Emma Mace

QTL analysis of ergot resistance in sorghum

Publisher: Springer Science and Business Media LLC

Date: 15-05-2008

DOI: 10.1007/S00122-008-0781-8

Abstract: Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP , 148 DArT and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.

Large-scale genome-wide association study reveals that drought-induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Publisher: Springer Science and Business Media LLC

Date: 24-08-2020

DOI: 10.1007/S00122-020-03665-2

Abstract: We detected 213 lodging QTLs and demonstrated that drought-induced stem lodging in grain sorghum is substantially associated with stay-green and plant height suggesting a critical role of carbon remobilisation. Sorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTLs, the majority of which showed a significant association with leaf senescence and plant height (72% and 71%, respectively). Only 16 lodging QTLs were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTLs indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se, which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots.

Genomic Regions Influencing Seminal Root Traits in Barley

Publisher: Wiley

Date: 03-2016

DOI: 10.3835/PLANTGENOME2015.03.0012

Abstract: Water availability is a major limiting factor for crop production, making drought adaptation and its many component traits a desirable attribute of plant cultivars. Previous studies in cereal crops indicate that root traits expressed at early plant developmental stages, such as seminal root angle and root number, are associated with water extraction at different depths. Here, we conducted the first study to map seminal root traits in barley ( Hordeum vulgare L.). Using a recently developed high‐throughput phenotyping method, a panel of 30 barley genotypes and a doubled‐haploid (DH) population (ND24260 × ‘Flagship’) comprising 330 lines genotyped with ersity array technology (DArT) markers were evaluated for seminal root angle (deviation from vertical) and root number under controlled environmental conditions. A high degree of phenotypic variation was observed in the panel of 30 genotypes: 13.5 to 82.2 and 3.6 to 6.9° for root angle and root number, respectively. A similar range was observed in the DH population: 16.4 to 70.5 and 3.6 to 6.5° for root angle and number, respectively. Seven quantitative trait loci (QTL) for seminal root traits (root angle, two QTL root number, five QTL) were detected in the DH population. A major QTL influencing both root angle and root number ( RAQ2 / RNQ4 ) was positioned on chromosome 5HL. Across‐species analysis identified 10 common genes underlying root trait QTL in barley, wheat ( Triticum aestivum L.), and sorghum [ Sorghum bicolor (L.) Moench]. Here, we provide insight into seminal root phenotypes and provide a first look at the genetics controlling these traits in barley.

Spot form of net blotch resistance in barley is under complex genetic control

Publisher: Springer Science and Business Media LLC

Date: 10-01-2015

DOI: 10.1007/S00122-014-2447-Z

Abstract: Evaluation of resistance to Pyrenophora teres f. maculata in barley breeding populations via association mapping revealed a complex genetic architecture comprising a mixture of major and minor effect genes. In the search for stable resistance to spot form of net blotch (Pyrenophora teres f. maculata, SFNB), association mapping was conducted on four independent barley (Hordeum vulgare L.) breeding populations comprising a total of 898 unique elite breeding lines from the Northern Region Barley Breeding Program in Australia for discovery of quantitative trait loci (QTL) influencing resistance at seedling and adult plant growth stages. A total of 29 significant QTL were validated across multiple breeding populations, with 22 conferring resistance at both seedling and adult plant growth stages. The remaining 7 QTL conferred resistance at either seedling (2 QTL) or adult plant (5 QTL) growth stages only. These 29 QTL represented 24 unique genomic regions, of which five were found to co-locate with previously identified QTL for SFNB. The results indicated that SFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H. A large proportion of the QTL acted in the same direction for both seedling and adult responses, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance. However, the accumulation of specific resistance alleles on several chromosomes must be considered in molecular breeding selection strategies.

Extensive variation within the pan-genome of cultivated and wild sorghum.

Publisher: Springer Science and Business Media LLC

Date: 20-05-2021

DOI: 10.1038/S41477-021-00925-X

Abstract: Sorghum is a drought-tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importance. Cultivated sorghum and its inter-fertile wild relatives constitute the primary gene pool for sorghum. Understanding and characterizing the ersity within this valuable resource is fundamental for its effective utilization in crop improvement. Here, we report analysis of a sorghum pan-genome to explore genetic ersity within the sorghum primary gene pool. We assembled 13 genomes representing cultivated sorghum and its wild relatives, and integrated them with 3 other published genomes to generate a pan-genome of 44,079 gene families with 222.6 Mb of new sequence identified. The pan-genome displays substantial gene-content variation, with 64% of gene families showing presence/absence variation among genomes. Comparisons between core genes and dispensable genes suggest that dispensable genes are important for sorghum adaptation. Extensive genetic variation was uncovered within the pan-genome, and the distribution of these variations was influenced by variation of recombination rate and transposable element content across the genome. We identified presence/absence variants that were under selection during sorghum domestication and improvement, and demonstrated that such variation had important phenotypic outcomes that could contribute to crop improvement. The constructed sorghum pan-genome represents an important resource for sorghum improvement and gene discovery.

Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping

Publisher: Springer Science and Business Media LLC

Date: 17-08-2006

DOI: 10.1186/1471-2105-7-383

The vegetative nitrogen response of sorghum lines containing different alleles for nitrate reductase and glutamate synthase

Publisher: Springer Science and Business Media LLC

Date: 25-10-2017

DOI: 10.1007/S11032-017-0738-1

Genetic diversity of Ethiopian sorghum reveals signatures of climatic adaptation.

Publisher: Springer Science and Business Media LLC

Date: 19-12-2021

DOI: 10.1007/S00122-020-03727-5

Abstract: A large collection of Ethiopian sorghum landraces, characterized by agro-ecology and racial-group, was found to contain high levels of ersity and admixture, with significant SNP associations identified for environmental adaptation. Sorghum [Sorghum bicolor L. (Moench)] is a major staple food crop in Ethiopia, exhibiting extensive genetic ersity with adaptations to erse agroecologies. The environmental and climatic drivers, as well as the genomic basis of adaptation, are poorly understood in Ethiopian sorghum and are critical elements for the development of climate-resilient crops. Exploration of the genome-environment association (GEA) is important for identifying adaptive loci and predicting phenotypic variation. The current study aimed to better understand the GEA of a large collection of Ethiopian sorghum landraces (n = 940), characterized with genome-wide SNP markers, to investigate key traits related to adaptation to temperature, precipitation and altitude. The Ethiopian sorghum landrace collection was found to consist of 12 subpopulations with high levels of admixture (47%), representing all the major racial groups of cultivated sorghum with the exception of kafir. Redundancy analysis indicated that agroecology explained up to 10% of the total SNP variation, and geographical location up to 6%. GEA identified 18 significant SNP markers for environmental variables. These SNPs were found to be significantly enriched (P < 0.05) for a priori QTL for drought and cold adaptation. The findings from this study improve our understanding of the genetic control of adaptive traits in Ethiopian sorghum. Further, the Ethiopian sorghum germplasm collection provides sources of adaptation to harsh environments (cold and/or drought) that could be deployed in breeding programs globally for abiotic stress adaptation.

Novel Grain Weight Loci Revealed in a Cross between Cultivated and Wild Sorghum

Publisher: Wiley

Date: 07-2018

DOI: 10.3835/PLANTGENOME2017.10.0089

Abstract: Grain weight has increased during domestication of cereals. Together with grain number it determines yield, but the two are often negatively correlated. Understanding the genetic architecture of grain weight and its relationship with grain number is critical to enhance crop yield. Sorghum is an important food, feed, and biofuel crop well‐known for its adaptation to drought and heat. This study aimed to dissect the genetic basis of thousand grain weight (TGW) in a BC 1 F 5 population between a domesticated sorghum accession and its wild progenitor, Sorghum bicolor subsp. verticilliflorum, and investigate its relationship with grain number. Thousand grain weight, grain number, and yield were measured in field trials in two successive years. A strong negative correlation between TGW and grain number was observed in both trials. In total, 17 TGW quantitative trait loci (QTL) were identified, with 11 of them exhibiting an opposing effect on grain number, implying the correlation between TGW and grain number is due to pleiotropy. Nine grain size candidate genes were identified within 6 TGW QTL, and of these 5 showed signatures of selection during sorghum domestication. Large‐effect QTL in this study that have not been identified previously in cultivated sorghum were found to contain candidate genes with domestication signal, indicating that these QTL were affected during sorghum domestication. This study sheds new light on the genetic basis of TGW, its relationship with grain number, and sorghum domestication.

Differences in temperature response of phenological development among diverse Ethiopian sorghum genotypes are linked to racial grouping and agroecological adaptation

Publisher: Wiley

Date: 03-2020

DOI: 10.1002/CSC2.20128

Abstract: Sorghum [ Sorghum bicolor (L.) Moench] is an important dryland crop in the semiarid tropics, and temperature and photoperiod are the main environmental factors affecting its phenology and thus adaptation. The objectives of this study were to quantify the response of development rate to temperature and photoperiod for 19 erse Ethiopian sorghum genotypes, and to determine if differences in these responses could be linked to racial grouping or agroecological adaptation. The genotypes, representing four major sorghum races and adaptation to four agroecological zones, were sown on 12 dates at two locations in Ethiopia with contrasting altitude. This created a range in photoperiod and temperatures relevant to Ethiopian conditions. Days from emergence to flag leaf appearance, anthesis, and maturity were recorded. A predictive phenology modeling framework was used to fit the effects of photoperiod and temperature on the rate of development for both the pre‐ and post‐anthesis periods. Results indicated that the pre‐anthesis development rate was independent of photoperiod for the range tested. This result differed from West African germplasm and likely reflects differences in agroecological adaptation and racial background. Significant genotypic differences were observed for the base temperature (0–9.8 °C) and for the optimum rate of development (0.011–0.022 d –1 , with low value indicating late anthesis), with differences related to agroecology and racial type. Post‐anthesis differences in the temperature response were minor. The observed differences in pre‐anthesis base temperature can positively affect sorghum breeding programs globally, especially in temperate regions where suitability for early spring plantings is often restricted by low temperatures.

Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea)

Publisher: Springer Science and Business Media LLC

Date: 15-05-2008

DOI: 10.1186/1471-2229-8-55

Abstract: Cultivated peanut or groundnut ( Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable licon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, ersity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.

Large‐scale GWAS in sorghum reveals common genetic control of grain size among cereals

Publisher: Wiley

Date: 11-11-2020

DOI: 10.1111/PBI.13284

Investigating successive Australian barley breeding populations for stable resistance to leaf rust

Publisher: Springer Science and Business Media LLC

Date: 23-08-2017

DOI: 10.1007/S00122-017-2970-9

Abstract: Genome-wide association studies of barley breeding populations identified candidate minor genes for pairing with the adult plant resistance gene Rph20 to provide stable leaf rust resistance across environments. Stable resistance to barley leaf rust (BLR, caused by Puccinia hordei) was evaluated across environments in barley breeding populations (BPs). To identify genomic regions that can be combined with Rph20 to improve adult plant resistance (APR), two BPs genotyped with the Diversity Arrays Technology genotyping-by-sequencing platform (DArT-seq) were examined for reaction to BLR at both seedling and adult growth stages in Australian environments. An integrated consensus map comprising both first- and second-generation DArT platforms was used to integrate QTL information across two additional BPs, providing a total of four interrelated BPs and 15 phenotypic data sets. This enabled identification of key loci underpinning BLR resistance. The APR gene Rph20 was the only active resistance region consistently detected across BPs. Of the QTL identified, RphQ27 on chromosome 6HL was considered the best candidate for pairing with Rph20. RphQ27 did not align or share proximity with known genes and was detected in three of the four BPs. The combination of RphQ27 and Rph20 was of low frequency in the breeding material however, strong resistance responses were observed for the lines carrying this pairing. This suggests that the candidate minor gene RphQ27 can interact additively with Rph20 to provide stable resistance to BLR across erse environments.

Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships.

Publisher: Springer Science and Business Media LLC

Date: 06-01-2020

DOI: 10.1007/S00122-019-03526-7

Abstract: Multi-environment models using marker-based kinship information for both additive and dominance effects can accurately predict hybrid performance in different environments. Sorghum is an important hybrid crop that is grown extensively in many subtropical and tropical regions including Northern NSW and Queensland in Australia. The highly varying weather patterns in the Australian summer months mean that sorghum hybrids exhibit a great deal of variation in yield between locations. To ultimately enable prediction of the outcome of crossing parental lines, both additive effects on yield performance and dominance interaction effects need to be characterised. This paper demonstrates that fitting a linear mixed model that includes both types of effects calculated using genetic markers in relationship matrices improves predictions. Genotype by environment interactions was investigated by comparing FA1 (single-factor analytic) and FA2 (two-factor analytic) structures. The G×E causes a change in hybrid rankings between trials with a difference of up to 25% of the hybrids in the top 10% of each trial. The prediction accuracies increased with the addition of the dominance term (over and above that achieved with an additive effect alone) by an average of 15% and a maximum of 60%. The percentage of dominance of the total genetic variance varied between trials with the trials with higher broad-sense heritability having the greater percentage of dominance. The inclusion of dominance in the factor analytic models improves the accuracy of the additive effects. Breeders selecting high yielding parents for crossing need to be aware of effects due to environment and dominance.

Genetic Diversity of C4 Photosynthesis Pathway Genes in Sorghum bicolor (L.)

Publisher: MDPI AG

Date: 16-07-2020

DOI: 10.3390/GENES11070806

Abstract: C4 photosynthesis has evolved in over 60 different plant taxa and is an excellent ex le of convergent evolution. Plants using the C4 photosynthetic pathway have an efficiency advantage, particularly in hot and dry environments. They account for 23% of global primary production and include some of our most productive cereals. While previous genetic studies comparing phylogenetically related C3 and C4 species have elucidated the genetic ersity underpinning the C4 photosynthetic pathway, no previous studies have described the genetic ersity of the genes involved in this pathway within a C4 crop species. Enhanced understanding of the allelic ersity and selection signatures of genes in this pathway may present opportunities to improve photosynthetic efficiency, and ultimately yield, by exploiting natural variation. Here, we present the first genetic ersity survey of 8 known C4 gene families in an important C4 crop, Sorghum bicolor (L.) Moench, using sequence data of 48 genotypes covering wild and domesticated sorghum accessions. Average nucleotide ersity of C4 gene families varied more than 20-fold from the NADP-malate dehydrogenase (MDH) gene family (θπ = 0.2 × 10−3) to the pyruvate orthophosphate dikinase (PPDK) gene family (θπ = 5.21 × 10−3). Genetic ersity of C4 genes was reduced by 22.43% in cultivated sorghum compared to wild and weedy sorghum, indicating that the group of wild and weedy sorghum may constitute an untapped reservoir for alleles related to the C4 photosynthetic pathway. A SNP-level analysis identified purifying selection signals on C4 PPDK and carbonic anhydrase (CA) genes, and balancing selection signals on C4 PPDK-regulatory protein (RP) and phosphoenolpyruvate carboxylase (PEPC) genes. Allelic distribution of these C4 genes was consistent with selection signals detected. A better understanding of the genetic ersity of C4 pathway in sorghum paves the way for mining the natural allelic variation for the improvement of photosynthesis.

A Graph-Based Pan-Genome Guides Biological Discovery

Publisher: Elsevier BV

Date: 09-2020

DOI: 10.1016/J.MOLP.2020.07.020

Assessment and rationalization of genetic diversity of Papua New Guinea taro (Colocasia esculenta) using SSR DNA fingerprinting

Publisher: Springer Science and Business Media LLC

Date: 03-11-2007

DOI: 10.1007/S10722-007-9286-6

How accurate are the marker orders in crop linkage maps generated from large marker datasets?

Publisher: CSIRO Publishing

Date: 2009

DOI: 10.1071/CP08099

Abstract: Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930–932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30–40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks ided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping.

Genetic dissection of root architecture in Ethiopian sorghum landraces

Publisher: Springer Science and Business Media LLC

Date: 16-09-2023

DOI: 10.1007/S00122-023-04457-0

Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor

Publisher: Frontiers Media SA

Date: 25-10-2016

DOI: 10.3389/FPLS.2016.01544

Mapping spot blotch resistance genes in four barley populations

Publisher: Springer Science and Business Media LLC

Date: 16-02-2010

DOI: 10.1007/S11032-010-9401-9

Rice-cold tolerance across reproductive stages

Publisher: CSIRO Publishing

Date: 2016

DOI: 10.1071/CP15331

Abstract: Cold temperature stress at the reproductive stage, particularly at booting and flowering stages can cause significant reductions in rice (Oryza sativa L.) yield particularly at high latitudes and elevation. Although genotypic variation for cold tolerance is known to exist, the tolerance mechanisms and genotypic consistency across the stages are yet to be understood for segregating populations. Three experiments were conducted under controlled temperature glasshouse conditions to determine floral characteristics that were associated with cold tolerance at the flowering stage and to determine genotypic consistency at the booting and flowering stages. Twenty F5 Reiziq × Lijiangheigu lines from two extreme phenotypic bulks selected for cold tolerance at booting stage in the F2 generation were utilised. Spikelet sterility under cold stress at booting was significantly correlated with spikelet sterility under cold stress at flowering (r = 0.62**) with five lines identified as cold tolerant across reproductive stages. There was also a positive correlation (r = 0.47*) between spikelet sterility under cold stress at booting at the F5 and at the F2 generation. The quantitative trait loci (QTL qLTSPKST10.1) previously identified on chromosome 10 contributing to spikelet sterility within the F2 generation, was also identified in the F5 generation. Additionally, genomic regions displaying significant segregation between the progenies contrasting for their cold tolerance response phenotype were identified on chromosomes 5 and 7 with Lijiangheigu as allelic donor and an estimated reduction in spikelet sterility of 25% and 27%, respectively. Although genotypic variation in spikelet sterility at the booting stage was not related to the development rate for heading or flowering, those cold-tolerant genotypes at the flowering stage were the quickest to complete flowering. Cold-tolerant genotypes at the flowering stage had larger numbers of dehisced anthers and subsequently pollen number on stigma, which contributed to reduced spikelet sterility. It is concluded that enhanced anther dehiscence plays a significant role in improved cold tolerance at the flowering stage.

Heterosis in locally adapted sorghum genotypes and potential of hybrids for increased productivity in contrasting environments in Ethiopia

Publisher: Elsevier BV

Date: 12-2016

DOI: 10.1016/J.CJ.2016.06.020

QTL for root angle and number in a population developed from bread wheats (Triticum aestivum) with contrasting adaptation to water-limited environments

Publisher: Springer Science and Business Media LLC

Date: 24-03-2013

DOI: 10.1007/S00122-013-2074-0

Abstract: Root architecture traits in wheat are important in deep soil moisture acquisition and may be used to improve adaptation to water-limited environments. The genetic architecture of two root traits, seminal root angle and seminal root number, were investigated using a doubled haploid population derived from SeriM82 and Hartog. Multiple novel quantitative trait loci (QTL) were identified, each one having a modest effect. For seminal root angle, four QTL (-log10(P) >3) were identified on 2A, 3D, 6A and 6B, and two suggestive QTL (-log10(P) >2) on 5D and 6B. For root number, two QTL were identified on 4A and 6A with four suggestive QTL on 1B, 3A, 3B and 4A. QTL for root angle and root number did not co-locate. Transgressive segregation was found for both traits. Known major height and phenology loci appear to have little effect on root angle and number. Presence or absence of the T1BL.1RS translocation did not significantly influence root angle. Broad sense heritability (h (2)) was estimated as 50 % for root angle and 31 % for root number. Root angle QTL were found to be segregating between wheat cultivars adapted to the target production region indicating potential to select for root angle in breeding programs.

Characterization of Linkage Disequilibrium and Population Structure in a Mungbean Diversity Panel

Publisher: Frontiers Media SA

Date: 12-01-2018

DOI: 10.3389/FPLS.2017.02102

Genetic differentiation analysis for the identification of complementary parental pools for sorghum hybrid breeding in Ethiopia

Publisher: Springer Science and Business Media LLC

Date: 30-05-2015

DOI: 10.1007/S00122-015-2545-6

Abstract: The potential for exploiting heterosis for sorghum hybrid production in Ethiopia with improved local adaptation and farmers preferences has been investigated and populations suitable for initial hybrid development have been identified. Hybrids in sorghum have demonstrated increased productivity and stability of performance in the developed world. In Ethiopia, the uptake of hybrid sorghum has been limited to date, primarily due to poor adaptation and absence of farmer's preferred traits in existing hybrids. This study aimed to identify complementary parental pools to develop locally adapted hybrids, through an analysis of whole genome variability of 184 locally adapted genotypes and introduced hybrid parents (R and B). Genetic variability was assessed using genetic distance, model-based STRUCTURE analysis and pair-wise comparison of groups. We observed a high degree of genetic similarity between the Ethiopian improved inbred genotypes and a subset of landraces adapted to lowland agro-ecology with the introduced R lines. This coupled with the genetic differentiation from existing B lines, indicated that these locally adapted genotype groups are expected to have similar patterns of heterotic expression as observed between introduced R and B line pools. Additionally, the hybrids derived from these locally adapted genotypes will have the benefit of containing farmers preferred traits. The groups most ergent from introduced B lines were the Ethiopian landraces adapted to highland and intermediate agro-ecologies and a subset of lowland-adapted genotypes, indicating the potential for increased heterotic response of their hybrids. However, these groups were also differentiated from the R lines, and hence are different from the existing complementary heterotic pools. This suggests that although these groups could provide highly ergent parental pools, further research is required to investigate the extent of heterosis and their hybrid performance.

Identification of genetic regions associated with black point in barley

Publisher: Elsevier BV

Date: 2010

DOI: 10.1016/J.FCR.2009.10.003

The Sorghum QTL Atlas: a powerful tool for trait dissection, comparative genomics and crop improvement

Publisher: Springer Science and Business Media LLC

Date: 20-10-2019

DOI: 10.1007/S00122-018-3212-5

Abstract: We describe the development and application of the Sorghum QTL Atlas, a high-resolution, open-access research platform to facilitate candidate gene identification across three cereal species, sorghum, maize and rice. The mechanisms governing the genetic control of many quantitative traits are only poorly understood and have yet to be fully exploited. Over the last two decades, over a thousand QTL and GWAS studies have been published in the major cereal crops including sorghum, maize and rice. A large body of information has been generated on the genetic basis of quantitative traits, their genomic location, allelic effects and epistatic interactions. However, such QTL information has not been widely applied by cereal improvement programs and genetic researchers worldwide. In part this is due to the heterogeneous nature of QTL studies which leads QTL reliability variation from study to study. Using approaches to adjust the QTL confidence interval, this platform provides access to the most updated sorghum QTL information than any database available, spanning 23 years of research since 1995. The QTL database provides information on the predicted gene models underlying the QTL CI, across all sorghum genome assembly gene sets and maize and rice genome assemblies and also provides information on the ersity of the underlying genes and information on signatures of selection in sorghum. The resulting high-resolution, open-access research platform facilitates candidate gene identification across 3 cereal species, sorghum, maize and rice. Using a number of trait ex les, we demonstrate the power and resolution of the resource to facilitate comparative genomics approaches to provide a bridge between genomics and applied breeding.

DArT markers: diversity analyses and mapping in Sorghum bicolor

Publisher: Springer Science and Business Media LLC

Date: 22-01-2008

DOI: 10.1186/1471-2164-9-26

Abstract: The sequential nature of gel-based marker systems entails low throughput and high costs per assay. Commonly used marker systems such as SSR and SNP are also dependent on sequence information. These limitations result in high cost per data point and significantly limit the capacity of breeding programs to obtain sufficient return on investment to justify the routine use of marker-assisted breeding for many traits and particularly quantitative traits. Diversity Arrays Technology (DArT™) is a cost effective hybridisation-based marker technology that offers a high multiplexing level while being independent of sequence information. This technology offers sorghum breeding programs an alternative approach to whole-genome profiling. We report on the development, application, mapping and utility of DArT™ markers for sorghum germplasm. A genotyping array was developed representing approximately 12,000 genomic clones using Pst I+ Ban II complexity with a subset of clones obtained through the suppression subtractive hybridisation (SSH) method. The genotyping array was used to analyse a erse set of sorghum genotypes and screening a Recombinant Inbred Lines (RIL) mapping population. Over 500 markers detected variation among 90 accessions used in a ersity analysis. Cluster analysis discriminated well between all 90 genotypes. To confirm that the sorghum DArT markers behave in a Mendelian manner, we constructed a genetic linkage map for a cross between R931945-2-2 and IS 8525 integrating DArT and other marker types. In total, 596 markers could be placed on the integrated linkage map, which spanned 1431.6 cM. The genetic linkage map had an average marker density of 1/2.39 cM, with an average DArT marker density of 1/3.9 cM. We have successfully developed DArT markers for Sorghum bicolor and have demonstrated that DArT provides high quality markers that can be used for ersity analyses and to construct medium-density genetic linkage maps. The high number of DArT markers generated in a single assay not only provides a precise estimate of genetic relationships among genotypes, but also their even distribution over the genome offers real advantages for a range of molecular breeding and genomics applications.

Identification of QTL for sugar-related traits in a sweet x grain sorghum (Sorghum bicolor L. Moench) recombinant inbred population

Publisher: Springer Science and Business Media LLC

Date: 20-04-2008

DOI: 10.1007/S11032-008-9182-6

Development of Genomic Prediction in Sorghum

Publisher: Wiley

Date: 03-2018

DOI: 10.2135/CROPSCI2017.08.0469

Abstract: Genomic selection can increase the rate of genetic gain in plant breeding programs by shortening the breeding cycle. Gain can also be increased through higher selection intensities, as the size of the population available for selection can be increased by predicting performance of non‐phenotyped, but genotyped, lines. This paper demonstrates the application of genomic prediction in a sorghum [ Sorghum bicolor (L.) Moench] breeding program and compares different genomic prediction models incorporating relationship information derived from molecular markers and pedigree information. In cross‐validation, the models using marker‐based relationships had higher selection accuracy than the selection accuracy for models that used pedigree‐based relationships. It was demonstrated that genotypes that have not been included in the trials could be predicted quite accurately using marker information alone. The accuracy of prediction declined as the genomic relationship of the predicted in idual to the training population declined. We also demonstrate that the accuracy of genomic breeding values from the prediction error variance derived from the mixed model equations is a useful indicator of the accuracy of prediction. This will be useful to plant breeders, as the accuracy of the genomic predictions can be assessed with confidence before phenotypes are available. Four distinct environments were studied and shown to perform very differently with respect to the accuracy of predictions and the composition of estimated breeding values. This paper shows that there is considerable potential for sorghum breeding programs to benefit from the implementation of genomic selection.

In silico development of simple sequence repeat markers within the aeschynomenoid/dalbergoid and genistoid clades of the Leguminosae family and their transferability to Arachis hypogaea, groundnut

Publisher: Elsevier BV

Date: 2008

DOI: 10.1016/J.PLANTSCI.2007.09.014

Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype

Publisher: Oxford University Press (OUP)

Date: 13-08-2022

DOI: 10.1093/JXB/ERAC336

Abstract: The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.

Association mapping of resistance to Puccinia hordei in Australian barley breeding germplasm

Publisher: Springer Science and Business Media LLC

Date: 14-03-2014

DOI: 10.1007/S00122-014-2291-1

Abstract: "To find stable resistance using association mapping tools, QTL with major and minor effects on leaf rust reactions were identified in barley breeding lines by assessing seedlings and adult plants." Three hundred and sixty (360) elite barley (Hordeum vulgare L.) breeding lines from the Northern Region Barley Breeding Program in Australia were genotyped with 3,244 polymorphic ersity arrays technology markers and the results used to map quantitative trait loci (QTL) conferring a reaction to leaf rust (Puccinia hordei Otth). The F3:5 (Stage 2) lines were derived or sourced from different geographic origins or hubs of international barley breeding ventures representing two breeding cycles (2009 and 2011 trials) and were evaluated across eight environments for infection type at both seedling and adult plant stages. Association mapping was performed using mean scores for disease reaction, accounting for family effects using the eigenvalues from a matrix of genotype correlations. In this study, 15 QTL were detected 5 QTL co-located with catalogued leaf rust resistance genes (Rph1, Rph3/19, Rph8/14/15, Rph20, Rph21), 6 QTL aligned with previously reported genomic regions and 4 QTL (3 on chromosome 1H and 1 on 7H) were novel. The adult plant resistance gene Rph20 was identified across the majority of environments and pathotypes. The QTL detected in this study offer opportunities for breeding for more durable resistance to leaf rust through pyramiding multiple genomic regions via marker-assisted selection.

Determining Crop Growth Dynamics in Sorghum Breeding Trials Through Remote and Proximal Sensing Technologies

Publisher: IEEE

Date: 07-2018

DOI: 10.1109/IGARSS.2018.8519296

Mapping of adult plant resistance to net form of net blotch in three Australian barley populations

Publisher: CSIRO Publishing

Date: 2007

DOI: 10.1071/AR07141

Abstract: Net form of net blotch (NFNB), caused by Pyrenophora teres Drechs. f. teres Smedeg., is a serious disease problem for the barley industry in Australia and other parts of the world. Three doubled haploid barley populations, Alexis/Sloop, WI2875-1/Alexis, and Arapiles/Franklin, were used to identify genes conferring adult plant resistance to NFNB in field trials. Quantitative trait loci (QTLs) identified were specific for adult plant resistance because seedlings of the parental lines were susceptible to the NFNB isolates used in this study. QTLs were identified on chromosomes 2H, 3H, 4H, and 7H in both the Alexis/Sloop and WI2875-1/Alexis populations and on chromosomes 1H, 2H, and 7H in the Arapiles/Franklin population. Using QTLNetwork, epistatic interactions were identified between loci on chromosomes 3H and 6H in the Alexis/Sloop population, between 2H and 4H in the WI2875-1/Alexis population, and between 5H and 7H in the Arapiles/Franklin population. Comparisons with earlier studies of NFNB resistance indicate the pathotype-dependent nature of many resistance QTLs and the importance of establishing an international system of pathotype nomenclature and differential testing.

Integrating modelling and phenotyping approaches to identify and screen complex traits: transpiration efficiency in cereals

Publisher: Oxford University Press (OUP)

Date: 21-02-2018

DOI: 10.1093/JXB/ERY059

Abstract: Following advances in genetics, genomics, and phenotyping, trait selection in breeding is limited by our ability to understand interactions within the plant and with the environment, and to identify traits of most relevance to the target population of environments. We propose an integrated approach that combines insights from crop modelling, physiology, genetics, and breeding to characterize traits valuable for yield gain in the target population of environments, develop relevant high-throughput phenotyping platforms, and identify genetic controls and their value in production environments. This paper uses transpiration efficiency (biomass produced per unit of water used) as an ex le of a complex trait of interest to illustrate how the approach can guide modelling, phenotyping, and selection in a breeding programme. We believe that this approach, by integrating insights from erse disciplines, can increase the resource use efficiency of breeding programmes for improving yield gains in target populations of environments.

Crop Genomics Goes Beyond a Single Reference Genome

Publisher: Elsevier BV

Date: 12-2019

DOI: 10.1016/J.TPLANTS.2019.10.001

Abstract: The inadequacy of a single reference genome to capture the full landscape of genetic ersity within a species constrains exploration of genetic variation for crop improvement. A recent study by Yang et al. has demonstrated the value of multiple reference-quality genomes in capturing structural variants and guiding biological discovery.

SorGSD: a sorghum genome SNP database

Publisher: Springer Science and Business Media LLC

Date: 07-01-2016

DOI: 10.1186/S13068-015-0415-8

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Publisher: Springer Science and Business Media LLC

Date: 26-09-2014

DOI: 10.1186/S12870-014-0253-Z

QTL for nodal root angle in sorghum (Sorghum bicolor L. Moench) co-locate with QTL for traits associated with drought adaptation

Publisher: Springer Science and Business Media LLC

Date: 22-09-2011

DOI: 10.1007/S00122-011-1690-9

Abstract: Nodal root angle in sorghum influences vertical and horizontal root distribution in the soil profile and is thus relevant to drought adaptation. In this study, we report for the first time on the mapping of four QTL for nodal root angle (qRA) in sorghum, in addition to three QTL for root dry weight, two for shoot dry weight, and three for plant leaf area. Phenotyping was done at the six leaf stage for a mapping population (n = 141) developed by crossing two inbred sorghum lines with contrasting root angle. Nodal root angle QTL explained 58.2% of the phenotypic variance and were validated across a range of erse inbred lines. Three of the four nodal root angle QTL showed homology to previously identified root angle QTL in rice and maize, whereas all four QTL co-located with previously identified QTL for stay-green in sorghum. A putative association between nodal root angle QTL and grain yield was identified through single marker analysis on field testing data from a subset of the mapping population grown in hybrid combination with three different tester lines. Furthermore, a putative association between nodal root angle QTL and stay-green was identified using data sets from selected sorghum nested association mapping populations segregating for root angle. The identification of nodal root angle QTL presents new opportunities for improving drought adaptation mechanisms via molecular breeding to manipulate a trait for which selection has previously been very difficult.

Exploring and Exploiting Pan-genomics for Crop Improvement

Publisher: Elsevier BV

Date: 02-2019

DOI: 10.1016/J.MOLP.2018.12.016

Abstract: Genetic variation ranging from single-nucleotide polymorphisms to large structural variants (SVs) can cause variation of gene content among in iduals within the same species. There is an increasing appreciation that a single reference genome is insufficient to capture the full landscape of genetic ersity of a species. Pan-genome analysis offers a platform to evaluate the genetic ersity of a species via investigation of its entire genome repertoire. Although a recent wave of pan-genomic studies has shed new light on crop ersity and improvement using advanced sequencing technology, the potential applications of crop pan-genomics in crop improvement are yet to be fully exploited. In this review, we highlight the progress achieved in understanding crop pan-genomics, discuss biological activities that cause SVs, review important agronomical traits affected by SVs, and present our perspective on the application of pan-genomics in crop improvement.

Development and characterization of polymorphic microsatellite markers in taro (Colocasia esculenta)

Publisher: Canadian Science Publishing

Date: 10-2002

DOI: 10.1139/G02-045

Abstract: Microsatellite-containing sequences were isolated from enriched genomic libraries of taro (Colocasia esculenta (L.) Schott). The sequencing of 269 clones yielded 77 inserts containing repeat motifs. The majority of these (81.7%) were dinucleotide or trinucleotide repeats. The GT/CA repeat motif was the most common, accounting for 42% of all repeat types. From a total of 43 primer pairs designed, 41 produced markers within the expected size range. Sixteen (39%) were polymorphic when screened against a restricted set of taro genotypes from Southeast Asia and Oceania, with an average of 3.2 alleles detected on each locus. These markers represent a useful resource for taro germplasm management, genome mapping, and marker-assisted selection.Key words: Colocasia esculenta, microsatellite-enriched genomic library, simple sequence repeats, germplasm characterization.

Large scale genome-wide association study reveals that drought induced lodging in grain sorghum is associated with plant height and traits linked to carbon remobilisation

Publisher: Cold Spring Harbor Laboratory

Date: 08-12-2019

DOI: 10.1101/865667

Abstract: Sorghum is generally grown in water limited conditions and often lodges under post-anthesis drought, which reduces yield and quality. Due to its complexity, our understanding on the genetic control of lodging is very limited. We dissected the genetic architecture of lodging in grain sorghum through genome-wide association study (GWAS) on 2308 unique hybrids grown in 17 Australian sorghum trials over 3 years. The GWAS detected 213 QTL, the majority of which showed a significant association with leaf senescence and plant height (72% and 71% respectively). Only 16 lodging QTL were not associated with either leaf senescence or plant height. The high incidence of multi-trait association for the lodging QTL indicates that lodging in grain sorghum is mainly associated with plant height and traits linked to carbohydrate remobilisation. This result supported the selection for stay-green (delayed leaf senescence) to reduce lodging susceptibility, rather than selection for short stature and lodging resistance per se , which likely reduces yield. Additionally, our data suggested a protective effect of stay-green on weakening the association between lodging susceptibility and plant height. Our study also showed that lodging resistance might be improved by selection for stem composition but was unlikely to be improved by selection for classical resistance to stalk rots. We detected 213 lodging QTL and demonstrated that drought induced stem lodging in grain sorghum is substantially associated with stay-green and plant height, suggesting a critical role of carbon remobilisation.

VERNALIZATION1 Modulates Root System Architecture in Wheat and Barley

Publisher: Elsevier BV

Date: 2018

DOI: 10.1016/J.MOLP.2017.10.005

Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy

Publisher: Wiley

Date: 11-06-2016

DOI: 10.1111/PBI.12578

Allelic variation at a single gene increases food value in a drought-tolerant staple cereal

Publisher: Springer Science and Business Media LLC

Date: 12-02-2013

DOI: 10.1038/NCOMMS2450

Abstract: The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency.

Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum

Publisher: Springer Science and Business Media LLC

Date: 11-07-2017

DOI: 10.1186/S13007-017-0206-2

Allelic variation of the β-, γ- and δ-kafirin genes in diverse Sorghum genotypes

Publisher: Springer Science and Business Media LLC

Date: 19-06-2010

DOI: 10.1007/S00122-010-1383-9

Abstract: The β-, γ- and δ-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic ersity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally erse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic α-kafirins. Significant ersity was found for each locus, with the cysteine-rich β-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce β-kafirin. An analysis of flour viscosity reveals that these β-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less ersity at the protein level within the cysteine-rich γ-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the δ-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the δ-kafirin locus displayed comparatively low genetic variation. This study has identified genetic ersity in all single copy seed storage protein genes, including a null mutant for β-kafirin in Sorghum.

Whole-Genome Analysis of Candidate genes Associated with Seed Size and Weight in Sorghum bicolor Reveals Signatures of Artificial Selection and Insights into Parallel Domestication in Cereal Crops

Publisher: Frontiers Media SA

Date: 18-07-2017

DOI: 10.3389/FPLS.2017.01237

QTL analysis in multiple sorghum populations facilitates the dissection of the genetic and physiological control of tillering

Publisher: Springer Science and Business Media LLC

Date: 28-08-2014

DOI: 10.1007/S00122-014-2377-9

Abstract: A QTL model for the genetic control of tillering in sorghum is proposed, presenting new opportunities for sorghum breeders to select germplasm with tillering characteristics appropriate for their target environments. Tillering in sorghum can be associated with either the carbon supply-demand (S/D) balance of the plant or an intrinsic propensity to tiller (PTT). Knowledge of the genetic control of tillering could assist breeders in selecting germplasm with tillering characteristics appropriate for their target environments. The aims of this study were to identify QTL for tillering and component traits associated with the S/D balance or PTT, to develop a framework model for the genetic control of tillering in sorghum. Four mapping populations were grown in a number of experiments in south east Queensland, Australia. The QTL analysis suggested that the contribution of traits associated with either the S/D balance or PTT to the genotypic differences in tillering differed among populations. Thirty-four tillering QTL were identified across the populations, of which 15 were novel to this study. Additionally, half of the tillering QTL co-located with QTL for component traits. A comparison of tillering QTL and candidate gene locations identified numerous coincident QTL and gene locations across populations, including the identification of common non-synonymous SNPs in the parental genotypes of two mapping populations in a sorghum homologue of MAX1, a gene involved in the control of tiller bud outgrowth through the production of strigolactones. Combined with a framework for crop physiological processes that underpin genotypic differences in tillering, the co-location of QTL for tillering and component traits and candidate genes allowed the development of a framework QTL model for the genetic control of tillering in sorghum.

Rationalization of taro germplasm collections in the Pacific Island region using simple sequence repeat (SSR) markers

Publisher: Cambridge University Press (CUP)

Date: 12-2006

DOI: 10.1079/PGR2006125

Abstract: A regional (Oceania) core collection for taro germplasm has been developed based on phenotypic and molecular characterization. In total, 2199 accessions of taro germplasm have been collected by TaroGen (Taro Genetic Resources: Conservation and Utilisation) from 10 countries in Oceania: Papua New Guinea, Solomon Islands, Vanuatu, New Caledonia, Fiji, Palau, Niue, Tonga, Cook Islands and Samoa. Our objective was to select 10% from each country to contribute to a regional core. The larger collections from Papua New Guinea, Vanuatu and New Caledonia were analysed based on phenotypic characters, and a erse subset representing 20% of these collections was fingerprinted. A erse 20% subs le was also taken from the Solomon Islands. All accessions from the other six countries were fingerprinted. In total, 515 accessions were genotyped (23.4% overall) using taro specific simple sequence repeat (SSR) markers. DNA fingerprint data showed that great allelic ersity existed in Papua New Guinea and the Solomon Islands. Interestingly, rare alleles were identified in taros from the Solomon Islands province of Choiseul which were not observed in any of the other collections. Overall, 211 accessions were recommended for inclusion in the final regional core collection based on the phenotypic and molecular characterization.

Large-scale GWAS in sorghum reveals common genetic control of grain size among cereals

Publisher: Cold Spring Harbor Laboratory

Date: 22-07-2019

DOI: 10.1101/710459

Abstract: Grain size is a key yield component of cereal crops and a major quality attribute. It is determined by a genotype’s genetic potential and its capacity to fill the grains. This study aims to dissect the genetic architecture of grain size in sorghum via an integrated genome wide association study (GWAS) using a ersity panel of 837 in iduals and a BC-NAM population of 1,421 in iduals. In order to isolate genetic effects associated with grain size, rather than the genotype’s capacity to fill grain, a field treatment of removing half of the panicle during flowering was imposed. Extensive variation in grain size with high heritability was observed in both populations across 5 field trials. Subsequent GWAS analyses uncovered 92 grain size QTL, which were significantly enriched for orthologues of known grain size genes in rice and maize. Significant overlap between the 92 QTL and grain size QTL in rice and maize was also found, supporting common genetic control of this trait among cereals. Further analysis found grain size genes with opposite effect on grain number were less likely to overlap with the grain size QTL from this study, indicating the treatment facilitated identification of genetic regions related to the genetic potential of grain size rather than the capacity to fill the grain. These results enhance understanding of the genetic architecture of grain size in cereal, and pave the way for exploration of underlying molecular mechanisms in cereal crops and manipulation of this trait in breeding practices.

Linkage Projects - Grant ID: LP200301540

Start Date: 01-2023

End Date: 01-2026

Amount: $607,411.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP0990626

Start Date: 04-2010

End Date: 12-2013

Amount: $234,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP120200699

Start Date: 07-2012

End Date: 06-2016

Amount: $282,500.00

Funder: Australian Research Council

Industrial Transformation Research Hubs - Grant ID: IH230100006

Start Date: 2023

End Date: 12-2027

Amount: $4,933,330.00

Funder: Australian Research Council

Industrial Transformation Training Centres - Grant ID: IC230100016

Start Date: 2023

End Date: 12-2027

Amount: $5,000,000.00

Funder: Australian Research Council

Linkage Projects - Grant ID: LP170100822

Start Date: 01-2019

End Date: 12-2023

Amount: $605,000.00

Funder: Australian Research Council

Discovery Projects - Grant ID: DP140102505

Start Date: 2014

End Date: 09-2017

Amount: $611,000.00

Funder: Australian Research Council