Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam
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 et...
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MDPI AG
2021-10-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/10/2094 |
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| author | Ngoc Ha Luong Le-Hung Linh Kyu-Chan Shim Cheryl Adeva Hyun-Sook Lee Sang-Nag Ahn |
| author_facet | Ngoc Ha Luong Le-Hung Linh Kyu-Chan Shim Cheryl Adeva Hyun-Sook Lee Sang-Nag Ahn |
| author_sort | Ngoc Ha Luong |
| collection | DOAJ |
| description | 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 <i>japonica</i> and <i>indica</i> 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 F<sub>ST</sub>) value of 0.130. We also detected subspecies-specific markers to classify rice (<i>Oryza sativa</i> L.) into <i>indica</i> and <i>japonica</i>. 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. |
| first_indexed | 2024-03-10T06:15:39Z |
| format | Article |
| id | doaj.art-cfc4ccf2648d4fbc99d9313729de3f5e |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T06:15:39Z |
| publishDate | 2021-10-01 |
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| series | Plants |
| spelling | doaj.art-cfc4ccf2648d4fbc99d9313729de3f5e2023-11-22T19:43:40ZengMDPI AGPlants2223-77472021-10-011010209410.3390/plants10102094Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern VietnamNgoc Ha Luong0Le-Hung Linh1Kyu-Chan Shim2Cheryl Adeva3Hyun-Sook Lee4Sang-Nag Ahn5Department of Agronomy, Chungnam National University, Daejeon 34134, KoreaAgricultural Genetics Institute, North Tu Liem District, Hanoi 100000, VietnamDepartment of Agronomy, Chungnam National University, Daejeon 34134, KoreaDepartment of Agronomy, Chungnam National University, Daejeon 34134, KoreaDepartment of Agronomy, Chungnam National University, Daejeon 34134, KoreaDepartment of Agronomy, Chungnam National University, Daejeon 34134, KoreaNorthern 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 <i>japonica</i> and <i>indica</i> 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 F<sub>ST</sub>) value of 0.130. We also detected subspecies-specific markers to classify rice (<i>Oryza sativa</i> L.) into <i>indica</i> and <i>japonica</i>. 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.https://www.mdpi.com/2223-7747/10/10/2094ricegenetic diversitypopulation structuregenetic differentiationmarker-trait associationnorthern Vietnam |
| spellingShingle | Ngoc Ha Luong Le-Hung Linh Kyu-Chan Shim Cheryl Adeva Hyun-Sook Lee Sang-Nag Ahn Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam Plants rice genetic diversity population structure genetic differentiation marker-trait association northern Vietnam |
| title | Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam |
| title_full | Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam |
| title_fullStr | Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam |
| title_full_unstemmed | Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam |
| title_short | Genetic Structure and Geographical Differentiation of Traditional Rice (<i>Oryza sativa</i> L.) from Northern Vietnam |
| title_sort | genetic structure and geographical differentiation of traditional rice i oryza sativa i l from northern vietnam |
| topic | rice genetic diversity population structure genetic differentiation marker-trait association northern Vietnam |
| url | https://www.mdpi.com/2223-7747/10/10/2094 |
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