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Analyses of African common bean (Phaseolus vulgaris L.) germplasm using a SNP fingerprinting platform: diversity, quality control and molecular breeding

Author: Raatz, B.
Author: Mukankusi, C.
Author: Lobaton, J.D.
Author: Male, A.
Author: Chisale, V.
Author: Amsalu, B.
Author: Fourie, D.
Author: Mukamuhirwa, F.
Author: Muimui, K.
Author: Mutari, B.
Author: Nchimbi-Msolla, S.
Author: Nkalubo, S.
Author: Tumsa, K.
Author: Chirwa, R.
Author: Maredia, M.K.
Author: He, Chunlin
Year: 2019
ISSN: ISSN: 1573-5109
ISSN: ISSN: 0925-9864
Abstract: 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: PDF
Language: English
Publisher: Springer Nature
Type: Article
Place of Publication: Dordrecht (Netherlands)
Pages: 707-722
Issue: 3
Volume: 66
DOI: 10.1007/s10722-019-00746-0
Keywords: SNP Genotyping
Keywords: Diversity Analysis
Keywords: Germplasm Purity
Agrovoc: GENOMES
Agrovoc: MAIZE
Agrovoc: BEANS
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Journal: Genetic Resources and Crop Evolution

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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP

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