Large-scale DNA polymorphism study of Oryza sativa and O. rufipogon reveals the origin and divergence of Asian rice

Author: Rakshit Sujay   Rakshit Arunita   Matsumura Hideo   Takahashi Yoshihiro   Hasegawa Yoshitaka   Ito Akiko   Ishii Takashige   Miyashita Naohiko   Terauchi Ryohei  

Publisher: Springer Publishing Company

ISSN: 0040-5752

Source: Theoretical and Applied Genetics, Vol.114, Iss.4, 2007-02, pp. : 731-743

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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, 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 ( = 0.0024), whereas ssp. japonica exhibited extremely low nucleotide diversity ( = 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 ∼50 kb in O. sativa ssp. indica.

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