Is drought tolerance a domestication trait in tepary bean?: Allelic diversity at abiotic stress responsive genes in cultivated Phaseolus acutifolius A. Gray and its wild relatives

Some of the major impacts of climate change are expected in the poorest
regions of the world where drought stress and nutrient deficiency are
already a main issue. Legumes are an essential food crop for the poorest
because of their high dietary protein and micronutrient contents. However,
they are generally drought susceptible. Therefore, our goal in this study
was to explore allele diversity at abiotic stress responsive candidate
genes in the only drought tolerant cultivated bean species of the genus
Phaseolus, tepary bean (P. acutifolius A. Gray) and its related species P.
parvifolius Freytag. Specifically, we estimated drought tolerance in 52
tepary bean s.l. geo-referenced germplasm accessions from the P.
acutifolius–parvifolius clade using climate information, and used this
estimated drought stress index to examine allele correlations with Asr2,
Dreb2B and ERECTA-encoding candidate genes for drought tolerance. Genetic
clustering showed that cultivated and wild P. acutifolius were
intermingled with P. acutifolius var. tenuifolius and P. parvifolius,
signifying that allele diversity at candidate genes for drought tolerance
was not scarce in tepary bean s.l. Dreb2B and ERECTA-encoding genes
harbored signatures of directional/purifying selection, likely in favor of
adaptive alleles selectively advantageous because each had two SNPs
significantly correlated (p-value < 0.05) with habitat drought
stress at six and 12 months. These results suggest that tepary bean s.l.
is a reservoir of novel alleles at candidate genes for drought tolerance,
as expected for a drought-tolerant species that originated in warmer and
arid environments. Abiotic stress responsive candidate genes also exhibit
comparable patterns of selective signatures when comparing orthologous
across species, which speaks for a predominant role of gene
sub-functionalization likely due to ecological constrains. Our study
therefore corroborates that the candidate gene approach is still an
effective alternative for marker validation across a broader genetic basis
of germplasm accessions. Further efforts to determine the genetic
architecture of drought tolerance will unlock novel alleles hidden in a
crop with limited modern relevance as tepary bean, but capable of acting
as a donor in backcrossing and genome editing strategies with elite common
bean lines aiming to meet the imminent demands of a drier world.