title: Genome-wide investigation on the genetic variations of rice disease resistance genes.
abstract: Exploitation of plant disease resistance (R) gene in breeding programs has been proven to be the most efficient strategy for coping with the threat of pathogens. An understanding of R-gene variation is the basis for this strategy. Here we report a genome-wide investigation on the variation of NBS-LRR-encoding genes, the common type of R genes, between two sequenced rice genomes, Oryza sativa L. var. Nipponbare and 93-11. We show that the allelic nucleotide diversity in 65.0% of 397 least-divergent pairs is not high (0.344% on average), while the remaining 35% display a greater diversity (5.4% on average). The majority of conserved R genes is single-copy and/or located as a singleton. The clustered, particularly the complex-clustered, R-genes contribute greatly to the rich genetic variation. Surprisingly only 11.2% of R-genes have remarkably high ratios of non-synonymous to synonymous rates, which is much less than the 17.4% observed between Arabidopsis genomes. Noticeable "artificially selective sweeping" could be detected in a large proportion of the conserved R-genes, a scenario described in the "arms race" co-evolutionary model. Based on our study, a variation pattern of R-genes is proposed and confirmed by the analysis of R-genes from other rice lines, indicating that the observed variation pattern may be common in all rice lines.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, 210093 Nanjing, China.
authors.forename: Sihai
authors.initials: S
authors.lastname: Yang
authors.forename: Zhumei
authors.initials: Z
authors.lastname: Feng
authors.forename: Xiuyan
authors.initials: X
authors.lastname: Zhang
authors.forename: Ke
authors.initials: K
authors.lastname: Jiang
authors.forename: Xinqing
authors.initials: X
authors.lastname: Jin
authors.forename: Yueyu
authors.initials: Y
authors.lastname: Hang
authors.forename: Jian-Qun
authors.initials: JQ
authors.lastname: Chen
authors.forename: Dacheng
authors.initials: D
authors.lastname: Tian
mesh_terms: D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D007113:Immunity, Innate / Q000235:genetics*; D005810:Multigene Family; D012275:Oryza / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010935:Plant Diseases / Q000235:genetics*