A Cluster of Nucleotide‐Binding Site–Leucine‐Rich Repeat Genes Resides in a Barley Powdery Mildew Resistance Quantitative Trait Loci on 7HL

Abstract

Powdery mildew causes severe yield losses in barley production worldwide. Although many resistance genes have been described, only a few have already been cloned. A strong QTL (quantitative trait locus) conferring resistance to a wide array of powdery mildew isolates was identified in a Spanish barley landrace on the long arm of chromosome 7H. Previous studies narrowed down the QTL position, but were unable to identify candidate genes or physically locate the resistance. In this study, the exome of three recombinant lines from a high-resolution mapping population was sequenced and analyzed, narrowing the position of the resistance down to a single physical contig. Closer inspection of the region revealed a cluster of closely related NBS-LRR (nucleotide-binding site-leucine-rich repeat containing protein) genes. Large differences were found between the resistant lines and the reference genome of cultivar Morex, in the form of PAV (presence-absence variation) in the composition of the NBS-LRR cluster. Finally, a template-guided assembly was performed and subsequent expression analysis revealed that one of the new assembled candidate genes is transcribed. In summary, 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 NGS (next-generation sequencing) tools to tackle the challenges of gene cloning when the target gene is absent from the reference genome.

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species

“…Of most interest to crop scientists is the fact that loci controlling adaptive responses to the environment are frequent transposition targets ( Quadrana et al, 2016 ). The description in barley of a cluster of accessory resistance genes in a transposon-rich region subscribes this observation ( Cantalapiedra et al, 2016 ). Unfortunately there are no physical maps of these genotypes to systematically test this hypothesis, for instance by checking for the co-occurrence of accessory loci and transposons.…”

High Resolution Genetic and Physical Mapping of a Major Powdery Mildew Resistance Locus in Barley

“…Although there is no further information on the location of the second copy gene, it is highly expected both NLR and RLK with the highest sequence identity (putative tandem duplications or local paralogs) to be typically found in close physical proximity and are the result of tandem duplication events (Baumgarten et al, 2003; Cantalapiedra et al, 2016).…”

“…Recently, Cantalapiedra et al (2016) analyzed the exome sequences of three recombinant lines with contrasting resistance phenotypes from a high-resolution mapping population. By narrowing the position of the resistance derived from a Spanish landrace – showing a wide array of powdery mildew isolates – down to a single physical contig, they found large differences between the resistant lines and cultivar Morex as the reference genome, in the form of PAV in the composition of the NBS-LRR cluster.…”

Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene Sen3

“…Moreover, the genotype used as a reference is often susceptible to the disease and lacks the causal R gene paralog segregating in a mapping population. This is exemplified by the case of the fine-mapping and candidate gene analysis of a powdery mildew resistance QTL in barley [11]. After an exome capture experiment was performed using homozygous recombinants, reads were mapped to the barley reference genome.…”