Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance.

Xiaolong Li,Shifeng Cheng

doi:10.3390/cimb43020069

Abstract

Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.

Highlights

Infectious diseases are the main challenge in agricultural production and lead to heavy yield losses of many crops [1,2]
A total of 2012 high-confidence Nucleotide-binding leucine-rich repeat (NLR) proteins were identified in the hexaploid wheat reference genome “Chinese Spring” (IWGSC RefSeq v1.1) [16], and 625 (31.06%), 785 (39.02%), and 602 (29.92%) NLRs were identified in the A, B, and D subgenomes, respectively (Table S1)
We provide a repertoire of NLR genes from hexaploid wheat and a landscape of dynamic diversity of NLRs in Triticum and Aegilops

Summary

Introduction

Infectious diseases are the main challenge in agricultural production and lead to heavy yield losses of many crops [1,2]. Bread wheat production is seriously threatened by varied diseases, such as Fusarium head blight (Fhb), powdery mildew, rust, and root rot, which are projected to lead to 20–30% yield loss, even up to 50% in wheat every year [6,7]. Nucleotide-binding leucine-rich repeat (NLR) proteins, encoded by one of the most variable gene families in plants, are intracellular immune receptors involved in disease resistance through their recognition of pathogen proteins [8]. Release of the wheat reference genome (IWGSC RefSeq v1.0) [16] and mass resequencing data [17,18,19,20] have allowed us to identify the genome-wide repertoire of NLRs in wheat, determine their diversity in wheat relatives, and recover the diverse NLR gene pool through breeding and improvement of disease resistance in wheat

Methods

Results

Discussion

Conclusion