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，对于未来开展定向培育新品种、特色茶加工研发，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，但目前尚无针对全非洲尺度的茶树遗传多样性研究。本研究采用23对核简单序列重复（nuclear Simple Sequence Repeats, nSSRs）标记与3个质体DNA（plastid DNA）区域，对采集自非洲8个国家的280份茶种质资源的遗传多样性、亲缘关系及育种模式进行了分析。共计280份非洲茶种质资源共扩增得到297个等位基因，平均每个位点含12.91个等位基因，遗传多样性（HS）均值为0.652。STRUCTURE群体结构分析表明，非洲茶种质资源可分为两个核心遗传类群，分别对应茶（Camellia sinensis）的两个变种——茶原变种（Camellia sinensis var. sinensis）与阿萨姆茶变种（Camellia sinensis var. assamica），同时存在一个混杂的“镶嵌”类群，该类群个体均为F2代及回交（BC）世代的杂种，且以阿萨姆茶变种作为主要母本来源。已知为阿萨姆茶变种的种质资源进一步被划分为两个类群，分别对应非洲两大主要茶叶育种中心：南部非洲的中非茶叶研究基金会（Tea Research Foundation of Central Africa, TRFCA）与东非的肯尼亚茶叶研究基金会（Tea Research Foundation of Kenya, TRFK）。茶种质资源在非洲各国间存在共享现象。非洲茶树整体遗传多样性水平相对偏低。阿萨姆茶变种是非洲当前主要栽培的茶树类型，且在非洲茶树育种改良中发挥了更为核心的作用。研究证实非洲各国间存在国际种质资源交流与种质迁移现象。阿萨姆茶变种的种质资源聚类为TRFCA与TRFK两大育种中心，这一结果暗示阿萨姆茶变种的部分性状及其关联基因可能在地理分化或当地育种偏好的作用下经历了定向选择。本研究首次利用不同遗传来源的分子标记开展非洲茶树育种现状的探究，为后续相关研究奠定了基础。本研究结果可为未来非洲茶树育种工作中茶种质资源的勘探、利用与保护规划提供重要参考。