Fine-mapping of a powdery mildew QTL by exome sequencing

Abstract

Powdery mildew in barley is caused by the biotrophic fungus Blumeria graminis f. sp. hordei. Colonization of leaf surfaces results in severe yield losses in temperate latitudes worldwide. Up to date, most mildew resistance loci (Ml genes) have not been cloned, with the exception of mlo and Mla genes. Cloning efforts to identify them relied on cumbersome procedures, due to the lack of genomic resources and the large and highly repetitive nature of barley genome. In the last decade, new resources have been made available which accelerate barley research and breeding. In this work, we take advantage of those resources to fine map a powdery mildew resistance QTL on 7HL, through the development of a high-resolution mapping population followed by exome sequencing of recombinant lines with contrasting resistance phenotypes. Exome capture data allowed delimiting the physical position of the QTL to a single physical contig. The analysis of available genomic references led to the characterization of the gene composition in the region, revealing a cluster of NBS-LRRs taking up most of the QTL. We followed a non-standard pipeline to assemble reads from mixed mappings, causing heterozygous variants in NBS-LRR loci. Overall, the results suggest that NBS-LRR genes, absent from the reference and the susceptible genotypes, could be functional and responsible for the powdery mildew resistance. The procedure followed is an example of the use of next generation sequencing tools to tackle the challenges of gene cloning when the template is absent from the reference.