Rakshit Sujay, Rakshit Arunita, Matsumura Hideo, Takahashi Yoshihiro, Hasegawa Yoshitaka, Ito Akiko, Ishii Takashige, Miyashita Naohiko T, Terauchi Ryohei
Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, 024-0003 Iwate, Japan.
Theor Appl Genet. 2007 Feb;114(4):731-43. doi: 10.1007/s00122-006-0473-1. Epub 2007 Jan 12.
Polymorphism over approximately 26 kb of DNA sequence spanning 22 loci and one region distributed on chromosomes 1, 2, 3 and 4 was studied in 30 accessions of cultivated rice, Oryza sativa, and its wild relatives. Phylogenetic analysis using all the DNA sequences suggested that O. sativa ssp. indica and ssp. japonica were independently domesticated from a wild species O. rufipogon. O. sativa ssp. indica contained substantial genetic diversity (pi = 0.0024), whereas ssp. japonica exhibited extremely low nucleotide diversity (pi = 0.0001) suggesting the origin of the latter from a small number of founders. O. sativa ssp. japonica contained a larger number of derived and fixed non-synonymous substitutions as compared to ssp. indica. Nucleotide diversity and genealogical history substantially varied across the 22 loci. A locus, RLD15 on chromosome 2, showed a distinct genealogy with ssp. japonica sequences distantly separated from those of O. rufipogon and O. sativa ssp. indica. Linkage disequilibrium (LD) was analyzed in two different regions. LD in O. rufipogon decays within 5 kb, whereas it extends to approximately 50 kb in O. sativa ssp. indica.
在30份栽培稻（亚洲栽培稻）及其野生近缘种中，研究了跨越22个位点和一个区域、分布于1号、2号、3号和4号染色体上约26 kb DNA序列的多态性。利用所有DNA序列进行的系统发育分析表明，亚洲栽培稻的籼亚种和粳亚种是从野生稻（普通野生稻）独立驯化而来的。亚洲栽培稻籼亚种具有丰富的遗传多样性（π = 0.0024），而粳亚种表现出极低的核苷酸多样性（π = 0.0001），这表明后者起源于少数几个奠基者。与籼亚种相比，亚洲栽培稻粳亚种含有更多衍生和固定的非同义替换。22个位点的核苷酸多样性和系统发育历史差异很大。位于2号染色体上的RLD15位点显示出独特的系统发育关系，粳亚种序列与普通野生稻和亚洲栽培稻籼亚种的序列相距甚远。在两个不同区域分析了连锁不平衡（LD）。普通野生稻中的LD在5 kb内衰减，而在亚洲栽培稻籼亚种中则延伸至约50 kb。
