Integrated Genome-Wide Association and QTL Mapping Elucidate the Genetic Basis of Fruit Yield and Quality Traits in Pepper under Water Stress

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ID: 322988
2026
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Abstract
Water deficit is a major constraint on pepper (Capsicum annuum) yield, yet the genetic architecture of reproductive-stage drought tolerance remains poorly resolved. We phenotyped a Balkan C. annuum diversity panel (n = 133) and an interspecific backcross inbred line (BIL) population (n = 76) under well-watered (WW) and water-stress (WS) conditions. WS was applied from anthesis of the second truss as a stepwise reduction in irrigation volume relative to WW (30% for 7 days, then 60% thereafter), maintained for 90 days across the reproductive period. We assessed yield components, soluble solids, and stress-tolerance (STI) and stress-susceptibility (SSI) indices. Genome-wide association study (GWAS) identified 104 SNP-trait associations (P < 1×10-5), and QTL mapping detected 38 significant QTLs (1,000 permutations, α = 0.01), with the QTL intervals defined at LOD ≥ 8. Integrating GWAS and QTL mapping under WS revealed overlapping loci on chromosomes 5 and 6, harboring two consensus intergenic SNPs associated with yield components and soluble solids. Haplotype analysis linked chromosome 5 alleles to higher fruit number and soluble solids. At chromosome 6, the G allele at SNP 6_28348737 was enriched in tolerant lines for fruit number. These regions harbor candidate genes for reproductive development and stress response, including GREEN RIPE-LIKE1 (GRL1), CYP77A19, Endoglucanase-like, and FLOWERING PROMOTING FACTOR 1 (FPF1), possibly through cis-regulatory variation. Together, these results advance understanding of the genetic basis of pepper yield under drought and identify candidate breeding markers.
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Authors Avanish Rai, Emil Vatov, Alicja Wieteska Georgieva, Stefka Bogdanova, Michael F. Wittenberg, Nikolay Anachkov, Pasquale Tripodi, Velichka Todorova, İvanka Trıngovska, Daniela Ganeva, Veselin Petrov, Tsanko Gechev, Saleh Alseekh
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Journal Journal of experimental botany
Year 2026
DOI
10.1093/jxb/erag385
URL
https://doi.org/10.1093/jxb/erag385
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