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Originally published as Genetics Published Articles Ahead of Print on February 3, 2008.
Genetics, Vol. 178, 2081-2091, April 2008, Copyright © 2008
doi:10.1534/genetics.107.086421
Genomic Organization, Rapid Evolution and Meiotic Instability of Nucleotide-Binding-Site-Encoding Genes in a New Fruit Crop, "Chestnut Rose"
Qiang Xu*,
Xiaopeng Wen
and
Xiuxin Deng*,1
* National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China and Guizhou Key Laboratory of Agricultural Bioengineering, Guizhou University, Guiyang 550025, Guizhou, People's Republic of China
1 Corresponding author: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Lion St. no.1, Wuhan 430070, People's Republic of China.
E-mail: xxdeng{at}mail.hzau.edu.cn
From chestnut rose, a promising fruit crop of the Rosa genus, powdery mildew disease-resistant and susceptible genotypes and their F1 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 F1 progeny. A phylogenetic tree was constructed, which revealed that NBS sequences from parents and F1 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.