Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding
Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping...
| Main Authors: | , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2019
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/99568 |
| _version_ | 1855538907378089984 |
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| author | Raatz, Bodo Mukankusi, Clare Mugisha Lobaton, Juan David Male, Alan Chisale, Virginia Amsalu, Berhanu Fourie, Deidre Mukamuhirwa, Floride Muimui, Kennedy K. Mutari, Bruce Nchimbi-Msolla, Susan Nkalubo, Stanley T. Tumsa, Kidane Chirwa, Rowland Maredia, Mywish K. He, Chunlin |
| author_browse | Amsalu, Berhanu Chirwa, Rowland Chisale, Virginia Fourie, Deidre He, Chunlin Lobaton, Juan David Male, Alan Maredia, Mywish K. Muimui, Kennedy K. Mukamuhirwa, Floride Mukankusi, Clare Mugisha Mutari, Bruce Nchimbi-Msolla, Susan Nkalubo, Stanley T. Raatz, Bodo Tumsa, Kidane |
| author_facet | Raatz, Bodo Mukankusi, Clare Mugisha Lobaton, Juan David Male, Alan Chisale, Virginia Amsalu, Berhanu Fourie, Deidre Mukamuhirwa, Floride Muimui, Kennedy K. Mutari, Bruce Nchimbi-Msolla, Susan Nkalubo, Stanley T. Tumsa, Kidane Chirwa, Rowland Maredia, Mywish K. He, Chunlin |
| author_sort | Raatz, Bodo |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools. |
| format | Journal Article |
| id | CGSpace99568 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace995682025-03-13T09:45:22Z Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding Raatz, Bodo Mukankusi, Clare Mugisha Lobaton, Juan David Male, Alan Chisale, Virginia Amsalu, Berhanu Fourie, Deidre Mukamuhirwa, Floride Muimui, Kennedy K. Mutari, Bruce Nchimbi-Msolla, Susan Nkalubo, Stanley T. Tumsa, Kidane Chirwa, Rowland Maredia, Mywish K. He, Chunlin phaseolus vulgaris l. common bean dna fingerprinting huellas genéticas adn germoplasm plant breeding colombia uganda Common bean (Phaseolus vulgaris L.) is an important staple crop for smallholder farmers, particularly in Eastern and Southern Africa. To support common bean breeding and seed dissemination, a high throughput SNP genotyping platform with 1500 established SNP assays has been developed at a genotyping service provider which allows breeders without their own genotyping infrastructure to outsource such service. A set of 708 genotypes mainly composed of germplasm from African breeders and CIAT breeding program were assembled and genotyped with over 800 SNPs. Diversity analysis revealed that both Mesoamerican and Andean gene pools are in use, with an emphasis on large seeded Andean genotypes, which represents the known regional preferences. The analysis of genetic similarities among germplasm entries revealed duplicated lines with different names as well as distinct SNP patterns in identically named samples. Overall, a worrying number of inconsistencies was identified in this data set of very diverse origins. This exemplifies the necessity to develop and use a cost-effective fingerprinting platform to ensure germplasm purity for research, sharing and seed dissemination. The genetic data also allows to visualize introgressions, to identify heterozygous regions to evaluate hybridization success and to employ marker-assisted selection. This study presents a new resource for the common bean community, a SNP genotyping platform, a large SNP data set and a number of applications on how to utilize this information to improve the efficiency and quality of seed handling activities, breeding, and seed dissemination through molecular tools. 2019-03 2019-02-25T14:26:43Z 2019-02-25T14:26:43Z Journal Article https://hdl.handle.net/10568/99568 en Open Access Springer Raatz, Bodo; Mukankusi, Clare; Lobaton, Juan David; Male, Alan; Chisale, Virginia; Amsalu, Berhanu; Fourie, Deidré; Mukamuhirwa, Floride; Muimui, Kennedy; Mutari, Bruce; Nchimbi-Msolla, Susan; Nkalubo, Stanley; Tumsa, Kidane; Chirwa, Rowland; Maredia, Mywish K. & He, Chunlin. (2019). Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding. Genetic Resources and Crop Evolution, 1-16 p. |
| spellingShingle | phaseolus vulgaris l. common bean dna fingerprinting huellas genéticas adn germoplasm plant breeding colombia uganda Raatz, Bodo Mukankusi, Clare Mugisha Lobaton, Juan David Male, Alan Chisale, Virginia Amsalu, Berhanu Fourie, Deidre Mukamuhirwa, Floride Muimui, Kennedy K. Mutari, Bruce Nchimbi-Msolla, Susan Nkalubo, Stanley T. Tumsa, Kidane Chirwa, Rowland Maredia, Mywish K. He, Chunlin Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title | Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title_full | Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title_fullStr | Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title_full_unstemmed | Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title_short | Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding |
| title_sort | analyses of african common bean phaseolus vulgaris l germplasm using a snp fingerprinting platform diversity quality control and molecular breeding |
| topic | phaseolus vulgaris l. common bean dna fingerprinting huellas genéticas adn germoplasm plant breeding colombia uganda |
| url | https://hdl.handle.net/10568/99568 |
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