Association mapping integrated with image-based phenomics identifies SNPs and candidate genes underpinning fruit morphology and development in chile pepper ( <i>Capsicum annum</i> L.)

Fruit morphology has a significant impact on the agronomic performance of chile peppers, influencing both yield potential and mechanical harvest efficiency. Through the integration of genome-wide association studies (GWAS) with Tomato Analyzer, an image-based phenomics tool, we aim to identify single-nucleotide polymorphism (SNP) markers associated with fruit architecture and morphology. A Capsicum association mapping panel (CAMP) consisting of 129 genotypes was evaluated under an augmented field design for the 2024 growing season. Best linear unbiased predictions (BLUPs) were reported for maximum fruit height (MAXH), maximum fruit width (MAXW), curved fruit height (CURH), width mid-height (WMH), height mid-width (HMW), area (ARA), perimeter (PER), ten pod weight (PODW), and yield (YLD). Medium to low narrow-sense heritability (h2), ranging between 0.18 and 0.33, was observed. A medium to high Pearson correlation (r=0.23-1.00) was observed for all traits except WHM. After filtration and imputation, 40,709 genotyping-by-sequencing (GBS) SNP markers were used to perform multi-locus GWAS. A total of 169 SNP markers associated with seven basic fruit measurements across 12 chromosomes were identified. A SNP marker, SCM002812.1_10016804 on chromosome 1, identified across multiple GWAS models was found to be associated with the potential candidate gene, YABBY4, which can regulate fruit development. Other candidate genes identified included FRIGIDA-like protein 3, COBRA-like protein, and Auxin-responsive protein SAUR65 regulating fruit, flower, and shoot development. The findings of this study will be relevant for the development of molecular markers for marker-assisted selection, genomic selection for basic fruit morphology traits, and studying expression levels of genes regulating fruit development in chile peppers.