10.5061/DRYAD.J2C24
Cortés, Andrés J.
University of Gothenburg
Blair, Matthew W.
Tennessee State University
Data from: Genotyping by sequencing and genome–environment associations in
wild common bean predict widespread divergent adaptation to drought
Dryad
dataset
2019
Phaseolus vulgaris
Holocene
National Science Foundation
https://ror.org/021nxhr62
Lundell and Tullberg grants
2019-01-31T00:00:00Z
2019-01-31T00:00:00Z
en
https://doi.org/10.3389/fpls.2018.00128
5398954 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
Hapmap fileHapmap file23k89.hmp.txtR codeR codeGBS_bean.R
Meso- and south-america