Population Genetic Structure of Wild Rice (Oryza rufipogon) in Mainland Southeast Asia as Revealed by Microsatellite Polymorphisms

Abstract

Strains of wild rice (Oryza rufipogon) distributed in mainland Southeast Asia have been classified into perennial type and annual type, based on their reproductive systems and habitats. However, only a few attempts have so far been made at evaluating genetic structure within, and among, populations. The purpose of this paper is to analyze the genetic structures of a total of seven wild rice populations in mainland Southeast Asia. These seven populations are composed of three perennial populations and four annual populations. Microsatellite (SSR) polymorphisms were used to estimate dynamics within, and among, populations through several statistical parameters. Results reveal that within-population genetic structures of the two types are different. The outcrossing rate of perennial populations, estimated by fixation index, ranged from 49% to 72%. The outcrossing rate for annual populations varied from 5% to 29%. Genetic variability between the two types, a high degree of gene differentiation was observed among annual populations (CST = 0.59) compared with among perennial populations (CST = 0.22), due to differential gene diversity within populations (Hs = 0.32 and 0.67, in annual and perennial populations, respectively), as well as gene diversity for all populations (HT = 0.80 and 0.86, in annual and perennial populations, respectively). SSR analysis revealed that the populations analyzed could be classified into three clades according to their geographic origin: those from the middle Mekong basin, the lower Mekong basin, and the Chao-Phraya basin. The results indicate not only that the mating systems within populations and genetic differentiation among populations are both clearly differentiated between perennials and annuals, but also that geographical differentiation occurs along major river basin systems in mainland Southeast Asia.