Genome-wide analysis of CNGC gene family in Brassica juncea (L.) Czern reveals key targets for stress resistance and crop improvement

Abstract

Cyclic nucleotide-gated ion channels (CNGCs) are important in cellular signaling, enabling ion passage, mainly calcium, across cell membranes in animals and plants. In plants, CNGCs are involved in cation transport, influencing growth, pathogen defense, and stress resistance. The CNGC gene family in Brassica juncea (L.) Czern (BjCNGCs) has not been well studied previously. We conducted a wide-ranging genome-wide analysis of BjCNGCs using available genomic data, covering genomic characterization, evolution, synteny analysis, gene mapping, structure, conserved motifs, cis-acting elements, potential protein association networks, post-translational modifications, and regulation. RT-qPCR assays were performed to investigate the expression patterns of selected BjCNGC genes in response to growth and stress. Our study identified 39 BjCNGC genes predicted to be present on fourteen chromosomes. Almost 49 % of these genes are positioned in conserved syntenic blocks of LF, MF-I, and MF-II sub-genomes, with a gene deletion (Bra024083 and BniB002576) from the MF-I block during intraspecific hybridization. The remaining genes evolved through segmental duplications 0.22 to 0.67 million years ago under purifying selection. Phylogenetic analysis classified the BjCNGC family into four groups, with groups III and IV further subdivided into A and B. We recognized 17 miRNA target sites, six of which are involved in stress resistance, coupled with phosphorylation for regulatory control. In-silico methods revealed gene structures, conserved motifs, and protein interaction networks. The study identified several CNGCs in Brassica juncea (L.) Czern showed significant responses to various stresses. Remarkably, certain CNGCs showed increased responses to black rot and TuMV, while others were more reactive to salinity and drought conditions. These findings suggest that targeting specific CNGCs through future genomic selection and breeding efforts could enhance crop production by introducing desirable stress-resistant traits in Brassica.