Characterization of novel wheat NBS domain-containing sequences and their utilization, in silico, for genome-scale R-gene mining

Mol Genet Genomics. 2014 Aug;289(4):599-613. doi: 10.1007/s00438-014-0834-4. Epub 2014 Mar 18.

Abstract

In crop improvement, the isolation, cloning and transfer of disease resistance genes (R-genes) is an ultimate goal usually starting from tentative R-gene analogs (RGAs) that are identified on the basis of their structure. For bread wheat, recent advances in genome sequencing are supporting the efforts of wheat geneticists worldwide. Among wheat R-genes, nucleotide-binding site (NBS)-encoding ones represent a major class. In this study, we have used a polymerase chain reaction-based approach to amplify and clone NBS-type RGAs from a bread wheat cultivar, 'Salambo 80.' Four novel complete ORF sequences showing similarities to previously reported R-genes/RGAs were used for in silico analyses. In a first step, where analyses were focused on the NBS domain, these sequences were phylogenetically assigned to two distinct groups: a first group close to leaf rust Lr21 resistance proteins; and a second one similar to cyst nematode resistance proteins. In a second step, sequences were used as initial seeds to walk up and downstream the NBS domain. This procedure enabled identifying 8 loci ranging in size between 2,115 and 7,653 bp. Ab initio gene prediction identified 8 gene models, among which two had complete ORFs. While GenBank survey confirmed the belonging of sequences to two groups, subsequent characterization using IWGSC genomic and proteomic data showed that the 8 gene models, reported in this study, were unique and their loci matched scaffolds on chromosome arms 1AS, 1BS, 4BS and 1DS. The gene model located on 1DS is a pseudo-Lr21 that was shown to have an NBS-LRR domain structure, while the potential association of the RGAs, here reported, is discussed. This study has produced novel R-gene-like loci and models in the wheat genome and provides the first steps toward further elucidation of their role in wheat disease resistance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Binding Sites
  • Chromosome Mapping
  • Chromosomes, Plant / genetics*
  • Cloning, Molecular
  • DNA Primers / genetics
  • Gene Library
  • Genome, Plant / genetics*
  • Genomics
  • Molecular Sequence Data
  • Phylogeny
  • Plant Diseases / immunology*
  • Plant Immunity
  • Plant Proteins / genetics*
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology
  • Triticum / genetics*
  • Triticum / immunology

Substances

  • DNA Primers
  • Plant Proteins

Associated data

  • GENBANK/JX566982
  • GENBANK/JX566983
  • GENBANK/JX566984
  • GENBANK/JX566985