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. 2017 Oct 5;7(10):3491-3507.
doi: 10.1534/g3.117.300222.

Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum

Ahmad H Sallam  1 , Priyanka Tyagi  2 , Gina Brown-Guedira  3 , Gary J Muehlbauer  4   5 , Alex Hulse  1 , Brian J Steffenson  6
Affiliations

Genome-Wide Association Mapping of Stem Rust Resistance in Hordeum vulgare subsp. spontaneum

Ahmad H Sallam et al. G3 (Bethesda). .

Abstract

Stem rust was one of the most devastating diseases of barley in North America. Through the deployment of cultivars with the resistance gene Rpg1, losses to stem rust have been minimal over the past 70 yr. However, there exist both domestic (QCCJB) and foreign (TTKSK aka isolate Ug99) pathotypes with virulence for this important gene. To identify new sources of stem rust resistance for barley, we evaluated the Wild Barley Diversity Collection (WBDC) (314 ecogeographically diverse accessions of Hordeum vulgare subsp. spontaneum) for seedling resistance to four pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) of the wheat stem rust pathogen (Puccinia graminis f. sp. tritici, Pgt) and one isolate (92-MN-90) of the rye stem rust pathogen (P. graminis f. sp. secalis, Pgs). Based on a coefficient of infection, the frequency of resistance in the WBDC was low ranging from 0.6% with HKHJC to 19.4% with 92-MN-90. None of the accessions was resistant to all five cultures of P. graminis A genome-wide association study (GWAS) was conducted to map stem rust resistance loci using 50,842 single-nucleotide polymorphic markers generated by genotype-by-sequencing and ordered using the new barley reference genome assembly. After proper accounting for genetic relatedness and structure among accessions, 45 quantitative trait loci were identified for resistance to P. graminis across all seven barley chromosomes. Three novel loci associated with resistance to TTKSK, QCCJB, MCCFC, and 92-MN-90 were identified on chromosomes 5H and 7H, and two novel loci associated with resistance to HKHJC were identified on chromosomes 1H and 3H. These novel alleles will enhance the diversity of resistance available for cultivated barley.

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Figures

Figure 1
Figure 1
Heatmap for the distribution of linkage disequilibrium (LD) across the genome of H. vulgare subsp. spontaneum accessions of the WBDC estimated as r2 using SNP markers, number of SNP markers for each chromosome, and average adjacent marker LD for each chromosome. The approximate positions of centromeres (C) are given for each chromosome.
Figure 2
Figure 2
(A) Population structure of the WBDC inferred from Bayesian grouping implemented in STRUCTURE where the number of subpopulations (SP) identified was seven. (B) PCA of the WBDC identified seven major groups that corresponded closely with the subpopulation assignment results found with STRUCTURE analysis. Accessions not belonging to any of the seven subpopulations are shown in black.
Figure 3
Figure 3
(A) Heatmap matrix displaying the genetic kinship among accessions of the WBDC calculated based on 50,842 SNP markers with corresponding subpopulations identified by STRUCTURE given above. (B) Heatmap for the average coefficient of infection (CI) of WBDC accessions to P. graminis f. sp. tritici pathotypes TTKSK, QCCJB, MCCFC, and HKHJC and P. graminis f. sp. secalis culture 92-MN-90 where lighter colors indicate higher resistance levels.
Figure 4
Figure 4
Geographic distribution of accessions in the WBDC and their subpopulation assignment as identified by structure analysis for (A) the entire region and (B) an enlarged insert of the Levant region.
Figure 5
Figure 5
Phenotypic distribution of the coefficient of infection to P. graminis f. sp. tritici pathotypes TTKSK, QCCJB, MCCFC, and HKHJC and P. graminis f. sp. secalis culture 92-MN-90 in the WBDC.
Figure 6
Figure 6
Manhattan plot displaying SNP markers significantly associated with resistance to four P. graminis f. sp. tritici pathotypes (TTKSK, QCCJB, MCCFC, and HKHJC) and one P. graminis f. sp. secalis culture 92-MN-90 in the WBDC. Two models were used: the K model (designated by circles) and the G model [designated by plus (+) signs]. All plotted G model hits are significant. The threshold for QTL detection for each P. graminis culture using the K model is shown with a horizontal dashed red line. Physical positions of the stem rust resistance genes Rpg1 and rpg4/Rpg5 are given on the map.
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