Genetic Analysis of NBS-LRR Gene Family in Chickpea and Their Expression Profiles in Response to Ascochyta Blight Infection

Abstract

Ascochyta blight is one of the major diseases of chickpea worldwide. The genetic resistance to ascochyta blight in chickpea is complex and governed by multiple QTLs. However, the molecular mechanism of quantitative disease resistance to ascochyta blight and the genes underlying these QTLs are still unknown. Most often disease resistance is determined by resistance (R) genes. The most predominant R-genes contain nucleotide binding site and leucine rich repeat (NBS-LRR) domains. A total of 121 NBS-LRR genes were identified in the chickpea genome. Ninety-eight of these genes contained all essential conserved domains while 23 genes were truncated. The NBS-LRR genes were grouped into eight distinct classes based on their domain architecture. Phylogenetic analysis grouped these genes into two major clusters based on their structural variation, the first cluster with toll or interleukin-1 like receptor (TIR) domain and the second cluster either with or without a coiled-coil domain. The NBS-LRR genes are distributed unevenly across the eight chickpea chromosomes and nearly 50% of the genes are present in clusters. Thirty of the NBS-LRR genes were co-localized with nine of the previously reported ascochyta blight QTLs and were tested as potential candidate genes for ascochyta blight resistance. Expression pattern of these genes was studied in two resistant (CDC Corinne and CDC Luna) and one susceptible (ICCV 96029) genotypes at different time points after ascochyta blight infection using real-time quantitative PCR. Twenty-seven NBS-LRR genes showed differential expression in response to ascochyta blight infection in at least one genotype at one time point. Among these 27 genes, the majority of the NBS-LRR genes showed differential expression after inoculation in both resistant and susceptible genotypes which indicates the involvement of these genes in response to ascochyta blight infection. Five NBS-LRR genes showed genotype specific expression. Our study provides a new insight of NBS-LRR gene family in chickpea and the potential involvement of NBS-LRR genes in response to ascochyta blight infection.

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

“…Ascochyta blight resistance QTLs have been reported on all chickpea chromosomes. However, most of these QTLs were identified using low‐density SSR marker‐based maps and the QTL interval varied from 0.3 to 30 Mb in CDC Frontier physical map (Li et al ., ; Sagi et al ., ). Genomic position of a few QTL flanking SSR markers was still undetected in the reference genome, and, hence, they were not used for comparative analysis in the present study.…”

“…Disease resistance genes, pathogenesis-related genes transcriptional activator PTI5, pathogenesis-related genes and multiple CC-NBS-LRR disease resistance genes were also identified in the QTL intervals (Table 3). Co-localization of NBS-LRR genes in QTL interval and differential expression profiles of NBS-LRR genes in response to ascochyta blight infection on the resistant and susceptible chickpea cultivars suggested the possible involvement of NBS-LRR genes in response to ascochyta blight in chickpea (Sagi et al, 2017). The interaction between flowering and resistance to diseases has been observed in multiple plants.…”

Genomic Organization and Comparative Phylogenic Analysis of NBS-LRR Resistance Gene Family inSolanum pimpinellifoliumandArabidopsis thaliana

“…Meanwhile, the LRR (leucine-rich repeat) domain has a higher variation than neighboring regions and is assumed to play a key role in the resistance function. 18 The NBS-LRR superfamily, accounting for the largest gene family among plant genomes, has become the core of the resistance research field. Currently, NBS-LRR genes have been studied in many monocotyledon and dicotyledon plants, including Arabidopsis, chickpea, potato, rice, cassava, maize, Brassica napus, poplar, Medicago, sorghum, papaya, grape, and lotus.…”

Integrated transcriptome, small RNA and degradome sequencing approaches provide insights into Ascochyta blight resistance in chickpea

“…For AB resistance, several QTLs have been reported until now (see Sagi et al, 2017). These QTLs were physically mapped on six chickpea pseudomolecules by using the markers flanking these QTLs.…”