Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines

Authors: AMONGI, W - Makerere University; NKALUBO, STANLEY - National Crops Resources Research Institute; OCHWO-SSEMAKULA, MILDRED - Alliance Of Bioversity International And The International Center For Tropical Agriculture (CIAT); BADJI, ARFANG - National Crops Resources Research Institute; DRAMADRI ONZIGA, ISAAC - Makerere University; ODONGO LAPAKA, THOMAS - Makerere University; NUWAMANYA, EPHRAIM - Makerere University; TUKAMUHHABWE, PHINEAS - Makerere University; IZQUIERDO, PAULO - Michigan State University; Cichy, Karen; KELLY, JAMES - Michigan State University; MUKANKUSI, CLARE - Alliance Of Bioversity International And The International Center For Tropical Agriculture (CIAT)

Submitted to: Genetic Resources and Crop Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/19/2023
Publication Date: 3/8/2023
Citation: Amongi, W., Nkalubo, S., Ochwo-Ssemakula, M., Badji, A., Dramadri Onziga, I., Odongo Lapaka, T., Nuwamanya, E., Tukamuhhabwe, P., Izquierdo, P., Cichy, K.A., Kelly, J., Mukankusi, C. 2023. Genetic clustering, and diversity of African panel of released common bean genotypes and breeding lines. Genetic Resources and Crop Evolution. https://doi.org/10.1007/s10722-023-01559-y.
DOI: https://doi.org/10.1007/s10722-023-01559-y

Interpretive Summary: Common bean is an important grain legume crop of global importance, especially in sub-Saharan Africa, where it is a staple food crop for calories, protein, and micronutrients, especially iron, zinc, thiamin, and folic acid. This study aimed to evaluate the genetic diversity and structure of breeding lines and released common bean varieties in East Africa to determine the relevance of the population for genomic selection, for use in the Pan African Bean Research Alliance (PABRA). Two populations consisting of 725 common bean genotypes were analyzed by single nucleotide polymorphic (SNP) markers. A subset of the germplasm was also characterized for agronomic traits, cooking time, and nutrition quality. The genotypes exhibited high genetic diversity and thus have high potential for use in plant breeding. Phenotypic evaluation indicated the usefulness of this population for improvement of cooking time and yield performance. Selection for early maturity, a common practice across African countries, is a probable contributor to lower yield in Andean beans. Fast cooking beans exist in all market classes but the small white beans were notably superior in this attribute.

Technical Abstract: Common bean is a grain legume of global importance especially for proteins and micronutrients. The crop is a staple food in sub-Saharan Africa, where it has gained importance in iron biofortification for people prone to anemia. However, biotic and abiotic constraints, long cooking time, and high phytic acid and polyphenols both of which affect bioavailable iron, hinder the production and health benefits. To inform breeding decisions, the study determined genetic diversity and population structure within 725 breeding lines, varieties, or landraces mostly from Uganda and South America. Genotyping by sequencing (GBS) and diversity array technology (DarTseq) were used to generate single nucleotide polymorphic (SNP) markers on Set1 (427) and Set2 (298) germplasm, respectively. The germplasm were grouped into Andean and Mesoamerican gene pools, with the latter as the larger subpopulation. Analysis of molecular variance revealed 46% (Set1) and 50% (Set2) of genetic variation among the subpopulations, with fixation indices (FST) of 0.54 (Set1) and 0.71 (Set2) among Andean and Mesoamerican beans, respectively. The overall germplasm’s gene diversities were 0.206 (Set1) and 0.332 (Set2). Admixtures were the most diverse (0.193) in both sets of germplasm. The germplasm exhibited high genetic diversity and as a result they have a high potential for use in plant breeding. Inter-gene pool crosses within and across market classes are possible and considering both approaches is expected to increase diversity to realize genetic gain. The structure and polymorphic information generated provided useful perspectives for genomic breeding and genome-wide association study using the population.