Genetic and epigenetic diversity of wild and cultivated soybean in local populations in Northern Huang Huai region of China

This study aimed to characterize genetic/epigenetic structures within and between cultivated and wild soybean at local population level in Northern Huang Huai region of China. We analyzed a total of 124 individuals including 94 wild accessions and 30 cultivars using 10 AFLP primer pairs and 8 MSAP primer pairs. The results revealed that the genetic and epigenetic diversity in cultivated soybean exceeded that of wild accessions at local population level. The reason for greater amount of diversity in cultivars could be due to bulking and mixing of cultivated gene pool from geographically distant populations by crossbreeding under condition of artificial domestication, while, gene flow was difficult in natural habitats between wild populations. Interestingly, the genetic and epigenetic diversity were differed slightly (F-test, P=0.181-0.531) in the cultivars, while, the epigenetic diversity was significantly higher (F-test, P<0.001) than the genetic diversity in the wild populations. A possible explanation was that a fluctuating environment in natural habitats might lead to more epigenetic variation in wild populations. Furthermore, the Structure, AMOVA, and PCA analyses indicated that genetic differentiation has occurred between the wild soybean and cultivars (o rt=0.12), and among wild populations (0.307 < ost < 0.352). Furthermore, existence of epigenetic divergence among the wild populations (0.133 < st < 0.168) was evidenced. This indicated that natural selection might act on epigenetic variation in a similar manner like genetics. Finally, AMOVA and Structure analyses reflected greater epigenetic similarity than genetics in the studied individuals. We suggest that the reason was basically due to adaptive convergence to similar environments.