Genetic Characterization of Stem Rust Resistance in a Global Spring Wheat Germplasm Collection

Abstract

Stem rust, caused by the fungus Puccinia graminis Pers. f. sp. tritici Ericks, is one of the most damaging diseases of wheat (Triticum aestivum L.). The recent emergence of the stem rust Ug99 race group poses a serious threat to world wheat production. Utilization of genetic resistance in cultivar development is the optimal way to control stem rust. Here, we report association mapping of stem rust resistance in a global spring wheat germplasm collection (2152 accessions) genotyped with the wheat iSelect 9K single‐nucleotide polymorphism array. Using a unified mixed model method (or QK method), we identified a total of 47 loci that were significantly associated with various stem rust resistance traits including field disease resistance and seedling resistance against multiple stem rust pathogen races including BCCBC, TRTTF, TTKSK (Ug99), and TTTTF. The 47 loci could be further condensed into 11 quantitative trait locus (QTL) regions according to linkage disequilibrium information among adjacent markers. We postulate that these QTLs represent known stem rust resistance genes including Sr2, Sr6, Sr7a, Sr8a, Sr9h, Sr13, Sr28, and Sr36. We further employed a multilocus mixed model to explore marker‐trait associations and identified two additional QTLs (one potentially represents Sr31) that were significantly associated with stem rust resistance against various races. Combinations of the most significant loci for each trait explained up to 38.6% of the phenotypic variance. Markers identified through this study could be used to track the genes or QTLs. Accessions with high numbers of resistance‐associated alleles may serve as important breeding materials for stem rust resistance.

Genome-Wide Association Studies in Diverse Spring Wheat Panel for Stripe, Stem, and Leaf Rust Resistance

“…In our study, LD decay was found strongly different in the three genomes with B genome to have the quickest decay followed by A genome, which is supported by previous reports (Gao et al, 2017;Riaz et al, 2018). This supports the practical use of D genome markers suitable for association tests even though less in number (Gao et al, 2017). D genome was found to have the highest LD than other genomes which has also been mentioned in several previous studies (Nielsen et al, 2014;Wang et al, 2014;Zegeye et al, 2014;Voss-Fels et al, 2015;Riaz et al, 2018).…”

“…It has an added advantage of capturing information on germplasm derived from secondary and tertiary gene pools as the array is developed using exome capture of wheat and its wild relatives (Allen et al, 2017;Rasheed and Xia, 2019). In our study, LD decay was found strongly different in the three genomes with B genome to have the quickest decay followed by A genome, which is supported by previous reports (Gao et al, 2017;Riaz et al, 2018). This supports the practical use of D genome markers suitable for association tests even though less in number (Gao et al, 2017).…”

“…Genotypes with COI scores of 0 to 20 were considered as resistant, with score ≥ 60 as susceptible and the remaining as moderate ( Table 1). COI was assumed to be suitable for GWAS and as a primary trait for the identification of significant marker-trait associations (MTAs) since it combines both the information from DS and IR for rust response (Yu et al, 2012;Gao et al, 2016Gao et al, , 2017Mihalyov et al, 2017).…”

Characterization of Ethiopian Wheat Germplasm for Resistance to Four Puccinia graminis f. sp. tritici Races Facilitated by Single-Race Nurseries

“…Previously, Sr11 was reported to be effective to race TKTTF and present in Ethiopian wheat germplasm (Nirmala et al 2016 ). Association mapping studies have confirmed the presence of Sr7a, which confers resistance to race TKTTF, and Sr8a, which confers resistance to TRTTF, in conventional germ-plasm (Bajgain et al 2015 ; Gao et al 2017 ; Mihalyov et al 2017 ). Although nearly all of the bread wheat lines were resistant to race JRCQC, the genes specifically responsible for conferring this resistance are unknown.…”

A Genome-Wide Association Study of Field and Seedling Response to Individual Stem Rust Pathogen Races Reveals Combinations of Race-Specific Genes in North American Spring Wheat

“…Though several studies have evaluated seedling and/or field response of wheat association mapping panels to Pgt isolates (Yu et al, 2011 , 2012 ; Letta et al, 2014 ; Zhang et al, 2014 ; Gao et al, 2017 ; Mihalyov et al, 2017 ; Muleta et al, 2017 ), only one has evaluated field response of the wheat population studied to more than one Pgt race (Chao et al, 2017 ). In that study, field response of a bulk of six Pgt isolates in Minnesota was compared to response to a bulk of Pgt isolates in Ethiopia, and differences between these datasets could be due to environment and/or race.…”