Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean
Snap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean d...
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| Format: | Article |
| Language: | English |
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American Society for Horticultural Science (ASHS)
2023-12-01
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| Series: | Journal of the American Society for Horticultural Science |
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| Online Access: | https://journals.ashs.org/jashs/view/journals/jashs/149/1/article-p1.xml |
| _version_ | 1797321189396316160 |
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| author | Ana Saballos Martin M. Williams II |
| author_facet | Ana Saballos Martin M. Williams II |
| author_sort | Ana Saballos |
| collection | DOAJ |
| description | Snap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean diversity panel composed of heirloom and improved cultivars used in North America and genome-wide association studies (GWAS) to investigate the genetic basis of pod morphological characteristics, including length, width, height, width/height ratio, and coefficients of variation (CVs). The GWAS detected multiple genomic regions associated with each pod trait, with a total of 20 quantitative trait loci (QTLs) for pod length, 9 for pod width, 14 for pod height, and 10 for pod width/height ratio. Regarding the CV of each pod trait, genome-wide association analyses detected six QTL for length CVs, five for width CVs, 15 for height CVs, and six for width/height ratio CVs. Thirteen regions in seven chromosomes were associated with two or more pod traits. Eighteen QTLs for pod traits in this study colocated with previously reported QTLs for pod and seed traits. The QTL intervals encompass gene models with homologues in other species that are involved in the control of developmental processes. These results capture the complex nature of the genetic control of snap bean pod traits and confirm the significance of genomic regions harboring overlapping QTLs identified in this and other studies. The phenotypic expression of pod traits in snap bean appears to be under the control of a few genomic regions with a strong effect with additional contributions of multiple small-effect regions. Validation of the function of the candidate genes identified in associated regions will contribute to our understanding of legume pod development. |
| first_indexed | 2024-03-08T04:54:58Z |
| format | Article |
| id | doaj.art-d32e7cca8af446fbab913e49412e21e9 |
| institution | Directory Open Access Journal |
| issn | 2327-9788 |
| language | English |
| last_indexed | 2024-03-08T04:54:58Z |
| publishDate | 2023-12-01 |
| publisher | American Society for Horticultural Science (ASHS) |
| record_format | Article |
| series | Journal of the American Society for Horticultural Science |
| spelling | doaj.art-d32e7cca8af446fbab913e49412e21e92024-02-07T17:47:41ZengAmerican Society for Horticultural Science (ASHS)Journal of the American Society for Horticultural Science2327-97882023-12-011491https://doi.org/10.21273/JASHS05318-23Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap BeanAna Saballos0Martin M. Williams II1Global Change and Photosynthesis Research Unit, US Department of Agriculture–Agricultural Research ServiceGlobal Change and Photosynthesis Research Unit, US Department of Agriculture–Agricultural Research ServiceSnap beans are cultivars of common bean (Phaseolus vulgaris) that are cultivated for their fleshy immature pods that exhibit a wide diversity of pod shapes and sizes. The genetic basis of the snap bean pod shape is complex and involves the interaction of multiple genes. This study used a snap bean diversity panel composed of heirloom and improved cultivars used in North America and genome-wide association studies (GWAS) to investigate the genetic basis of pod morphological characteristics, including length, width, height, width/height ratio, and coefficients of variation (CVs). The GWAS detected multiple genomic regions associated with each pod trait, with a total of 20 quantitative trait loci (QTLs) for pod length, 9 for pod width, 14 for pod height, and 10 for pod width/height ratio. Regarding the CV of each pod trait, genome-wide association analyses detected six QTL for length CVs, five for width CVs, 15 for height CVs, and six for width/height ratio CVs. Thirteen regions in seven chromosomes were associated with two or more pod traits. Eighteen QTLs for pod traits in this study colocated with previously reported QTLs for pod and seed traits. The QTL intervals encompass gene models with homologues in other species that are involved in the control of developmental processes. These results capture the complex nature of the genetic control of snap bean pod traits and confirm the significance of genomic regions harboring overlapping QTLs identified in this and other studies. The phenotypic expression of pod traits in snap bean appears to be under the control of a few genomic regions with a strong effect with additional contributions of multiple small-effect regions. Validation of the function of the candidate genes identified in associated regions will contribute to our understanding of legume pod development.https://journals.ashs.org/jashs/view/journals/jashs/149/1/article-p1.xmlgreen beanlegume pod morphologyphaseolus vulgariprocessing traitsquality |
| spellingShingle | Ana Saballos Martin M. Williams II Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean Journal of the American Society for Horticultural Science green bean legume pod morphology phaseolus vulgari processing traits quality |
| title | Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean |
| title_full | Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean |
| title_fullStr | Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean |
| title_full_unstemmed | Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean |
| title_short | Genome-wide Association Study Identifies Candidate Loci with Major Contributions to the Genetic Control of Pod Morphological Traits in Snap Bean |
| title_sort | genome wide association study identifies candidate loci with major contributions to the genetic control of pod morphological traits in snap bean |
| topic | green bean legume pod morphology phaseolus vulgari processing traits quality |
| url | https://journals.ashs.org/jashs/view/journals/jashs/149/1/article-p1.xml |
| work_keys_str_mv | AT anasaballos genomewideassociationstudyidentifiescandidatelociwithmajorcontributionstothegeneticcontrolofpodmorphologicaltraitsinsnapbean AT martinmwilliamsii genomewideassociationstudyidentifiescandidatelociwithmajorcontributionstothegeneticcontrolofpodmorphologicaltraitsinsnapbean |