Tropical Research and Education Center, Horticultural Sciences Department, University of Florida, 18905 SW 280th St, Homestead, FL, 33033, USA.
Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), CINVESTAV, Km 9.6 Carretera Irapuato-León, Guanajuato, CP 36824, Mexico.
Plant Sci. 2021 Oct;311:111019. doi: 10.1016/j.plantsci.2021.111019. Epub 2021 Aug 13.
Genomics-based diversity analysis of natural vanilla populations is important in order to guide conservation efforts and genetic improvement through plant breeding. Vanilla is a cultivated, undomesticated spice that originated in Mesoamerica prior to spreading globally through vegetative cuttings. Vanilla extract from the commercial species, mainly V. planifolia and V. × tahitensis, is used around the world as an ingredient in foods, beverages, cosmetics, and pharmaceuticals. The global reliance on descendants of a few foundational clones in commercial production has resulted in an industry at heightened risk of catastrophic failure due to extremely narrow genetic diversity. Conversely, national and institutional collections including those near the center of cultivation contain previously undiscovered diversity that could bolster the genetic improvement of vanilla and guide conservation efforts. Towards this goal, an international vanilla genotyping effort generated and analyzed 431,204 single nucleotide polymorphisms among 412 accessions and 27 species from eight collections. Phylogenetic and STRUCTURE analysis sorted vanilla by species and identified hybrid accessions. Principal Component Analysis and the Fixation Index (FST) were used to refine relationships among accessions and showed differentiation among species. Analysis of the commercial species split V. planifolia into three types with all V. × tahitensis accessions being most similar to V. planifolia type 2. Finally, an in-depth analysis of V. × tahitensis identified seven V. planifolia and six V. odorata accessions as most similar to the estimated parental genotypes providing additional data in support of the current hybrid theory. The prevalence of probable V. × tahitensis parental accessions from Belize suggests that V. × tahitensis could have originated from this area and highlights the need for vanilla conservation throughout Central and South America. The genetic groupings among accessions, particularly for V. planifolia, can now be used to focus breeding efforts on fewer accessions that capture the greatest diversity.
基于基因组的天然香草群体多样性分析对于指导保护工作和通过植物育种进行遗传改良非常重要。香草是一种栽培的、未经驯化的香料，起源于中美洲，通过营养繁殖在全球范围内传播。商业品种（主要是 V. planifolia 和 V. × tahitensis）的香草提取物在世界各地被用作食品、饮料、化妆品和制药的成分。全球对商业生产中少数基础克隆后代的依赖，导致该行业由于遗传多样性极其狭窄而面临灾难性失败的高风险。相反，包括靠近种植中心的国家和机构收藏在内的收藏，包含了以前未被发现的多样性，这可以增强香草的遗传改良，并指导保护工作。为此，一项国际香草基因分型工作生成并分析了来自八个收藏的 27 个物种的 412 个样本中的 431,204 个单核苷酸多态性。系统发育和 STRUCTURE 分析根据物种对香草进行了分类，并鉴定了杂交样本。主成分分析和固定指数（FST）用于细化样本之间的关系，并显示了物种之间的分化。对商业品种的分析将 V. planifolia 分为三种类型，所有 V. × tahitensis 样本与 V. planifolia 类型 2 最为相似。最后，对 V. × tahitensis 的深入分析确定了七个 V. planifolia 和六个 V. odorata 样本与估计的亲本基因型最为相似，为支持当前的杂交理论提供了更多数据。伯利兹存在大量可能的 V. × tahitensis 亲本样本，这表明 V. × tahitensis 可能起源于该地区，突显了在中美洲和南美洲各地保护香草的必要性。样本之间的遗传分组，特别是对 V. planifolia 的分组，现在可以用于集中精力在少数样本上，这些样本可以捕捉到最大的多样性。
