Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers
Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for r...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-05-01
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| Series: | Agronomy |
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| Online Access: | https://www.mdpi.com/2073-4395/11/5/995 |
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| author | Wanchana Aesomnuk Siriphat Ruengphayak Vinitchan Ruanjaichon Tanee Sreewongchai Chanate Malumpong Apichart Vanavichit Theerayut Toojinda Samart Wanchana Siwaret Arikit |
| author_facet | Wanchana Aesomnuk Siriphat Ruengphayak Vinitchan Ruanjaichon Tanee Sreewongchai Chanate Malumpong Apichart Vanavichit Theerayut Toojinda Samart Wanchana Siwaret Arikit |
| author_sort | Wanchana Aesomnuk |
| collection | DOAJ |
| description | Rice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to <i>indica</i> and <i>japonica</i> groups. The <i>indica</i> group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise <i>F<sub>ST</sub></i> showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding. |
| first_indexed | 2024-03-10T11:20:11Z |
| format | Article |
| id | doaj.art-9924d35bb4704166b27b737bb0c86a28 |
| institution | Directory Open Access Journal |
| issn | 2073-4395 |
| language | English |
| last_indexed | 2024-03-10T11:20:11Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agronomy |
| spelling | doaj.art-9924d35bb4704166b27b737bb0c86a282023-11-21T20:04:50ZengMDPI AGAgronomy2073-43952021-05-0111599510.3390/agronomy11050995Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP MarkersWanchana Aesomnuk0Siriphat Ruengphayak1Vinitchan Ruanjaichon2Tanee Sreewongchai3Chanate Malumpong4Apichart Vanavichit5Theerayut Toojinda6Samart Wanchana7Siwaret Arikit8Center for Agricultural Biotechnology (CAB), Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, ThailandRice Science Center, Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom 73140, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandDepartment of Agronomy, Faculty of Agriculture, Kasetsart University, Bangkhen, Bangkok 10900, ThailandDepartment of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom 73140, ThailandRice Science Center, Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom 73140, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandNational Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Pahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, ThailandRice Science Center, Kamphaeng Saen Campus, Kasetsart University, Nakhon Pathom 73140, ThailandRice is a staple food for more than half of the world’s population. Modern rice varieties have been developed for high yield and quality; however, there has been a substantial loss of diversity. A greater number of genetically dynamic landraces could offer valuable and useful genetic resources for rice improvement. In this study, the genetic diversity and population structure of 365 accessions of lowland and upland landraces from four populations from different geographical regions of Thailand were investigated using 75 SNP markers. Clustering analyses using maximum likelihood, Principal Coordinate Analysis (PCoA), and Discriminant Analysis of Principal Components (DAPC) clustered these landraces into two main groups, corresponding to <i>indica</i> and <i>japonica</i> groups. The <i>indica</i> group was further clustered into two subgroups according to the DAPC and STRUCTURE analyses (K = 3). The analysis of molecular variance (AMOVA) analysis results revealed that 91% of the variation was distributed among individuals, suggesting a high degree of genetic differentiation among rice accessions within the populations. Pairwise <i>F<sub>ST</sub></i> showed the greatest genetic differentiation between the northeastern and southern populations and the smallest genetic differentiation between the northern and northeastern populations. Isolation-by-distance analysis based on a Mantel test indicated a significant relationship between the genetic distance and geographic distance among the Thai rice landraces. The results from this study provide insight into the genetic diversity of Thai rice germplasm, which will enhance the germplasm characterization, conservation, and utilization in rice genetics and breeding.https://www.mdpi.com/2073-4395/11/5/995rice (<i>Oryza sativa)</i>genetic diversitypopulation structurelandraceThai riceSNPs |
| spellingShingle | Wanchana Aesomnuk Siriphat Ruengphayak Vinitchan Ruanjaichon Tanee Sreewongchai Chanate Malumpong Apichart Vanavichit Theerayut Toojinda Samart Wanchana Siwaret Arikit Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers Agronomy rice (<i>Oryza sativa)</i> genetic diversity population structure landrace Thai rice SNPs |
| title | Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers |
| title_full | Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers |
| title_fullStr | Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers |
| title_full_unstemmed | Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers |
| title_short | Estimation of the Genetic Diversity and Population Structure of Thailand’s Rice Landraces Using SNP Markers |
| title_sort | estimation of the genetic diversity and population structure of thailand s rice landraces using snp markers |
| topic | rice (<i>Oryza sativa)</i> genetic diversity population structure landrace Thai rice SNPs |
| url | https://www.mdpi.com/2073-4395/11/5/995 |
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