ORCID Profile
0000-0002-9653-2700
Current Organisation
Murdoch University
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Publisher: Oxford University Press (OUP)
Date: 11-09-2020
DOI: 10.1093/JXB/ERAA416
Abstract: Barley possesses a branchless, spike-shaped inflorescence where determinate spikelets attach directly to the main axis, but the developmental mechanism of spikelet identity remains largely unknown. Here we report the functional analysis of the barley gene BRANCHED AND INDETERMINATE SPIKELET 1 (BDI1), which encodes a TCP transcription factor and plays a crucial role in determining barley inflorescence architecture and spikelet development. The bdi1 mutant exhibited indeterminate spikelet meristems that continued to grow and differentiate after producing a floret meristem some spikelet meristems at the base of the spike formed two fully developed seeds or converted to branched spikelets, producing a branched inflorescence. Map-based cloning analysis showed that this mutant has a deletion of ~600 kb on chromosome 5H containing three putative genes. Expression analysis and virus-induced gene silencing confirmed that the causative gene, BDI1, encodes a CYC/TB1-type TCP transcription factor and is highly conserved in both wild and cultivated barley. Transcriptome and regulatory network analysis demonstrated that BDI1 may integrate regulation of gene transcription cell wall modification and known trehalose-6-phosphate homeostasis to control spikelet development. Together, our findings reveal that BDI1 represents a key regulator of inflorescence architecture and meristem determinacy in cereal crop plants.
Publisher: Elsevier BV
Date: 09-2009
DOI: 10.1016/J.PLAPHY.2009.05.005
Abstract: The effects of exogenous abscisic acid (ABA) and polyethylene glycol (PEG 6000) treatments on grain H(2)O(2), ABA and beta-amylase activity were studied during grain development in the spike culture experiments with variety Triumph and its ABA-insensitive mutant TL43 as the plant materials. The results showed that during grain development the two genotypes were similar in the pattern of ABA concentration change, but differed greatly in the pattern of H(2)O(2) concentration and beta-amylase activity changes. The beta-amylase activity was positively correlated with H(2)O(2) concentration, negatively correlated with ABA concentration, and it is mainly closely associated with continued high levels of ABA with respect to H(2)O(2). Water stress (PEG treatment) induced beta-amylase was associated with H(2)O(2) concentration but not with ABA concentration. Exogenous application of H(2)O(2) and Ascorbic acid (AsA) increased beta-amylase activity in Triumph but reduced that of TL43. However, the endogenous H(2)O(2) concentration in grains was always consistent with beta-amylase activity. A novel model was hypothesized from the current results to illustrate the relationship between H(2)O(2), ABA and beta-amylase synthesis for the barley exposed to abiotic stresses.
Publisher: Springer Science and Business Media LLC
Date: 19-10-2018
DOI: 10.1007/S00122-017-2997-Y
Abstract: An ultra-high density genetic map containing 34,574 sequence-defined markers was developed in Lupinus angustifolius. Markers closely linked to nine genes of agronomic traits were identified. A physical map was improved to cover 560.5 Mb genome sequence. Lupin (Lupinus angustifolius L.) is a recently domesticated legume grain crop. In this study, we applied the restriction-site associated DNA sequencing (RADseq) method to genotype an F
Publisher: Frontiers Media SA
Date: 22-04-2022
Abstract: Drought stress is a common environmental stress, which adversely affects the yield and quality of crops. Due to its excellent drought tolerance, wild barley from the Middle East region is considered a valuable source for barley improvement. Here, we compared the growth rate, stomatal regulation and capacity to metabolize reactive oxygen species (ROS) of two barley cultivars and one wild barley accession. The results indicated the wild barley EC_S1 showed a more significant decline in stomatal aperture and less ROS production. Transcriptomic analysis revealed that EC_S1 has slower transcriptional regulation (5,050 DEGs) in the early stage of drought stress (14 days) than Baudin (7,022 DEGs) and Tadmor (6,090 DEGs). In addition, 30 hub genes, including nine known drought-related genes were identified by WGCNA analysis. Then, we cloned a novel bZIP transcription factor, HvbZIP21 , from EC_S1. HvbZIP21 was subcellularly targeted to the nucleus. Overexpression of HvbZIP21 in Arabidopsis enhanced drought tolerance due to increasing activities of superoxide dismutase, peroxidase, and catalase activities as well as glutathione content. Silencing of HvbZIP21 in EC_S1 suppressed drought tolerance in BSMV:HvbZIP21-inoculated plants. Taken together, our findings suggest that HvbZIP21 play a critical role in drought tolerance by manipulating ROS scavenging.
Publisher: Frontiers Media SA
Date: 05-08-2022
Abstract: Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al 3+ ) and Al treatments (15, 30 μM Al 3+ ). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be ided into 4 major phylogenetic groups. Four chickpea MATE genes ( CaMATE1-4 ) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula . Transcriptome data showed that CaMATE1-4 have erse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root. Protein structural modeling analyses revealed that CaMATE2 has a ergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic ersity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al 3+ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.
Publisher: Informa UK Limited
Date: 09-2008
Publisher: Springer Science and Business Media LLC
Date: 22-09-2020
Publisher: Springer Science and Business Media LLC
Date: 12-2000
Publisher: Springer Science and Business Media LLC
Date: 26-05-2016
Publisher: Springer Science and Business Media LLC
Date: 07-09-2014
Publisher: Springer Science and Business Media LLC
Date: 2015
Publisher: Elsevier BV
Date: 03-2020
Publisher: Springer Science and Business Media LLC
Date: 02-09-2015
Publisher: Springer Science and Business Media LLC
Date: 17-08-2016
DOI: 10.1038/SREP31741
Abstract: A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.
Publisher: Springer Science and Business Media LLC
Date: 2023
DOI: 10.1007/S00122-023-04272-7
Abstract: Map-based cloning, subcellular localization, virus-induced-gene-silencing and transcriptomic analysis reveal HvTUB8 as a candidate gene with pleiotropic effects on barley spike and leaf development via ethylene and chlorophyll metabolism. Barley lateral spikelet morphology and grain shape play key roles in grain physical quality and yield. Several genes and QTLs for these traits have been cloned or fine mapped previously. Here, we report the phenotypic and genotypic analysis of a barley mutant with round lateral spikelet (rls) from cv. Edamai 934. rls had round lateral spikelet, short but round grain, shortened awn, thick glume and dark green leaves. Histocytologic and ultrastructural analysis revealed that the difference of grain shape of rls was caused by change of cell arrangement in glume, and the dark leaf color resulted from enlarged chloroplast. HvTUBULIN8 ( HvTUB8 ) was identified as the candidate gene for rls by combination of RNA-Seq, map-based-cloning, virus-induced-gene-silencing (VIGS) and protein subcellular location. A single G-A substitution at the third exon of HvTUB8 resulted in change of Cysteine 354 to tyrosine. Furthermore, the mutant isoform Hvtub8 could be detected in both nucleus and cytoplasm, whereas the wild-type protein was only in cytoplasm and granular organelles of wheat protoplasts. Being consistent with the rare phenotype, the “A” allele of HvTUB8 was only detected in rls , but not in a worldwide barley germplasm panel with 400 accessions. VIGS confirmed that HvTUB8 was essential to maintain spike integrity. RNA-Seq results suggested that HvTUB8 may control spike morphogenesis via ethylene homeostasis and signaling, and control leaf color through chlorophyll metabolism. Collectively, our results support HvTUB8 as a candidate gene for barley spike and leaf morphology and provide insight of a novel mechanism of it in barley development.
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR03002
Abstract: Barley kernel discoloration (KD) leads to substantial annual loss in value through downgrading and discounting of malting barley. KD is a difficult trait to introgress into elite varieties as it is controlled by multiple genes and strongly influenced by environment and maturity. As the first step towards marker assisted selection for KD tolerance, we mapped quantitative trait loci (QTLs) controlling KD measured by grain brightness [Minolta L (Min L)], redness (Min a), and yellowness (Min b) in 7 barley populations. One to 3 QTLs were detected for grain brightness in various populations, and one QTL could account for 5–31% of the phenotypic variation. The QTL located around the centromere region of chromosome 2H was consistently detected in 6 of the 7 populations, explaining up to 28% of the phenotypic variation. In addition, QTLs for grain brightness were most frequently identified on chromosomes 3H and 7H in various populations. Australian varieties Galleon, Chebec, and Sloop contribute an allele to increase grain brightness on chromosome 7H in 3 different populations. A major gene effect was detected for grain redness. One QTL on chromosome 4H explained 54% of the phenotypic variation in the Sloop/Halcyon population, and was associated with the blue aleurone trait. A second QTL was detected on the long arm of chromosome 2H in 3 populations, accounting for 23–47% of the phenotypic variation. The major QTLs for grain yellowness were mapped on chromosomes 2H and 5H. There were strong associations between the QTLs for heading date, grain brightness, and yellowness. The molecular markers linked with the major QTLs should be useful for marker assisted selection for KD.
Publisher: MDPI AG
Date: 10-09-2022
Abstract: Salt stress is a major abiotic stress factor affecting crop production, and understanding of the response mechanisms of seed germination to salt stress can help to improve crop tolerance and yield. The differences in regulatory pathways during germination in different salt-tolerant barley seeds are not clear. Therefore, this study investigated the responses of different salt-tolerant barley seeds during germination to salt stress at the proteomic and metabolic levels. To do so, the proteomics and metabolomics of two barley seeds with different salt tolerances were comprehensively examined. Through comparative proteomic analysis, 778 differentially expressed proteins were identified, of which 335 were upregulated and 443 were downregulated. These proteins, were mainly involved in signal transduction, propanoate metabolism, phenylpropanoid biosynthesis, plant hormones and cell wall stress. In addition, a total of 187 salt-regulated metabolites were identified in this research, which were mainly related to ABC transporters, amino acid metabolism, carbohydrate metabolism and lipid metabolism 72 were increased and 112 were decreased. Compared with salt-sensitive materials, salt-tolerant materials responded more positively to salt stress at the protein and metabolic levels. Taken together, these results suggest that salt-tolerant germplasm may enhance resilience by repairing intracellular structures, promoting lipid metabolism and increasing osmotic metabolites. These data not only provide new ideas for how seeds respond to salt stress but also provide new directions for studying the molecular mechanisms and the metabolic homeostasis of seeds in the early stages of germination under abiotic stresses.
Publisher: Wiley
Date: 09-2012
Publisher: Bentham Science Publishers Ltd.
Date: 05-12-2007
Publisher: Frontiers Media SA
Date: 05-10-2017
Publisher: The Institute of Brewing & Distilling
Date: 07-2016
DOI: 10.1002/JIB.353
Publisher: Public Library of Science (PLoS)
Date: 22-06-2017
Publisher: Springer Science and Business Media LLC
Date: 12-02-2011
DOI: 10.1007/S00122-011-1544-5
Abstract: The use of dwarfing genes has resulted in the most significant improvements in yield and adaptation in cereal crops. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. The sdw1 gene has never been used successfully for malting barley, but only for a large number of feed varieties. One of the gibberellin 20-oxidase genes (Hv20ox₂) was identified as the candidate gene for sdw1/denso. Semi-quantitative real-time RT-PCR revealed that Hv20ox₂ was expressed at different levels in various organs of barley. Transcriptional levels were reduced in leaf blade, sheath, stem and rachis tissue in the barley variety Baudin with the denso gene. Subsequently, the relative expression levels of Hv20ox₂ were determined by quantitative real-time RT-PCR in a doubled haploid population and mapped as a quantitative trait. A single expression quantitative trait locus (eQTL) was identified and mapped to its structural gene region on chromosome 3H. The eQTL was co-located with QTLs for yield, height, development score, hectolitre weight and grain plumpness. The expression level of Hv20ox₂ was reduced fourfold in the denso mutant, but around 60-fold in the sdw1 mutant, compared to the control variety. The reduced expression level of Hv20ox₂ enhanced grain yield by increasing the number of effective tillers, but had negative effects on grain and malting quality. The sdw1 gene can be used only in feed barley due to its severe reduction of Hv20ox₂ expression. The gene expression marker for Hv20ox₂ can be used to distinguish different alleles of sdw1/denso.
Publisher: Springer Science and Business Media LLC
Date: 22-07-2020
DOI: 10.1186/S12870-020-02547-5
Abstract: Drought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions. In this study, we detected large genetic variation in a panel of 328 erse barley ( Hordeum vulgare L.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were germinated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. The Squamosa promoter-binding-like protein 3 gene ( SPL3 ) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity. This study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.
Publisher: Springer Science and Business Media LLC
Date: 20-03-2015
Publisher: Elsevier BV
Date: 05-2020
Publisher: Springer Science and Business Media LLC
Date: 10-08-2023
DOI: 10.1038/S41597-023-02434-2
Abstract: Wild barley, from “Evolution Canyon (EC)” in Mount Carmel, Israel, are ideal models for cereal chromosome evolution studies. Here, the wild barley EC_S1 is from the south slope with higher daily temperatures and drought, while EC_N1 is from the north slope with a cooler climate and higher relative humidity, which results in a differentiated selection due to contrasting environments. We assembled a 5.03 Gb genome with contig N50 of 3.53 Mb for wild barley EC_S1 and a 5.05 Gb genome with contig N50 of 3.45 Mb for EC_N1 using 145 Gb and 160.0 Gb Illumina sequencing data, 295.6 Gb and 285.35 Gb Nanopore sequencing data and 555.1 Gb and 514.5 Gb Hi-C sequencing data, respectively. BUSCOs and CEGMA evaluation suggested highly complete assemblies. Using full-length transcriptome data, we predicted 39,179 and 38,373 high-confidence genes in EC_S1 and EC_N1, in which 93.6% and 95.2% were functionally annotated, respectively. We annotated repetitive elements and non-coding RNAs. These two wild barley genome assemblies will provide a rich gene pool for domesticated barley.
Publisher: MDPI AG
Date: 28-02-2023
DOI: 10.3390/IJMS24054706
Abstract: Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 2023
DOI: 10.34133/PLANTPHENOMICS.0015
Abstract: Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation. Domestication and crop breeding often target the scaling traits in the opposite directions. The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored. Here, we revisited a erse barley ( Hordeum vulgare L.) panel with genome-wide single-nucleotide polymorphisms (SNPs) profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling. Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit. Genomic structural equation modeling systematically evaluated the pleiotropic effect of in idual SNP on the plant height and seed weight within a trait correlation network. We discovered seventeen novel SNPs (quantitative trait locus) conferring pleiotropic effect on plant height and seed weight, involving genes with function in erse traits related to plant growth and development. Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome. We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley. Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.
Publisher: American Chemical Society (ACS)
Date: 08-07-2009
DOI: 10.1021/JF900988H
Abstract: The hydrolysis of starch is a key factor for controlling the glycemic index (GI). Slow digestion properties of starch lead to slower glucose release and lower glycemic response. Food with high resistant starch (RS) possesses great value for controlling the GI. To elucidate the factors that play a role in slow digestibility, seven rice mutants different in RS contents were selected for comparative studies. The degree of hydrolysis showed highly significant correlation with RS, apparent amylose content (AAC), lipid content (LC), and other starch physiochemical properties in all these materials with different RS contents. The rate of in vitro digestible starch correlated positively with RS, whereas digestibility was affected mostly by lipid content for those mutants with similar RS. Starch-lipid complexes and short chains with degrees of polymerization (DP) of 8-12 strongly influenced starch digestion. The integrity of aggregated starch and the number of round starch granules might influence the digestibility of starch directly.
Publisher: Wiley
Date: 29-05-2022
DOI: 10.1002/TPG2.20221
Abstract: Bread wheat ( Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence–absence variation (PAV) between cultivars, h ering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high‐quality reference genomes are becoming available, reflecting the genetic content of a erse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes.
Publisher: Springer Science and Business Media LLC
Date: 07-07-2016
Publisher: Wiley
Date: 03-2020
DOI: 10.1111/TPJ.14557
Abstract: Functional ergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional ergence for plant ersity and environmental adaptation.
Publisher: Springer Science and Business Media LLC
Date: 08-10-2010
Abstract: Dwarfing genes have widely been used in barley breeding program. More than 30 types of dwarfs or semidwarfs have been reported, but a few has been exploited in barley breeding because pleiotropic effects of dwarfing genes cause some undesired traits. The plant architecture of newly discovered dwarfing germplasm "Huaai 11" consisted of desirable agronomic traits such as shortened stature and early maturity. Genetic factor controlling the plant height in dwarf line Huaai 11 was investigated. The Huaai 11 was crossed with tall varieties Monker, Mpyt, Zhenongda 3, Zaoshu 3, Advance, Huadamai 1, Huadamai 6, Hyproly and Ris01508. All the F 1 plants displayed tall trait. Both tall and dwarf plants appeared in all the F 2 populations with a 3:1 segregation ratio, suggesting that dwarfism of Huaai 11 is controlled by a single recessive gene, btwd1 . Allelism test indicated that this dwarfing gene in the Huaai 11 is nonallelic with the gene br , uzu , sdw1 and denso . Using a double haploid population derived from a cross of Huadamai 6 and Huaai 11 and SSR markers the novel dwarfing gene was mapped onto the long arm of chromosome 7H, and closely linked to Bmac031 and Bmac167 with genetic distance of 2.2 cM. Huaai 11 is a new source of dwarf for broadening the genetic base of dwarfism. This dwarf source was controlled by a recessive dwarfing gene btwd1 , was mapped onto the long arm of chromosome 7H.
Publisher: Springer Netherlands
Date: 2013
Publisher: Public Library of Science (PLoS)
Date: 30-03-2016
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/CP09187
Abstract: Heading date is a major determinant of the regional and seasonal adaptation of barley varieties. The dogma is that introduced germplasm is more likely to be adapted if it is derived from a similar latitude. However, barley germplasm introduced from similar latitudes of South-East Asia is extremely early heading in the Australian environments and vice versa. A doubled-haploid population from a cross of an Australian barley Galleon and a Japanese barley Haruna Nijo was evaluated for heading date in Australia (Perth, 31°56′S) and China (Wuhan, 30°33′N) under normal autumn sowing, late sowing in the field, and extended-light glasshouse conditions. One major QTL was identified on chromosome 5H under the three conditions in China. The single QTL accounted for up to 50% of phenotypic variation for heading date. The Australian variety contributed to late heading date. Two QTLs on chromosomes 4H and 5H were detected for controlling heading date in Australia. The QTL/QTL interaction contributed up to 35.8% of phenotypic variation for heading date in Australia, which is the major reason for the extremely early heading date of the Japanese variety in the Australian environment. The chromosome 5H QTL was detected at the same chromosomal location when the population was grown in either China or Australia. In both environments the Australian variety contributed to the late heading date. Selection against the Japanese alleles of chromosomes 4H and 5H QTLs could eliminate the extremely early genotype in Australia and selection against the Australian allele of chromosome 5H QTL could eliminate the extremely late genotype in China when Australian and Japanese germplasms are used in the breeding programs.
Publisher: Springer Science and Business Media LLC
Date: 16-10-2015
Publisher: Public Library of Science (PLoS)
Date: 08-02-2018
Publisher: Burleigh Dodds Science Publishing
Date: 04-02-2020
Publisher: Springer Science and Business Media LLC
Date: 25-07-2022
DOI: 10.1007/S00122-022-04169-X
Abstract: Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley ( Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic ersity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic ersity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.
Publisher: Cold Spring Harbor Laboratory
Date: 04-03-2020
DOI: 10.1101/2020.03.04.976324
Abstract: The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact breeding had on the genetic ersity of barley released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic ersity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a erse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined dataset and germplasm collection provide a rich source of genetic ersity that can be applied to understanding and improving environmental adaptation and enhanced yields. Today’s gene pool of crop genetic ersity has been shaped during domestication and more recently by breeding. Genetic ersity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic ersity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties. Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic ersity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive ersity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.
Publisher: Springer Science and Business Media LLC
Date: 06-02-2023
DOI: 10.1186/S12915-022-01503-Z
Abstract: Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date. Taking advantage of recently published genomic data in Triticeae , we dissected a ergent homogentisate phytyltransferase ( HPT2 ) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional ergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint. Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication. Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.
Publisher: Frontiers Media SA
Date: 14-07-2021
Abstract: Phosphorus (P) deficiency is a major threat to the crop production, and for understanding the response mechanism of plant roots, P stress may facilitate the development of crops with increased tolerance. Phosphorylation plays a critical role in the regulation of proteins for plant responses to biotic and abiotic stress however, its functions in P starvation/resupply are largely unknown for barley ( Hordeum vulgare ) growth. Here, we performed a global review of phosphorylation in barley roots treated by P starvation/resupply. We identified 7,710 phosphorylation sites on 3,373 proteins, of which 76 types of conserved motifs were extracted from 10,428 phosphorylated peptides. Most phosphorylated proteins were located in the nucleus (36%) and chloroplast (32%). Compared with the control, 186 and 131 phosphorylated proteins under P starvation condition and 156 and 111 phosphorylated proteins under P resupply condition showed significant differences at 6 and 48 h, respectively. These proteins mainly participated in carbohydrate metabolism, phytohormones, signal transduction, cell wall stress, and oxidases stress. Moreover, the pathways of the ribosome, RNA binding, protein transport, and metal binding were significantly enriched under P starvation, and only two pathways of ribosome and RNA binding were greatly enriched under Pi resupply according to the protein–protein interaction analysis. The results suggested that the phosphorylation proteins might play important roles in the metabolic processes of barley roots in response to Pi deficiency/resupply. The data not only provide unique access to phosphorylation reprogramming of plant roots under deficiency/resupply but also demonstrate the close cooperation between these phosphorylation proteins and key metabolic functions.
Publisher: Springer Science and Business Media LLC
Date: 20-10-2012
DOI: 10.1007/S00122-012-1997-1
Abstract: Selection for phomopsis stem blight disease (PSB) resistance is one of the key objectives in lupin (Lupinus angustifolius L.) breeding programs. A cross was made between cultivar Tanjil (resistant to PSB) and Unicrop (susceptible). The progeny was advanced into F(8) recombinant inbred lines (RILs). The RIL population was phenotyped for PSB disease resistance. Twenty plants from the RIL population representing disease resistance and susceptibility was subjected to next-generation sequencing (NGS)-based restriction site-associated DNA sequencing on the NGS platform Solexa HiSeq2000, which generated 7,241 single nucleotide polymorphisms (SNPs). Thirty-three SNP markers showed the correlation between the marker genotypes and the PSB disease phenotype on the 20 representative plants, which were considered as candidate markers linked to a putative R gene for PSB resistance. Seven candidate markers were converted into sequence-specific PCR markers, which were designated as PhtjM1, PhtjM2, PhtjM3, PhtjM4, PhtjM5, PhtjM6 and PhtjM7. Linkage analysis of the disease phenotyping data and marker genotyping data on a F(8) population containing 187 RILs confirmed that all the seven converted markers were associated with the putative R gene within the genetic distance of 2.1 CentiMorgan (cM). One of the PCR markers, PhtjM3, co-segregated with the R gene. The seven established PCR markers were tested in the 26 historical and current commercial cultivars released in Australia. The numbers of "false positives" (showing the resistance marker allele band but lack of the putative R gene) for each of the seven PCR markers ranged from nil to eight. Markers PhtjM4 and PhtjM7 are recommended in marker-assisted selection for PSB resistance in the Australian national lupin breeding program due to its wide applicability on breeding germplasm and close linkage to the putative R gene. The results demonstrated that application of NGS technology is a rapid and cost-effective approach in development of markers for molecular plant breeding.
Publisher: Oxford University Press (OUP)
Date: 27-08-2019
DOI: 10.1093/JXB/ERZ332
Abstract: Using gene-set association test and epistasis analysis, this research achieved higher statistical power with potentially high accuracy, and detected significant genes and gene networks that influence flowering time in barley.
Publisher: Springer Science and Business Media LLC
Date: 05-2014
Publisher: Springer Science and Business Media LLC
Date: 07-11-2017
Publisher: Springer Science and Business Media LLC
Date: 1999
Publisher: Wiley
Date: 08-02-2023
DOI: 10.1111/PBI.13998
Abstract: The green revolution was based on genetic modification of the gibberellin (GA) hormone system with “dwarfing” gene mutations that reduces GA signals, conferring shorter stature, thus enabling plant adaptation to modern farming conditions. Strong GA‐related mutants with shorter stature often have reduced coleoptile length, discounting yield gain due to their unsatisfactory seedling emergence under drought conditions. Here we present gibberellin ( GA ) 3‐oxidase1 ( GA3ox1 ) as an alternative semi‐dwarfing gene in barley that combines an optimal reduction in plant height without restricting coleoptile and seedling growth. Using large‐scale field trials with an extensive collection of barley accessions, we showed that a natural GA3ox1 haplotype moderately reduced plant height by 5–10 cm. We used CRISPR/Cas9 technology, generated several novel GA3ox1 mutants and validated the function of GA3ox1 . We showed that altered GA3ox1 activities changed the level of active GA isoforms and consequently increased coleoptile length by an average of 8.2 mm, which could provide essential adaptation to maintain yield under climate change. We revealed that CRISPR/Cas9‐induced GA3ox1 mutations increased seed dormancy to an ideal level that could benefit the malting industry. We conclude that selecting HvGA3ox1 alleles offers a new opportunity for developing barley varieties with optimal stature, longer coleoptile and additional agronomic traits.
Publisher: Frontiers Media SA
Date: 18-08-2020
Publisher: Burleigh Dodds Science Publishing
Date: 21-01-2020
Publisher: Elsevier BV
Date: 03-2011
Publisher: Springer Science and Business Media LLC
Date: 13-05-2020
DOI: 10.1007/S00122-020-03599-9
Abstract: An effective and stable quantitative resistance locus, QSc.VR4, was fine mapped, characterized and physically anchored to the short arm of 4H, conferring adult plant resistance to the fungus Rhynchosporium commune in barley. Scald caused by Rhynchosporium commune is one of the most destructive barley diseases worldwide. Accumulation of adult plant resistance (APR) governed by multiple resistance alleles is predicted to be effective and long-lasting against a broad spectrum of pathotypes. However, the molecular mechanisms that control APR remain poorly understood. Here, quantitative trait loci (QTL) analysis of APR and fine mapping were performed on five barley populations derived from a common parent Vlamingh, which expresses APR to scald. Two QTLs, designated QSc.VR4 and QSc.BR7, were detected from a cross between Vlamingh and Buloke. Our data confirmed that QSc.VR4 is an effective and stable APR locus, residing on the short arm of chromosome 4H, and QSc.BR7 derived from Buloke may be an allele of reported Rrs2. High-resolution fine mapping revealed that QSc.VR4 is located in a 0.38 Mb genomic region between InDel markers 4H2282169 and 4H2665106. The gene annotation analysis and sequence comparison suggested that a gene cluster containing two adjacent multigene families encoding leucine-rich repeat receptor kinase-like proteins (LRR-RLKs) and germin-like proteins (GLPs), respectively, is likely contributing to scald resistance. Adult plant resistance (APR) governed by QSc.VR4 may confer partial levels of resistance to the fungus Rhynchosporium commune and, furthermore, be an important resource for gene pyramiding that may contribute broad-based and more durable resistance.
Publisher: MDPI AG
Date: 16-06-2023
Abstract: Crop genetic ersity is essential for adaptation and productivity in agriculture. A previous study revealed that poor allele ersity in wheat commercial cultivars is a major barrier to its further improvement. Homologs within a variety, including paralogs and orthologs in polyploid, account for a large part of the total genes of a species. Homolog ersity, intra-varietal ersity (IVD), and their functions have not been elucidated. Common wheat, an important food crop, is a hexaploid species with three subgenomes. This study analyzed the sequence, expression, and functional ersity of homologous genes in common wheat based on high-quality reference genomes of two representative varieties, a modern commercial variety Aikang 58 (AK58) and a landrace Chinese Spring (CS). A total of 85,908 homologous genes, accounting for 71.9% of all wheat genes, including inparalogs (IPs), outparalogs (OPs), and single-copy orthologs (SORs), were identified, suggesting that homologs are an important part of the wheat genome. The levels of sequence, expression, and functional variation in OPs and SORs were higher than that of IPs, which indicates that polyploids have more homologous ersity than diploids. Expansion genes, a specific type of OPs, made a great contribution to crop evolution and adaptation and endowed crop with special characteristics. Almost all agronomically important genes were from OPs and SORs, demonstrating their essential functions for polyploid evolution, domestication, and improvement. Our results suggest that IVD analysis is a novel approach for evaluating intra-genomic variations, and exploitation of IVD might be a new road for plant breeding, especially for polyploid crops, such as wheat.
Publisher: Springer Science and Business Media LLC
Date: 27-04-2017
Abstract: Barley ( Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
Publisher: Springer Science and Business Media LLC
Date: 19-10-2011
Publisher: Elsevier BV
Date: 02-2014
DOI: 10.1016/J.PLAPHY.2013.11.025
Abstract: Aluminum (Al) toxicity is a major limiting factor for plant production in acid soils. Wild barley germplasm is a treasure trove of useful genes and offers rich sources of genetic variation for crop improvement. Al-stress-hydroponic-experiments were performed, and the physiochemical characteristic of two contrasting Tibetan wild barley genotypes (Al-resistant XZ16 and Al-sensitive XZ61) and Al-resistant cv. Dayton were compared. Ultrastructure of chloroplasts and root cells in XZ16 was less injured than that in Dayton and XZ61. Moreover, XZ16 secreted significantly more malate besides citrate and exhibited less Al uptake and distribution than both of XZ61 and Dayton in response to Al stress, simultaneously maintained higher H⁺-, Ca²⁺Mg²⁺- and total-ATPase activities over XZ61. The protein synthesis inhibitor cycloheximide reduced citrate secretion from XZ16, but not from Dayton. In Tibetan wild barley, our findings highlight the significant correlations between Al tolerance, ATPase activity and citrate secretion, providing some insights into the physiological basis for Al-detoxification.
Publisher: CSIRO Publishing
Date: 12-2022
DOI: 10.1071/CP22281
Abstract: Context The legume shrub/tree leucaena (Leucaena leucocephala (Lam.) de Wit.) is highly regarded as a cattle fodder, although it is considered an environmental weed in many parts of Australia. Aims We investigated the feasibility of developing a forage variety of triploid leucaena through interspecific hybridisation that is sterile (without seeds) as a strategy to mitigate its weed risk. Methods A conventional breeding strategy was used to create triploid hybrids from hand-crosses between tetraploid and diploid species of leucaena. Molecular markers were developed to confirm successful crosses and flow cytometry was used to confirm the ploidy level. The plants are being evaluated for flowering behaviour, seed and herbage production across two environmentally erse sites at Carnarvon and Kununurra in northern Western Australia. Key results During 2018/19 and 2019/20, 2260 crosses between 45 different combinations of diploid females by tetraploid males and their reciprocals have created over 3000 putative triploid hybrid plants. This is the first time that triploids have successfully been created in Australia and 10 new parental combinations were created as a world-first. Conclusions A cohort of sterile triploid plants has been identified and selections will be made based on their edible biomass productivity, insect tolerance, capacity for regrowth after cutting, nutritive value and plant chemistry (including anti-methanogenic responses). A sterile leucaena variety will have application not only in Australian grazing systems but also in other tropical regions of the world. Implications A cost-effective technology for mass vegetative propagation of leucaena will be required for commercialisation of a sterile variety.
Publisher: Springer Science and Business Media LLC
Date: 15-08-2009
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer Science and Business Media LLC
Date: 28-03-2015
DOI: 10.1007/S00122-015-2499-8
Abstract: Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding. The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.
Publisher: Public Library of Science (PLoS)
Date: 31-03-2016
Publisher: Springer Science and Business Media LLC
Date: 08-08-2019
Publisher: Springer Science and Business Media LLC
Date: 29-10-2019
DOI: 10.1186/S12864-019-6182-3
Abstract: Artificial mutagenesis not only provides a new approach to increase the ersity of desirable traits for breeding new varieties but are also beneficial for characterizing the genetic basis of functional genes. In recent decades, many mutation genes have been identified which are responsible for phenotype changes in mutants in various species including Arabidopsis and rice. However, the mutation feature in induced mutants and the underlying mechanisms of various types of artificial mutagenesis remain unclear. In this study, we adopted a transcriptome sequencing strategy to characterize mutations in coding regions in a barley dwarf mutant induced by gamma-ray radiation. We detected 1193 genetic mutations in gene transcription regions introduced by gamma-ray radiation. Interestingly, up to 97% of the gamma irradiation mutations were concentrated in certain regions in chromosome 5H and chromosome 7H. Of the 26,745 expressed genes, 140 were affected by gamma-ray radiation their biological functions included cellular and metabolic processes. Our results indicate that mutations induced by gamma-ray radiation are not evenly distributed across the whole genome but located in several concentrated regions. Our study provides an overview of the feature of genetic mutations and the genes affected by gamma-ray radiation, which should contribute to a deeper understanding of the mechanisms of radiation mutation and their application in gene function analysis.
Publisher: Frontiers Media SA
Date: 31-03-2021
Abstract: Barley ( Hordeum vulgare L.)—a major cereal crop—has low Pi demand, which is a distinct advantage for studying the tolerance mechanisms of phosphorus deficiency. We surveyed dynamic protein succinylation events in barley roots in response to and recovery from Pi starvation by firstly evaluating the impact of Pi starvation in a Pi-tolerant (GN121) and Pi-sensitive (GN42) barley genotype exposed to long-term low Pi (40 d) followed by a high-Pi recovery for 10 d. An integrated proteomics approach involving label-free, immune-affinity enrichment, and high-resolution LC-MS/MS spectrometric analysis was then used to quantify succinylome and proteome in GN121 roots under short-term Pi starvation (6, 48 h) and Pi recovery (6, 48 h). We identified 2,840 succinylation sites (Ksuc) across 884 proteins of which, 11 representative Ksuc motifs had the preferred amino acid residue (lysine). Furthermore, there were 81 differentially abundant succinylated proteins (DFASPs) from 119 succinylated sites, 83 DFASPs from 110 succinylated sites, 93 DFASPs from 139 succinylated sites, and 91 DFASPs from 123 succinylated sites during Pi starvation for 6 and 48 h and during Pi recovery for 6 and 48 h, respectively. Pi starvation enriched ribosome pathways, glycolysis, and RNA degradation. Pi recovery enriched the TCA cycle, glycolysis, and oxidative phosphorylation. Importantly, many of the DFASPs identified during Pi starvation were significantly overexpressed during Pi recovery. These results suggest that barley roots can regulate specific Ksuc site changes in response to Pi stress as well as specific metabolic processes. Resolving the metabolic pathways of succinylated protein regulation characteristics will improve phosphate acquisition and utilization efficiency in crops.
Publisher: Springer Science and Business Media LLC
Date: 05-2004
DOI: 10.1007/S10142-004-0104-3
Abstract: Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable. A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy re-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified as a candidate gene controlling the seed dormancy re-harvest sprouting QTL on 5HL. This chromosomal region also shared synteny with the telomere region of wheat chromosome 4AL, but was located outside of the QTL reported for seed dormancy in wheat. The wheat chromosome 4AL QTL region for seed dormancy was syntenic to both rice chromosome 3 and 11. In both cases, corresponding QTLs for seed dormancy have been mapped in rice.
Publisher: Oxford University Press (OUP)
Date: 10-06-2023
Abstract: Drought stress poses a serious threat to crop production worldwide. Genes encoding homocysteine methyltransferase (HMT) have been identified in some plant species in response to abiotic stress, but its molecular mechanism in plant drought tolerance remains unclear. Here, transcriptional profiling, evolutionary bioinformatics, and population genetics were conducted to obtain insight into the involvement of HvHMT2 from Tibetan wild barley (Hordeum vulgare ssp. agriocrithon) in drought tolerance. We then performed genetic transformation coupled with physio-biochemical dissection and comparative multiomics approaches to determine the function of this protein and the underlying mechanism of HvHMT2-mediated drought tolerance. HvHMT2 expression was strongly induced by drought stress in tolerant genotypes in a natural Tibetan wild barley population and contributed to drought tolerance through S-adenosylmethionine (SAM) metabolism. Overexpression of HvHMT2 promoted HMT synthesis and efficiency of the SAM cycle, leading to enhanced drought tolerance in barley through increased endogenous spermine and less oxidative damage and growth inhibition, thus improving water status and final yield. Disruption of HvHMT2 expression led to hypersensitivity under drought treatment. Application of exogenous spermine reduced accumulation of reactive oxygen species (ROS), which was increased by exogenous mitoguazone (inhibitor of spermine biosynthesis), consistent with the association of HvHMT2-mediated spermine metabolism and ROS scavenging in drought adaptation. Our findings reveal the positive role and key molecular mechanism of HvHMT2 in drought tolerance in plants, providing a valuable gene not only for breeding drought-tolerant barley cultivars but also for facilitating breeding schemes in other crops in a changing global climate.
Publisher: Springer Science and Business Media LLC
Date: 02-03-2017
DOI: 10.1038/SREP43766
Abstract: A poly-row branched spike ( prbs ) barley mutant was obtained from soaking a two-rowed barley inflorescence in a solution of maize genomic DNA. Positional cloning and sequencing demonstrated that the prbs mutant resulted from a 28 kb deletion including the inflorescence architecture gene HvRA2 . Sequence annotation revealed that the HvRA2 gene is flanked by two LTR (long terminal repeat) retrotransposons ( BARE ) sharing 89% sequence identity. A recombination between the integrase (IN) gene regions of the two BARE copies resulted in the formation of an intact BARE and loss of HvRA2. No maize DNA was detected in the recombination region although the flanking sequences of HvRA2 gene showed over 73% of sequence identity with repetitive sequences on 10 maize chromosomes. It is still unknown whether the interaction of retrotransposons between barley and maize has resulted in the recombination observed in the present study.
Publisher: Springer Science and Business Media LLC
Date: 07-2021
Publisher: Zhejiang University Press
Date: 11-2011
Publisher: Springer Science and Business Media LLC
Date: 21-12-2023
Publisher: Wiley
Date: 07-01-2018
DOI: 10.1111/TPJ.13794
Abstract: Pseudogenes have a reputation of being 'evolutionary relics' or 'junk DNA'. While they are well characterized in mammals, studies in more complex plant genomes have so far been h ered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole-genome assessment of pseudogenes on the barley genome. We identified, characterized and classified 89 440 gene fragments and pseudogenes scattered along the chromosomes, with occasional hotspots and higher densities at the chromosome ends. Full-length pseudogenes (11 015) have preferentially retained their exon-intron structure. Retrotransposition of processed mRNAs only plays a marginal role in their creation. However, the distribution of retroposed pseudogenes reflects the Rabl configuration of barley chromosomes and thus hints at founding mechanisms. While parent genes related to the defense-response were found to be under-represented in cultivated barley, we detected several defense-related pseudogenes in wild barley accessions. The percentage of transcriptionally active pseudogenes is 7.2%, and these may potentially adopt new regulatory roles.The barley genome is rich in pseudogenes and small gene fragments mainly located towards chromosome tips or as tandemly repeated units. Our results indicate non-random duplication and pseudogenization preferences and improve our understanding of the dynamics of gene birth and death in large plant genomes and the mechanisms that lead to evolutionary innovations.
Publisher: Oxford University Press (OUP)
Date: 19-08-2019
DOI: 10.1104/PP.19.00717
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/CP10154
Abstract: A genetic map of barley (Hordeum vulgare L.) with 163 lified fragment length polymorphism and 69 simple sequence repeat (SSR) markers was constructed using a population of 178 doubled haploid lines from a cross between the varieties ‘Baudin’ and ‘AC Metcalfe’. Linkage groups were assigned to barley chromosomes using published map locations of SSR markers as reference points. The total length of the map was 1307.2 cM with an average interval length of 5.6 cM between markers. The genetic map was used to locate quantitative trait loci (QTLs) for several disease resistance traits. The population was tested for spot type net blotch, caused by Pyrenophora teres f. maculata, and net type net blotch, caused by Pyrenophora teres f. teres, in greenhouse experiments and in a range of field environments in Western Australia and Queensland. The response of the lines to leaf rust (caused by Puccinia hordei L.) at adult plant growth stages was evaluated in Western Australia. Significant marker–trait associations were found for seedling resistance and symptom severity in adult plants to these diseases. A new locus conferring resistance to P. teres f. maculata at both seedling and adult plant stages was detected on the short arm of chromosome 6H. From the seedling testing against P. teres f. teres, five highly repeatable QTLs were detected, on chromosomes 2HS, 2HL, 3HS, 4HL, and 6HS. For leaf rust, one highly significant QTL was detected on chromosome 2HL. The markers within these QTL regions present an opportunity for marker-assisted selection for these traits in barley-breeding programs.
Publisher: Wiley
Date: 09-03-2021
DOI: 10.1111/TPJ.15173
Publisher: MDPI AG
Date: 27-10-2022
Abstract: Cuticular waxes comprise the hydrophobic layer that protects crops against nonstomatal water loss and biotic and abiotic stresses. Expanding on our current knowledge of the genes that are involved in cuticular wax biosynthesis and regulation plays an important role in dissecting the processes of cuticular wax metabolism. In this study, we identified the Cer-GN1 barley (Hordeum vulgare L.) mutant that is generated by ethyl methanesulfonate mutagenesis with a glossy spike phenotype that is controlled by a single recessive nuclear gene. A physiological analysis showed that the total cuticular wax loads of Cer-GN1 were one-third that of the progenitor wild-type (WT), and its water loss rate was significantly accelerated (p 0.05). In addition, Cer-GN1 was defective in the glume’s cuticle according to the toluidine blue dye test, and it was deficient in the tubule-shaped crystals which were observed on the glume surfaces by scanning electron microscopy. Using metabolomics and transcriptomics, we investigated the impacts of cuticular wax composition and waxy regulatory genes on the loss of the glaucous wax in the spikes of Cer-GN1. Among the differential metabolites, we found that 16-hydroxyhexadecanoic acid, which is one of the predominant C16 and C18 fatty acid-derived cutin monomers, was significantly downregulated in Cer-GN1 when it was compared to that of WT. We identified two novel genes that are located on chromosome 4H and are downregulated in Cer-GN1 (HvMSTRG.29184 and HvMSTRG.29185) that encode long-chain fatty acid omega-monooxygenase CYP704B1, which regulates the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid. A quantitative real-time PCR revealed that the expression levels of HvMSTRG.29184 and HvMSTRG.29185 were downregulated at 1, 4, 8, 12, and 16 days after the heading stage in Cer-GN1 when it was compared to those of WT. These results suggested that HvMSTRG.29184 and HvMSTRG.29185 have CYP704B1 activity, which could regulate the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid in barley. Their downregulation in Cer-GN1 reduced the synthesis of the cuticular wax components and ultimately caused the loss of the glaucous wax in the spikes. It is necessary to verify whether HvMSTRG.29184 and HvMSTRG.29185 truly encode a CYP704B1 that regulates the conversion of C16 palmitic acid to 16-hydroxyhexadecanoic acid in barley.
Publisher: Oxford University Press (OUP)
Date: 2020
Abstract: Barley (Hordeum vulgare L.) is one of the first domesticated grain crops and represents the fourth most important cereal source for human and animal consumption. BarleyVarDB is a database of barley genomic variation. It can be publicly accessible through the website at 146.118.64.11/BarleyVar. This database mainly provides three sets of information. First, there are 57 754 224 single nuclear polymorphisms (SNPs) and 3 600 663 insertions or deletions (InDels) included in BarleyVarDB, which were identified from high-coverage whole genome sequencing of 21 barley germplasm, including 8 wild barley accessions from 3 barley evolutionary original centers and 13 barley landraces from different continents. Second, it uses the latest barley genome reference and its annotation information publicly accessible, which has been achieved by the International Barley Genome Sequencing Consortium (IBSC). Third, 522 212 whole genome-wide microsatellites/simple sequence repeats (SSRs) were also included in this database, which were identified in the reference barley pseudo-molecular genome sequence. Additionally, several useful web-based applications are provided including JBrowse, BLAST and Primer3. Users can design PCR primers to asses polymorphic variants deposited in this database and use a user-friendly interface for accessing the barley reference genome. We envisage that the BarleyVarDB will benefit the barley genetic research community by providing access to all publicly available barley genomic variation information and barley reference genome as well as providing them with an ultra-high density of SNP and InDel markers for molecular breeding and identification of functional genes with important agronomic traits in barley. Database URL: 146.118.64.11/BarleyVar
Publisher: Springer Science and Business Media LLC
Date: 02-04-2009
Publisher: Elsevier BV
Date: 12-2014
DOI: 10.1016/J.FOODCHEM.2014.05.058
Abstract: Our previous study found that the critical protein in SE (silica eluted) proteins is BTI-CMe, and assumed that SE-ve malt for brewing may improve the haze stability in beer. In this study, we investigated the difference in gene sequence and corresponding amino acid sequence of BTI-CMe between SE+ve and SE-ve types. The results showed that there were 7 amino acid differences between Yerong (SE-ve) and Franklin (SE+ve). Two types BTI-CMe were expressed in vitro and purified successfully. By adding the purified BTI-CMe into commercial beer, we found that both original turbidity and alcohol chill haze degree of beer were increased. BTI-CMe of SE-ve haplotype showed a lower level of haze formation in beer than SE+ve haplotype. Response surface methodology (RSM) was conducted to determine the relationship between BTI-CMe and tannic acid, and their effects on haze formation. It was found that (1) higher content of BTI-CMe and/or tannic acid in beer would give rise to higher turbidity (2) there was a significant interaction between BTI-CMe and tannic acid (3) haze activity disparity of BTI-CMe between two types was significantly and positively correlated with the tannic acid concentration.
Publisher: Springer Science and Business Media LLC
Date: 04-2017
DOI: 10.1038/NATURE22043
Abstract: Cereal grasses of the Triticeae tribe have been the major food source in temperate regions since the dawn of agriculture. Their large genomes are characterized by a high content of repetitive elements and large pericentromeric regions that are virtually devoid of meiotic recombination. Here we present a high-quality reference genome assembly for barley (Hordeum vulgare L.). We use chromosome conformation capture mapping to derive the linear order of sequences across the pericentromeric space and to investigate the spatial organization of chromatin in the nucleus at megabase resolution. The composition of genes and repetitive elements differs between distal and proximal regions. Gene family analyses reveal lineage-specific duplications of genes involved in the transport of nutrients to developing seeds and the mobilization of carbohydrates in grains. We demonstrate the importance of the barley reference sequence for breeding by inspecting the genomic partitioning of sequence variation in modern elite germplasm, highlighting regions vulnerable to genetic erosion.
Publisher: Public Library of Science (PLoS)
Date: 14-05-2013
Publisher: Zhejiang University Press
Date: 02-2020
Publisher: Springer Science and Business Media LLC
Date: 26-08-2014
Publisher: MDPI AG
Date: 08-2023
Abstract: Enhancing the water-use efficiency (WUE) of barley cultivars may safeguard yield deficits during periods of low rainfall. Reduced stomatal density is linked to enhanced WUE, leading to improved drought resistance across plant genera. In this study, 10 barley varieties exhibiting a range of stomatal density phenotypes were grown under differing soil water contents to determine whether stomatal density influences the capacity of genotypes to resist low water availability. The low-stomatal-density genotype Hindmarsh showed the least impact on biomass production during early development, with a 37.13% decrease in dry biomass during drought treatment. Low-stomatal-density genotypes additionally outcompeted high-stomatal-density genotypes under water-deprivation conditions during the reproductive phase of development, exhibiting 19.35% greater wilting resistance and generating 54.62% more heads relative to high-stomatal-density genotypes (p 0.05). Finally, a correlation analysis revealed a strong negative linear relationship between stomatal density and the traits of head number (r = −0.71) and the number of days until wilting symptoms (r = −0.67) (p 0.05). The combined results indicate that low-stomatal-density genotypes show promising attributes for high WUE, revealing novel barley varieties that may be useful to future breed improvement for drought tolerance.
Publisher: Frontiers Media SA
Date: 14-11-2017
Publisher: Elsevier BV
Date: 10-2020
Publisher: Public Library of Science (PLoS)
Date: 03-2018
Publisher: Springer Science and Business Media LLC
Date: 23-06-2016
Publisher: Institute of Electrical and Electronics Engineers (IEEE)
Date: 06-2018
Publisher: Springer Science and Business Media LLC
Date: 20-03-2008
Publisher: Wiley
Date: 2001
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02179
Abstract: A genetic linkage map consisting of 435 molecular markers has been constructed using a doubled-haploid mapping population derived from a cross between the Australian barley feed variety Galleon and Haruna Nijo, a Japanese barley cultivar of high malting quality. This map was used to locate the genes conferring CCN and SFNB resistance from Galleon and to locate malting and brewing quality genes from Haruna Nijo. Closely linked markers to the trait loci have been identified and are now being widely implemented in Australian breeding programs.
Publisher: Elsevier BV
Date: 06-2022
Publisher: Springer Science and Business Media LLC
Date: 28-01-2012
Publisher: Elsevier BV
Date: 2002
Publisher: Elsevier BV
Date: 02-2016
DOI: 10.1016/J.FOODCHEM.2015.07.090
Abstract: Sugar degradation during grain germination is important for malt quality. In malting industry, gibberellin (GA) is frequently used for improvement of malting quality. In this study, the changes of metabolite profiles and starch-degrading enzymes during grain germination, and as affected by GA and abscisic acid (ABA) were investigated using two wild barley accessions XZ72 and XZ95. Totally fifty-two metabolites with known structures were detected and the change of metabolite during germination was time- and genotype dependent. Sugars and amino acids were the most dramatically changed compounds. Addition of GA enhanced the activities of starch-degrading enzymes, and increased most metabolites, especially sugars and amino acids, whereas ABA had the opposite effect. The effect varied with the barley accessions. The current study is the first attempt in investigating the effect of hormones on metabolite profiles in germinating barley grain, being helpful for identifying the factors affecting barley germination or malt quality.
Publisher: Wiley
Date: 11-2000
DOI: 10.2135/CROPSCI2000.4061755X
Abstract: The genus Avena contains 30 different species from diploid through tetraploid to hexaploid with different genome compositions. Research regarding the origin of the different genomes in the polyploid species has been inconclusive. The objectives of this research were to investigate the phylogenetic relationships of the Avena species by means of polymorphisms in satellite, minisatellite, and microsatellite DNA. A satellite DNA sequence, ASS49, was isolated from a microsatellite‐enriched library of the hexaploid oat Avena sativa L. Southern hybridization showed that ASS49 was a species‐specific rather than a genome‐specific satellite. ASS49 was able to distinguish species that may be the diploid and tetraploid progenitors of hexaploid oat. The phylogenetic relationship of Avena species was further investigated using 40 microsatellite and four minisatellite primers. These results appeared to support the findings with ASS49. It appears that the Ac‐genome diploid species ( A. canariensis Baum Raj. et S .) is the progenitor and A‐genome donor of the hexaploid oat rather than the generally believed As‐genome species ( A. strigosa Schreber). Instead, A. strigosa appears to be a member of a separate lineage of diploid and tetraploid species including the tetraploid species A. abyssinica Hochst.
Publisher: Springer Science and Business Media LLC
Date: 11-09-2020
Publisher: Springer Science and Business Media LLC
Date: 11-12-2019
DOI: 10.1038/S41598-019-53620-5
Abstract: Grain filling is an important growth process in formation of yield and quality for barley final yield determination. To explore the grain development behavior during grain filling period in barley, a high-density genetic map with 1962 markers deriving from a doubled haploid (DH) population of 122 lines was used to identify dynamic quantitative trait locus (QTL) for grain filling rate (GFR) and five grain size traits: grain area (GA), grain perimeter (GP), grain length (GL), grain width (GW) and grain diameter (GD). Unconditional QTL mapping is to detect the cumulative effect of genetic factors on a phenotype from development to a certain stage. Conditional QTL mapping is to detect a net effect of genetic factors on the phenotype at adjacent time intervals. Using unconditional, conditional and covariate QTL mapping methods, we successfully detected 34 major consensus QTLs. Moreover, certain candidate genes related to grain size, plant height, yield, and starch synthesis were identified in six QTL clusters, and in idual gene was specifically expressed in different grain filling stages. These findings provide useful information for understanding the genetic basis of the grain filling dynamic process and will be useful for molecular marker-assisted selection in barley breeding.
Publisher: Centro Internacional de Agricultura Tropical
Date: 31-05-2019
Abstract: Keynote paper presented at the International Leucaena Conference, 1‒3 November 2018, Brisbane, Queensland, Australia.Strategies to breed sterile leucaena for Western Australia include plant breeding and biotechnology tools to generate sterile lines at both the tetraploid and triploid ploidy levels. For tetraploids, the main target species is the commercial Leucaena leucocephala, that is well known for its potential as a high-quality, productive and persistent forage. Gene editing technologies (CRISPR) will be utilized to edit out flowering genes and develop a non-flowering L. leucocephala. For triploids, the strategy is to cross tetraploid species (L. leucocephala and/or L. ersifolia) with diploid species to generate sterile triploid hybrids. The diploid parents will include species that have good forage attributes such as L. collinsii, L. macrophylla, L. shannonii and L. pulverulenta. Several of these triploid crosses have already been created by the Department of Primary Industries and Regional Development (Perth, Western Australia) and will be evaluated in the Kimberley and Pilbara regions of Western Australia for their agronomic performance and sterility. Vegetative propagation will be required for the tetraploid gene-edited non-flowering L. leucocephala. Triploids can either be vegetatively propagated, once generated, or generated via a seed production nursery.
Publisher: Wiley
Date: 09-11-2011
Publisher: Frontiers Media SA
Date: 05-08-2021
DOI: 10.3389/FGENE.2021.695791
Abstract: Selection for resistance against gray leaf spot (GLS) is a major objective in the lupin breeding programs. A segregation ratio of 1:1 (resistant:susceptible) in F 8 recombinant inbred lines (RIL 8 ) derived from a cross between a breeding line 83A:476 (resistant to GLS) and a wild accession P27255 (susceptible to GLS) indicated that GLS was controlled by a single major gene. To develop molecular markers linked to GLS, in the beginning, only 11 resistant lines and six susceptible lines from the 83A:476 and P27255 population were genotyped with MFLP markers, and three MFLP markers were identified to be co-segregated with GLS. This method was very efficient, but the markers were located outside of the gene, and could not be used in other germplasms. Then QTL analysis and fine mapping were conducted to identify the gene. Finally, the gene was narrowed down to a 241-kb region containing two disease resistance genes. To further identify the candidate gene, DNA variants between accessions Tanjil (resistant to GLS) and Unicrop (susceptible to GLS) were analyzed. The results indicated that only one SNP was detected in the 241 kb region. This SNP was located in the TMV resistance protein N-like gene region and also identified between 83A:476 and P27255. Genotyping the Tanjil/Unicrop RIL 8 population showed that this SNP co-segregated with GLS resistance. The phylogenetic tree analysis of this gene among 18 lupin accessions indicates that Australian resistant breeding line/varieties were clustered into one group and carry two resistant alleles, while susceptible accessions were clustered into different groups.
Publisher: Frontiers Media SA
Date: 08-01-2018
Publisher: Zhejiang University Press
Date: 06-2020
Publisher: Springer Science and Business Media LLC
Date: 05-2018
Publisher: Elsevier BV
Date: 10-2022
DOI: 10.1016/J.PLAPHY.2022.07.027
Abstract: Extreme weather events have become more frequent, increasing crop yield fluctuations in many regions and thus the risk to global food security. Breeding crop cultivars with improved tolerance to a combination of abiotic stresses is an effective solution to counter the adverse impact of climate change. The ever-increasing genomic data and analytical tools provide unprecedented opportunities to mine genes with tolerance to multiple abiotic stresses through bioinformatics analysis. We undertook an integrated meta-analysis using 260 transcriptome data of barley related to drought, salt, heat, cold, and waterlogging stresses. A total of 223 shared differentially expressed genes (DEGs) were identified in response to five abiotic stresses, and significantly enriched in 'glutathione metabolism' and 'monoterpenoid biosynthesis' pathways. Using weighted gene co-expression network analysis (WGCNA), we further identified 15 hub genes (e.g., MYB, WRKY, NADH, and GST4) and selected the GST4 gene for functional validation. HvGST4 overexpression in Arabidopsis thaliana enhanced the tolerance to multiple abiotic stresses, likely through increasing the content of glutathione to scavenge reactive oxygen species and alleviate cell membrane peroxidation. Furthermore, we showed that virus-induced gene silencing (VIGS) of HvGST4 in barley leaves exacerbated cell membrane peroxidation under five abiotic stresses, reducing tolerance to multiple abiotic stress. Our study provides a new solution for identifying genes with tolerance to multiple abiotic stresses based on meta-analysis, which could contribute to breeding new varieties adapted genetically to adverse environmental conditions.
Publisher: Elsevier BV
Date: 02-2021
Publisher: CSIRO Publishing
Date: 2020
DOI: 10.1071/CP20169
Abstract: The gene HvDEP1, on barley (Hordeum vulgare L.) chromosome 5H, encodes a γ-subunit of the heterotrimeric G-protein complex and was previously determined to be a candidate gene underlying a major quantitative trait locus for grain length. In the present study, we identified a 9 bp indel (insertion–deletion mutation) at position –84 bp from the start codon within a reported upstream open reading frame located in the 5′ UTR (untranslated region) and developed a diagnostic molecular marker. We also identified a 13 bp indel (–514 bp) in linkage disequilibrium that bridges an important regulatory motif. Using a doubled-haploid population and a barley ersity panel, we were able to show that the effects of these indels were environmentally stable and consistently delineated phenotypic groups based on grain length and 1000-grain weight. Genotypes represented by deletions at these two positions relative to the reference cv. Morex had consistently shorter grains, by 3.69–3.96%, and lower 1000-grain weight, by 2.38–4.21%, in a doubled-haploid population studied. Additionally, a ersity panel was tested but consistent differences were observed only for grain length, reinforcing literature indicating the importance of this gene for grain-length regulation. The frequency of the longer and heavier grained reference allele was higher in modern cultivars, suggesting that indirect selection for longer grain may have occurred through direct selection for grain yield via grain-weight improvement. These results indicate that grain length and 1000-grain weight in barley can be manipulated by targeting variation in gene promoters through marker-assisted selection.
Publisher: Springer Science and Business Media LLC
Date: 13-04-2013
Publisher: Frontiers Media SA
Date: 31-03-2016
Publisher: Springer Netherlands
Date: 2007
Publisher: MDPI AG
Date: 17-05-2022
Abstract: Crop heat stress is a threat to food supply, with heatwaves expected to increase in frequency and intensity globally. In addition to yield loss, heat stress dramatically reduces fertility and seed-setting rate, grain quality and weight, and seed germination and growth. Genetic variability for heat stress tolerance can be used in breeding programs to develop tolerant genotypes. The availability of genome assemblies with high-confidence sequences for many cereal crops, including rice, maize, wheat and barley, now allows the identification of heat stress tolerance-associated genes and gene networks. This review focuses on synthesizing current advances in understanding the detrimental effects of heat stress on cereal crop production at the physiological and genetic levels. It provides an account of available genomic resources, genetic variation, candidate genes, and molecular markers for heat stress tolerance. Lastly, this review offers insight into crop genetic improvement for heat stress tolerance, including germplasm screening in glasshouse and field trials, marker-assisted selection, mapping genomic loci and identification of candidate genes, and genomic-assisted breeding.
Publisher: Informa UK Limited
Date: 2009
Publisher: Wiley
Date: 29-04-2014
DOI: 10.1111/JAC.12068
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR03037
Abstract: A genetic linkage map of Hordeum vulgare L. 1280 cM in length, composed of 257 AFLP, RFLP, SNP, and microsatellite markers, has been constructed. The map was based on a doubled haploid population made from the cross Sloop (spring type) × Halcyon (winter type). The genetic map was used to identify qualitative major genes and quantitative trait loci (QTLs) affecting traits related to growth and flowering, grain colour, and disease resistance. Nine QTLs associated with grain colour (brightness, redness, yellowness, blue aleurone colour), plant height, 'intrinsic lateness', awn emergence, response to photoperiod, and spring or winter habit were located on 1H, 2H, 3H, 4H, and 5H. Eight QTLs associated with resistance to scald, net form of net blotch, leaf rust and powdery mildew were identified on chromosomes 1H, 2H, 3H, 4H, 5H, and 7H. The estimated magnitude of the QTL effects ranged from 9 to 85% of the total phenotypic variance. Resistances to leaf scald, net blotch, and leaf rust, and photoperiod and grain colour, were each controlled by at least one major gene.
Publisher: Springer Science and Business Media LLC
Date: 26-01-2023
DOI: 10.1186/S13059-023-02861-9
Abstract: A pangenome aims to capture the complete genetic ersity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking. To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants’ position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 erse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic ersity. We characterize a new locus ( qPH8-1 ) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS). Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.
Publisher: Wiley
Date: 27-07-2023
DOI: 10.1111/PBI.14077
Publisher: Canadian Science Publishing
Date: 10-2009
DOI: 10.1139/G09-058
Abstract: Fifty-two SSR markers were used to evaluate the genetic ersity of 33 Qinghai-Tibetan wild barley accessions, 56 landraces collected primarily from other parts of China, and 1 Israeli wild barley accession. At the 52 SSR loci, 206 alleles were detected for the 90 accessions, among which 111 were common alleles. The number of alleles per locus ranged from 1 to 9, with an average of 4.0. Polymorphism information content (PIC) values ranged from 0 to 0.856 among all the markers, with an average of 0.547. The PIC value of Qinghai-Tibetan wild barley varied from 0 to 0.813 with an average of 0.543, while in landraces, the markers showed a range of 0 to 0.790 with an average of 0.490. The SSR markers could clearly differentiate the Qinghai-Tibetan wild barley from the landraces. Twenty-four unique alleles were observed in Qinghai-Tibetan wild barley, and the frequency of unique alleles in Qinghai-Tibetan wild barley was about 2.1 times higher than that in the landraces, on average. Five of the 7 chromosomes had more unique alleles in the Qinghai-Tibetan wild barley, but chromosome 2H had more unique alleles in the landraces. The presence of many unique alleles may reflect the adaptation of this barley germplasm to erse environments and production systems.
Publisher: Elsevier
Date: 2016
Publisher: Elsevier BV
Date: 03-2021
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02186
Abstract: Single nucleotide polymorphisms (SNPs) have been identified in a range of plant genomes. Development of rapid, low-cost methods to enable their validation and implementation as molecular markers is now required for practical applications. We report the development of single and multi-nucleotide primer extension assays to genotype co-dominant SNPs from small quantities of barley leaf tissue. In the single nucleotide primer extension assay, a genotyping primer with its 3′ end directly flanking a SNP was annealed to a target sequence and extended by a single dideoxynucleotide triphosphate complementary to the polymorphic base. In the multi-nucleotide primer extension assay, designed to facilitate allele calling, the genotyping primer with its 3′ end flanking the SNP was extended by either 1 or 2 nucleotides, depending on the allele encountered. Extension products were analysed using MALDI-ToF mass spectrometry and, making use of the molecular weight difference between DNA bases, the incorporated nucleotides were identified by the increase in mass of the extended primers. Based on a SNP identified in the barley Mlo gene, primer extension assays were designed and used for co-dominant marker-assisted selection of barley seedlings segregating for mlo-mediated resistance to powdery mildew. This allowed accurate selection of progeny lines carrying alleles for resistance to powdery mildew, including heterozygotes. Doubled haploid barley progenies were screened for Mlo alleles and a complete correlation between mlo/mlo genotype and resistant phenotype was found The method has been used by barley breeders for routine selection of barley genotypes resistant to powdery mildew.
Publisher: Springer Science and Business Media LLC
Date: 18-02-2011
Publisher: Frontiers Media SA
Date: 12-2022
DOI: 10.3389/FPLS.2022.1063988
Abstract: Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.
Publisher: Cold Spring Harbor Laboratory
Date: 17-10-2020
DOI: 10.1101/2020.10.17.343632
Abstract: MYB transcription factors (TFs) represents one of the largest TF families in plants. In this study, we performed genome-wide MYB-domain screening and identified a total of 997 MYBs in wheat (Triticum aestivum), among which 445 were 2-domain MYBs (R2R3-MYBs) that were clustered into 15 subgroups with varied conservation profiles. Homologous genes were highly conserved across the three subgenomes, with minor variations contributed by segmental duplications. Tandem and proximal gene duplications have contributed significantly to the expansion of the wheat Myb gene family. Furthermore, comprehensive transcriptome profiling of R2R3-Myb genes in 61 different tissue and time point s les revealed a clear pattern of temporal and spatial variations within six expression groups. The comprehensive genomic and transcriptional analyses provided valuable insights into the evolution and biological functions of R2R3-Myb genes in wheat. They would serve as a useful guide to further investigate the potential agronomic traits controlled by this large TF family.
Publisher: Springer Science and Business Media LLC
Date: 12-2019
DOI: 10.1186/S13059-019-1899-5
Abstract: Chromosome-scale genome sequence assemblies underpin pan-genomic studies. Recent genome assembly efforts in the large-genome Triticeae crops wheat and barley have relied on the commercial closed-source assembly algorithm DeNovoMagic. We present TRITEX, an open-source computational workflow that combines paired-end, mate-pair, 10X Genomics linked-read with chromosome conformation capture sequencing data to construct sequence scaffolds with megabase-scale contiguity ordered into chromosomal pseudomolecules. We evaluate the performance of TRITEX on publicly available sequence data of tetraploid wild emmer and hexaploid bread wheat, and construct an improved annotated reference genome sequence assembly of the barley cultivar Morex as a community resource.
Publisher: Springer Science and Business Media LLC
Date: 19-03-2020
DOI: 10.1007/S00122-020-03579-Z
Abstract: A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing in idual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.
Publisher: Elsevier BV
Date: 10-2014
Publisher: CSIRO Publishing
Date: 2008
DOI: 10.1071/AR07205
Abstract: We report the first quantitative trait loci (QTL) mapped in an F8 recombinant inbred line (RIL) population of Lupinus angustifolius. Traits mapped were early vigour, days to flowering, height at maturity, and seed size. Twenty-two QTLs were found, located on 13 linkage groups, with alleles beneficial to the crop contributed by both parents. Early vigour was controlled by 8 QTLs on 7 linkage groups. Time to flowering was controlled by 10 QTLs and the height at maturity was found to be under the control of 4 QTLs. Seed size was linked to 2 QTLs. A region linked to the Ku gene that promotes early flowering by removal of the vernalisation requirement appeared to play a role in all 4 traits. The gene mollis controlling soft-seededness appeared to also be linked to early vigour, and iucundis controlling alkaloid production was linked to seed size. Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use these data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula highlighted.
Publisher: Frontiers Media SA
Date: 30-11-2018
Publisher: MDPI AG
Date: 29-07-2021
Abstract: Waterlogging occurs when soil is saturated with water, leading to anaerobic conditions in the root zone of plants. Climate change is increasing the frequency of waterlogging events, resulting in considerable crop losses. Plants respond to waterlogging stress by adventitious root growth, aerenchyma formation, energy metabolism, and phytohormone signalling. Genotypes differ in biomass reduction, photosynthesis rate, adventitious roots development, and aerenchyma formation in response to waterlogging. We reviewed the detrimental effects of waterlogging on physiological and genetic mechanisms in four major cereal crops (rice, maize, wheat, and barley). The review covers current knowledge on waterlogging tolerance mechanism, genes, and quantitative trait loci (QTL) associated with waterlogging tolerance-related traits, the conventional and modern breeding methods used in developing waterlogging tolerant germplasm. Lastly, we describe candidate genes controlling waterlogging tolerance identified in model plants Arabidopsis and rice to identify homologous genes in the less waterlogging-tolerant maize, wheat, and barley.
Publisher: Zhejiang University Press
Date: 03-07-2023
Abstract: Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
Publisher: Public Library of Science (PLoS)
Date: 03-09-2013
Publisher: Springer Science and Business Media LLC
Date: 19-03-2014
Publisher: Bentham Science Publishers Ltd.
Date: 10-2022
DOI: 10.2174/2210298102666220324112842
Abstract: Environmental stresses adversely impact crop production, crop quality, and product safety. Climate change is predicted to exacerbate the impacts of stresses on current cropping systems with multilateral impacts on crop productivity and yield, bio ersity, soil fertility, microbial activity, and carbon sequestration. Transforming crop production systems and developing stress and climate- resilient crops are paramount to alleviate pervasive food and nutrition security and food safety issues and achieve a world free from hunger and malnutrition. Modern breeding techniques have been the key to transforming crop production systems and developing stress- and climate-resilient crops. As a rapidly evolving technology, the Nobel Prize-winning CRISPR method is a leading choice for genome editing and a possible major contributor to solving environmental and food insecurity issues. Here, a background on the stressors with far-reaching impacts on food security has been provided, and the principles and advances in classical genome editing (CRISPR/Cas9) that generate DNA double-strand breaks (DSB) have been reviewed. Base editing and prime editing platforms, which are DSB- and template-free, enabling targeted base substitutions, have been discussed. The application of such tools for trait improvement has been evaluated to develop stressresilient crops and high-throughput mutant libraries. Recent developments in the regulatory landscape for genome-edited crops in various countries have been examined. Finally, the challenges and future perspectives toward crop improvement have been highlighted.
Publisher: Cold Spring Harbor Laboratory
Date: 25-02-2022
DOI: 10.1101/2022.02.23.481560
Abstract: Bread wheat is one of humanity’s most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, h ering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a erse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes. Database URL: www.appliedbioinformatics.com.au/wheat_panache
Publisher: Springer Science and Business Media LLC
Date: 18-01-2019
Publisher: Public Library of Science (PLoS)
Date: 20-08-2012
Publisher: Frontiers Media SA
Date: 28-06-2016
Publisher: Elsevier BV
Date: 12-2022
Publisher: Elsevier
Date: 2016
Publisher: Frontiers Media SA
Date: 19-12-2016
Publisher: MDPI AG
Date: 22-02-2020
DOI: 10.3390/IJMS21041516
Abstract: Salt stress is one of the major environmental factors impairing crop production. In our previous study, we identified a major QTL for salinity tolerance on chromosome 2H on barley (Hordeum vulgare L.). For further investigation of the mechanisms responsible for this QTL, two pairs of near-isogenic lines (NILs) differing in this QTL were developed. Sensitive NILs (N33 and N53) showed more severe damage after exposure to 300 mM NaCl than tolerant ones (T46 and T66). Both tolerant NILs maintained significantly lower Na+ content in leaves and much higher K+ content in the roots than sensitive lines under salt conditions, thus indicating the presence of a more optimal Na+/K+ ratio in plant tissues. Salinity stress caused significant accumulation of H2O2, MDA, and proline in salinity-sensitive NILs, and a greater enhancement in antioxidant enzymatic activities at one specific time or tissues in tolerant lines. One pair of NILs (N33 and T46) were used for proteomic studies using two-dimensional gel electrophoresis. A total of 53 and 51 differentially expressed proteins were identified through tandem mass spectrometry analysis in the leaves and roots, respectively. Proteins which are associated with photosynthesis, reactive oxygen species (ROS) scavenging, and ATP synthase were found to be specifically upregulated in the tolerant NIL. Proteins identified in this study can serve as a useful resource with which to explore novel candidate genes for salinity tolerance in barley.
Publisher: Wiley
Date: 29-03-2011
Publisher: MDPI AG
Date: 26-11-2021
Abstract: Root-derived mobile signals play critical roles in coordinating a shoot’s response to underground conditions. However, the identification of root-to-shoot long-distance mobile signals has been scant. In this study, we aimed to characterize root-to-shoot endogenous mobile miRNAs by using an Arabidopsis/Nicotiana interfamilial heterograft in which these two taxonomically distant species with clear genetic backgrounds had sufficient ersity in differentiating miRNA sources. Small RNA deep sequencing analysis revealed that 82 miRNAs from the Arabidopsis scion could travel through the graft union to reach the rootstock, whereas only a very small subset of miRNA (6 miRNAs) preferred the root-to-shoot movement. We demonstrated in an ex vivo RNA imaging experiment that the root-to-shoot mobile Nb-miR164, Nb-miR395 and Nb-miR397 were targeted to plasmodesmata using the bacteriophage coat protein MS2 system. Furthermore, the Nb-miR164 was shown to move from the roots to the shoots to induce phenotypic changes when its overexpressing line was used as rootstock, strongly supporting that root-derived Nb-miR164 was able to modify the scion trait via its long-distance movement.
Publisher: Wiley
Date: 05-10-2018
DOI: 10.1111/PBI.12826
Publisher: Frontiers Media SA
Date: 04-09-2020
Publisher: Wiley
Date: 16-11-2022
DOI: 10.1111/PBI.13917
Abstract: Divergent selection of populations in contrasting environments leads to functional genomic ergence. However, the genomic architecture underlying heterogeneous genomic differentiation remains poorly understood. Here, we de novo assembled two high-quality wild barley (Hordeum spontaneum K. Koch) genomes and examined genomic differentiation and gene expression patterns under abiotic stress in two populations. These two populations had a shared ancestry and originated in close geographic proximity but experienced different selective pressures due to their contrasting micro-environments. We identified structural variants that may have played significant roles in affecting genes potentially associated with well-differentiated phenotypes such as flowering time and drought response between two wild barley genomes. Among them, a 29-bp insertion into the promoter region formed a cis-regulatory element in the HvWRKY45 gene, which may contribute to enhanced tolerance to drought. A single SNP mutation in the promoter region may influence HvCO5 expression and be putatively linked to local flowering time adaptation. We also revealed significant genomic differentiation between the two populations with ongoing gene flow. Our results indicate that SNPs and small SVs link to genetic differentiation at the gene level through local adaptation and are maintained through ergent selection. In contrast, large chromosome inversions may have shaped the heterogeneous pattern of genomic differentiation along the chromosomes by suppressing chromosome recombination and gene flow. Our research offers novel insights into the genomic basis underlying local adaptation and provides valuable resources for the genetic improvement of cultivated barley.
Publisher: Springer Science and Business Media LLC
Date: 08-02-2014
Publisher: Springer Science and Business Media LLC
Date: 21-11-2018
DOI: 10.1007/S00122-018-3243-Y
Abstract: A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection.
Publisher: Springer Science and Business Media LLC
Date: 14-11-2015
Publisher: Frontiers Media SA
Date: 20-11-2018
Publisher: Canadian Science Publishing
Date: 02-2003
DOI: 10.1139/G02-099
Abstract: Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota × Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed in idually within the most likely framework interval using χ 2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.Key words: molecular marker, RFLP, linkage map, oat, Avena.
Publisher: Springer Netherlands
Date: 13-08-2012
Publisher: Elsevier
Date: 2016
Publisher: Springer Netherlands
Date: 13-08-2012
Publisher: Springer Science and Business Media LLC
Date: 23-06-2020
Publisher: Springer Netherlands
Date: 13-08-2012
Publisher: Public Library of Science (PLoS)
Date: 29-05-2013
Publisher: Wiley
Date: 08-02-2022
DOI: 10.1111/JIPB.13214
Abstract: Nitrogen is a major determinant of grain yield and quality. As excessive use of nitrogen fertilizer leads to environmental pollution and high production costs, improving nitrogen use efficiency (NUE) is fundamental for a sustainable agriculture. Here, we dissected the role of the barley abnormal cytokinin response1 repressor 1 ( HvARE1 ) gene, a candidate for involvement in NUE previously identified in a genome‐wide association study, through natural variation analysis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9)‐mediated gene editing. HvARE1 was predominantly expressed in leaves and shoots, with very low expression in roots under low nitrogen conditions. Agrobacterium ‐mediated genetic transformation of immature embryos ( cv . Golden Promise) with single guide RNAs targeting HvARE1 generated 22 T 0 plants, from which four T 1 lines harbored missense and/or frameshift mutations based on genotyping. Mutant are1 lines exhibited an increase in plant height, tiller number, grain protein content, and yield. Moreover, we observed a 1.5‐ to 2.8‐fold increase in total chlorophyll content in the flag leaf at the grain filling stage. Delayed senescence by 10–14 d was also observed in mutant lines. Barley are1 mutants had high nitrogen content in shoots under low nitrogen conditions. These findings demonstrate the potential of ARE1 in NUE improvement in barley.
Publisher: Springer Science and Business Media LLC
Date: 12-2017
Publisher: Springer Science and Business Media LLC
Date: 04-12-2020
DOI: 10.1007/S00122-019-03498-8
Abstract: In the original publication of this article, the acknowledgement section has been missed to publish. Now the same has been provided in this correction.
Publisher: Springer Science and Business Media LLC
Date: 31-07-2010
Publisher: Springer Science and Business Media LLC
Date: 2001
Publisher: MDPI AG
Date: 07-01-2021
Abstract: Seed germination and seedling establishment are the most critical stages in the barley (Hordeum vulgare ssp. vulgare L.) life cycle that contribute substantially to grain yield. These two phases are exposed to several forms of environmental stresses such as salinity due to high level of salt accumulation in the soil rhizosphere where seed germination takes place and seedlings emerge from. Previously, we have reported genotypic variability and independent QTLs associated with salinity tolerance at seedling and germination stages. However, genotypic studies on revival of a seedling germinating under salinity stress are yet to close the lack of information between germination and seedling stages. Here, we attempt to close the genetic gap by targeting early seedling survival traits in barley after germination under salinity (NaCl) stress and the various seedling vigour indices. Seedling vigour parameters formed the basis for Quantitative trait locus (QTL) linkage mapping in 103 Doubled Haploid (DH) lines of CM72/Gairdner population, and validated the phenotypic response using a selected erse panel of 85 barley germplasm. The results indicate that 150 mM NaCl stress significantly reduced all the recorded phenotypic traits compared to 75, 90 and 120 mM NaCl. In both DH population and ersity panel barley germplasm, the highest percentage reduction was recorded in shoot length (65.6% and 50.3%) followed by seedling vigour index length (56.5% and 41.0%), while root length (28.6% and 15.8%) and root dry weight (29.3% and 28.0%) were least reduced when control was compared to150 mM NaCl stress treatment. Six QTLs containing 13 significant markers were detected in the DH population, 3 on chromosomes 1H, 8 on 3H and 2 on 4H with LOD values ranging from 3 to 8 associated with seedling survival traits under salinity stress. Three QTLs one on 1H and two on 3H with closely linked significant markers (Bmac0032, bPb-9418 and bPb-4741), (bPb-4576 and bPb-9624) and (bPb-3623, bPb-5666 and bPb-6383) for 1H and two on 3H respectively formed the regions with high possibility of candidate genes. A QTL on 3H flanked with markers bPb-4576 and bPb-9624 that were detected in more than one salinity survival trait and were closely linked to each other will form a basis for detailed studies leading to gene functional analysis, genetic transformation and marker assisted selection (MAS).
Publisher: Elsevier BV
Date: 10-2013
Publisher: Springer Science and Business Media LLC
Date: 11-06-2015
Publisher: Springer Netherlands
Date: 13-08-2012
Publisher: Springer Science and Business Media LLC
Date: 29-07-2015
Publisher: Springer Science and Business Media LLC
Date: 31-05-2021
DOI: 10.1007/S00122-021-03865-4
Abstract: Using genomic structural equation modelling, this research demonstrates an efficient way to identify genetically correlating traits and provides an effective proxy for multi-trait selection to consider the joint genetic architecture of multiple interacting traits in crop breeding. Breeding crop cultivars with optimal value across multiple traits has been a challenge, as traits may negatively correlate due to pleiotropy or genetic linkage. For ex le, grain yield and grain protein content correlate negatively with each other in cereal crops. Future crop breeding needs to be based on practical yet accurate evaluation and effective selection of beneficial trait to retain genes with the best agronomic score for multiple traits. Here, we test the framework of whole-system-based approach using structural equation modelling (SEM) to investigate how one trait affects others to guide the optimal selection of a combination of agronomically important traits. Using ten traits and genome-wide SNP profiles from a worldwide barley panel and SEM analysis, we revealed a network of interacting traits, in which tiller number contributes positively to both grain yield and protein content we further identified common genetic factors affecting multiple traits in the network of interaction. Our method demonstrates an efficient way to identify genetically correlating traits and underlying pleiotropic genetic factors and provides an effective proxy for multi-trait selection within a whole-system framework that considers the joint genetic architecture of multiple interacting traits in crop breeding. Our findings suggest the promise of a whole-system approach to overcome challenges such as the negative correlation of grain yield and protein content to facilitating quantitative and objective breeding decisions in future crop breeding.
Publisher: Informa UK Limited
Date: 17-09-2009
Publisher: Springer Science and Business Media LLC
Date: 18-10-2020
DOI: 10.1007/S00122-019-03448-4
Abstract: An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F
Publisher: Springer Science and Business Media LLC
Date: 17-11-2012
Publisher: Springer Science and Business Media LLC
Date: 04-2019
DOI: 10.1038/S41597-019-0011-Z
Abstract: In barley and other cereal crops, phenological ersity drives adaptation to different cultivation areas. Improvement of barley yield and quality traits requires adaptation to specific production areas with introgression of favorable alleles dependent upon precise identification of the underlying genes. Combining targeted sequence capture systems with next-generation sequencing provides an efficient approach to explore target genetic regions at high resolution, and allows rapid discovery of thousands of genetic polymorphisms. Here, we apply a versatile target-capture method to detect genome-wide polymorphisms in 174 flowering time-related genes, chosen based on prior knowledge from barley, rice, and Arabidopsis thaliana . Sequences were generated across a phenologically erse panel of 895 barley varieties, resulting a high mean depth coverage of ~25x allowing reliable discovery and calling of insertion-deletion (InDel) and single nucleotide polymorphisms (SNPs). Sequences of InDel and SNPs from the targeted enrichment were utilized to develop 67 Kompetitive Allele Specific PCR (KASP) markers for validation. This work provides researchers and breeders a comprehensive molecular toolkit for the selection of phenology-related traits in barley.
Publisher: MDPI AG
Date: 22-08-2021
Abstract: Increased drought frequency due to climate change is limiting the agronomic performance of cereal crops globally, where cultivars often experience negative impacts on yield. Stomata are the living interface responsible for % of plant water loss through transpiration. Thus, stomata are a prospective target for improving drought tolerance by enhancing water-use efficiency (WUE) in economically important cereals. Reducing stomatal density through molecular approaches has been shown to improve WUE in many plant species, including the commercial cereals barley, rice, wheat and maize. Rice with reduced stomatal density exhibit yields 27% higher than controls under drought conditions, reflecting the amenability of grasses to stomatal density modification. This review presents a comprehensive overview of stomatal development, with a specific emphasis on the genetic improvement of WUE in the grass lineage. Improved understanding of the genetic regulation of stomatal development in the grasses, provides significant promise to improve cereal adaptivity in drought-prone environments whilst maximising yield potential. Rapid advances in gene-editing and ‘omics’ technologies may allow for accelerated adaption of future commercial varieties to water restriction. This may be achieved through a combination of genomic sequencing data and CRISPR-Cas9-directed genetic modification approaches.
Publisher: Springer Science and Business Media LLC
Date: 23-02-2016
DOI: 10.1007/S00122-016-2693-3
Abstract: Aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilized approach for the selection of waterlogging tolerant barley genotypes. One major QTL for aerenchyma formation after 7 days of waterlogging treatment was identified and the newly developed markers explained 44 % of the phenotypic variance. This QTL can now be effectively used in barley breeding programs. Waterlogging is one of the important limiting conditions for crop yield and productivity. The main feature of waterlogged soils is oxygen deprivation, due to slow gas diffusion in water. Decreased oxygen content in waterlogged soils leads to the oxygen deficiency in plant tissues, resulting in reduced energy availability for plants. Rapidly induced aerenchyma formation is critical to maintaining adequate oxygen supply and overall waterlogging tolerance in barley. In this study, we have proved that quantifying aerenchyma formation after 7 days of waterlogging in commercial potting mixture can be a reliable, fast, and widely utilised approach for the selection of waterlogging tolerant barley genotypes, which is supported by measurements of redox potential (an indicator of anaerobic conditions). This protocol was also used to identify quantitative trait loci (QTL) in a doubled haploid population of barley from the cross between Yerong (tolerant) and Franklin (sensitive) genotypes. The QTL for aerenchyma formation and root porosity were at the same location as the waterlogging tolerance QTL. Seven new markers were developed and added onto this region on chromosome 4H. One major QTL for aerenchyma formation after 7 days waterlogging treatment explained 44.0 % of the phenotypic variance. This successful QTL for aerenchyma formation can be effectively used in the marker assisted selection to improve waterlogging tolerance in barley.
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02237
Abstract: The quality of barley for the range of end uses from animal feed to brewing is determined by many genes, making the breeding of new barley varieties difficult. Understanding of the molecular basis of barley quality has been advanced by biochemical studies. More recently, molecular genetic tools are allowing the analysis of the biochemical factors contributing to grain quality. Many genetic loci influencing key quality attributes have been identified by gene mapping. Limited success has been reported in using this information to select for quantitative trait loci for these quality traits in plant breeding. Genomic techniques allowing more detailed analysis of variations in the barley genome in relation to quality promise to extend significantly the value of molecular genetic approaches to barley quality improvement. Definition of the genetic basis of malting quality requires the identification of the genes involved in germination and endosperm modification. Feed quality remains difficult to define. Recent advances are likely to accelerate the rate of discovery, providing new options for analysis of barley quality.
Publisher: Frontiers Media SA
Date: 24-04-2019
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02238
Abstract: A genetic map of barley with 224 AFLP and 39 simple sequence repeat (SSR) markers was constructed using a doubled haploid (DH) mapping population from a cross between the varieties Tallon and Kaputar. Linkage groups were assigned to in idual barley chromosomes using the published map locations of the SSR markers as reference points. This genetic map was used to identify markers with linkage to agronomic, disease, and quality traits in barley. The population, which comprised 65 lines, was tested in a range of environments across Australia. Quantitative trait loci (QTLs) analyses were performed using software packages MapMaker, MapManager, and Qgene. Significant associations with markers were found for several traits. Grain yield showed significant association with regions on chromosomes 2H, 3H, and 5H over a range of sites throughout Australia. Regions on chromosomes 2H and 3H explained 30% and 26% of variation in lodging, respectively. Among quality traits, diastatic power was associated with regions on chromosomes 1H, 2H, and 5H (R2 = 37%). Hot water extract was associated with a region on chromosome 6H and a marker not assigned to a chromosome (R2 = 45%). There were also environment-specific QTLs for the traits analysed. The markers identified here present an opportunity for marker assisted selection of lines for these traits in barley breeding programs.Mapping and QTL analysis of Tallon × Kaputar
Publisher: Springer Science and Business Media LLC
Date: 08-02-2006
DOI: 10.1007/S00122-006-0228-Z
Abstract: Male sterility of wheat-breeding line 337S (Triticum aestivum L.) is sensitive to both short day-length/low temperature and long day-length/high temperature. 337S was crossed with the common wheat variety, Huamai No. 8 and the F1 was highly fertile. The F2 population segregated in a 15:1 ratio for fertility/sterility in 243 in iduals under long day-length/high-temperature. The two thermophotoperiod-responsive male sterile genes were mapped to chromosomes 5B and 2B using Simple Sequence Repeat (SSR) markers and bulked segregant analysis. Partial linkage maps around the sterility loci of chromosomes 2B and 5B were constructed using the 243 in iduals in the F2 population. One gene (wptms1) for male sterility was flanked by the SSR markers Xgwm335 and Xgwm371 at a genetic distance in chromosome 5B of 4.1 and 24.4 cM, respectively. The second gene (wptms2) was mapped between markers Xgwm374 and Xgwm120 at a genetic distance of 6.6 and 20.9 cM, respectively. The closest linked markers Xgwm335 (wptms1) and Xgwm374 (wptms2) explained 53 and 38% of phenotypic variation for the fertility. The SSR markers provide a useful tool to transfer the male sterile genes into elite wheat germplasm.
Publisher: Springer Science and Business Media LLC
Date: 05-03-2016
Publisher: The Institute of Brewing & Distilling
Date: 2010
Publisher: Springer Berlin Heidelberg
Date: 2010
Publisher: Frontiers Media SA
Date: 21-02-2020
Publisher: Informa UK Limited
Date: 26-06-2015
Publisher: Research Square Platform LLC
Date: 16-11-2021
DOI: 10.21203/RS.3.RS-1037957/V1
Abstract: Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley ( Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhance yield potential. Bi-parental populations were used intensively to map genes controlling flowering. However, the lack of genetic ersity in bi-parental populations can lead to low mapping resolution and low allele richness, rendering the identification of underlying functional alleles difficult. Multiparent mapping populations such as nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) can overcome these limitations. The higher genetic and phenotypic ersity of multiple parents allows high-resolution quantitative trait loci (QTL) mapping. In this study, we use a MAGIC population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq) and Kompetitive allele-specific polymerase chain reaction (KASP) genotyping. Phenotypic data was collected from 15 trials at different sites, across three consecutive years, various sowing times with/without vernalisation and extended photoperiod. This study detected 14 stable regions associated with flowering time across multiple environments. Minor regions associated with flowering time in certain environmental conditions were also identified. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. These associations provide opportunities to utilise specific genes/alleles to create barley varieties with better grain yield and adaptation to growing conditions.
Publisher: Springer Science and Business Media LLC
Date: 25-11-2020
DOI: 10.1038/S41586-020-2947-8
Abstract: Genetic ersity is key to crop improvement. Owing to pervasive genomic structural variation, a single reference genome assembly cannot capture the full complement of sequence ersity of a crop species (known as the ‘pan-genome’ 1 ). Multiple high-quality sequence assemblies are an indispensable component of a pan-genome infrastructure. Barley ( Hordeum vulgare L.) is an important cereal crop with a long history of cultivation that is adapted to a wide range of agro-climatic conditions 2 . Here we report the construction of chromosome-scale sequence assemblies for the genotypes of 20 varieties of barley—comprising landraces, cultivars and a wild barley—that were selected as representatives of global barley ersity. We catalogued genomic presence/absence variants and explored the use of structural variants for quantitative genetic analysis through whole-genome shotgun sequencing of 300 gene bank accessions. We discovered abundant large inversion polymorphisms and analysed in detail two inversions that are frequently found in current elite barley germplasm one is probably the product of mutation breeding and the other is tightly linked to a locus that is involved in the expansion of geographical range. This first-generation barley pan-genome makes previously hidden genetic variation accessible to genetic studies and breeding.
Publisher: Springer Science and Business Media LLC
Date: 21-10-2014
Publisher: Springer Science and Business Media LLC
Date: 18-01-2011
DOI: 10.1007/S10142-011-0209-4
Abstract: Low phytic acid grains can provide a solution to dietary micronutrient deficiency and environmental pollution. A low phytic acid 1-1 (lpa1-1) barley mutant was identified using forward genetics and the mutant gene was mapped to chromosome 2HL. Comparative genomic analysis revealed that the lpa1-1 gene was located in the syntenic region of the rice Os-lpa-MH86-1 gene on chromosome 4. The gene ortholog of rice Os-lpa-MH86-1 (designated as HvST) was isolated from barley using polymerase chain reaction and mapped to chromosome 2HL in a doubled haploid population of Clipper×Sahara. The results demonstrate the collinearity between the rice Os-lpa-MH86-1 gene and the barley lpa1-1 region. Sequence analysis of HvST revealed a single base pair substitution (C→T transition) in the last exon of the gene in lpa1-1 (M422), which resulted in a nonsense mutation. These results will facilitate our understanding of the molecular mechanisms controlling the low phytic acid phenotype and assist in the development of a diagnostic marker for the selection of the lpa1-1 gene in barley.
Publisher: Springer Science and Business Media LLC
Date: 13-01-2017
Publisher: Elsevier
Date: 2016
Publisher: MDPI AG
Date: 19-09-2022
Abstract: Salinity is a natural and anthropogenic process that plants overcome using various responses. Salinity imposes a two-phase effect, simplified into the initial osmotic challenges and subsequent salinity-specific ion toxicities from continual exposure to sodium and chloride ions. Plant responses to salinity encompass a complex gene network involving osmotic balance, ion transport, antioxidant response, and hormone signaling pathways typically mediated by transcription factors. One particular transcription factor mega family, WRKY, is a principal regulator of salinity responses. Here, we categorize a collection of known salinity-responding WRKYs and summarize their molecular pathways. WRKYs collectively play a part in regulating osmotic balance, ion transport response, antioxidant response, and hormone signaling pathways in plants. Particular attention is given to the hormone signaling pathway to illuminate the relationship between WRKYs and abscisic acid signaling. Observed trends among WRKYs are highlighted, including group II WRKYs as major regulators of the salinity response. We recommend renaming existing WRKYs and adopting a naming system to a standardized format based on protein structure.
Publisher: Cold Spring Harbor Laboratory
Date: 27-04-2020
DOI: 10.1101/2020.04.27.063065
Abstract: Chickpea is an economically important legume crop with high nutritional value in human diets. Aluminium-toxicity poses a significant challenge for the yield improvement of this increasingly popular crop in acidic soils. The wild progenitors of chickpea may provide a more erse gene pool for Al-tolerance in chickpea breeding. However, the genetic basis of Al-tolerance in chickpea and its wild relatives remains largely unknown. Here, we assessed the Al-tolerance of six selected wild Cicer accessions by measuring the root elongation in solution culture under control (0 µM Al 3+ ) and Al-treatment (30 µM Al 3+ ) conditions. Al-treatment significantly reduced the root elongation in all target lines compared to the control condition after 2-day’s growth. However, the relative reduction of root elongation in different lines varied greatly: 3 lines still retained significant root growth under Al-treatment, whilst another 2 lines displayed no root growth at all. We performed genome-wide identification of multidrug and toxic compound extrusion (MATE) encoding genes in the Cicer genome. A total of 56 annotated MATE genes were identified, which ided into 4 major phylogeny groups (G1-4). Four homologues to lupin LaMATE ( 50% aa identity named CaMATE1-4 ) were clustered with previously characterised MATEs related to Al-tolerance in various other plants. qRT-PCR showed that CaMATE2 transcription in root tips was significantly up-regulated upon Al-treatment in all target lines, whilst CaMATE1 was up-regulated in all lines except Bari2_074 and Deste_064, which coincided with the lines displaying no root growth under Al-treatment. Transcriptional profiling in five Cicer tissues revealed that CaMATE1 is specifically transcribed in the root tissue, further supporting its role in Al-detoxification in roots. This first identification of MATE-encoding genes associated with Al-tolerance in Cicer paves the ways for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.
Publisher: CABI
Date: 2012
Publisher: Springer Science and Business Media LLC
Date: 30-11-2015
Publisher: Frontiers Media SA
Date: 18-08-2022
Abstract: Phosphate (Pi) stress is an important environmental factor that limits plant growth and development. Of various posttranslational modifications (PTMs), protein phosphorylation and succinylation are the two most important PTMs that regulate multiple biological processes in response to Pi stress. However, these PTMs have been investigated in idually but their interactions with proteins in response to Pi stress remain poorly understood. In this study, to elucidate the underlying mechanisms of protein phosphorylation and succinylation in response to Pi stress, we performed a global analysis of the barley root phosphorylome and succinylome in Pi starvation and recovery stages, respectively. A total of 3,634 and 884 unique phosphorylated and succinylated proteins, respectively, corresponding to 11,538 and 2,840 phospho- and succinyl-sites, were identified of these, 275 proteins were found to be simultaneously phosphorylated and succinylated. Gene Set Enrichment Analysis was performed with a Kyoto Encyclopedia of Genes and Genomes pathway database revealing pathways that significantly enriched in the phosphorylome and succinylome. Such pathways, were dynamically regulated by Pi starvation and recovery treatments, and could be partitioned into distinct metabolic processes. In particular, phosphorylated proteins related to purine, the mitogen-activated protein kinase (MAPK) signaling pathway, pyrimidine, and ATP-binding cassette (ABC) transporters were upregulated in both Pi deprivation and recovery stages. Succinylated proteins, significantly upregulated by both Pi starvation and recovery, were enriched in nitrogen metabolism and phenylpropanoid biosynthesis. Meanwhile, succinylated proteins that were significantly downregulated by both Pi starvation and recovery were enriched in lysine degradation and tryptophan metabolism. This highlighted the importance of these metabolic pathways in regulating Pi homeostasis. Furthermore, protein–protein interaction network analyses showed that the response of central metabolic pathways to Pi starvation and recovery was significantly modulated by phosphorylation or succinylation, both in idually and together. In addition, we discovered relevant proteins involved in MAPK signaling and phenylpropanoid biosynthetic pathways existing in interactions between phosphorylated and succinylated proteins in response to Pi recovery. The current study not only provides a comprehensive analysis of phosphorylated and succinylated proteins in plant responses to Pi starvation and recovery, but also reveals detailed interactions between phosphorylated and succinylated proteins in barley roots.
Publisher: Frontiers Media SA
Date: 05-07-2021
Abstract: Halogeton glomeratus is a succulent annual herbaceous halophyte belonging to the Chenopodiaceae family, has attracted wide attention as a promising candidate for phytoremediation and as an oilseed crop and noodle-improver. More importantly, H. glomeratus has important medicinal value in traditional Chinese medicine. However, there are few comprehensive studies on the nutrients, particularly secondary metabolites. Here, we adopted untargeted metabolomics to compare the differences in metabolites of different tissues (root, stem, leaf, and seed) and identify the compounds related to pharmacological effects and response to abiotic stress in H. glomeratus. A total of 2,152 metabolites were identified, and the metabolic profiles of root, stem, leaf, and seed s les were clearly separated. More than 50% of the metabolites showed significant differences among root, stem, leaf, and seed. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of differential metabolites suggested an extensive alteration in the metabolome among the different organs. Furthermore, the identified metabolites related to pharmacological effects and response to abiotic stress included flavones, flavonols, flavandiols, glucosinolates, isoquinolines, pyridines, indoles, amino acids, lipids, carbohydrates, and ATP-binding cassette transporters. These metabolites have application in treating human cardiovascular diseases, cancers, diabetes, and heart disease, induce sleeping and have nutritive value. In plants, they are related to osmotic adjustment, alleviating cell damage, adjusting membrane lipid action and avoiding toxins. To the best of our knowledge, this is the first metabolomics-based report to overview the metabolite compounds in H. glomeratus and provide a reference for future development and utilization of H. glomeratus .
Publisher: Elsevier BV
Date: 03-2020
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02215
Abstract: A doubled haploid population of 120 in iduals was produced from the parents Chebec, an Australian 2-row barley of feed quality with resistance to the cereal cyst nematode, and Harrington, a 2-rowed, Canadian variety of premium malting quality. This paper describes 18 field and laboratory experiments conducted with the population and summarises the traits mapped and analysed. The genomic location of 25 traits and genes is described and marker–trait associations for 5 traits (malt extract, diastatic power, resistance to cereal cyst nematode, early flowering, resistance to pre-harvest sprouting) important to Australian efforts to improve malting barley varieties have been used in practical breeding programs. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.
Publisher: Elsevier BV
Date: 12-2013
Publisher: Springer Science and Business Media LLC
Date: 15-03-2015
DOI: 10.1007/S00122-015-2481-5
Abstract: One major QTL-controlling malt extract was identified on 2H, based on the data from four different environments and a large number of DH lines, determining 48% of phenotypic variation. This QTL is of a high value for marker-assisted selection. Improving malting quality traits is one of the major breeding objectives for barley breeding programmes. Among different quality traits, malt extract is one of the most important, determining the yield of beer production. The use of molecular markers linked to loci affecting the quality traits can greatly improve selection efficiency. However, the discovery of closely linked markers relies on not only the availability of the loci, but the accuracy of phenotyping. In this experiment, 188 doubled-haploid lines derived from the cross between a Japanese malting barley and a Chinese feed barley were grown in four different environments (two sites × 2 years). Different quality traits were determined and used to map QTL for these traits. Several QTLs were identified for different quality traits. One major QTL-controlling malt extract was identified on 2H and determined 48% of phenotypic variation with the closest marker of GBM1121. This QTL was consistently expressed in all four environments and is of a high value for marker-assisted selection in malting barley breeding.
Publisher: Springer Science and Business Media LLC
Date: 30-12-2014
Publisher: Public Library of Science (PLoS)
Date: 06-08-2015
Publisher: MDPI AG
Date: 08-05-2020
Abstract: Nitrogen (N) fertilization plays an important role in crop production however, excessive and inefficient use of N fertilizer is a global issue that incurs high production costs, pollutes the environment and increases the emission of greenhouse gases. To overcome these negative consequences, improving nitrogen use efficiency (NUE) would be a key factor for profitable crop production either by increasing yield or reducing fertilizer cost. In contrast to soil and crop management practices, understanding the molecular mechanisms in NUE and developing new varieties with improved NUE is more environmentally and economically friendly. In this review, we highlight the recent progress in understanding and improving nitrogen use efficiency in barley, with perspectives on the impact of N on plant morphology and agronomic performance, NUE and its components such as N uptake and utilization, QTLs and candidate genes controlling NUE, and new strategies for NUE improvement.
Publisher: CSIRO Publishing
Date: 2008
DOI: 10.1071/AR07345
Abstract: A genetic linkage map of barley with 128 molecular markers was constructed using a doubled haploid (DH) mapping population derived from a cross between barley (Hordeum vulgare) cvv. Stirling and Harrington. Quantitative trait loci controlling seed dormancy were characterised in the population. A major quantitative trait locus (QTL) controlling seed dormancy and accounting for over half the phenotypic variation (52.17%) was identified on the distal end of the long arm of chromosome 5H. Minor QTLs were also detected near the centromeric region of 5H and on chromosomes 1H and 3H. These minor QTLs with additive effects accounted for 7.52% of the phenotypic variance measured. Examination of epistatic interactions further detected additional minor QTLs near the centromere of 2H and on the long arm and short arms of 4H. Combinations of parental alleles at the QTL locations in predictive analyses indicated dramatic differences in germination. These results emphasise the potential differences in dormancy that can be achieved through the use of specific gene combinations and highlights the importance of minor genes and the epistatic interactions that occur between them. This study found that the combination of Stirling alleles at the two QTL locations on the 5H chromosome and Harrington alleles at the 1H and 3H QTL locations significantly produced the greatest dormancy. Uncovering gene complexes controlling the trait may enable breeders to produce superior genotypes with the desirable allele combinations necessary for manipulating seed dormancy in barley.
Publisher: Springer Berlin Heidelberg
Date: 2009
Publisher: CSIRO Publishing
Date: 2003
DOI: 10.1071/AR02210
Abstract: Barley seed dormancy is controlled by multiple genes that have a strong interaction with the environment. Lack of adequate dormancy results in pre-harvest sprouting in the field under wet weather conditions. On the other hand, too much dormancy has a detrimental effect in the malting house. There is only a very 'narrow window' of dormancy for malting barley. Harrington barley, which has been a dominant malting variety in the international market and widely used in Australia barley breeding programs, is highly susceptible to pre-harvest sprouting. A doubled haploid (DH) population derived from a cross of Chebec/Harrington was used to search for molecular markers linked with seed dormancy and pre-harvest sprouting. One major quantitative trait locus (QTL) was identified to control pre-harvest sprouting measured by α-amylase activity in barley grains, and could explain % of the phenotypic variation. This QTL was located on chromosome 5HL and flanked by restriction fragment length polymorphism (RFLP) marker CDO506 and simple sequence repeat (SSR) marker GMS1. The SSR marker (GMS1) linked with this QTL was further validated in a Stirling/Harrington DH population. A minor QTL on chromosome 2H accounted for 8% of phenotypic variation. Two QTLs for seed dormancy were located on chromosomes 2H and 5HL. The major QTL for dormancy coincided with the QTL for pre-harvest sprouting at chromosome 5HL and explained 61% of phenotypic variation. Since the presence of the Harrington allele at this locus favoured not only pre-harvest sprouting, but also increased malting extract, diastatic power, α-amylase, and free amino acid nitrogen, development of high malting quality varieties with pre-harvest sprouting tolerance would appear to be difficult.
Publisher: Springer Berlin Heidelberg
Date: 2010
Publisher: Springer Berlin Heidelberg
Date: 2009
Publisher: CSIRO Publishing
Date: 2006
DOI: 10.1071/AR05161
Abstract: The fertility of a wheat male sterile line 337S was investigated in 4 consecutive years with 18 different sowing dates. Line 337S showed high sterility under both short daylength/low temperature and long daylength/high temperature during ear development. It has 2 time windows to be used as a male sterile line for hybrid seed production. Its fertility rate can be % with suitable sowing time thus, it can be self-maintained as a male sterile line. Line 337S was reciprocally crossed with 7 common wheat varieties and the fertility of their F1, F2, and BC1 hybrids was investigated at different sowing dates. The results showed that recessive nuclear genes controlled male sterility in 337S and no cytoplasmic effect was observed. All common wheat varieties were able to restore its fertility. The male sterility was controlled by a pair of recessive genes under short daylength/low temperature, but was governed by 2 pairs of recessive genes under long daylength/high temperature. This novel male sterile line provides a new tool for using heterosis in wheat.
Publisher: The Institute of Brewing & Distilling
Date: 31-10-2018
DOI: 10.1002/JIB.532
Publisher: Springer Science and Business Media LLC
Date: 11-11-2016
Publisher: Springer Science and Business Media LLC
Date: 14-03-2019
DOI: 10.1038/S41598-019-40703-6
Abstract: Leaf is the main organ of photosynthesis, which significantly impacts crop yield. A high-density linkage map containing 1894 single nucleotide polymorphism (SNP) and 68 simple sequence repeats (SSR) markers was used to identify quantitative trait locus (QTL) for flag leaf length (FLL), second leaf length (SLL), third leaf length (TLL), fourth leaf length (FOLL), flag leaf area (FLA), second leaf area (SLA), third leaf area (TLA) and fourth leaf area (FOLA). In total, 57 QTLs underlying the top four leaf length and area traits were identified and mapped on chromosome 2H, 3H, 4H and 7H. In idual QTL accounted for 5.17% to 37.11% of the phenotypic variation in 2015 and 2016. A major stable QTL qFLL 2 - 2 close to the marker 2HL_25536047 was identified on the long arm of chromosome 2H. The most important QTL clustered region at M_256210_824 - 2HL_23335246 on chromosome 2H was associated with FLL, SLL, FLA and SLA and explained high phenotypic variation. These findings provide genetic basis for improving the leaf morphology of barley. In addition, our results suggested that the top four leaves were significantly positively correlated with plant height and some yield-related traits.
Publisher: Springer Science and Business Media LLC
Date: 2012
Publisher: MDPI AG
Date: 14-11-2022
Abstract: The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The “Green Revolution” beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth (3) GA interacts with other phytohormones manipulating plant development and reproduction and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.
Publisher: Springer Science and Business Media LLC
Date: 12-03-2009
DOI: 10.1007/S10142-009-0120-4
Abstract: The barley sdw1/denso gene not only controls plant height but also yield and quality. The sdw1/denso gene was mapped to the long arm of chromosome 3H. Comparative genomic analysis revealed that the sdw1/denso gene was located in the syntenic region of the rice semidwarf gene sd1 on chromosome 1. The sd1 gene encodes a gibberellic acid (GA)-20 oxidase enzyme. The gene ortholog of rice sd1 was isolated from barley using polymerase chain reaction. The barley and rice genes showed a similar gene structure consisting of three exons and two introns. Both genes share 88.3% genomic sequence similarity and 89% amino acid sequence identity. A single nucleotide polymorphism was identified in intron 2 between barley varieties Baudin and AC Metcalfe with Baudin known to contain the denso semidwarf gene. The single nucleotide polymorphism (SNP) marker was mapped to chromosome 3H in a doubled haploid population of Baudin x AC Metcalfe with 178 DH lines. Quantitative trait locus analysis revealed that plant height cosegregated with the SNP. The sdw1/denso gene in barley is the most likely ortholog of the sd1 in rice. The result will facilitate understanding of the molecular mechanism controlling semidwarf phenotype and provide a diagnostic marker for selection of semidwarf gene in barley.
Publisher: Wiley
Date: 06-12-2019
DOI: 10.1111/PBI.13029
Publisher: Wiley
Date: 11-01-2021
DOI: 10.1111/TPJ.15100
Publisher: Springer Science and Business Media LLC
Date: 15-08-2008
Publisher: Frontiers Media SA
Date: 06-07-2023
DOI: 10.3389/FPLS.2023.1189743
Abstract: Multiple nodes and dwarf mutants in barley are a valuable resource for identifying genes that control shoot branching, vegetative growth and development. In this study, physiological, microscopic and genetic analysis were conducted to characterize and fine-map the underling gene of a barley mutant with Multiple Stem Nodes and Spikes and Dwarf ( msnsd ), which was selected from EMS- and 60 Co-treated barley cv . Edamai 934. The msnsd mutant had more stem nodes, lower plant height and a shorter plastochron than Edamai 934. Moreover, the mutant had two or more spikes on each tiller. Microscopic analysis showed that the dwarf phenotype of msnsd resulted from reduced cell lengths and cell numbers in the stem. Further physiological analysis showed that msnsd was GA 3 -deficient, with its plant height increasing after external GA 3 application. Genetic analysis revealed that a single recessive nuclear gene, namely, Hv MSNSD , controlled the msnsd phenotype. Using a segregating population derived from Harrington and the msnsd mutant, Hv MSNSD was fine-mapped on chromosome 5H in a 200 kb interval using bulked segregant analysis (BSA) coupled with RNA-sequencing (BSR-seq), with a C-T substitution in the exon of HvTCP25 co-segregating with the msnsd phenotype. RNA-seq analysis showed that a gene encoding gibberellin 2-oxidase 8, a negative regulator of GA biosynthesis, was upregulated in the msnsd mutant. Several known genes related to inflorescence development that were also upregulated and enriched in the msnsd mutant. Collectively, we propose that Hv MSNSD regulates the plastochron and morphology of reproductive organs, likely by coordinating GA homeostasis and changed expression of floral development related genes in barley. This study offers valuable insights into the molecular regulation of barley plant architecture and inflorescence development.
Publisher: Wiley
Date: 2201
Publisher: Public Library of Science (PLoS)
Date: 16-07-2015
Publisher: Cold Spring Harbor Laboratory
Date: 11-04-2020
DOI: 10.1101/2020.04.09.034942
Abstract: Monitoring the mutation dynamics of SARS-CoV-2 is critical for the development of effective approaches to contain the pathogen. By analyzing 106 SARS-CoV-2 and 39 SARS genome sequences, we provided direct genetic evidence that SARS-CoV-2 has a much lower mutation rate than SARS. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. The discrepant phylogenies for the spike protein and its receptor binding domain proved a previously reported structural rearrangement prior to the emergence of SARS-CoV-2. Despite that we found the spike glycoprotein of SARS-CoV-2 is particularly more conserved, we identified a receptor binding domain mutation that leads to weaker ACE2 binding capability based on in silico simulation, which concerns a SARS-CoV-2 s le collected on 27 th January 2020 from India. This represents the first report of a significant SARS-CoV-2 mutant, and requires attention from researchers working on vaccine development around the world. Based on the currently available genome sequence data, we provided direct genetic evidence that the SARS-COV-2 genome has a much lower mutation rate and genetic ersity than SARS during the 2002-2003 outbreak. The spike (S) protein encoding gene of SARS-COV-2 is found relatively more conserved than other protein-encoding genes, which is a good indication for the ongoing antiviral drug and vaccine development. Minimum Evolution phylogeny analysis revealed the putative original status of SARS-CoV-2 and the early-stage spread history. We confirmed a previously reported rearrangement in the S protein arrangement of SARS-COV-2, and propose that this rearrangement should have occurred between human SARS-CoV and a bat SARS-CoV, at a time point much earlier before SARS-COV-2 transmission to human. We provided first evidence that a mutated SARS-COV-2 with reduced human ACE2 receptor binding affinity have emerged in India based on a s le collected on 27th January 2020.
Publisher: Frontiers Media SA
Date: 13-05-2022
Abstract: Heat stress is a primary constraint to Australia's barley production. In addition to impacting grain yield, it adversely affects physical grain quality (weight and plumpness) and market value. The incidence of heat stress during grain filling is rising with global warming. However, breeding for new superior heat-tolerant genotypes has been challenging due to the narrow window of sensitivity, the unpredictable nature of heat stress, and its frequent co-occurrence with drought stress. Greater scientific knowledge regarding traits and mechanisms associated with heat tolerance would help develop more efficient selection methods. Our objective was to assess 157 barley varieties of contrasting genetic backgrounds for various developmental, agro-morphological, and physiological traits to examine the effects of heat stress on physical grain quality. Delayed sowing (i.e., July and August) increased the likelihood of daytime temperatures above 30°C during grain-filling. Supplementary irrigation of field trials ensured a reduced impact of drought stress. Heat tolerance appeared to be the primary factor determining grain plumpness. A wide variation was observed for heat tolerance, particularly among the Australian varieties. Genotypic variation was also observed for grain weight, plumpness, grain growth components, stay-green and stem water-soluble carbohydrates (WSC) content, and mobilisation under normal and delayed sown conditions. Compared to normal sowing, delayed sowing reduced duration of developmental phases, plant height, leaf size, head length, head weight, grain number, plumpness, grain width and thickness, stem WSC content, green leaf area retention, and harvest index (HI), and increased screenings, grain length, grain-filling rate (GFR), WSC mobilisation efficiency (WSCME), and grain protein content. Overall, genotypes with heavier and plumper grains under high temperatures had higher GFR, longer grain-filling duration, longer green leaf area retention, higher WSCME, taller stature, smaller leaf size, greater HI, higher grain weight lumpness potentials, and earlier flowering. GFR played a significant role in determining barley grain weight and plumpness under heat-stress conditions. Enhancing GFR may provide a new avenue for improving heat tolerance in barley.
No related grants have been discovered for Chengdao Li.