ORCID Profile
0000-0003-3966-8596
Current Organisation
University of Adelaide
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Springer US
Date: 2020
DOI: 10.1007/978-1-0716-0235-5_9
Abstract: Genomic selection (GS) is rapidly being adopted by many plant and animal breeding programs. New statistical methods that increase prediction accuracy are needed to enable effective GS. This chapter will introduce a prediction method that makes use of the biological functions of DNA markers.
Publisher: Public Library of Science (PLoS)
Date: 27-06-2016
Publisher: Elsevier BV
Date: 09-2016
Publisher: Wiley
Date: 16-11-2022
DOI: 10.1002/TPG2.20166
Abstract: Achieving yield potential in chickpea ( Cicer arietinum L.) is limited by many constraints that include biotic and abiotic stresses. Combining next‐generation sequencing technology with advanced statistical modeling has the potential to increase genetic gain efficiently. Whole genome resequencing data was obtained from 315 advanced chickpea breeding lines from the Australian chickpea breeding program resulting in more than 298,000 single nucleotide polymorphisms (SNPs) discovered. Analysis of population structure revealed a distinct group of breeding lines with many alleles that are absent from recently released Australian cultivars. Genome‐wide association studies (GWAS) using these Australian breeding lines identified 20 SNPs significantly associated with grain yield in multiple field environments. A reduced level of nucleotide ersity and extended linkage disequilibrium suggested that some regions in these chickpea genomes may have been through selective breeding for yield or other traits. A large introgression segment that introduced from C. echinospermum for phytophthora root rot resistance was identified on chromosome 6, yet it also has unintended consequences of reducing yield due to linkage drag. We further investigated the effect of genotype by environment interaction on genomic prediction of yield. We found that the training set had better prediction accuracy when phenotyped under conditions relevant to the targeted environments. We also investigated the effect of SNP functional annotation on prediction accuracy using different subsets of SNPs based on their genomic locations: regulatory regions, exome, and alternative splice sites. Compared with the whole SNP dataset, a subset of SNPs did not significantly decrease prediction accuracy for grain yield despite consisting of a smaller number of SNPs.
Publisher: Springer Science and Business Media LLC
Date: 10-04-2013
DOI: 10.1038/HDY.2013.16
Publisher: Springer Science and Business Media LLC
Date: 10-01-2011
Abstract: Rye ( Secale cereale L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific ersity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic ersity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations. A total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype ersity of candidate genes were high with average values π = 5.6 × 10 -3 and Hd = 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between in iduals within populations. Haplotype frequencies varied markedly between the candidate genes. ScCbf14 , ScVrn1 , and ScDhn1 were dominated by a single haplotype, while the other 8 genes ( ScCbf2 , ScCbf6 , ScCbf9b , ScCbf11 , ScCbf12 , ScCbf15 , ScIce2 , and ScDhn3 ) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low. The Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide ersity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.
Publisher: Frontiers Media SA
Date: 28-04-2021
Abstract: A better understanding of the genetics of salinity tolerance in chickpea would enable breeding of salt tolerant varieties, offering potential to expand chickpea production to marginal, salinity-affected areas. A Recombinant Inbred Line population was developed using accelerated-Single Seed Descent of progeny from a cross between two chickpea varieties, Rupali (salt-sensitive) and Genesis836 (salt-tolerant). The population was screened for salinity tolerance using high-throughput image-based phenotyping in the glasshouse, in hydroponics, and across 2 years of field trials at Merredin, Western Australia. A genetic map was constructed from 628 unique in-silico DArT and SNP markers, spanning 963.5 cM. Markers linked to two flowering loci identified on linkage groups CaLG03 and CaLG05 were used as cofactors during genetic analysis to remove the confounding effects of flowering on salinity response. Forty-two QTL were linked to growth rate, yield, and yield component traits under both control and saline conditions, and leaf tissue ion accumulation under salt stress. Residuals from regressions fitting best linear unbiased predictions from saline conditions onto best linear unbiased predictions from control conditions provided a measure of salinity tolerance per se , independent of yield potential. Six QTL on CaLG04, CaLG05, and CaLG06 were associated with tolerance per se . In total, 21 QTL mapped to two distinct regions on CaLG04. The first distinct region controlled the number of filled pods, leaf necrosis, seed number, and seed yield specifically under salinity, and co-located with four QTL linked to salt tolerance per se . The second distinct region controlled 100-seed weight and growth-related traits, independent of salinity treatment. Positional cloning of the salinity tolerance-specific loci on CaLG04, CaLG05, and CaLG06 will improve our understanding of the key determinants of salinity tolerance in chickpea.
Publisher: Springer Science and Business Media LLC
Date: 27-10-2011
Abstract: Frost is an important abiotic stress that limits cereal production in the temperate zone. As the most frost tolerant small grain cereal, rye ( Secale cereale L.) is an ideal cereal model for investigating the genetic basis of frost tolerance (FT), a complex trait with polygenic inheritance. Using 201 genotypes from five Eastern and Middle European winter rye populations, this study reports a multi-platform candidate gene-based association analysis in rye using 161 single nucleotide polymorphisms (SNPs) and nine insertion-deletion (Indel) polymorphisms previously identified from twelve candidate genes with a putative role in the frost responsive network. Phenotypic data analyses of FT in three different phenotyping platforms, controlled, semi-controlled and field, revealed significant genetic variations in the plant material under study. Statistically significant ( P 0.05) associations between FT and SNPs/haplotypes of candidate genes were identified. Two SNPs in ScCbf15 and one in ScCbf12 , all leading to amino acid exchanges, were significantly associated with FT over all three phenotyping platforms. Distribution of SNP effect sizes expressed as percentage of the genetic variance explained by in idual SNPs was highly skewed towards zero with a few SNPs obtaining large effects. Two-way epistasis was found between 14 pairs of candidate genes. Relatively low to medium empirical correlations of SNP-FT associations were observed across the three platforms underlining the need for multi-level experimentation for dissecting complex associations between genotypes and FT in rye. Candidate gene based-association studies are a powerful tool for investigating the genetic basis of FT in rye. Results of this study support the findings of bi-parental linkage mapping and expression studies that the Cbf gene family plays an essential role in FT.
Publisher: Oxford University Press (OUP)
Date: 13-06-2016
DOI: 10.1093/JXB/ERW221
Abstract: We measured yield components, nitrogen fixation, soil nitrogen uptake and carbon isotope composition (δ(13)C) in a collection of chickpea genotypes grown in environments where water availability was the main source of yield variation. We aimed to quantify the phenotypic plasticity of these traits using variance ratios, and to explore their genetic basis using FST genome scan. Fifty-five genes in three genomic regions were found to be under selection for plasticity of yield 54 genes in four genomic regions for the plasticity of seeds per m(2) 48 genes in four genomic regions for the plasticity of δ(13)C 54 genes in two genomic regions for plasticity of flowering time 48 genes in five genomic regions for plasticity of nitrogen fixation and 49 genes in three genomic regions for plasticity of nitrogen uptake from soil. Plasticity of yield was related to plasticity of nitrogen uptake from soil, and unrelated to plasticity of nitrogen fixation, highlighting the need for closer attention to nitrogen uptake in legumes. Whereas the theoretical link between δ(13)C and transpiration efficiency is strong, the actual link with yield is erratic due to trade-offs and scaling issues. Genes associated with plasticity of δ(13)C were identified that may help to untangle the δ(13)C-yield relationship. Combining a plasticity perspective to deal with complex G×E interactions with FST genome scan may help understand and improve both crop adaptation to stress and yield potential.
Publisher: Frontiers Media SA
Date: 22-10-2019
Publisher: Frontiers Media SA
Date: 17-03-2017
Publisher: Springer Science and Business Media LLC
Date: 13-10-2021
DOI: 10.1007/S00122-021-03954-4
Abstract: QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in erse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple ersity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two ersity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1-FTa2-FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and ersity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the ersity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.
Publisher: Springer Science and Business Media LLC
Date: 07-12-2018
DOI: 10.1007/S00122-018-3256-6
Abstract: Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F
Publisher: Springer Science and Business Media LLC
Date: 02-05-2017
DOI: 10.1038/S41598-017-01211-7
Abstract: Soil salinity results in reduced productivity in chickpea. However, breeding for salinity tolerance is challenging because of limited knowledge of the key traits affecting performance under elevated salt and the difficulty of high-throughput phenotyping for large, erse germplasm collections. This study utilised image-based phenotyping to study genetic variation in chickpea for salinity tolerance in 245 erse accessions. On average salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the ersity panel with seed number being the major determinant for salinity tolerance measured as yield. This study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.
Publisher: Frontiers Media SA
Date: 22-11-2016
Publisher: Frontiers Media SA
Date: 19-02-2018
No related grants have been discovered for Yongle Li.