Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers
Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice....
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MDPI AG
2021-11-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/10/12/2564 |
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| author | Aye Aye Thant Hein Zaw Marie Kalousova Rakesh Kumar Singh Bohdan Lojka |
| author_facet | Aye Aye Thant Hein Zaw Marie Kalousova Rakesh Kumar Singh Bohdan Lojka |
| author_sort | Aye Aye Thant |
| collection | DOAJ |
| description | Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release. |
| first_indexed | 2024-03-10T03:17:48Z |
| format | Article |
| id | doaj.art-c270d380844549919d20bcbe2e654ad0 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T03:17:48Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-c270d380844549919d20bcbe2e654ad02023-11-23T10:10:01ZengMDPI AGPlants2223-77472021-11-011012256410.3390/plants10122564Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT MarkersAye Aye Thant0Hein Zaw1Marie Kalousova2Rakesh Kumar Singh3Bohdan Lojka4Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech RepublicPlant Biotechnology Center, Pale Myothit, Shwe Nanthar, Mingaladon, Yangon 110 23, MyanmarDepartment of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech RepublicInternational Center for Biosaline Agriculture, Crop Diversification and Genetics, Al Rwayyah 2, Academic City, Dubai P.O. Box 14660, United Arab EmiratesDepartment of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech RepublicMyanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.https://www.mdpi.com/2223-7747/10/12/2564DArT markersgenetic diversityMyanmarrice (<i>Oryza sativa</i> L.)silicoDArTSNP |
| spellingShingle | Aye Aye Thant Hein Zaw Marie Kalousova Rakesh Kumar Singh Bohdan Lojka Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers Plants DArT markers genetic diversity Myanmar rice (<i>Oryza sativa</i> L.) silicoDArT SNP |
| title | Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers |
| title_full | Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers |
| title_fullStr | Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers |
| title_full_unstemmed | Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers |
| title_short | Genetic Diversity and Population Structure of Myanmar Rice (<i>Oryza sativa</i> L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers |
| title_sort | genetic diversity and population structure of myanmar rice i oryza sativa i l varieties using dartseq based snp and silicodart markers |
| topic | DArT markers genetic diversity Myanmar rice (<i>Oryza sativa</i> L.) silicoDArT SNP |
| url | https://www.mdpi.com/2223-7747/10/12/2564 |
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