Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), 84098 Pontecagnano Faiano, Italy;
Genome Diversity, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland, Germany.
Proc Natl Acad Sci U S A. 2021 Aug 24;118(34). doi: 10.1073/pnas.2104315118.
Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding. Genetic characterization of such collections has the potential to elucidate the genetic histories of important crops, use marker-trait associations to identify loci controlling traits of interest, search for loci undergoing selection, and contribute to genebank management by identifying taxonomic misassignments and duplicates. We conducted a genomic scan with genotyping by sequencing (GBS) derived single nucleotide polymorphisms (SNPs) of 10,038 pepper ( spp.) accessions from worldwide genebanks and investigated the recent history of this iconic staple. Genomic data detected up to 1,618 duplicate accessions within and between genebanks and showed that taxonomic ambiguity and misclassification often involve interspecific hybrids that are difficult to classify morphologically. We deeply interrogated the genetic diversity of the commonly consumed to investigate its history, finding that the kinds of peppers collected in broad regions across the globe overlap considerably. The method using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions-was developed to supplement traditional population genetic analyses. The results reflect a vision of pepper as a highly desirable and tradable cultural commodity, spreading rapidly throughout the globe along major maritime and terrestrial trade routes. Marker associations and possible selective sweeps affecting traits such as pungency were observed, and these traits were shown to be distributed nonuniformly across the globe, suggesting that human preferences exerted a primary influence over domesticated pepper genetic structure.
基因库收集和保存了大量的植物和详细的护照信息，旨在为保护和繁殖保存遗传多样性。对这些收藏的遗传特征分析有可能阐明重要作物的遗传历史，利用标记-性状关联来识别控制感兴趣性状的基因座，寻找正在经历选择的基因座，并通过识别分类学上的错误分配和重复来为基因库管理做出贡献。我们对来自世界各地基因库的 10038 个辣椒（ spp.）样本进行了基于测序（GBS）的基因型单核苷酸多态性（SNP）的基因组扫描，并研究了这一标志性作物的近期历史。基因组数据在基因库内和基因库之间检测到多达 1618 个重复样本，表明分类学上的模糊性和错误分类通常涉及到难以进行形态分类的种间杂种。我们深入研究了普遍食用的 的遗传多样性，以了解其历史，发现全球广泛地区收集的辣椒种类重叠相当大。利用遗传数据来量化焦点地区和其他地区辣椒之间相似性的方法是为了补充传统的群体遗传分析而开发的。结果反映了辣椒作为一种非常受欢迎和可交易的文化商品的形象，沿着主要的海上和陆地贸易路线迅速在全球传播。观察到了与辣度等性状相关的标记关联和可能的选择压力，这些性状在全球的分布不均匀，表明人类的偏好对驯化辣椒的遗传结构产生了主要影响。
