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

Susana Trindade Leitão,Marcos Malosetti,Maria Catarina Bicho,Maria João Paulo,Susana De Sousa Araújo,Maria Carlota Vaz Patto,Fred Van Eeuwijk,Priscila Pereira

doi:10.1038/s41438-020-00434-6

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.

Highlights

Common bean (Phaseolus vulgaris L.) is one of the most important food-grain legumes worldwide, with recognized benefits for health and nutrition[1]
Phenotypic trait variation under contrasting water treatments Several physiological and morphological traits were evaluated in the Portuguese common bean collection under well-watered (WW) and water-deficit (WD) conditions, namely, stomatal CO2 conductance, net CO2 assimilation rate (A), transpiration rate (E), substomatal CO2 concentration (Ci), instantaneous and intrinsic water-use efficiencies (WUE = A/E and WUEi = A/gs, respectively), chlorophylls a (Ca) and b (Cb) contents, carotene and xanthophyll (Ccx) contents, leaf fresh weight (FW), turgid weight (TW) and dry weight (DW), leaf relative water content (RWC (%) = [(FW − DW)/(TW − DW)] × 100), specific leaf area (SLA), and leaf thickness (LT)
Drought is a major concern in agriculture affecting a wide range of crops, including common bean

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is one of the most important food-grain legumes worldwide, with recognized benefits for health and nutrition[1]. Water availability is the major abiotic factor affecting crop productivity. Drought periods may result in up to 70% of yield reduction[2]. It is estimated that 60% of common bean production occurs in regions prone to water deficit[3]. Many physiological processes, including photosynthesis, are negatively affected. Most plants respond to a mild-to-moderate water deficit by

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Conclusion