Vigna unguiculata Raw sequence reads

Cowpea is one of the most important food and forage legumes in drier regions of the tropics and subtropics. Cowpea is a susceptible host of root-knot nematodes (Meloidogyne spp., RKN) and infection results in significant yield loss. Previous studies demonstrated that RKN resistance in cowpea is controlled by at least two dominant genes Rk and Rk2, localized in two major QTLs, Rkn-1 and Rkn-2. The aim of the present work was to select candidate genes for RKN resistance based on transcriptome profiling of roots of two near-isogenic lines (NILs), CB46 NULL (susceptible) and CB46 72-1-3 (resistant, Rkn-1/2). Transcriptome analyses were performed 3 and 9 days after RKN inoculation and sequence reads were aligned to the common bean whole genome, resulting in 19,922 unique genes mapped to the reference genome. Comparison between resistant and susceptible NILs 3 and 9 days after inoculation revealed up-regulation of 109 and 98 genes and down-regulation of 110 and 89 genes, respectively. Functional annotation showed that differentially expressed genes are mostly involved in metabolic and cellular processes, biological regulation and defense. Among the genes assigned to defense, few genes showed contrasting expression patterns between the NILs, including NBS-LRR genes and peroxidases. For the resistance conferred by Rk and Rk2, analysis was performed on differentially expressed genes specifically localized in the respective QTLs regions. Based on candidate genes localized in the QTL regions and RNA-seq results, 8 genes were chosen for validation using quantitative RT-PCR. Three of these genes were highly expressed in resistant plants and are members of the TIR-NB-LRR family of proteins. Current work is investigating the role of these genes in cowpea resistance to RKN.