Genomics of the Barley Immune System

Positional cloning of resistance (R) loci to biotrophic pathogens in angiosperms has revealed that the majority of genes encode proteins with two critical domains: a nucleotide binding (NB) domain and tandem arrays of leucine rich repeats (LRRs) [reference]. Localized to the cytoplasm, NB-LRRs recognize the presence of pathogens through direct recognition of pathogen-derived elicitors or through indirect recognition of host proteins that are modified by the pathogen. NB-LRR encoding loci are highly complex, exhibiting substantial copy number variation, structural rearrangements, and novel gene content between allelic variants. Collectively, these characteristics render this gene family a major challenge with modern assembly and annotation from next-generation sequencing. Using the Morex whole genome shotgun reference assembly as a starting point, we identified 328 NB-LRRs are present in the annotated Morex genome. The NB-LRRs are unequally distributed across the genome, with particular enrichment on chromosome arms: 1HS, 2HS, 6HL, and 7HS. Here, we describe a substantial extension of the number of annotated NB-LRRs to 355, which was achieved by integrating a transcriptome-based discovery pipeline and RenSeq/PacBio, an exome capture that specifically targets the NB-LRRs from barley. We are now leveraging the leaf transcriptomes derived from 39 elite, landrace, and wild barley accessions to assess allelic diversity including phylogenetic relationship and degree of presence/absence variation relative to the reference genome. High expression was observed for many NB-LRR encoding R genes, including Mla and Rpg5. The annotated NB-LRRome, RenSeq capture design, and physical anchoring will be a critical resource in the rapid identification of R genes in barley.