Genome-wide and Mla locus-specific characterisation of Latvian barley varieties

Abstract

Genetic diversity in locally adapted germplasm forms the basis for crop improvement through breeding. While single loci have been routinely used for studies of genetic diversity, the highthroughput genotyping platforms that have recently become available for large genome cro plants offer an unbiased view on genetic diversity on a genome-wide scale. We assessed genetic diversity in Latvian barley varieties and some progenitors using DArT markers and studied the extent of linkage disequilibrium in Latvian germplasm. Further, genetic diversity at three loci flanking the barley powdery mildew Mla locus conferring race-specific resistance was studied in Latvian barley germplasm. The Mla locus encompasses several closely related resistance gene homologues with a complex evolutionary history, which complicates the design of molecular markers for different Mla genes. We observed significant linkage disequilibrium between the single nucleotide polymorphisms (SNPs) at the three loci, 206i20_T7, ABC15612, and 538P8, flanking the Mla locus. SNP haplotypes were largely in agreement with known phenotypic data and, thus, may be potentially diagnostic for Mla resistance genes in hybrids.