Peter Bulli, Junli Zhang, Shiaoman Chao, Xianming Chen and Michael Pumphrey

Abstract

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.

See http://www.g3journal.org/content/6/8/2237.abstract?etoc

G3 (Genes, Genomes, and Genetics) August 1, 2016 vol. 6 no. 8 2237-2253

Figure 2

Relationship of population structure and stripe rust resistance. (A) Fast Ward clustering. Vertical dotted lines indicate genetic similarity thresholds used to classify accessions into two major groups and three subgroups. (B) Heat map of identity-by-descent (IBD) kinship matrix. The two major cluster groups and three cluster subgroups are separated by dashed and dotted lines, respectively. (C) Membership of accessions in the STRUCTURE-derived population structure subgroups. (D) Heat map of reactions of the accessions to stripe rust. IT, infection type; SEV, disease severity. Blue lines indicate resistance and red lines susceptibility based on BLUE-ALL for infection type and disease severity. (E) Frequency of population structure subgroups in geographical regions of origin. (F) Frequency of population structure subgroups in improvement status of accessions (ACIMPT).