Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, USA.
Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, 27275, Torreon, Coahuila, Mexico.
Theor Appl Genet. 2024 May 14;137(6):130. doi: 10.1007/s00122-024-04635-8.
Genome-wide association study of color spaces across the four cultivated Capsicum spp. revealed a shared set of genes influencing fruit color, suggesting mechanisms and pathways across Capsicum species are conserved during the speciation. Notably, Cytochrome P450 of the carotenoid pathway, MYB transcription factor, and pentatricopeptide repeat-containing protein are the major genes responsible for fruit color variation across the Capsicum species. Peppers (Capsicum spp.) rank among the most widely consumed spices globally. Fruit color, serving as a determinant for use in food colorants and cosmeceuticals and an indicator of nutritional contents, significantly influences market quality and price. Cultivated Capsicum species display extensive phenotypic diversity, especially in fruit coloration. Our study leveraged the genetic variance within four Capsicum species (Capsicum baccatum, Capsicum chinense, Capsicum frutescens, and Capsicum annuum) to elucidate the genetic mechanisms driving color variation in peppers and related Solanaceae species. We analyzed color metrics and chromatic attributes (Red, Green, Blue, L*, a*, b*, Luminosity, Hue, and Chroma) on samples cultivated over six years (2015-2021). We resolved genomic regions associated with fruit color diversity through the sets of SNPs obtained from Genotyping by Sequencing (GBS) and genome-wide association study (GWAS) with a Multi-Locus Mixed Linear Model (MLMM). Significant SNPs with FDR correction were identified, within the Cytochrome P450, MYB-related genes, Pentatricopeptide repeat proteins, and ABC transporter family were the most common among the four species, indicating comparative evolution of fruit colors. We further validated the role of a pentatricopeptide repeat-containing protein (Chr01:31,205,460) and a cytochrome P450 enzyme (Chr08:45,351,919) via competitive allele-specific PCR (KASP) genotyping. Our findings advance the understanding of the genetic underpinnings of Capsicum fruit coloration, with developed KASP assays holding potential for applications in crop breeding and aligning with consumer preferences. This study provides a cornerstone for future research into exploiting Capsicum's diverse fruit color variation.
对四个栽培辣椒属植物的颜色空间进行全基因组关联研究，揭示了一套共同的影响果实颜色的基因，表明在物种形成过程中，辣椒属物种之间的机制和途径是保守的。值得注意的是，类胡萝卜素途径的细胞色素 P450、MYB 转录因子和五肽重复蛋白是导致辣椒属物种间果实颜色变异的主要基因。辣椒（Capsicum spp.）是全球消费最广泛的香料之一。果实颜色是作为食品着色剂和化妆品的决定因素，也是营养成分的指标，显著影响市场质量和价格。栽培的辣椒属植物表现出广泛的表型多样性，特别是在果实颜色方面。我们的研究利用四个辣椒属物种（Capsicum baccatum、Capsicum chinense、Capsicum frutescens 和 Capsicum annuum）的遗传变异来阐明驱动辣椒和相关茄科物种颜色变异的遗传机制。我们分析了在六年（2015-2021 年）种植的样本的颜色度量和色度属性（红、绿、蓝、L*、a*、b*、亮度、色调和色度）。我们通过从测序（GBS）和全基因组关联研究（GWAS）获得的 SNP 集，利用多基因混合线性模型（MLMM）解析与果实颜色多样性相关的基因组区域。通过 FDR 校正识别出具有显著 SNP 的基因，在 Cytochrome P450、MYB 相关基因、Pentatricopeptide repeat 蛋白和 ABC 转运家族中，在四个物种中最为常见，表明果实颜色的比较进化。我们进一步通过竞争性等位基因特异性 PCR（KASP）基因分型验证了一个五肽重复蛋白（Chr01:31,205,460）和一个细胞色素 P450 酶（Chr08:45,351,919）的作用。我们的研究结果提高了对辣椒果实着色遗传基础的理解，开发的 KASP 检测方法有可能应用于作物育种，并与消费者的偏好保持一致。这项研究为未来利用辣椒丰富的果实颜色变异提供了基础。
