Meng Yaning, Li Xinxin, Zhang Hongxiao, Yu Zhanghong, Zhang Zhe, Fan Yanqin, Yan Libin
Institute of Economic Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, China.
College of Horticultural Science & Technology, Hebei Normal University of Science & Technology, Qinhuangdao, China.
Sci Rep. 2025 Apr 3;15(1):11392. doi: 10.1038/s41598-025-95552-3.
This study aims to enhance the coloration of pepper fruit by identifying valuable genetic resources through the analysis of single nucleotide polymorphism (SNP). markers and candidate genes associated with fruit pigmentation. Utilizing 197 natural populations of both hot and sweet peppers, we employed specific-locus amplified fragment sequencing (SLAF-seq) to examine 1496 high-quality SNP markers, thereby identifying significant loci contributing to fruit color variation. Our genome-wide association study pinpointed 30 significant SNP sites located on chromosome 6. Further analysis using kompetitive allele-specific PCR(KASP) and phenotypic correlation with fruit color led to the identification of the CA.PGAv.1.6.scaffold919.44 gene, which is implicated in anthocyanin synthesisregulation via the NAC domain, thereby influencing pepper fruit coloration. These findings offer a valuable reference for the advancement of molecular-assisted breeding strategies aimed at improving the fruit color of both sweet and hot peppers.To improve the fruit color of sweet peppers, this study aimed to identify single nucleotide polymorphism (SNP) loci and candidate genes significantly associated with fruit color. A natural population of 197 sweet pepper accessions was used as the material. SLAF-seq was conducted with 1496 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. Combining KASP genotyping technology with field phenotypes, the gene CAPGAv.1.6.scaffold919.44 was identified as a candidate gene regulating mature fruit color. It is related to the NAC domain and is 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.
本研究旨在通过分析单核苷酸多态性（SNP）标记和与果实色素沉着相关的候选基因来鉴定有价值的遗传资源，从而增强辣椒果实的色泽。利用197个辣椒（包括辣椒和甜椒）自然群体，我们采用特定位点扩增片段测序（SLAF-seq）技术检测了1496个高质量SNP标记，从而确定了导致果实颜色变异的显著位点。我们的全基因组关联研究确定了位于6号染色体上的30个显著SNP位点。进一步使用竞争性等位基因特异性PCR（KASP）分析以及与果实颜色的表型相关性分析，鉴定出了CA.PGAv.1.6.scaffold919.44基因，该基因通过NAC结构域参与花青素合成调控，进而影响辣椒果实的色泽。这些发现为推进旨在改善甜椒和辣椒果实颜色的分子辅助育种策略提供了有价值的参考。为了改善甜椒果实颜色，本研究旨在鉴定与果实颜色显著相关的单核苷酸多态性（SNP）位点和候选基因。以197份甜椒种质的自然群体为材料。利用1496个高质量SNP标记进行SLAF-seq分析，挖掘优良变异位点并预测候选基因。通过曼哈顿图分析以及与果实颜色的最佳线性无偏预测（BLUP）值进行关联分析，在6号染色体上检测到30个显著位点。结合KASP基因分型技术和田间表型，鉴定出基因CAPGAv.1.6.scaffold919.44为调控成熟果实颜色的候选基因。它与NAC结构域相关，推测通过调控花青素生物合成来改变果实颜色。本研究为甜椒果实颜色相关的分子辅助育种奠定了基础。
