Data from: Genetic Architecture of Resistance to Stripe Rust in a Global Winter Wheat Germplasm Collection

Virulence shifts in populations of Puccinia striiformis f. sp. tritici (Pst), the causal pathogen of wheat stripe rust, are a major challenge to resistance breeding. The majority of known resistance genes are already ineffective against current races of Pst, necessitating the identification and introgression of new sources of resistance. Germplasm core collections that reflect the range of genetic and phenotypic diversity of crop species are ideal platforms for examining the genetic architecture of complex traits such as resistance to stripe rust. We report the results of genetic characterization and genome-wide association analysis (GWAS) for resistance to stripe rust in a core subset of 1175 accessions in the National Small Grains Collection (NSGC) winter wheat germplasm collection, based on genotyping with the wheat 9K single nucleotide polymorphism (SNP) iSelect assay and phenotyping of seedling and adult plants under natural disease epidemics in four environments. High correlations among the field data translated into high heritability values within and across locations. Population structure was evident when accessions were grouped by stripe rust reaction. GWAS identified 127 resistance loci that were effective across at least two environments, including 20 with significant genome-wide adjusted P-values. Based on relative map positions of previously reported genes and QTL, five of the QTL with significant genome-wide adjusted P-values in this study represent potentially new loci. This study provides an overview of the diversity of Pst resistance in the NSGC winter wheat germplasm core collection, which can be exploited for diversification of stripe rust resistance in breeding programs.

• Resource Title: SUPPLEMENTAL MATERIAL FOR BULLI, ET AL, 2016.

  File Name: Web Page, url: http://www.g3journal.org/content/suppl/2016/05/25/g3.116.028407.DC1

  Files in this Data Supplement:

  • Table S2 - Pearson correlation coefficients among the best linear unbiased estimates (BLUEs) of infection type (IT) and disease severity (SEV) for individual locations (MTV and PLM) and across locations (ALL). (.pdf, 257 KB)
  • Table S1 - Predominant races of Puccinia striiformis f. sp. tritici during the 2011 to 2014 crop seasons. (.pdf, 336 KB)
  • Table S3 - Loci associated with resistance to Puccinia striiformis f. sp. tritici in the global winter wheat germplasm collection in at least two environments (with marker-wise P <0.01 in at least one of the environments). (.pdf, 478 KB)
  • Table S4 - Loci associated with partial resistance to Puccinia striiformis f. sp. tritici in the global winter wheat germplasm collection in at least two environments with (marker-wise P <0.01 in at least one of the environments). (.pdf, 481 KB)
  • Table S5 - Frequencies of favorable alleles of QTL-tag SNPs in population structure subgroups of the global winter wheat germplasm collection. (.pdf, 360 KB)
  • Table S6 - Frequencies of favorable alleles of QTL-tag SNPs associated with partial resistance in population structure subgroups of the global winter wheat germplasm collection. (.pdf, 361 KB)
  • Table S7 - Analysis of variance for infection type (IT) and disease severity (SEV) using 20 quantitative trait loci (QTL) with significant genome-wide associations (adjusted P <0.1). (.pdf, 372 KB)
  • Table S8 - Analysis of molecular variance (AMOVA), and FST values between pairs of subpopulations of subset of the global winter wheat core germplasm collection based on 5,347 SNPs. (.pdf, 335 KB)
  • Table S9 - Summary of enrichment of genomic regions with significant marker-trait associations with reactions to Puccinia striiformis f. sp. tritici, and loci annotations. (.pdf, 364 KB)
  • File S3 - Supporting information for Figure 6. (.pdf, 635 KB)
  • Figure S1 - Country-specific distribution of the improvement status (ACIMPT) of the global winter wheat germplasm collection. (.pptx, 129 KB)
  • Figure S2 - Box plots. (.pptx, 104 KB)
  • File S1 - Genetic profiles of the 1,175 winter wheat accessions based on the 127 QTL-tag SNPs. (.xlsx, 618 KB)
  • File S2 - Control resistance genes Yr18/Lr34 and Yr46/Lr67. (.xlsx, 126 KB)
  • File S4 - Results of Blastx search against Brachypodium and rice proteins using contigs of SNPs within confidence intervals of the 20 QTL with genome-wide significant association with stripe rust reaction. (.xlsx, 299 KB)