scholarly journals Genome-Wide Association Analysis of Stable Stripe Rust Resistance Loci in a Chinese Wheat Landrace Panel Using the 660K SNP Array

2021 ◽  
Vol 12 ◽  
Author(s):  
Fangjie Yao ◽  
Fangnian Guan ◽  
Luyao Duan ◽  
Li Long ◽  
Hao Tang ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Snp Array ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide ◽  
A Genome ◽  
Wheat Landraces ◽  
Chinese Wheat ◽  
Kasp Markers

Stripe rust (caused by Puccinia striiformis f. sp. tritici) is one of the most severe diseases affecting wheat production. The disease is best controlled by developing and growing resistant cultivars. Chinese wheat (Triticum aestivum) landraces have excellent resistance to stripe rust. The objectives of this study were to identify wheat landraces with stable resistance and map quantitative trait loci (QTL) for resistance to stripe rust from 271 Chinese wheat landraces using a genome-wide association study (GWAS) approach. The landraces were phenotyped for stripe rust responses at the seedling stage with two predominant Chinese races of P. striiformis f. sp. tritici in a greenhouse and the adult-plant stage in four field environments and genotyped using the 660K wheat single-nucleotide polymorphism (SNP) array. Thirteen landraces with stable resistance were identified, and 17 QTL, including eight associated to all-stage resistance and nine to adult-plant resistance, were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 3B, 5A, 5B, 6D, and 7A. These QTL explained 6.06–16.46% of the phenotypic variation. Five of the QTL, QYrCL.sicau-3AL, QYrCL.sicau-3B.4, QYrCL.sicau-3B.5, QYrCL.sicau-5AL.1 and QYrCL.sicau-7AL, were likely new. Five Kompetitive allele specific PCR (KASP) markers for four of the QTL were converted from the significant SNP markers. The identified wheat landraces with stable resistance to stripe rust, significant QTL, and KASP markers should be useful for breeding wheat cultivars with durable resistance to stripe rust.

scholarly journals Genome-wide association analysis of stripe rust resistance in modern Chinese wheat

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Mengjie Jia ◽  
Lijun Yang ◽  
Wei Zhang ◽  
Garry Rosewarne ◽  
Junhui Li ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Amplification Refractory Mutation System ◽  
Post Inoculation ◽  
Genome Wide ◽  
A Genome ◽  
Chinese Wheat

Abstract Background Stripe rust (yellow rust) is a significant disease for bread wheat (Triticum aestivum L.) worldwide. A genome-wide association study was conducted on 240 Chinese wheat cultivars and elite lines genotyped with the wheat 90 K single nucleotide polymorphism (SNP) arrays to decipher the genetic architecture of stripe rust resistance in Chinese germplasm. Results Stripe rust resistance was evaluated at the adult plant stage in Pixian and Xindu in Sichuan province in the 2015–2016 cropping season, and in Wuhan in Hubei province in the 2013–2014, 2016–2017 and 2018–2019 cropping seasons. Twelve stable loci for stripe rust resistance were identified by GWAS using TASSEL and GAPIT software. These loci were distributed on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 4B (3), 4D, 6D, and 7B and explained 3.6 to 10.3% of the phenotypic variation. Six of the loci corresponded with previously reported genes/QTLs, including Sr2/Yr30/Lr27, while the other six (QYr.hbaas-1BS, QYr.hbaas-2BL, QYr.hbaas-3AL, QYr.hbaas-4BL.3, QYr.hbaas-4DL, and QYr.hbaas-6DS) are probably novel. The results suggest high genetic diversity for stripe rust resistance in this population. The resistance alleles of QYr.hbaas-2AS, QYr.hbaas-3BS, QYr.hbaas-4DL, and QYr.hbaas-7BL were rare in the present panel, indicating their potential use in breeding for stripe rust resistance in China. Eleven penta-primer amplification refractory mutation system (PARMS) markers were developed from SNPs significantly associated with seven mapped QTLs. Twenty-seven genes were predicted for mapped QTLs. Six of them were considered as candidates for their high relative expression levels post-inoculation. Conclusion The resistant germplasm, mapped QTLs, and PARMS markers developed in this study are resources for enhancing stripe rust resistance in wheat breeding.

Genome-wide association studies revealed novel stripe rust resistance QTL in barley at seedling and adult-plant stages

Euphytica ◽  
2021 ◽  
Vol 217 (1) ◽  
Author(s):  
Sanjaya Gyawali ◽  
Sujan Mamidi ◽  
Shiaoman Chao ◽  
Subhash C. Bhardwaj ◽  
Pradeep S. Shekhawat ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Association Studies ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide Association Studies ◽  
Resistance Qtl ◽  
Genome Wide

scholarly journals Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)

Plant Disease ◽  
2020 ◽  
Vol 104 (8) ◽  
pp. 2174-2180 ◽  
Author(s):  
Fangping Yang ◽  
Jindong Liu ◽  
Ying Guo ◽  
Zhonghu He ◽  
Awais Rasheed ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Common Wheat ◽  
Stripe Rust ◽  
Resistance Genes ◽  
Rust Resistance ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Economic Losses ◽  
Genome Wide ◽  
A Genome

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.

scholarly journals Genome-Wide Association Mapping of Loci for Resistance to Stripe Rust in North American Elite Spring Wheat Germplasm

2018 ◽  
Vol 108 (2) ◽  
pp. 234-245 ◽  
Author(s):  
Jayfred Gaham Godoy ◽  
Sheri Rynearson ◽  
Xianming Chen ◽  
Michael Pumphrey
Keyword(s):  
Stripe Rust ◽  
Spring Wheat ◽  
Puccinia Striiformis ◽  
Single Nucleotide Polymorphism Array ◽  
Infection Type ◽  
Genome Wide Association ◽  
Adult Plant ◽  
Wheat Germplasm ◽  
Genome Wide ◽  
A Genome

Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a major yield-limiting foliar disease of wheat (Triticum aestivum) worldwide. In this study, the genetic variability of elite spring wheat germplasm from North America was investigated to characterize the genetic basis of effective all-stage and adult plant resistance (APR) to stripe rust. A genome-wide association study was conducted using 237 elite spring wheat lines genotyped with an Illumina Infinium 90K single-nucleotide polymorphism array. All-stage resistance was evaluated at seedling stage in controlled conditions and field evaluations were conducted under natural disease pressure in eight environments across Washington State. High heritability estimates and correlations between infection type and severity were observed. Ten loci for race-specific all-stage resistance were confirmed from previous mapping studies. Three potentially new loci associated with race-specific all-stage resistance were identified on chromosomes 1D, 2A, and 5A. For APR, 11 highly significant quantitative trait loci (QTL) (false discovery rate < 0.01) were identified, of which 3 QTL on chromosomes 3A, 5D, and 7A are reported for the first time. The QTL identified in this study can be used to enrich the current gene pool and improve the diversity of resistance to stripe rust disease.

scholarly journals Genome-wide association analysis of stripe rust resistance loci in wheat accessions from southwestern China

2020 ◽  
Vol 61 (1) ◽  
pp. 37-50 ◽  
Author(s):  
Bin Cheng ◽  
Xu Gao ◽  
Ning Cao ◽  
Yanqing Ding ◽  
Yu Gao ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Stripe Rust ◽  
Rust Resistance ◽  
Puccinia Striiformis ◽  
Genome Wide Association ◽  
Southwestern China ◽  
Stripe Rust Resistance ◽  
Wheat Stripe Rust ◽  
Genome Wide ◽  
A Genome

AbstractWheat stripe rust can cause considerable yield losses, and genetic resistance is the most effective approach for controlling the disease. To identify the genomic regions responsible for Puccinia striiformis f. sp. tritici (Pst) resistance in a set of winter wheat strains mainly from southwestern China, and to identify DNA markers in these regions, we carried out a genome-wide association study (GWAS) of 120 China winter wheat accessions using single nucleotide polymorphism (SNP) markers from 90K wheat SNP arrays. In total, 16 SNP loci were significantly associated with wheat stripe rust in field and greenhouse trials. Of these, three distinctive SNPs on chromosomes 1B, 4A, and 6A were identified at a site in Mianyang in 2014, where the most prevalent wheat stripe rust races since 2009 have been V26 (G22-9, G22-14). This suggests that the three SNP loci were linked to the new quantitative trait loci (QTL)/genes resistant to the V26 races. Germplasm with immunity to Pst is a good source of stripe rust resistance for breeding, and after further validation, SNPs closely linked to resistance QTLs/genes could be converted into user-friendly markers and facilitate marker-assisted selection to improve wheat stripe rust resistance.

scholarly journals Mendelization and Molecular Mapping of a Large-effect QTL Conferring Durable Adult-plant Resistance to Stripe Rust in a Chinese Wheat Landrace ‘Gaoxianguangtoumai’

2021 ◽  
Author(s):  
Yuqi Wang ◽  
Fengying Liang ◽  
Fangnian Guan ◽  
Fangjie Yao ◽  
Long Li ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Plant Resistance ◽  
Adult Plant Resistance ◽  
Puccinia Striiformis ◽  
Snp Array ◽  
Adult Plant ◽  
Isogenic Line ◽  
Wheat Landrace ◽  
Chinese Wheat ◽  
Kasp Markers

Abstract The Chinese wheat landrace ‘Gaoxianguangtoumai’ (GX) has exhibited a high degree of adult-plant resistance (APR) to stripe rust in field environments for more than a decade. To reveal the genetic basis for APR to stripe rust in GX, a set of 249 F6:8 recombinant inbred lines (RILs) was developed from a cross between GX and the susceptible cultivar ‘Taichung 29’. The parents and RILs were evaluated for disease severity at the adult-plant stage in field environments by artificial inoculation with the currently predominant Chinese Puccinia striiformis f. sp. tritici races during three cropping seasons, and genotyped using the Wheat 55K single-nucleotide polymorphism (SNP) array to construct a genetic map with 1,871 SNP markers. Two stable APR quantitative trait loci (QTL), QYr.GX-2AS and QYr.GX-7DS from GX, were detected on chromosomes 2AS and 7DS, which explained 15.5–27.0% and 9.6–15.6% of the total phenotypic variation, respectively. Compared with published genes and QTL, QYr.GX-7DS is likely Yr18, whereas QYr.GX-2AS is probably novel. Haplotype analysis revealed that QYr.GX-2AS is likely to be rare which present in 5.3% of the 325 surveyed Chinese wheat landraces. By analyzing a near-isogenic line population, QYr.GX-2AS was further mapped to an interval with a physical distance of about 1.37 Mb and co-segregated with a Kompetitive allele-specific PCR (KASP) marker. Furthermore, three tightly linked KASP markers were highly polymorphic among 109 Chinese wheat cultivars. The short physical interval and tightly linked KASP markers developed in this study will facilitate marker-assisted selection and map-based cloning of QYr.GX-2AS.

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