Genome-wide association mapping dissects the selective breeding of determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.)

Denning-James, Kate E., Chater, Caspar, Cortés, Andrés J., Blair, Matthew W., Peláez, Diana, Hall, Anthony and De Vega, José J. (2025) Genome-wide association mapping dissects the selective breeding of determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris L.). G3: Genes, Genomes, Genetics, 15 (6). ISSN 2160-1836

[thumbnail of jkaf090]
Preview
PDF (jkaf090) - Published Version
Available under License Creative Commons Attribution.

Download (11MB) | Preview

Abstract

The common bean (Phaseolus vulgaris L.) is a legume pulse crop that provides significant dietary and ecosystem benefits globally. We investigated 2 key traits, determinacy and photoperiod sensitivity, that are integral to its management and crop production, and that were early selected during the domestication of both Mesoamerican and Andean gene pools. Still, significant variation exists among common bean landraces for these traits. Since landraces form the basis for trait introgression in prebreeding, understanding these traits’ genetic underpinnings and relation with population structure is vital for guiding breeding and genetic studies. We explored genetic admixture, principal component, and phylogenetic analyses using whole-genome sequencing to define subpopulations and gene pools. We used genome-wide association mapping (GWAS) to identify marker-trait associations in a diversity panel of common bean landraces. We observed a clear correlation between these traits, gene pool, and subpopulation structure. We found extensive admixture between the Andean and Mesoamerican gene pools in some regions. We identified 13 QTLs for determinacy and 10 QTLs for photoperiod sensitivity and underlying causative genes. Our study identified known and novel causative genes and a high proportion of pleiotropic effects for these traits in common bean, and likely translatable to other legume species.

Item Type: Article
Additional Information: A correction has been published: G3 Genes|Genomes|Genetics, Volume 15, Issue 8, August 2025, jkaf141, https://doi.org/10.1093/g3journal/jkaf141. The correction only affects author affiliation and not the scientific content of the article. Data availability statement: We thank CIAT's Genebank and IPK's Genebank for their generous provision of germplasm. Germplasm held in the CIAT and IPK collections is available on request. Raw reads are deposited in the SRA under accession PRJEB81566. The scripts used in this study are publicly available in Github (https://github.com/DeVegaGroup/KDJ-CBeans/). Supplemental material available at G3 online. Funding information: KED.-J is supported by the Biotechnology and Biological Sciences Research Council (UKRI-BBSRC) to the Norwich Research Park Doctoral Training program (#2578607). This research was partially funded by the British Council throughout the “2019 Newton Fund Institutional Links binational Bioeconomy” call in grant ID 527023146 to AJC and JJDV. This study was also partially funded by the Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation (UKRI), to the Earlham Institute's Grant “Decoding Biodiversity” (BBX011089/1), and its constituent work package BBS/E/ER/230002B (Decode WP2 Genome Enabled Analysis of Diversity to Identify Gene Function, Biosynthetic Pathways, and Variation in Agri/Aquacultural Traits). Funding was also received from the BBSRC through the “Core Strategic Programme Grant” BB/CSP1720/1 (Genomes to Food Security) and its constituent work package BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation), as well as the BBSRC-funded “Core Capability Grant” BB/CCG1720/1.
Uncontrolled Keywords: common bean,determinacy,domestication,genomics,gwas,legume,photoperiod,plant genetics,molecular biology,genetics,genetics(clinical) ,/dk/atira/pure/subjectarea/asjc/1300/1312
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 20 Aug 2025 12:30
Last Modified: 24 Aug 2025 06:30
URI: https://ueaeprints.uea.ac.uk/id/eprint/100169
DOI: 10.1093/g3journal/jkaf090

Downloads

Downloads per month over past year

Actions (login required)

View Item View Item