Data from: Insights into the genetic relationships and breeding patterns of the African tea germplasm based on nSSR markers and cpDNA sequences

Africa is one of the key centers of global tea production. Understanding the genetic diversity and relationships of cultivars of African tea is important for future targeted breeding efforts for new crop cultivars, specialty tea processing, and to guide germplasm conservation efforts. Despite the economic importance of tea in Africa, no research work has been done so far on its genetic diversity at a continental scale. Twenty-three nSSRs and three plastid DNA regions were used to investigate the genetic diversity, relationships, and breeding patterns of tea accessions collected from eight countries of Africa. A total of 280 African tea accessions generated 297 alleles with a mean of 12.91 alleles per locus and a genetic diversity (HS) estimate of 0.652. A STRUCTURE analysis suggested two main genetic groups of African tea accessions which corresponded well with the two tea types Camellia sinensis var. sinensis and C. sinensis var. assamica, respectively, as well as an admixed “mosaic” group whose individuals were defined as hybrids of F2 and BC generation with a high proportion of C. sinensis var. assamica being maternal parents. Accessions known to be C. sinensis var. assamica further separated into two groups representing the two major tea breeding centers corresponding to southern Africa (Tea Research Foundation of Central Africa, TRFCA), and East Africa (Tea Research Foundation of Kenya, TRFK). Tea accessions were shared among countries. African tea has relatively lower genetic diversity. C. sinensis var. assamica is the main tea type under cultivation and contributes more in tea breeding improvements in Africa. International germplasm exchange and movement among countries within Africa was confirmed. The clustering into two main breeding centers, TRFCA, and TRFK, suggested that some traits of C. sinensis var. assamica and their associated genes possibly underwent selection during geographic differentiation or local breeding preferences. This study represents the first step toward effective utilization of differently inherited molecular markers for exploring the breeding status of African tea. The findings here will be important for planning the exploration, utilization, and conservation of tea germplasm for future breeding efforts in Africa.

非洲是全球茶叶生产的核心产区之一。解析非洲茶树栽培品种的遗传多样性与亲缘关系，对于未来开展靶向性新品种选育、特色茶叶加工，以及指导种质资源保护工作均具有重要意义。尽管茶叶在非洲经济中占据重要地位，但目前尚无针对全大陆尺度的茶树遗传多样性研究。本研究采用23个核简单序列重复（nuclear Simple Sequence Repeats, nSSRs）标记与3个质体DNA区域，对采自非洲8个国家的茶树种质的遗传多样性、亲缘关系及育种模式展开分析。共计280份非洲茶树种质共扩增得到297个等位基因，每个位点平均等位基因数为12.91，遗传多样性（HS）估值为0.652。STRUCTURE群体结构分析结果显示，非洲茶树种质可划分为两个主要遗传类群，分别对应山茶属茶原变种（Camellia sinensis var. sinensis）与山茶属茶阿萨姆变种（C. sinensis var. assamica），同时存在一个混杂的“镶嵌”类群，其个体被鉴定为F2代与回交（BC）世代的杂交后代，且以阿萨姆变种作为主要母本来源。经鉴定为阿萨姆变种的种质进一步被划分为两个类群，分别对应两大主要茶叶育种中心：南部非洲（中非茶叶研究基金会，TRFCA）与东非（肯尼亚茶叶研究基金会，TRFK）。各国间存在茶树种质的共享现象。非洲茶树的遗传多样性相对偏低。阿萨姆变种是非洲当前主栽茶树类型，且在非洲茶叶育种改良中贡献更为突出。研究证实了国际间以及非洲内部各国间的茶树种质交流与流动。聚类结果显示阿萨姆变种种质可划分为TRFCA与TRFK两大育种中心类群，这表明阿萨姆变种的部分性状及其相关基因可能在地理分化或当地育种偏好的作用下经历了选择。本研究首次利用不同遗传模式的分子标记探究非洲茶树的育种现状，为后续研究迈出了关键一步。本研究结果对于规划非洲未来茶树育种工作中的种质资源勘探、利用与保护具有重要指导意义。