Data from: Last generation genome – environment associations reveal the genetic basis of heat tolerance in common bean (Phaseolus vulgaris L.)

Genome-Environment Associations (GEA) are a powerful strategy for the
study of adaptive traits in wild plant populations, yet they still lack
behind in the use of modern statistical methods as the ones suggested for
Genome-Wide Association Studies (GWAS). In order to bridge this gap, we
couple GEA with last generation GWAS algorithms in common bean to identify
novel sources of heat tolerance across naturally heterogeneous ecosystems.
Common bean (Phaseolus vulgaris L.) is the most important legume for human
consumption, and breeding it for resistance to heat stress is key because
annual increases in atmospheric temperature are causing decreases in yield
of up to 9% for every 1°C. A total of 78 geo-referenced wild accessions,
spanning the two gene pools of common bean, were Genotyped by Sequencing
(GBS) leading to the discovery of 23,373 SNP markers. Three indices of
heat stress were developed for each accession and inputted in last
generation algorithms (i.e. SUPER, FARMCPU and BLINK) to identify putative
associated loci with the environmental heterogeneity in heat stress.
Best-fit models revealed 120 significantly associated alleles distributed
in all 11 common bean chromosomes. Flanking candidate genes were
identified using 1kb genomic windows centered in each associated SNP
marker. Some of these genes were directly linked to heat-responsive
pathways, such as the activation of heat shock proteins (MED23, MED25,
HSFB1, HSP40 and HSP20). We also found protein domains related to thermo
stability in plants such as S1 and Zinc finger A20 & AN1. Other
genes were related to biological processes that may correlate with plant
tolerance to high temperature, such as time to flowering (MED25, MBD9 and
PAP), germination and seedling development (Pkinase_Tyr, Ankyrin-B and
Family Glicosil-hydrolase), cell wall stability (GAE6), and signaling
pathway of abiotic stress via Abscisic Acid (Histone-like transcription
factors NFYB and phospholipase C) and Auxin (Auxin response factor and
AUX_IAA). This work offers putative associated loci for marker-assisted
and genomic selection for heat tolerance in common bean. It also
demonstrates that it is feasible to identify genome-wide environmental
associations with modest sample sizes by using a combination of various
carefully chosen environmental indices and last generation GWAS
algorithms.