Population genetic structure of Japanese wild soybean (Glycine soja) based on microsatellite variation

Abstract

The research objectives were to determine aspects of the population dynamics relevant to effective monitoring of gene flow in the soybean crop complex in Japan. Using 20 microsatellite primers, 616 individuals from 77 wild soybean (Glycine soja) populations were analysed. All samples were of small seed size (< 0.03 g), were directly collected in the field and came from all parts of Japan where wild soybeans grow, except Hokkaido. Japanese wild soybean showed significant reduction in observed heterozygosity, low outcrossing rate (mean 3.4%) and strong genetic differentiation among populations. However, the individual assignment test revealed evidence of rare long-distance seed dispersal (> 10 km) events among populations, and spatial autocorrelation analysis revealed that populations within a radius of 100 km showed a close genetic relationship to one another. When analysis of graphical ordination was applied to compare the microsatellite variation of wild soybean with that of 53 widely grown Japanese varieties of cultivated soybean (Glycine max), the primary factor of genetic differentiation was based on differences between wild and cultivated soybeans and the secondary factor was geographical differentiation of wild soybean populations. Admixture analysis revealed that 6.8% of individuals appear to show introgression from cultivated soybeans. These results indicated that population genetic structure of Japanese wild soybean is (i) strongly affected by the founder effect due to seed dispersal and inbreeding strategy, (ii) generally well differentiated from cultivated soybean, but (iii) introgression from cultivated soybean occurs. The implications of the results for the release of transgenic soybeans where wild soybeans grow are discussed.

DNA methylation polymorphism in annual wild soybean (Glycine soja Sieb. et Zucc.) and cultivated soybean (G. max L. Merr.)

“…1a, 2a and 3a). This is interesting, though incompatible with the naturally occurring introgression events that were shown always to occur from cultivated to wild (Kuroda et al 2006). One possibility may be that these cultivated soybean plants indeed contained introgression from wild soybean, maybe under some unrecorded human-mediated crossing in their pedigrees.…”

“…The biological diversity in both cultivated and annual wild soybeans has been investigated by phenotypic analysis (Dong et al 2001, as well as by using various molecular markers like isozymes, RFLP, SSR (Keim et al 1992;Yu and Kiang 1993;Skorupska et al 1993;Dong et al 2001Dong et al , 2004Abe et al 2003;Kuroda et al 2006;. As expected for a large and complex genome of polyploid origin Walling et al 2006), the soybean genome is heavily methylated by 5-methyl-cytosines, predominantly at repetitive sequences located in the heterochromatic centromeric regions (Zhu et al 1994;Young et al 1999).…”

Global legume diversity assessment: Concepts, key indicators, and strategies

“…Multiple genetic studies have been carried out on crop legumes and their wild relatives including soybean (Glycine max; Vaughan & al., 2006;Li & al., 2010), peanut (Arachis hypogaea L.; Varshney & al., 2009), common bean (Phaseolus vulgaris; Mensack & al., 2011), lima bean (Phaseolus lunatus L.; Martínez-Castillo & al., 2006), pea (Pisum sativum L.), mungbean (Vigna radiata (L.) R. Wilczek, . However, the geographic sampling of the wild species in most of these previous studies is limited to certain countries and/or regions, and most used accessions from seed banks.…”

Hybridization between GM soybean (Glycine max(L.) Merr.) and wild soybean (Glycine sojaSieb. et Zucc.) under field conditions in Japan

“…The pollen parents of the hybrids were identified by using 20 SSR markers (Kuroda et al, 2006). Total DNA was extracted from young leaf tissue from each surviving plant.…”