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Introduction: Rice, Oryza sativa, is a cultivated, inbreeding species that is estimated to have been domesticated in Asia from a complex ancestral species, O. rufipogon (Oka, 1988; Vaughan et al., 2005). Evidence from fossilized remains of rice grains found in tombs in China, India and Vietnam suggest that domestication occurred approximately 10,000 years ago (Matsuo et al., 1997; Zhao, 1998; Higham and Lu, 1998; Jiang and Liu, 2006; Pei, 1998).
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Two major sub-species within O. sativa have been recognized since ancient times, namely indica and japonica (Matsuo et al., 1997; Oka, 1988). The time since divergence of the indica and japonica groups is estimated to be greater than 100,000 years, based on analysis of transposon insertion polymorphism (Cheng et al., 2003; Vitte et al. 2004; Hu et al., 2006) and full-genome sequence comparisons (Ma and Bennetzen, 2004). This time estimate suggests that the genetic differentiation of the indica and japonica groups pre-dates the domestication of O. sativa by at least one hundred thousand years. This is consistent with the belief that rice was independently domesticated on at least two occasions from a pre-differentiated ancestral pool (Cheng et al., 2003; Garris et al., 2005; Hu et al., 2006; Londo et al., 2006; Roy, 1921; Second, 1982 and 1991).
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Five subpopulations have been clearly identified within O. sativa using SSRs (Garris et al., 2005). Of these, the indica and aus subpopulations cluster within the Indica sub-species group, and the tropical japonica, temperate japonica and aromatic subpopulations cluster with the Japonica sub-species group (Garris et al., 2005). This subpopulation structure is deep and ancient, with overall estimates of divergence showing Fst values of 0.375 (Garris et al., 2005), compared to Fst values of 0.08-0.09 for heterotic groups in maize (Matsuoka et al., 2002). The number and identity of the subpopulations identified by Garris et al. (2005) using 169 SSRs is consistent with those detected by (Glaszmann, 1987) using only 17 isozyme markers or by SNP’s assayed at 111 random genes using the same germplasm accessions (Caicedo et al., 2007).
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