Cloning and characterization of NBS-LRR encoding resistance gene candidates from Tomato Leaf Curl New Delhi Virus resistant genotype of Luffa cylindrica Roem

We employed degenerate primers to amplify nucleotide-binding site (NBS) domain of resistance gene candidates (RGCs) from Tomato Leaf Curl New Delhi Virus (ToLCNDV) resistant Luffa cylindrica (sponge gourd) genotype, DSG-6. Sixteen non-redundant sequences of RGCs were identified with un-interrupted open reading frames (ORFs) and high amino acid sequence homologies (60–98%) to various nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins from GenBank database. Alignment of the deduced amino acid sequence and phylogenetic analysis of the NBS domain revealed six and ten sponge gourd (sg) RGCs belong to the Toll Interleukin Receptor (TIR) and non-TIR group of NBS-LRR genes, respectively. The sgRGCs consisted of conserved NB-ARC [homologous region shared with APAF-1 (apoptotic protease-activating factor-1), R proteins and CED-4 (Caenorhabditis elegans death-4 protein)] domain from P-loop nucleoside triphosphatase (NTPase) family and characteristic P-loop, Kinase-2, RNBS-A, Kinase-3A and GLPL motifs. The comparative analysis of expression profiles of sgRGCs in asymptomatic and field-driven symptomatic leaf tissues of ToLCNDV resistant and susceptible genotypes revealed RGCLc28 is expressed consistently in resistant genotypes. The differentially expressed RGCLc28 of DSG-6 is predicted to have strong association with the resistance trait against the leaf curl and mosaic disease in sponge gourd and may serve as important genomic resource for candidate gene discovery. ► Sixteen sgRGCs isolated from ToLCNDV-resistant sponge gourd genotype using degenerate primers. ► Conserved motifs of NBS-LRR domain identified on sgRGCs. ► Sixteen sgRGCs belong to TIR and non-TIR class NBS-LRRs. ► One sgRGC differentially expressed between ToLCNDV-resistant and susceptible genotypes.