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

• Published in: Conservation genetics Vol. 8; no. 1; pp. 149 - 158
• Main Authors: Kuroda, Yosuke, Sato, Yo-Ichiro, Bounphanousay, Chay, Kono, Yasuyuki, Tanaka, Koji
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Nature B.V 01-02-2007
• Subjects: Cereal crops; Genetic diversity; Genetic structure; Natural populations; Oryza nivara; Oryza rufipogon; Oryza sativa
• ISSN: 1566-0621; 1572-9737
• DOI: 10.1007/s10592-006-9156-3

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 ^sub ST^ = 0.77, R ^sub ST^ = 0.71) than O. rufipogon populations (G ^sub ST^ = 0.29, R ^sub ST^ = 0.28), whereas genetic diversity for all populations of these two wild species showed similar values (H ^sub 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 ^sub 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.[PUBLICATION ABSTRACT]