VCF and Metadata for Capsicum annuum XP-GWAS on β-Carotene

Carotenoids are essential plant pigments with critical roles in stress adaptation and human nutrition. β-Carotene, a major provitamin A carotenoid, is an important nutritional target in Capsicum annuum; however, its accumulation is a complex quantitative trait shaped by multiple metabolic and regulatory pathways. To explore the genetic basis underlying natural variation in β-carotene content, an extreme-phenotype genome-wide association approach was applied using accessions representing contrasting carotenoid levels. A total of 91 single nucleotide polymorphisms (SNPs) showed significant allele frequency differentiation between high- and low–β-carotene groups (FDR < 0.05), with a subset located on assembled chromosomes and the remainder on unanchored scaffolds. The strongest and most consistent association signal was detected at the 4-hydroxyphenylpyruvate dioxygenase (HPPD) locus on chromosome 5, where multiple significant SNPs clustered within the gene region. HPPD is known to contribute to plastoquinone biosynthesis, a pathway that indirectly supports carotenoid desaturation, suggesting a plausible biological link to β-carotene accumulation. Additional associated loci were identified near genes related to sulfur metabolism, ribosomal function, cellular signaling, and non-coding RNAs, although these signals should be considered exploratory. Overall, this study prioritizes HPPD and several additional genomic regions as candidate loci associated with β-carotene variation in C. annuum. Given the pooled design and the prevalence of signals on unanchored scaffolds, the identified associations are hypothesis-generating and require independent validation before functional interpretation or application in breeding programs.