ASHS 2025 Conference

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 128 genotypes with three checks evaluated in Las Cruces, NM under an augmented design for the 2024 growing season. The design consisted of ten blocks, each with a different number of test genotypes whereas checks were replicated in each block. Ten green and ten red fruits (N=20) for each genotype were scanned using a flatbed scanner and images were processed using Tomato Analyzer software to record fruit architecture. Best linear unbiased predictions (BLUPs) were calculated for maximum fruit height (MAXH; cm), maximum fruit width (MAXW; cm), curved fruit height (CURH; cm), width mid-height (WMH; cm), area (ARA; cm2), and perimeter (PER; cm). High narrow sense heritability (h2) ranging between 0.80 and 0.98 was observed. A medium to high Pearson correlation (r=0.56–1.00) 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 129 SNP markers associated with seven basic fruit measurements across 10 chromosomes were identified. The SNP marker SCM002812.1_10016804 on chromosome 1 at 10.02 Mb was found to be associated with the potential candidate gene YABBY4, which can regulate fruit developmental processes. Other candidate genes identified included Gibberellin receptor GID1B, Cyclin-L1-1, and U6 small nuclear RNA (adenine-(43)-N(6))-methyltransferase), regulating plant growth hormones, cell division, and methylation, respectively. The findings of this study will be relevant for the development of molecular markers for marker-assisted selection and studying expression levels of genes regulating fruit development in a comparative analysis using chile pepper genotypes with contrasting fruit morphology.