Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers

Abstract

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.

Genetic structure of Brazilian wild rice (Oryza glumaepatula Steud., Poaceae) populations analyzed using microsatellite markers

“…In microsatellite marker studies of O. rufipogon (Table 7) similar results were obtained by Gao et al (2002a), who found 3.10 alleles per locus (H e = 0.345), and Zhou et al (2003) who obtained 3.35 alleles per locus (H e = 0.413). Gao et al (2000aGao et al ( , 2002b) also found lower indices in O. rufipogon studied with allozyme markers.…”

“…Molecular markers have been used for germplasm characterization, phylogenetic and population genetic studies in O. glumaepatula and several other Oryza species (Akimoto et al, 1998;Buso et al, 1998;Ge et al, 1999;Doi et al, 2000;Bautista et al, 2001;Oliveira, 2002;Gao et al, 2002aGao et al, , 2002bGao, 2004;Brondani et al, 2005). Buso et al (1998) used isozyme and random amplified polymorphic DNA (RAPD) markers to estimate genetic parameters for four South American O. glumaepatula populations and found high values for interpopulation differentiation.…”

Gene Flow Across Species Boundaries in Sympatric, Sexually Deceptive Ophrys (Orchidaceae) Species

“…Direct comparisons of both markers in plants and animals have reported higher microsatellite variation than allozyme variation, but found inconsistent results with respect to genetic differentiation among populations. In wild rice, microsatellites detected higher genetic differentiation among populations (Gao et al 2002), whereas the opposite was found for Anopheles mosquitoes (Lehmann et al 1996).…”

Assessing the genetic structure of Oryza glumaepatula populations with isozyme markers

“…Using random amplified polymorphic DNA (RAPD) markers, Ge et al (1999) confirmed the taxonomic classification of O. glumaepatula as a distinct species and not as an American form of O. rufipogon. Isozymic markers have been widely used in the cultivated and wild Oryza species, thus elucidating the processes of the domestication of the cultivated rice, assessing the genetic diversity and genetic structure of populations associated with aspects of their life history (Second, 1982;Barbier, 1989;Grover and Pental, 1992;Suh et al, 1997;Akimoto et al, 1998;Buso et al, 1998;Gao et al, 2000a;Gao et al, 2000b;Gao et al, 2000c;Gao et al, 2002a;Gao et al, 2002b;Quesada et al, 2002;Ishikawa et al, 2005). Buso et al (1998) observed in four populations of O. glumaepatula collected at the basins of Rio Amazonas and Rio Paraguay, based on isozymes and RAPD, a pattern of greater variation among rather than within populations, suggesting a self-fertilization breeding system.…”