Characterization and Molecular Analysis of NBS-LRR Class Resistance Gene Homologues Isolated from Zingiber spp. of North East India

Rhizome rot or Fusarium yellows on ginger is a serious soil-borne disease of ginger in areas it is grown and found to be prevalent in the Northeastern region of India as well. In this region, it is mainly caused by the fungus Fusarium oxysporum f. sp. Zingiberi. Most of the plant disease resistance (R) genes encode a highly conserved nucleotide binding site and leucine-rich repeat structure (NBS-LRR). Therefore, degenerate primers based on the conserved domains of resistance genes were obtained to target PCR to amplify resistance gene candidates (RGCs) from Zingiber spp. Of Northeast India. PCR amplication from genomic DNA yielded a group of fragments of approximately 350bp and 600bp DNA sequences. Cloning, sequencing and characterization of the sequences showed that the amino acid sequences of the RGCs, detected the presence of conserved motifs of superfamilies NS-ARC and significant homology with R-genes in the GenBank database from other plant species. The level of sequence identity between Zingiber RGC sequences and known resistance genes in the top blast hits varied from 87 % to 91 % between Zne19p6 and Zne31p6 respectively to Zingiber officinale clone ZoP26 (e-value 1e-106) and Zingiber zerumbet clone ZzP226 (e-value 1e-81). RGCs were also detected using the RGC-specific primers designed. However, in RT-PCR analysis, the expression of the disease resistance seems to be very low or absent in the Zingiber species found in the region. The RGCs can be used to characterize resistance gene in related plant species to further study the organisation and functioning of such NBS-LRR encoding R-genes in asexually reproducing plant species. This study reports for the first time on characterization and molecular analysis of Fusarium RGCs from Zingiber spp. Of North East India.