Journal of Integrative Agriculture

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基于全基因组SNP和儿茶素构建陕西省茶树核心种质

  

  • 修回日期:2025-03-27

Core germplasm construction of tea plant populations based on genome-wide SNP and catechins in Shaanxi Province, China

Xinyu Wang1*, Xiufeng Li2*, Dan Chen1*, Jingwen Gao1, Shuangqian Hao1, He Zhang1, Ziyan Zhao1, Mengwei Shen1, Huirui Chen1, Fuqiang Qi1, Keyi Zhang1, Haozhe Zhou1, Yanjun Xi2, Jie Zhou1, Youben Yu1# , Qingshan Xu1#   

  1. 1 College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China

    2 Hanzhong Agricultural Technology Extension and Training Center, Hanzhong, Shaanxi 723000, China

  • Revised:2025-03-27
  • About author: #Qingshan Xu, E-mail: xuqingshan@nwsuaf.edu.cn; Youben Yu, E-mail: yyben@163.com *These authors contributed equally to this study.
  • Supported by:

    This work was supported by the National Natural Science Foundation of China (32472795), the Natural Science Basic Research Program of Shaanxi (2024JC-YBMS-145), the China Agriculture Research System of MOF and MARA (CARS-19), the Agricultural Special Fund Project of Shaanxi Province (2024NYGG009), the Natural Science Basic Research Program of Shaanxi (2021JQ-162), and Chinese Universities Scientific Fund (2452023481) to Q.X. 

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摘要：

遗传多样性在遗传研究和育种中起着关键作用，而核心种质是获取遗传多样性的重要资源。目前，茶树核心种质的构建主要基于表型数据或分子标记；然而，有效构建植物育种计划的核心种质需要综合考虑多个因素。本研究收集了320份茶树种质资源，分析了其单核苷酸多态性（SNP）和代谢物数据。基于2,118,060个高质量SNP标记，分析结果表明陕西省茶树种质资源具有丰富的遗传多样性，表现为较高的观察杂合度（Ho=0.340）、期望杂合度（He=0.327）、次要等位基因频率（MAF=0.229）和多态信息含量（PIC=0.268）。此外，较高的遗传多样性指数（H'=1.902）表明代谢变异显著。系统发育分析将320份茶树种质资源分为6个聚类分支，反映了地理因素对茶树遗传多样性的影响。在遗传和代谢数据的基础上，我们开发了一个包含106份材料的核心集合，旨在有效地代表原始种质资源的基因、代谢、种群和区域多样性。核心集合的全基因组关联分析成功地验证了在原始集合中发现的标记-性状关联。本研究为茶树种质资源的保护与管理提供了理论依据。

Abstract:

Genetic diversity is crucial for genetic research and breeding, and the core collections are important resources for capturing this diversity. Recently, the core germplasm of tea plants was constructed mainly based on phenotypic data or molecular markers; however, the effective construction of a core germplasm resource for plant breeding programs requires the consideration of various aspects. In this study, we collected 320 tea germplasm resources and analyzed their single-nucleotide polymorphisms (SNPs) and metabolite data. Abundant genetic diversity in tea plants was inferred from the mean values of observed heterozygosity (Ho=0.340), expected heterozygosity (He=0.327), minor allele frequency (MAF=0.229), and polymorphic information content (PIC=0.268), based on the data from 2,118,060 high-quality SNP markers. A mean genetic diversity index (H') value of 1.902 suggested significant metabolic variation. The 320 tea samples were categorized into six groups based on phylogenetic analysis, reflecting the influence of geographical factors on genetic diversity. Based on the genetic and metabolic data, a preliminary core collection of 106 accessions was developed to effectively represent the majority of the molecular, metabolic, population, and regional diversity present in the original panel. Genome-wide association studies of the core panel successfully replicated the marker-trait associations found in the original panel. This study contributes to the conservation and management of tea plant germplasm.

Key words: tea plant , core collection ,  genetic diversity ,  SNPs ,  catechin index