Fig 1.
Geographic origin of the 959 spring wheat accessions.
The number of accessions (No) from a particular country is indicated by the size of the pie chart. Color within the chart indicates accession type (Acc).
Fig 2.
Frequency distribution of the response to the accessions to stripe rust.
A) Best linear unbiased prediction (BLUP) values of the infection type (IT) responses of adult plants under field condition, B) BLUP values of the severity (SEV) responses of adult plants under field condition, and C) seedling resistance screening against three Puccinia striiformis f. sp. tritici races (PSTv_14, PSTv_37 and PSTv_40) under greenhouse experiments. MTV_SEV = Mount Vernon severity, MTV_IT = Mount Vernon infection type, PLM_SEV = Pullman severity, PLM_IT = Pullman infection type.
Table 1.
Means and variance components of infection type (IT) and severity (SEV) of stripe rust in the 959 global collection of spring wheat accessions.
Fig 3.
Population structure and its relationship to stripe rust resistance.
A) Dendrogram based on Ward clustering of the spring wheat core collection, B) pairwise kinship matrix depicting clustering of the accessions based on identity-by-decent (IBD), C) population structure based on principal component analysis (PCA). Both genetic relatedness and principal component analyses grouped the accessions into two subpopulations, Subpopulation 1 (SP1) and Subpopulation 2 (SP2). Clustering pattern based on PCA also explained geographic origin and improvement status of the spring wheat core collection. D) Effect of population structure on stripe rust infection type (IT) and severity (SEV). Box plots show trait distribution and compare the levels of stripe rust between the two subpopulations. MTV_12 = Mount Vernon 2012, MTV_13 = Mount Vernon 2013, MTV_14 = Mount Vernon 2014, PLM_12 = Pullman 2012, PLM_13 = Pullman 2013, PLM_14 = Pullman 2014.
Fig 4.
Patterns of genome wide linkage disequilibrium (LD) in the germplasm panel.
A) Scatter plot of average LD (r2) as a function of genetic distance between markers, B) chromosome-wise distribution of the number of marker pairs that showed LD due to physical linkage (B).
Fig 5.
Allelic effects of the 11 highly significant markers on BLUP values of stripe rust severity (upper) and infection type (lower).
Blue colored boxes indicate effect due to the resistance associated alleles, while the red colored boxes indicated effect due to the unfavorable allele.
Table 2.
Genomic regions significantly associated with field-based resistance to stripe rust infection type (IT) and severity (SEV) in the 959 spring wheat accessions based on marker-wise P value <0.01 in at least two of the five environments and false-discovery-rate (FDR) adjusted P values < 0.1 in at least one environment.
Table 3.
Genomic regions significantly associated with seedling resistance to stripe rust in the 959 global collection of spring wheat accessions based on FDR adjusted P values <0.1.
Fig 6.
Relationships between the number of favorable alleles of the significant SNPs in each of the accessions and responses to Puccinia striiformis f. sp. tritici.
(A) Infection type (IT), (B) Disease severity (SEV).