Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)
Abstract Background Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-10-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-020-02579-x |
| _version_ | 1819014876354314240 |
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| author | Alena Sokolkova Marina Burlyaeva Tatjana Valiannikova Margarita Vishnyakova Roland Schafleitner Cheng-Ruei Lee Chau-Ti Ting Ramakrishnan Madhavan Nair Sergey Nuzhdin Maria Samsonova Eric von Wettberg |
| author_facet | Alena Sokolkova Marina Burlyaeva Tatjana Valiannikova Margarita Vishnyakova Roland Schafleitner Cheng-Ruei Lee Chau-Ti Ting Ramakrishnan Madhavan Nair Sergey Nuzhdin Maria Samsonova Eric von Wettberg |
| author_sort | Alena Sokolkova |
| collection | DOAJ |
| description | Abstract Background Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. Conclusions The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts. |
| first_indexed | 2024-12-21T02:22:48Z |
| format | Article |
| id | doaj.art-6da00ed44ae34728b0e9e9e76ed65db4 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T02:22:48Z |
| publishDate | 2020-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-6da00ed44ae34728b0e9e9e76ed65db42022-12-21T19:19:05ZengBMCBMC Plant Biology1471-22292020-10-0120S11910.1186/s12870-020-02579-xGenome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)Alena Sokolkova0Marina Burlyaeva1Tatjana Valiannikova2Margarita Vishnyakova3Roland Schafleitner4Cheng-Ruei Lee5Chau-Ti Ting6Ramakrishnan Madhavan Nair7Sergey Nuzhdin8Maria Samsonova9Eric von Wettberg10Peter the Great St. Petersburg Polytechnic University, Department of Applied MathematicsFederal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR)Kuban Branch of Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR)Federal Research Centre All-Russian N.I. Vavilov Institute of Plant Genetic Resources (VIR)World Vegetable CenterNational Taiwan UniversityNational Taiwan UniversityWorld Vegetable Center, South and Central Asia, ICRISAT Campus, PatancheruPeter the Great St. Petersburg Polytechnic University, Department of Applied MathematicsPeter the Great St. Petersburg Polytechnic University, Department of Applied MathematicsPeter the Great St. Petersburg Polytechnic University, Department of Applied MathematicsAbstract Background Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. Conclusions The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts.http://link.springer.com/article/10.1186/s12870-020-02579-xMungbeanCore-collectionPhenotypingGWASPopulation structurePhenology traits |
| spellingShingle | Alena Sokolkova Marina Burlyaeva Tatjana Valiannikova Margarita Vishnyakova Roland Schafleitner Cheng-Ruei Lee Chau-Ti Ting Ramakrishnan Madhavan Nair Sergey Nuzhdin Maria Samsonova Eric von Wettberg Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) BMC Plant Biology Mungbean Core-collection Phenotyping GWAS Population structure Phenology traits |
| title | Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) |
| title_full | Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) |
| title_fullStr | Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) |
| title_full_unstemmed | Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) |
| title_short | Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan) |
| title_sort | genome wide association study in accessions of the mini core collection of mungbean vigna radiata from the world vegetable gene bank taiwan |
| topic | Mungbean Core-collection Phenotyping GWAS Population structure Phenology traits |
| url | http://link.springer.com/article/10.1186/s12870-020-02579-x |
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