title: Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice.
abstract: 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.
authors.affiliation: Iwate Biotechnology Research Center, Narita 22-174-4, Kitakami, 024-0003 Iwate, Japan.
authors.forename: Sujay
authors.initials: S
authors.lastname: Rakshit
authors.forename: Arunita
authors.initials: A
authors.lastname: Rakshit
authors.forename: Hideo
authors.initials: H
authors.lastname: Matsumura
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Takahashi
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Hasegawa
authors.forename: Akiko
authors.initials: A
authors.lastname: Ito
authors.forename: Takashige
authors.initials: T
authors.lastname: Ishii
authors.forename: Naohiko T
authors.initials: NT
authors.lastname: Miyashita
authors.forename: Ryohei
authors.initials: R
authors.lastname: Terauchi
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics*; D016000:Cluster Analysis; D017931:DNA Primers; D019143:Evolution, Molecular; D018703:Founder Effect; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D017931:DNA Primers