Genetic Structure and Geographical Differentiation of Traditional Rice (Oryza sativa L.) from Northern Vietnam

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.

Integrated Metabolomics and Transcriptomics Analyses Reveal the Metabolic Differences and Molecular Basis of Nutritional Quality in Landraces and Cultivated Rice

“…Landraces have been attracting attention due to their local environmental adaptability, abiotic stress tolerance, and specific metabolic components [ 39 ]. During continuous domestication and improvement, landraces have displayed some different characteristics with cultivated rice [ 40 ].…”

Exploring japonica rice epigenetic diversity in the main production regions of Heilongjiang Province

“…Previous research on rice has generally studied the genetic diversity of varieties and accessions using molecular marker techniques such as SSR (simple sequence repeat) and SNPs (single nucleotide polymorphism), and the impact of geographical environment and varieties on population structure has been analysed and clarified 7 , 8 , 26 , 27 . Apart from genetic mechanisms, increasing evidence has shown that epigenetic processes have important evolutionary significance in plant adaptation to stressful environments 12 , 28 .…”

“…Many extrinsic and intrinsic factors affect the growth and development of plants during the vegetative and reproductive phases of the lifecycle and thus affect grain yield 33 . Meteorological conditions such as temperature, precipitation, and sunshine undoubtedly cause epigenetic effects, which then cause phenotypic variation 34 , and will eventually affect the yield and quality of rice 35 . In this study, six environmental factors that significantly affect the growth and development of rice and five phenotypic indicators that reflect rice quality were selected to discuss the effect of environmental conditions on phenotypic and epigenetic diversity.…”

“…The phenotypic data were analysed using the Standard Evaluation System for Rice (SES) 34 , which was slightly modified ( http://www.knowledgebank.irri.org/images/docs/rice-standard-evaluation-system.pdf ). The five evaluation standard indicators at mature stages were selected to analyse the phenotypic diversity of rice in different regions, since the samples were all from mature rice landraces.…”

“…To adapt to different environmental and developmental conditions, environmental factors and developmental signals will induce certain adjustments in genes, leading to changes in the final phenotype 6 . Many previous studies have focused on the environmental heterogeneity and wide distribution of varieties, exploring the impact of different geographical distances and environmental factors on genetic diversity 7 – 9 . Few studies, however, attempted to explain the influence of environmental and geographic factors on phenotypic polymorphism by epigenetic factors.…”