Genome-wide identification, expression, and characterization of CaLysM-RLKs in chickpea root nodule symbiosis

Abstract

Legumes establish a nitrogen-fixing symbiosis with rhizobia which depends on the exchange of chemical signals between the two partners. Successful interaction between legumes and rhizobia depends on the perception of Nod factors (NFs) by the receptor-like kinases. A few cell surface receptors have been identified that perceive the rhizobial NFs and activate the downstream signaling pathway for nodulation in model legumes like Lotus japonicus and Medicago truncatula . However, crop legume such as chickpea lacks detailed analysis of LysM-RLKs genes for NFs perception. Here, we identified and characterized CaLysM-RLK genes and analyzed their gene structure, motif composition, chromosomal localization, phylogenetic relationship with Arabidopsis, Oryza sativa , and Medicago truncatula . To understand the spatiotemporal expression patterns, we performed transcript profiling of Ca LysM-RLKs genes at a different time interval of the chickpea-rhizobia symbiotic interaction that revealed CaNFP and CaLYK3 can act as candidate genes for NF perception. Down-regulation of CaNFP and CaLYK3 in chickpea by agrobacterium rhizogenes mediated hairy root sysytem leads to signifificant reduction in nodule numbers. This study will be useful for improving root nodule symbiosis in chickpea. • Seventeen CaLysM-RLKs genes were identified in chickpea. • Based on the structure CaLysM-RLKs family members were classified into three main groups LYS-I, LYS-II, and LYS-III. • Analysis of paralogous gene pair (PGP) leads to the identification of a total of 6 PGPs. • CaLYK3 , and CaNFP regulate root nodule symbiosis in chickpea.