Southwest Landscape Architecture Engineering Research Center of State Forestry and Grassland Administration, College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China.
Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650225, China.
Int J Mol Sci. 2024 Mar 13;25(6):3241. doi: 10.3390/ijms25063241.
The market value of tea is largely dependent on the tea species and cultivar. Therefore, it is important to develop efficient molecular markers covering the entire tea genome that can be used for the identification of tea varieties, marker-assisted breeding, and mapping important quantitative trait loci for beneficial traits. In this study, genome-wide molecular markers based on intron length polymorphism (ILP) were developed for tea trees. A total of 479, 1393, and 1342 tea ILP markers were identified using the PCR method in silico from the 'Shuchazao' scaffold genome, the chromosome-level genome of 'Longjing 43', and the ancient tea DASZ chromosome-level genome, respectively. A total of 230 tea ILP markers were used to amplify six tea tree species. Among these, 213 pairs of primers successfully characterize products in all six species, with 112 primer pairs exhibiting polymorphism. The polymorphism rate of primer pairs increased with the improvement in reference genome assembly quality level. The cross-species transferability analysis of 35 primer pairs of tea ILP markers showed an average amplification rate of 85.17% through 11 species in 6 families, with high transferability in and tobacco. We also used 40 pairs of tea ILP primers to evaluate the genetic diversity and population structure of with 176 plants from Puan County, Guizhou Province, China. These genome-wide markers will be a valuable resource for genetic diversity analysis, marker-assisted breeding, and variety identification in tea, providing important information for the tea industry.
茶叶的市场价值在很大程度上取决于茶树品种和栽培品种。因此，开发覆盖整个茶树基因组的高效分子标记，用于鉴定茶树品种、辅助标记选择育种以及定位对有益性状的重要数量性状基因座，是非常重要的。本研究利用内含子长度多态性（ILP）开发了茶树的全基因组分子标记。利用 PCR 方法，分别从“树茶”支架基因组、“龙井 43”染色体水平基因组和古老茶树 DASZ 染色体水平基因组中，在计算机上鉴定出 479、1393 和 1342 个茶树 ILP 标记。总共使用了 230 个茶树 ILP 标记来扩增 6 个茶树物种。其中，213 对引物在所有 6 个物种中成功扩增出产物，112 对引物表现出多态性。随着参考基因组组装质量水平的提高，引物多态性率也随之增加。35 对茶树 ILP 标记的种间转移能力分析表明，在 6 个科的 11 个种中，平均扩增率为 85.17%，在 和烟草中具有较高的转移能力。我们还使用 40 对茶树 ILP 引物评估了来自中国贵州省普安县的 176 株茶树的遗传多样性和群体结构。这些全基因组标记将成为茶树遗传多样性分析、辅助标记选择育种和品种鉴定的宝贵资源，为茶产业提供重要信息。
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