This study seeks to enhance pepper fruit coloration by identifying valuable genetic resources through the analysis of single nucleotide polymorphism (SNP) markers and candidate genes related to fruit pigmentation.
Utilizing 197 natural populations of both hot and sweet peppers, researchers employed specific-locus amplified fragment sequencing (SLAF-seq) to examine 1,496 high-quality SNP markers, identifying significant loci contributing to fruit color variation. The genome-wide association study highlighted 30 significant SNP sites on chromosome 6. Further analysis using kompetitive allele-specific PCR (KASP) and phenotypic correlation with fruit color identified the gene CA.PGAv.1.6.scaffold919.44, which is implicated in anthocyanin synthesis regulation via the NAC domain, influencing pepper fruit coloration. These findings provide a valuable reference for developing molecular-assisted breeding strategies to improve the fruit color of both sweet and hot peppers. Specifically, for sweet peppers, the study aimed to identify SNP loci and candidate genes significantly associated with fruit color. A natural population of 197 sweet pepper accessions served as the material. SLAF-seq was conducted with 1,496 high-quality SNP markers to mine excellent variant loci and predict candidate genes. Through Manhattan plot analysis and association analysis with the best linear unbiased prediction (BLUP) values of fruit color, 30 significant loci were detected on chromosome 6. By combining KASP genotyping technology with field phenotypes, the gene CAPGAv.1.6.scaffold919.44 was identified as a candidate gene regulating mature fruit color, related to the NAC domain and hypothesized to alter fruit color by regulating anthocyanin biosynthesis.
This study lays the foundation for molecular-assisted breeding of sweet peppers related to fruit color.
Meng, Y., Li, X., Zhang, H., Yu, Z., Zhang, Z., Fan, Y., & Yan, L. (2025). Research on the mining of candidate genes for pepper fruit color and development of SNP markers based on SLAF-seq technology. Scientific Reports, 15(1), 1-10. https://doi.org/10.1038/s41598-025-95552-3
Source: Nature Magazine