Genomic organization, rapid evolution and meiotic instability of nucleotide-binding-site-encoding genes in a new fruit crop, "chestnut rose".
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.
Xu
Qiang
Q
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China.
Wen
Xiaopeng
X
Deng
Xiuxin
X
D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping; D018556:Crops, Agricultural / Q000166:cytology / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D005638:Fruit / Q000166:cytology / Q000235:genetics*; D017343:Genes, Plant; D018745:Genome, Plant / Q000235:genetics*; D042822:Genomic Instability; D007113:Immunity, Innate / Q000235:genetics / Q000276:immunology; D008540:Meiosis; D008969:Molecular Sequence Data; D005810:Multigene Family; D009711:Nucleotides / Q000378:metabolism*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics / Q000276:immunology; D027826:Rosa / Q000166:cytology / Q000235:genetics*; D012641:Selection, Genetic
D004251:DNA Transposable Elements; D009711:Nucleotides