Analysis of Vietnamese rice germplasm provides an insight into Japonica rice differentiation

Genetic differentiation among landraces of rice in northern Vietnam that lie in the centre of genetic diversity of Asian cultivated rice was analysed using DNA markers, and morphological and physiological traits to obtain an insight into the genetic differentiation of Asian rice. Principle coordinate analysis, based on nuclear RFLP data, divided Vietnamese rice varieties into three groups, designated A, B and C. Chloroplast DNA variation discriminated group A, which corresponded to the Indica rice varieties, from both groups B and C, which corresponded to the Japonica rice varieties. Physiological characteristics for Indica-Japonica and tropical-temperate Japonica discrimination suggested groups A and B consisted of typical Indica and Japonica varieties, respectively, while the characteristics of group C were distinct from those of the other two groups. This suggests that the genetic differences between groups B and C represent a new aspect of genetic variation that has not been previously reported in Japonica rice. Groups C and B corresponded with upland and lowland rice, respectively. Eight marker loci were associated with upland-lowland differentiation in Japonica rice. Highlighted chromosomal regions might have been selected during the history of cultivation under different cultural conditions, and thus contain genes related to adaptation.