Genetic analysis and physical mapping of oat adult plant resistance loci against Puccinia coronata f. sp. avenae.

Abstract

Six quantitative trait loci (QTL) for adult plant resistance (APR) against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations (RILs). Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTL were mapped on six different chromosomes, namely: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTL for coefficient of infection range from 12.2 to 46.9%, while heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking SNP markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTL in each population were determined using SNP haplotype data, which showed significantly lower coefficient of infection (CI) in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, Polymerase Chain Reaction Allelic Competitive Extension (PACE) markers for the APR loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.