Loci associated with resistance to stripe rust (<i>Puccinia striiformis</i> f. sp. <i>tritici</i>) in a core collection of spring wheat (<i>Triticum aestivum</i>)

<div><p>Stripe rust, caused by <i>Puccinia striiformis</i> Westend. f. sp. <i>tritici</i> Erikss. (<i>Pst</i>) remains one of the most significant diseases of wheat worldwide. We investigated stripe rust resistance by genome-wide association analysis (GWAS) in 959 spring wheat accessions from the United States Department of Agriculture-Agricultural Research Service National Small Grains Collection, representing major global production environments. The panel was characterized for field resistance in multi-environment field trials and seedling resistance under greenhouse conditions. A genome-wide set of 5,619 informative SNP markers were used to examine the population structure, linkage disequilibrium and marker-trait associations in the germplasm panel. Based on model-based analysis of population structure and hierarchical Ward clustering algorithm, the accessions were clustered into two major subgroups. These subgroups were largely separated according to geographic origin and improvement status of the accessions. A significant correlation was observed between the population sub-clusters and response to stripe rust infection. We identified 11 and 7 genomic regions with significant associations with stripe rust resistance at adult plant and seedling stages, respectively, based on a false discovery rate multiple correction method. The regions harboring all, except three, of the QTL identified from the field and greenhouse studies overlap with positions of previously reported QTL. Further work should aim at validating the identified QTL using proper germplasm and populations to enhance their utility in marker assisted breeding.</p></div

Means and variance components of infection type (IT) and severity (SEV) of stripe rust in the 959 global collection of spring wheat accessions.

<p>Means and variance components of infection type (IT) and severity (SEV) of stripe rust in the 959 global collection of spring wheat accessions.</p

Patterns of genome wide linkage disequilibrium (LD) in the germplasm panel.

<p>A) Scatter plot of average LD (<i>r</i>^<i>2</i>) 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).</p

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 <i>P</i> value <0.01 in at least two of the five environments and false-discovery-rate (FDR) adjusted <i>P</i> values < 0.1 in at least one environment.

<p>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 <i>P</i> value <0.01 in at least two of the five environments and false-discovery-rate (FDR) adjusted <i>P</i> values < 0.1 in at least one environment.</p

Population structure and its relationship to stripe rust resistance.

<p>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.</p

Relationships between the number of favorable alleles of the significant SNPs in each of the accessions and responses to <i>Puccinia striiformis</i> f. sp. <i>tritici</i>.

<p>(A) Infection type (IT), (B) Disease severity (SEV).</p

Genomic regions significantly associated with seedling resistance to stripe rust in the 959 global collection of spring wheat accessions based on FDR adjusted <i>P</i> values <0.1.

<p>Genomic regions significantly associated with seedling resistance to stripe rust in the 959 global collection of spring wheat accessions based on FDR adjusted <i>P</i> values <0.1.</p

Frequency distribution of the response to the accessions to stripe rust.

<p>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 <i>Puccinia striiformis</i> f. sp. <i>tritici</i> 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.</p

Allelic effects of the 11 highly significant markers on BLUP values of stripe rust severity (upper) and infection type (lower).

<p>Blue colored boxes indicate effect due to the resistance associated alleles, while the red colored boxes indicated effect due to the unfavorable allele.</p

Additional file 6: of Characterization of molecular diversity and genome-wide mapping of loci associated with resistance to stripe rust and stem rust in Ethiopian bread wheat accessions

Frequency of favorable alleles of the molecular markers linked to previously mapped stripe rust and stem rust resistance genes/QTL in the Ethiopian wheat accessions. (DOCX 16 kb