Genetic structure of three Oryza AA genome species (O. rufipogon, O. nivara and O. sativa) as assessed by SSR analysis on the Vientiane Plain of Laos

Abstract

Microsatellite (SSR) markers can reveal a high level of polymorphic loci, and are increasingly being used in population genetic structure studies. On the Vientiane plain of Laos all components of the rice crop complex exist, wild annual (O. nivara), wild perennial (O. rufipogon) and weedy relatives of rice as well as rice itself. To understand gene flow in the rice complex, the genetic structures of O. rufipogon (10 populations), O. nivara (10 populations) and O. sativa (24 samples) from across the Vientiane Plain, Laos, were compared. Higher genetic differentiation was detected among O. nivara populations (G ST = 0.77, R ST = 0.71) than O. rufipogon populations (G ST = 0.29, R ST = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H T = 0.77 and 0.64 in O. rufipogon and O. nivara, respectively). Based on neighbor-joining tree constructed on the basis of genetic distance (D A ), three genetic clusters were detected, corresponding to (1) O. sativa samples, (2) O. nivara populations and (3) O. rufipogon populations. Pairwise tests confirmed the genetic differentiation of the three species. Although none of the wild rice individuals used in this study had any cultivated-specific phenotypic traits, genetic admixture analysis detected more than 10% O. sativa membership in three O. rufipogon and one O. nivara populations, indicating that O. sativa alleles may cryptically persist in natural populations of O. rufipogon and O. nivara on the Vientiane Plain.

Ecogeographic Variation in the Morphology of Two Asian Wild Rice Species, Oryza nivara and Oryza rufipogon

“…This contrasting variation pattern agrees with the genetic diversity patterns observed in the two species (Kuroda et al 2007;Zhou et al 2008;Zheng and Ge 2010) in which O. nivara showed higher interpopulation genetic differentiation than O. rufipogon. Again, differences in habitat and breeding system may have influenced the different behavior of the two species.…”

“…species (Sharma and Shastry 1965;Ng et al 1981;Aggarwal et al 1999;Lu 1999;Lu et al 2001;Duan et al 2007;Kuroda et al 2007;Xu et al 2012), some rice scientists consider O. nivara to be the annual ecotype or subspecies of O. rufipogon (with O. rufipogon sensu stricto as the perennial ecotype) due to their continuous (morphological and genetic) variation and interfertility (Tateoka 1963;Second 1985;Oka 1988;Hiroi et al 1990; Morishima et al 1992;Iwamoto et al 1999;Vaughan et al 2003;Park et al 2003;Zhu and Ge 2005;Kwon et al 2006;Zhou et al 2008;Zheng and Ge 2010). In this study, O. nivara and O. rufipogon are provisionally treated as separate species.…”

Genetic analysis of a local population of Oryza glumaepatula using SSR markers: implications for management and conservation programs

“…In comparison to other Oryza species, variable numbers of alleles were detected. For 127 individuals of O. rufipogon and 197 individuals of O. nivara, analyzed with seven SSR markers, 55 and 36 alleles were identified, respectively (Kuroda et al 2007). However, 134 alleles were found in 813 individuals of four O. rufipogon populations, using 21 SSR markers (Xu et al 2006).…”

“…Several studies using molecular tools to assess the level and distribution of the genetic diversity of rice have elucidated aspects related to population structure of natural populations and germplasm collections of the wild relatives of rice, such as O. officinalis (Gao 2005), O. rufipogon (Gao et al 2002;Gao 2004), O. glaberrima (Semon et al 2004) and O. nivara (Kuroda et al 2007). These studies have allowed scientists to explore in situ and ex situ conservation strategies under different conditions, to maintain the genetic integrity of the populations and to maximize the preservation of a high proportion of the genetic diversity (Song et al 2003;Semon et al 2004).…”

Was Asian Rice (Oryza sativa) Domesticated More Than Once?

“…It is known that many populations of Asian wild rice have introgressed genes from cultivated rice [7,34,65,86]. Among wild rice accessions for which bacterial artificial chromosome libraries are available [82], at least one accession appears to have introgressed genes from cultivated rice.…”