Loci associated with resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a core collection of spring wheat (Triticum aestivum)

Abstract

Stripe rust, caused by Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.

Developing KASP Markers on a Major Stripe Rust Resistance QTL in a Popular Wheat TAM 111 Using 90K Array and Genotyping‐by‐Sequencing SNPs

“…However, the latter four markers were mapped on 2BL at 595.0 to 696.7 Mb of 2B in this study ( Fig. This is also consistent with what Muleta et al (2017) found through genome-wide association mapping, which was that SNPs IWA3621, IWA2977, IWA4983, IWA4984, IWA5149, IWA6875, and IWA6818 linked to Yr QTL in TAM 111, UC1110, Opata 85, Louise, and IDO444 clustered at 189 MB, of which three SNPs (IWA2977, IWA6818, and IWA5149) were mapped in the same genetic region and IWA2977 was mapped next to the peak SNP (IWB47487) linked to QYr.tamu-2B (Supplemental Table S5, Fig. The flanking markers for this 2B major QTL from this study indicated that QYr.tamu-2B was located at the 154.3 Mb physical position on the Chinese Spring reference genome IWGSC RefSeq v1.0 (IWGSC, 2014), which is on 2BS instead of 2BL.…”

“…1C) were identified as flanking markers for Yr5. 1C) was reported to be close to the regions of Yr53 (5-11 cM) and Yr43 (9-18 cM) by Muleta et al (2017). PI 480148 showed resistance in all seeding tests to several predominant Pst races in the United States.…”

“…(A) Modified genetic map of 2BL of QYr.tam-2BL for disease severity average using diversity arrays technology markers(Basnet et al, 2014). The SNPs linked to QYr.tamu-2B are bold, and several markers linked to known genes or SNPs found linked to TAM 111 stripe rust resistance gene inMuleta et al (2017) are bold and underlined in Panels B and C. (C) Fragment of wheat chromosome 2B map showing the physical location of the corresponding SNPs in Mb.…”

Genome‐wide mapping of resistance to stripe rust caused by Puccinia striiformis f. sp. tritici in hexaploid winter wheat

“…The prospect of developing varieties with complex resistance backgrounds is increasingly facilitated by the capacity for developing high‐density molecular markers to perform genome‐wide association mapping that has a higher mapping resolution and genome‐wide prediction, which are more feasible due to the recent availability of genotyping‐by‐sequencing (Davey et al., 2011; Poland, Brown, Sorrells, & Jannink, 2012) and high‐density single nucleotide polymorphism (SNP) genotyping platforms (Cavanagh et al., 2013; Wang et al., 2014). In particular, the Illumina iSelect 9K and 90K wheat SNP chip assays have enabled robust and affordable genotyping of wheat and were successfully used for genome‐wide association mapping, linkage mapping, and genome‐wide predictions of various traits (Bajgain et al., 2015; Bulli, Zhang, Chao, Chen, & Pumphrey, 2016; Kertho, Mamidi, Bonman, McClean, & Acevedo, 2015; Maccaferri et al., 2015b; Muleta et al., 2017a,b; Naruoka et al., 2016; Turner et al., 2017; Wu et al., 2015). The objectives of this study were (i) to explore genetic diversity among accessions in a worldwide collection of winter wheat accessions and identify new sources of seedling and adult plant resistance to stripe rust, and (ii) to identify genomic regions underlying resistance to stripe rust in the winter wheat accessions through genome‐wide association analysis.…”

INLUENCE OF ALIEN GENETIC MATERIAL ON THE MANIFESTATION OF AGRONOMICALLY IMPORTANT TRAITS OF COMMON WHEAT (T. aestivum L.)

“…Новым методическим подходом является полногеном ный поиск ассоциаций (genome wide association study -GWAS), который позволяет в геномах культивируемых сортов идентифицировать генетические локусы как с главными, так и с минорными эффектами (Gao et al, 2016;Gerard et al, 2017;Muleta et al, 2017). В качестве дополнительного преимущества этого метода отметим де тальную информацию по генотипированию сортов и се лекционных линий большим числом молекулярных мар керов и возможность применения этих данных для се лекции по большому числу признаков.…”