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Front. Plant Sci. | doi: 10.3389/fpls.2018.00128

Genotyping by Sequencing and Genome–Environment Associations in Wild Common Bean Predict Widespread Divergent Adaptation to Drought

  • 1Department of Biological & Environmental Sciences, University of Gothenburg, Sweden
  • 2Department of Agricultural and Environmental Sciences, Tennessee State University, United States

Drought will reduce global crop production by >10% in 2050 substantially worsening global malnutrition. Breeding for resistance to drought will require accessing crop genetic diversity found in the wild accessions from the driest high stress ecosystems. Genome–environment associations in crop wild relatives reveal natural adaptation, and therefore can be used to identify adaptive variation. We explored this approach in the food crop Phaseolus vulgaris L., characterizing 86 geo-referenced wild accessions using Genotyping by Sequencing (GBS) to discover single-nucleotide-polymorphisms (SNPs). The wild beans represented Mesoamerica, Guatemala, Colombia, Ecuador/Northern Peru and Andean groupings. We found high polymorphism with a total of 22,845 SNPs across the 86 accessions loci that confirmed genetic relationships for the groups. As a second objective, we quantified allelic associations with a bioclimatic-based drought index using 10 different statistical models that accounted for population structure. Based on the optimum model, 115 SNPs in 90 regions, widespread in all 11 common bean chromosomes, were associated with the bioclimatic-based drought index. A gene coding for an Ankyrin repeat-containing protein and a phototropic-responsive NPH3 gene were identified as potential candidates. Genomic windows of 1Mb containing associated SNPs had more positive Tajima’s D scores than windows without associated markers. This indicates that adaptation to drought, as estimated by bioclimatic variables, has been under natural divergent selection, suggesting that drought tolerance may be favorable under dry conditions but harmful in humid conditions. Our work exemplifies that genomic signatures of adaptation are useful for germplasm characterization, potentially enhancing future marker-assisted selection and crop improvement.

Keywords: drought tolerance, adaptation, Genomic Signatures of Selection, Divergent selection, SNP markers, Tajima’s D

Received: 06 Nov 2017; Accepted: 23 Jan 2018.

Edited by:

Nicholas Provart, University of Toronto, Canada

Reviewed by:

Frédéric Marsolais, Agriculture and Agri-Food Canada (AAFC), Canada
Umesh K. Reddy, West Virginia State University, United States  

Copyright: © 2018 Cortés and Blair. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Andrés J. Cortés, University of Gothenburg, Department of Biological & Environmental Sciences, Gothenburg, Sweden, andres.cortes@bioenv.gu.se