Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean
Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition arou...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1014282/full |
| _version_ | 1798023029018591232 |
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| author | Samson Ugwuanyi Samson Ugwuanyi Obi Sergius Udengwu Rod J. Snowdon Christian Obermeier |
| author_facet | Samson Ugwuanyi Samson Ugwuanyi Obi Sergius Udengwu Rod J. Snowdon Christian Obermeier |
| author_sort | Samson Ugwuanyi |
| collection | DOAJ |
| description | Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently. |
| first_indexed | 2024-04-11T17:39:37Z |
| format | Article |
| id | doaj.art-1b481f194aac4fa896c5416b949ee1f9 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T17:39:37Z |
| publishDate | 2022-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-1b481f194aac4fa896c5416b949ee1f92022-12-22T04:11:31ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-11-011310.3389/fpls.2022.10142821014282Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common beanSamson Ugwuanyi0Samson Ugwuanyi1Obi Sergius Udengwu2Rod J. Snowdon3Christian Obermeier4Department of Plant Breeding, Justus Liebig University, Giessen, GermanyDepartment of Plant Science and Biotechnology, University of Nigeria, Nsukka, NigeriaDepartment of Plant Science and Biotechnology, University of Nigeria, Nsukka, NigeriaDepartment of Plant Breeding, Justus Liebig University, Giessen, GermanyDepartment of Plant Breeding, Justus Liebig University, Giessen, GermanyPhaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.https://www.frontiersin.org/articles/10.3389/fpls.2022.1014282/fullPhaseolus vulgarisGWASmarker-trait associationsingle nucleotide polymorphismstargeted genotyping-by-sequencingpod shattering |
| spellingShingle | Samson Ugwuanyi Samson Ugwuanyi Obi Sergius Udengwu Rod J. Snowdon Christian Obermeier Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean Frontiers in Plant Science Phaseolus vulgaris GWAS marker-trait association single nucleotide polymorphisms targeted genotyping-by-sequencing pod shattering |
| title | Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean |
| title_full | Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean |
| title_fullStr | Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean |
| title_full_unstemmed | Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean |
| title_short | Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean |
| title_sort | novel candidate loci for morpho agronomic and seed quality traits detected by targeted genotyping by sequencing in common bean |
| topic | Phaseolus vulgaris GWAS marker-trait association single nucleotide polymorphisms targeted genotyping-by-sequencing pod shattering |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1014282/full |
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