Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose"

Genetics. 2008 Apr;178(4):2081-91. doi: 10.1534/genetics.107.086421. Epub 2008 Feb 3.

Abstract

From chestnut rose, a promising fruit crop of the Rosa genus, powdery mildew disease-resistant and susceptible genotypes and their F(1) progeny were used to isolate nucleotide-binding-site (NBS)-encoding genes using 19 degenerate primer pairs and an additional cloning method called overlapping extension amplification. A total of 126 genes were harvested; of these, 38 were from a resistant parent, 37 from a susceptible parent, and 51 from F(1) progeny. A phylogenetic tree was constructed, which revealed that NBS sequences from parents and F(1) progeny tend to form a mixture and are well distributed among the branches of the tree. Mapping of these NBS genes suggested that their organization in the genome is a "tandem duplicated cluster" and, to a lesser extent, a "heterogeneous cluster." Intraspecific polymorphisms and interspecific divergence were detected by Southern blotting with NBS-encoding genes as probes. Sequencing on the nucleotide level revealed even more intraspecific variation: for the R4 gene, 9.81% of the nucleotides are polymorphic. Amino acid sites under positive selection were detected in the NBS region. Some NBS-encoding genes were meiotically unstable, which may due to recombination and deletion events. Moreover, a transposon-like element was isolated in the flanking region of NBS genes, implying a possible role for transposon in the evolutionary history of resistance genes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Binding Sites
  • Chromosome Mapping
  • Crops, Agricultural / cytology
  • Crops, Agricultural / genetics
  • DNA Transposable Elements / genetics
  • Evolution, Molecular*
  • Fruit / cytology
  • Fruit / genetics*
  • Genes, Plant
  • Genome, Plant / genetics*
  • Genomic Instability*
  • Immunity, Innate / genetics
  • Immunity, Innate / immunology
  • Meiosis*
  • Molecular Sequence Data
  • Multigene Family
  • Nucleotides / metabolism*
  • Phylogeny
  • Plant Diseases / genetics
  • Plant Diseases / immunology
  • Rosa / cytology
  • Rosa / genetics*
  • Selection, Genetic

Substances

  • DNA Transposable Elements
  • Nucleotides