Nuclear microsatellites reveal the genetic architecture and breeding history of tea germplasm of East Africa

Tea is the most popular non-alcoholic beverage worldwide and is one of the most important tree cash crops in East Africa. However, no comprehensive study has been carried out on the genetic structure and diversity of tea germplasm for this region to date. In the present study, 193 tea accessions held at the ex situ Germplasm Bank of the Tea Research Institute (TRI), Kenya, were analysed using genetic data from 23 polymorphic simple sequence repeat (SSR) loci. A total of 266 alleles were detected with the number of alleles per locus ranging from 4 to 19 with an average of 7.88. Genetic clustering by STRUCTURE was used to correct misidentified accessions based on morphological characters. After reassignment of the tea accessions, Camellia assamica exhibited the lowest genetic diversity (Hs = 0.648) despite being the most widely cultivated tea type in the East African region. C. assamica subsp. lasiocalyx showed the highest genetic diversity (Hs = 0.76), which supported its origin by hybridization among tea types. Tea cultivars cultivated across the region exhibited lower genetic diversity (Hs = 0.661) compared to material held at the ex situ Germplasm Bank of TRI. Tea accessions clustered in the neighbour-joining tree on the basis of geographical origin, pedigree and leaf pigmentation, indicating their common origin. Our results indicated further that East African tea germplasm has a complex breeding history with a majority of the hybrids being F2 generation and backcross plants. C. assamica contributed significantly more genetic materials in the tea breeding programmes in East Africa. This study highlights the importance of ex situ germplasm banks to conserve the highest genetic diversity, which is an important resource for future tea crop improvements in East Africa.

茶叶是全球最受欢迎的非酒精饮品，同时也是东非地区最重要的木本经济作物之一。然而迄今为止，针对该地区茶种质资源的遗传结构与多样性尚未开展过全面研究。本研究针对肯尼亚茶叶研究所（Tea Research Institute, TRI）迁地种质库保存的193份茶种质材料，利用23个多态性简单序列重复（Simple Sequence Repeat, SSR）位点的遗传数据进行了分析。本次检测共得到266个等位基因，每个位点的等位基因数量介于4至19之间，平均值为7.88。研究采用STRUCTURE软件进行遗传聚类，以校正基于形态性状鉴定错误的种质材料。完成茶种质材料的重新归类后，尽管阿萨姆茶（Camellia assamica）是东非地区种植最广泛的茶类类型，但其遗传多样性最低（Hs = 0.648）。阿萨姆茶毛萼亚种（C. assamica subsp. lasiocalyx）的遗传多样性最高（Hs = 0.76），这一结果支持其起源于不同茶类类型间的杂交。该地区广泛种植的茶树品种的遗传多样性（Hs = 0.661）低于肯尼亚茶叶研究所迁地种质库保存的材料。基于地理起源、系谱关系以及叶片色素表型，茶种质材料在邻接树（neighbour-joining tree）中形成聚类，表明其具有共同的起源。本研究结果进一步显示，东非茶种质资源具有复杂的育种历史，多数杂交品种为F2代及回交植株。阿萨姆茶（Camellia assamica）在东非茶树育种项目中贡献了更多的遗传物质。本研究凸显了迁地种质库在保存最高水平遗传多样性方面的重要价值，而这些遗传资源是未来东非茶树品种改良的重要基础。