Genotyping the ex situ genetic resources of wild and cultivated tepary bean

Authors: Hart, John; VARGAS, ANA - University Of Puerto Rico; BEAVER, JAMES - University Of Puerto Rico; DEBOUCK, DANIEL - International Center For Tropical Agriculture (CIAT); Porch, Timothy - Tim

Submitted to: Bean Improvement Cooperative Annual Report
Publication Type: Research Notes
Publication Acceptance Date: 3/1/2019
Publication Date: 4/1/2019
Citation: Hart, J.P., Vargas, A.G., Beaver, J.S., Debouck, D.G., Porch, T.G. 2019. Genotyping the ex situ genetic resources of wild and cultivated tepary bean. Bean Improvement Cooperative Annual Report. 62:109-110.

Interpretive Summary: The tepary bean is a relatively untapped source of novel allelic diversity both as a donor for common bean improvement, and as an intrinsically stress-tolerant and nutritious food crop. The objectives of this research were to assemble, increase, and genotype all of the available wild and cultivated tepary bean accessions held by the USDA, CIAT, and TARS germplasm collections, and to investigate the genetic diversity and population structure of this germplasm as it relates to domestication status, morphological classification, and geographical distribution. An initial total of 314 accessions (158 wild, 156 cultivated) were obtained and genotyped as part of a genotyping-by-sequencing (GBS) library. After alignment, 20,364 SNP molecular markers were selected that were present in at least 80% of the accessions. The results suggested that the number of subpopulations present in the germplasm is equal to eight and that the membership of each accession in the eight subpopulations is structured based on domestication status, geographic origin, and morphological variation. These preliminary results confirm the strong bottleneck caused by tepary domestication, identify subpopulations of tepary germplasm in both the wild and cultivated genepools according to geographical origin, and present extensive opportunities for further research into the evolution, domestication, diversity, and improvement of tepary bean.

Technical Abstract: The tepary bean (Phaseolus acutifolius A. Gray) is a relatively untapped source of novel allelic diversity both as a donor for common bean improvement, and as an intrinsically stress-tolerant and nutritious food crop. The objectives of this research were to assemble, increase, and genotype all of the available wild and cultivated tepary bean accessions held by the USDA, CIAT, and TARS germplasm collections, and to investigate the genetic diversity and population structure of this germplasm as it relates to domestication status, morphological classification, and geographical distribution. An initial total of 314 accessions (158 wild, 156 cultivated) were obtained and genotyped as part of a 384-plex ApeKI genotyping-by-sequencing (GBS) library. After alignment with BWA we were able to discover and genotype 20,364 SNPs (with MAF = 0.05) that were present in at least 80% of the accessions. The results suggested that the number of subpopulations present in the germplasm is equal to eight and that the membership of each accession in the eight subpopulations is structured based on domestication status, geographic origin, and morphological variation. These preliminary results confirm the strong bottleneck caused by tepary domestication, identify subpopulations of tepary germplasm in both the wild and cultivated genepools according to geographical origin, and present extensive opportunities for further research into the evolution, domestication, diversity, and improvement of tepary bean.