Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes
Abstract Malnutrition due to macro‐ and micro‐nutrient deficiencies is one of the major global health concerns, especially in developing countries. Using genomics‐assisted breeding to enhance the nutritional value of important crops such as chickpea (Cicer arietinum L.) can help to address the probl...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-12-01
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| Series: | Agrosystems, Geosciences & Environment |
| Online Access: | https://doi.org/10.1002/agg2.20437 |
| _version_ | 1797389607892942848 |
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| author | Deus Mugabe Cristen M. Frieszell Marilyn L. Warburton Clarice J. Coyne Hatice Sari Renan Uhdre Lyle Wallace Yu Ma Ping Zheng Rebecca J. McGee Girish M. Ganjyal |
| author_facet | Deus Mugabe Cristen M. Frieszell Marilyn L. Warburton Clarice J. Coyne Hatice Sari Renan Uhdre Lyle Wallace Yu Ma Ping Zheng Rebecca J. McGee Girish M. Ganjyal |
| author_sort | Deus Mugabe |
| collection | DOAJ |
| description | Abstract Malnutrition due to macro‐ and micro‐nutrient deficiencies is one of the major global health concerns, especially in developing countries. Using genomics‐assisted breeding to enhance the nutritional value of important crops such as chickpea (Cicer arietinum L.) can help to address the problem. In this study, we conducted genome‐wide association studies to identify genes associated with protein, starch, oil, and fiber in chickpea to create resources to speed the breeding process. The USDA kabuli chickpea mini‐core of 88 accessions was genotyped using genotyped‐by‐sequencing, and 36,645 single nucleotide polymorphisms (SNPs) were identified across the eight chromosomes of the chickpea genome. A genome‐wide marker‐trait analysis using the FarmCPU model was conducted to identify SNP markers that can enable marker‐assisted breeding for seed protein, fiber, oil, and starch concentrations. The most significantly associated markers for seed protein concentration (p = 8.82E‐12), starch (p = 2.79E‐12), fiber (p = 7.65E‐12), and oil (p = 1.37E‐08) were found on chromosomes 1, 2, 6, and 7, controlling 11%, 12%, 20%, and 16% of the phenotypic variation, respectively. Validation of the SNP markers in a broader set of plant genetic resources and environments will be needed to determine their usefulness in breeding for end‐use characteristics. |
| first_indexed | 2024-03-08T22:58:25Z |
| format | Article |
| id | doaj.art-52c48cdad1c64c5184311facbb820b97 |
| institution | Directory Open Access Journal |
| issn | 2639-6696 |
| language | English |
| last_indexed | 2024-03-08T22:58:25Z |
| publishDate | 2023-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | Agrosystems, Geosciences & Environment |
| spelling | doaj.art-52c48cdad1c64c5184311facbb820b972023-12-16T02:28:30ZengWileyAgrosystems, Geosciences & Environment2639-66962023-12-0164n/an/a10.1002/agg2.20437Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genesDeus Mugabe0Cristen M. Frieszell1Marilyn L. Warburton2Clarice J. Coyne3Hatice Sari4Renan Uhdre5Lyle Wallace6Yu Ma7Ping Zheng8Rebecca J. McGee9Girish M. Ganjyal10Department of Crop and Soil Sciences Washington State University Pullman Washington USADepartment of Food Sciences Washington State University Pullman Washington USADepartment of Crop and Soil Sciences Washington State University Pullman Washington USADepartment of Crop and Soil Sciences Washington State University Pullman Washington USADepartment of Crop and Soil Sciences Washington State University Pullman Washington USADepartment of Crop and Soil Sciences Washington State University Pullman Washington USAUSDA ARS, Western Regional Plant Introduction Station Pullman Washington USADepartment of Horticulture Washington State University Pullman Washington USADepartment of Horticulture Washington State University Pullman Washington USAUSDA ARS, Grain Legume Genetics Physiology Research Pullman Washington USADepartment of Food Sciences Washington State University Pullman Washington USAAbstract Malnutrition due to macro‐ and micro‐nutrient deficiencies is one of the major global health concerns, especially in developing countries. Using genomics‐assisted breeding to enhance the nutritional value of important crops such as chickpea (Cicer arietinum L.) can help to address the problem. In this study, we conducted genome‐wide association studies to identify genes associated with protein, starch, oil, and fiber in chickpea to create resources to speed the breeding process. The USDA kabuli chickpea mini‐core of 88 accessions was genotyped using genotyped‐by‐sequencing, and 36,645 single nucleotide polymorphisms (SNPs) were identified across the eight chromosomes of the chickpea genome. A genome‐wide marker‐trait analysis using the FarmCPU model was conducted to identify SNP markers that can enable marker‐assisted breeding for seed protein, fiber, oil, and starch concentrations. The most significantly associated markers for seed protein concentration (p = 8.82E‐12), starch (p = 2.79E‐12), fiber (p = 7.65E‐12), and oil (p = 1.37E‐08) were found on chromosomes 1, 2, 6, and 7, controlling 11%, 12%, 20%, and 16% of the phenotypic variation, respectively. Validation of the SNP markers in a broader set of plant genetic resources and environments will be needed to determine their usefulness in breeding for end‐use characteristics.https://doi.org/10.1002/agg2.20437 |
| spellingShingle | Deus Mugabe Cristen M. Frieszell Marilyn L. Warburton Clarice J. Coyne Hatice Sari Renan Uhdre Lyle Wallace Yu Ma Ping Zheng Rebecca J. McGee Girish M. Ganjyal Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes Agrosystems, Geosciences & Environment |
| title | Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes |
| title_full | Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes |
| title_fullStr | Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes |
| title_full_unstemmed | Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes |
| title_short | Kabuli chickpea seed quality diversity and preliminary genome‐wide association study identifies markers and potential candidate genes |
| title_sort | kabuli chickpea seed quality diversity and preliminary genome wide association study identifies markers and potential candidate genes |
| url | https://doi.org/10.1002/agg2.20437 |
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