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Ref ID: 28620
Ref Type: Journal Article
Authors: Rakshit, Sujay
Rakshit, Arunita
Matsumura, Hideo
Takahashi, Yoshihiro
Hasegawa, Yoshitaka
Ito, Akiko
Ishii, Takashige
Miyashita, Naohiko T.
Terauchi, Ryohei
Title: Large-scale DNA polymorphism study of <i>Oryza sativa</i> and <i>O. rufipogon</i> reveals the origin and divergence of Asian rice
Date: 2007
Source: Theoretical and Applied Genetics
DOI: 10.1007/s00122-006-0473-1
Abstract: Polymorphism over ∼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, <i>Oryza sativa</i>, and its wild relatives. Phylogenetic analysis using all the DNA sequences suggested that <i>O. sativa</i> ssp. <i>indica</i> and ssp. <i>japonica</i> were independently domesticated from a wild species <i>O. rufipogon</i>. <i>O. sativa</i> ssp. <i>indica</i> contained substantial genetic diversity (π = 0.0024), whereas ssp. <i>japonica</i> exhibited extremely low nucleotide diversity (π = 0.0001) suggesting the origin of the latter from a small number of founders. <i>O. sativa</i> ssp. <i>japonica</i> contained a larger number of derived and fixed non-synonymous substitutions as compared to ssp. <i>indica</i>. Nucleotide diversity and genealogical history substantially varied across the 22 loci. A locus, RLD15 on chromosome 2, showed a distinct genealogy with ssp. <i>japonica</i> sequences distantly separated from those of <i>O. rufipogon</i> and <i>O. sativa</i> ssp. <i>indica</i>. Linkage disequilibrium (LD) was analyzed in two different regions. LD in <i>O. rufipogon</i> decays within 5 kb, whereas it extends to ∼50 kb in <i>O. sativa</i> ssp. <i>indica</i>.
Date Created: 10/5/2011
Volume: 114
Number: 4
Page Start: 731
Page End: 743