Common bean SNP alleles and candidate genes affecting photosynthesis under contrasting water regimes

Abstract

Water deficit is a major worldwide constraint to common bean (Phaseolus vulgaris L.) production, being photosynthesis one of the most affected physiological processes. To gain insights into the genetic basis of the photosynthetic response of common bean under water-limited conditions, a collection of 158 Portuguese accessions was grown under both well-watered and water-deficit regimes. Leaf gas-exchange parameters were measured and photosynthetic pigments quantified. The same collection was genotyped using SNP arrays, and SNP-trait associations tested considering a linear mixed model accounting for the genetic relatedness among accessions. A total of 133 SNP-trait associations were identified for net CO2 assimilation rate, transpiration rate, stomatal conductance, and chlorophylls a and b, carotenes, and xanthophyll contents. Ninety of these associations were detected under water-deficit and 43 under well-watered conditions, with only two associations common to both treatments. Identified candidate genes revealed that stomatal regulation, protein translocation across membranes, redox mechanisms, hormone, and osmotic stress signaling were the most relevant processes involved in common bean response to water-limited conditions. These candidates are now preferential targets for common bean water-deficit-tolerance breeding. Additionally, new sources of water-deficit tolerance of Andean, Mesoamerican, and admixed origin were detected as accessions valuable for breeding, and not yet explored.

Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics

“…Wu et al[171] identified 196 association loci containing 230 candidate SNPs as being linked to drought resistance in common bean. on the other hand Leitão et al[172], determined a total of 133 SNPs for transpiration rate, net Co2 assimilation rate, stomatal conductance, chlorophylls a/b, carotenes, and xanthophyll contents. Ninety of these associations were found under water-deficit conditions.…”

Shared and tailored common bean transcriptomic responses to combined fusarium wilt and water deficit

“…The recent advances in genomic selection research for complex traits in many crops, including legumes 56 , foresee an increase in the efficiency of breeding for multi-stress resistance 57 . In the case of common bean, the availability of resistant accessions from both gene pools—Andean and Mesoamerican—and of intermediate origin, as the ones identified within the Portuguese germplasm 27 , 28 might bring favorable genetic combination useful for multi-stress breeding.…”

“…Also, accession R-645 was more resilient than S-1955 to water deprivation, with photosynthesis-related traits showing higher variation in the latter accession when comparing plants, with the second trifoliate leaf established, under well-watered and water deficit conditions. For example, in accession R-645, the net CO 2 assimilation rate was only 10% lower under water deficit (defined as 40% of field capacity) than under well-watered conditions, while for accession S-1955 it was 3.4 times lower under water deficit 28 .…”

“…Two Portuguese common bean accessions—R-645 of Andean origin, and S-1955 of Mesoamerican origin—were chosen based on their contrasting response to water deficit and fusarium wilt 27 , 28 . Accession R-645 is resistant and accession S-1955 is susceptible to both stresses.…”

“…To attain this objective, we focused on two Portuguese common bean accessions, with contrasting responses to both WD and Fop 27 , 28 . The two accessions were exposed to single and combined stresses and the root transcriptome profiling was compared using massive analysis of cDNA ends (MACE).…”