Extreme-Phenotype Genome-Wide Association Study (XP-GWAS) of Beta-Carotene Content in Capsicum annuum Using Genotyping-by-Sequencing

This project investigates the genetic basis of beta-carotene variation in Capsicum annuum using a genotyping-by-sequencing (GBS)-based extreme-phenotype genome-wide association study (XP-GWAS). Ninety-two accessions were phenotypically evaluated and classified into high and low beta-carotene groups (46 accessions per group). Genomic DNA extracted from leaf tissue was pooled within each phenotype group and sequenced in 2023 using the Illumina NovaSeq 6000 platform (paired-end, 151 bp). Sequence reads were mapped to the Capsicum annuum reference genome (GCF_002878395.1), and variants were called using GATK. After quality filtering, 1,025,269 SNPs were retained for association analysis. The study identified significant genomic regions associated with carotenoid accumulation, providing insights for pepper breeding and nutritional improvement.