PLOS ONE · 6 authors, 6 centres
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This study identified 68 genetic markers and 22 candidate genes associated with drought tolerance in dry beans by screening 185 genotypes under drought-stressed and well-watered conditions. Drought stress reduced grain yield by 29.6%, and the markers explained up to 70% of the variation in traits like days to flowering and seed weight. These findings provide potential targets for marker-assisted breeding to improve drought tolerance in common bean.
**Background:** Common bean (*Phaseolus vulgaris* L.) is a major pulse crop, but its production is severely limited by drought stress, especially in Sub-Saharan Africa where up to 73% of production occurs under moderate to severe drought. Grain yield losses can reach 80% under severe drought. Understanding the genetic basis of drought tolerance is essential for marker-assisted breeding. This study aimed to identify SNP markers and candidate genes associated with agronomic and physiological traits under drought-stressed and well-watered conditions.
**Methods:** A diversity panel of 185 genotypes (landraces, cultivars, and elite lines) was evaluated at Save Valley Experiment Station, Zimbabwe, during the 2019 and 2020 dry winter seasons. The experiment used a 5×37 alpha lattice design with two replications under both drought-stressed and well-watered treatments. Drought stress was imposed after 80% flowering by withholding irrigation to 30% of field capacity. Phenotypic data were collected for days to 50% flowering (DFW), plant height (PH), days to physiological maturity (DPM), grain yield (GYD), 100-seed weight (SW), leaf temperature (LT), leaf chlorophyll content (LCC), and stomatal conductance (SC). Genotyping was performed using DArTseq, yielding 9370 filtered SNP markers. Population structure was assessed using STRUCTURE and PCA. Marker-trait associations (MTAs) were identified using a compressed mixed linear model (Q+K) in GAPIT, with significance set at p < 0.001. Candidate genes were identified within 200 kb windows around significant SNPs.
**Key Results:** Drought stress reduced mean PH by 12.1%, GYD by 29.6%, SW by 10.3%, DPM by 12.6%, LCC by 28.5%, and SC by 62.0%, while LT increased by 21.6%. Broad-sense heritability was high for most traits under drought stress (0.83–0.97) except SC (0.32), LT (0.46), and LCC (0.54). Population structure revealed two sub-populations (Andean and Middle-American). Under drought stress, 29 significant MTAs were identified for six traits (excluding DPM and LCC). Markers explained 0.08–0.10 (SC), 0.22–0.23 (LT), 0.29–0.32 (PH), 0.43–0.44 (GYD), 0.65–0.66 (SW), and 0.69–0.70 (DFW) of phenotypic variation. For GYD, four SNPs were identified on chromosomes Pv04 and Pv11, with allele effects ranging from -174.56 to 202.90 kg/ha. Under well-watered conditions, 39 significant MTAs were detected for six traits (excluding SW and SC). The highest R² was 0.70 for DPM (SNP 100117381 on Pv02). No common SNPs were found across environments. Twenty-two putative candidate genes were identified, including Phvul.001G254100 (CCCH zinc finger, associated with SC), Phvul.004G150500 (phosphoethanolamine N-methyltransferase, associated with GYD), and Phvul.002G122100 (RNA-recognition motif, associated with DFW).
**Clinical Implications:** This study provides a comprehensive genetic framework for drought tolerance in dry beans. The identified SNPs and candidate genes can be used in marker-assisted selection to develop drought-tolerant varieties, which is critical for food security in drought-prone regions. The Andean gene pool showed greater progress in drought tolerance, suggesting breeding efforts should also target Middle-American germplasm. The admixed genotypes identified may serve as bridges for transferring favorable alleles. Validation in segregating populations is needed before these markers are deployed in breeding programs.