Abstract
Northern Vietnam is one of the most important centers of genetic diversity for cultivated rice. Over thousands of years of cultivation, natural and artificial selection has preserved many traditional rice landraces in northern Vietnam due to its geographic situation, climatic conditions, and many ethnic groups. These local landraces serve as a rich source of genetic variation—an important resource for future crop improvement. In this study, we determined the genetic diversity and population structure of 79 rice landraces collected from northern Vietnam and 19 rice accessions collected from different countries. In total, 98 rice accessions could be differentiated into japonica and indica with moderate genetic diversity and a polymorphism information content of 0.382. Moreover, we found that genetic differentiation was related to geographical regions with an overall PhiPT (analog of fixation index FST) value of 0.130. We also detected subspecies-specific markers to classify rice (Oryza sativa L.) into indica and japonica. Additionally, we detected five marker-trait associations and rare alleles that can be applied in future breeding programs. Our results suggest that rice landraces in northern Vietnam have a dynamic genetic system that can create different levels of genetic differentiation among regions, but also maintain a balanced genetic diversity between regions.
Highlights
Despite the controversy over its origins, rice (Oryza sativa L.), which is one of the most important components of the human diet, is a staple food for almost half of the world’s population [1]
A set of 79 rice landraces collected from five ecological zones including the northwest (17 accessions), northeast (14), Red River Delta (26), northcentral coast (21), and south-central coast (1), was used in this study (Figure 1, Table S1)
We tested the statistical significance of the difference in gene diversity (GD) and PIC between the two subgroups as well as between the six regions, and the results indicated that the difference in GD and PIC values between the two subgroups or between each pair of regions were not statistically significant, except for the GD and PIC values of the southern Vietnam group, which were significantly (p < 0.001) lower than those of the other five regions
Summary
Despite the controversy over its origins, rice (Oryza sativa L.), which is one of the most important components of the human diet, is a staple food for almost half of the world’s population [1]. Rice production faces big challenges, including sustaining a growing population, conserving biodiversity, and adapting to climate change. These challenges must be tackled together for progress to be made in rice production. Cultivated rice should produce higher yields, and genetic resources should be both efficient and resistant to biotic and abiotic stresses, such as unpredictable climate change. Among genetic resources for breeding, rice landraces have a greater genetic diversity than elite cultivars and represent an intermediate stage in domestication between wild rice and elite cultivars [2]. Rice landraces are more convenient to use in rice breeding than wild rice, and maintain almost all potential sources of beneficial alleles in rice germplasm. Breeders can increase the yield of released varieties through gene pools by combining high-yielding genes/QTLs from various genetic resources of local landraces
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