Physical and transcriptional organisation of the bread wheat intracellular immune receptor repertoire

Abstract

1Disease resistance genes encoding intracellular immune receptors of the nucleotide-binding 2 and leucine-rich repeat (NLR) class of proteins detect pathogens by the presence of pathogen 3 effectors. Plant genomes typically contain hundreds of NLR encoding genes. The availability 4 of the hexaploid wheat cultivar Chinese Spring reference genome now allows a detailed study 5 of its NLR complement. However, low NLR expression as well as high intra-family sequence 6 homology hinders their accurate gene annotation. Here we developed NLR-Annotator for in 7 silico NLR identification independent of transcript support. Although developed for wheat, we 8 demonstrate the universal applicability of NLR-Annotator across diverse plant taxa. Applying 9 our tool to wheat and combining it with a transcript-validated subset of genes from the 10 reference gene annotation, we characterized the structure, phylogeny and expression profile of 11 the NLR gene family. We detected 3,400 full-length NLR loci of which 1,540 were confirmed 12 as complete genes. NLRs with integrated domains mostly group in specific sub-clades. 13Members of another subclade predominantly locate in close physical proximity to NLRs 14 carrying integrated domains suggesting a paired helper-function. Most NLRs (88%) display 15 low basal expression (in the lower 10 percentile of transcripts), which may be tissue-specific 16 and/or induced by biotic stress. As a case study for applying our tool to the positional cloning 17 of resistance genes, we estimated the number of NLR genes within the intervals of mapped rust 18 resistance genes. Our study will support the identification of functional resistance genes in 19 wheat to accelerate the breeding and engineering of disease resistant varieties. 20 22All rights reserved. No reuse allowed without permission.(which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/339424 doi: bioRxiv preprint first posted online Jun. 5, 2018; 3 Background 1The status of wheat as the world's most widely grown and important food crop [1] is 2 threatened by the emergence and spread of new and old diseases. For example, 3 wheat stem rust, long considered a vanquished foe of the past, has in the last 20 years 4 caused devastating epidemics in Africa [2, 3] and eastern Russia [4], while, in 2013 5and 2016 large outbreaks occurred for the first time in >50 years in western Europe 6 [5, 6]. The spread of disease into new regions can be attributed to the very success of 7 wheat as a globally traded commodity. In that context, wheat blast, a new disease for 8 wheat, which had until recently been confined to Brazil and other countries in South 9America, appearead in 2016 in Bangladesh, possibly as a result of importing 10 contaminated grain [7, 8]. The warm, wet climates in the wheat belts of India and 11China, which supply ~30% of the worlds wheat [1], favour the further proliferation of 12 this deva...

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