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 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.

scholarly journals Identifying Loci Conferring Resistance to Leaf and Stripe Rusts in a Spring Wheat Population (Triticum aestivum) via Genome-Wide Association Mapping

2019 ◽  
Vol 109 (11) ◽  
pp. 1932-1940 ◽  
Author(s):  
Weizhen Liu ◽  
James Kolmer ◽  
Sheri Rynearson ◽  
Xianming Chen ◽  
Liangliang Gao ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Stripe Rust ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Leaf Rust Resistance ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide

A previous genome-wide association study (GWAS) for leaf rust (caused by Puccinia triticina) resistance identified 46 resistance quantitative trait loci (QTL) in an elite spring wheat leaf rust resistance diversity panel. With the aim of characterizing the pleiotropic resistance sources to both leaf rust and stripe rust (caused by P. striiformis f. sp. tritici), stripe rust responses were tested in five U.S. environments at the adult-plant stage and to five U.S. races at the seedling stage. The data revealed balanced phenotypic distributions in this population except for the seedling response to P. striiformis f. sp. tritici race PSTv-37. GWAS for stripe rust resistance discovered a total of 21 QTL significantly associated with all-stage or field resistance on chromosomes 1B, 1D, 2B, 3B, 4A, 5A, 5B, 5D, 6A, 6B, 7A, and 7B. Previously documented pleiotropic resistance genes Yr18/Lr34 and Yr46/Lr67 and tightly linked genes Yr17-Lr37 and Yr30-Sr2-Lr27 were also detected in this population. In addition, stripe rust resistance QTL Yrswp-2B.1, Yrswp-3B, and Yrswp-7B colocated with leaf rust resistance loci 2B_3, 3B_t2, and 7B_4, respectively. Haplotype analysis uncovered that Yrswp-3B and 3B_t2 were either tightly linked genes or the same gene for resistance to both stripe and leaf rusts. Single nucleotide polymorphism markers IWB35950, IWB74350, and IWB72134 for the 3B QTL conferring resistance to both rusts should be useful in incorporating the resistance allele(s) in new cultivars.

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 Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance

2020 ◽  
Vol 11 ◽  
Author(s):  
Deepender Kumar ◽  
Animesh Kumar ◽  
Vinod Chhokar ◽  
Om Prakash Gangwar ◽  
Subhash Chander Bhardwaj ◽  
...  
Keyword(s):  
Leaf Rust ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Association Studies ◽  
Leaf Rust Resistance ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide

scholarly journals Correction to: Genome-wide mapping of adult plant stripe rust resistance in wheat cultivar Toni

2019 ◽  
Vol 132 (7) ◽  
pp. 2167-2168
Author(s):  
Xinli Zhou ◽  
Tian Hu ◽  
Xin Li ◽  
Ma YU ◽  
Yuanyuan Li ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Wheat Cultivar ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide

Genome-wide mapping of adult plant stripe rust resistance in wheat cultivar Toni

2019 ◽  
Vol 132 (6) ◽  
pp. 1693-1704 ◽  
Author(s):  
Xinli Zhou ◽  
Tian Hu ◽  
Xin Li ◽  
Ma YU ◽  
Yuanyuan Li ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Wheat Cultivar ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Genome Wide

Identification of Stripe Rust Resistance Loci in U.S. Spring Wheat Cultivars and Breeding Lines Using Genome-Wide Association Mapping and Yr Gene Markers

Plant Disease ◽  
2020 ◽  
Vol 104 (8) ◽  
pp. 2181-2192 ◽  
Author(s):  
Lu Liu ◽  
Meinan Wang ◽  
Zhiwu Zhang ◽  
Deven R. See ◽  
Xianming Chen
Keyword(s):  
Stripe Rust ◽  
Spring Wheat ◽  
Resistance Genes ◽  
Rust Resistance ◽  
The United States ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Wheat Cultivars ◽  
Breeding Lines ◽  
Genome Wide

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a major threat to wheat production worldwide, especially in the United States. To identify loci for effective stripe rust resistance in U.S. wheat, a genome-wide association study (GWAS) was conducted using a panel of 616 spring wheat cultivars and breeding lines. The accessions in this panel were phenotyped for stripe rust response in the greenhouse at seedling stage with five predominant and highly virulent races of Pst and in different field environments at adult-plant stage in 2017 and 2018. In total, 2,029 single-nucleotide polymorphism markers that cover the whole genome were generated with genotyping by multiplexed sequencing and used in GWAS. In addition, 23 markers of previously reported resistance genes or quantitative trait loci (QTLs) were used to genotype the population. This spring panel was grouped into three subpopulations based on principal component analysis. A total of 37 genes or QTLs including 10 potentially new QTLs for resistance to stripe rust were detected by GWAS and linked marker tests. The frequencies of the resistance genes or QTLs in various nurseries were determined, indicating different intensities of these genes or QTLs used in breeding programs of different regions. These resistance loci and the information on their markers, effectiveness, and distributions should be useful for improving stripe rust resistance in wheat cultivars.

scholarly journals Barley Stripe Rust Resistance QTL: Development and Validation of SNP Markers for Resistance to Puccinia striiformis f. sp. hordei

2016 ◽  
Vol 106 (11) ◽  
pp. 1344-1351 ◽  
Author(s):  
K. Esvelt Klos ◽  
T. Gordon ◽  
P. Bregitzer ◽  
P. Hayes ◽  
X. M. Chen ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Rust Resistance ◽  
Puccinia Striiformis ◽  
Recombinant Inbred Lines ◽  
Snp Markers ◽  
Stripe Rust Resistance ◽  
Adult Plant ◽  
Seedling Resistance ◽  
Resistance Qtl ◽  
Barley Stripe Rust

Quantitative trait loci (QTL) for barley stripe rust resistance were mapped in recombinant inbred lines (RIL) from a ‘Lenetah’ × ‘Grannelose Zweizeilige’ (GZ) cross. GZ is known for a major seedling resistance QTL on chromosome 4H but linked markers suitable for marker-assisted selection have not been developed. This study identified the 4H QTL (log of the likelihood [LOD] = 15.94 at 97.19 centimorgans [cM]), and additional QTL on chromosomes 4H and 6H (LOD = 5.39 at 72.7 cM and 4.24 at 34.46 cM, respectively). A QTL on chromosome 7H (LOD = 2.04 at 81.07 cM) was suggested. All resistance alleles were derived from GZ. Evaluations of adult plant response in Corvallis, OR in 2013 and 2015 provided evidence of QTL at the same positions. However, the minor QTL on 4H was not statistically significant in either location/year, while the 7H QTL was significant in both. The single-nucleotide polymorphism markers flanking the resistance QTL were validated in RIL from a ‘95SR316A’ × GZ cross for their ability to predict seedling resistance. In 95SR316A × GZ, 91 to 92% of RIL with GZ alleles at the major 4H QTL and at least one other were resistant to moderate in reaction. In these populations, at least two QTL were required to transfer the barley stripe rust resistance from GZ.

scholarly journals Genomic Regions Associated With Stripe Rust Resistance Against the Egyptian Race Revealed by Genome-Wide Association Study

2020 ◽  
Author(s):  
Abou-Zeid A. Mohamed ◽  
Amira M. I. Mourad
Keyword(s):  
Stripe Rust ◽  
Spring Wheat ◽  
Rust Resistance ◽  
Genome Wide Association Study ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Stripe Rust Resistance ◽  
Wheat Genotypes ◽  
Genome Wide ◽  
Resistant Genotypes

Abstract Background: Wheat stripe rust (caused by Puccinia striiformis f. sp. Tritici), is a major disease that causes huge yield damage. New pathogen races appeared in the last few years and caused a broke down in the resistant genotypes. In Egypt, some of the resistant genotypes began to be susceptible to stripe rust in recent years. This situation increases the need to produce new genotypes with durable resistance. Besides, looking for a new resistant source from the available wheat genotypes all over the world help in enhancing the breeding programs. Results: In the recent study, a set of 103-spring wheat genotypes from different fourteen countries were evaluated to their field resistant to stripe rust for two years. These genotypes included 17 Egyptian genotypes from the old and new cultivars. The 103-spring wheat genotypes were reported to be well adapted to the Egyptian environmental conditions. Out of the tested genotypes, eight genotypes from four different countries were found to be resistant in both years. Genotyping was carried out using genotyping-by-sequencing and a set of 26,703 SNPs were used in the genome-wide association study. Five SNP markers, located on chromosomes 2A and 4A, were found to be significantly associated with the resistance in both years. Three gene models associated with disease resistance and underlying these significant SNPs were identified. One immune Iranian genotype, with the highest number of different alleles from the most resistant Egyptian genotypes, was detected. Conclusion: the high variation among the tested genotypes in their resistance to the Egyptian stripe rust race confirming the possible improvement of stripe rust resistance in the Egyptian wheat genotypes. The identified five SNP markers are stable and could be used in marker-assisted selection after validation in different genetic backgrounds. Crossing between the immune Iranian genotype and the Egyptian genotypes will improve stripe rust resistance in Egypt.

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