The Key Laboratory of Plant Resources Conservation and Germplasm Innovationin Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering / College of Tea Science, Guizhou University, Guiyang, 550025, Guizhou Province, People's Republic of China.
Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Molecular and Environmental Plant Sciences Program, MS2133 Texas A&M University, College Station, TX, 77843-2133, USA.
BMC Plant Biol. 2019 Jul 23;19(1):328. doi: 10.1186/s12870-019-1917-5.
To efficiently protect and exploit germplasm resources for marker development and breeding purposes, we must accurately depict the features of the tea populations. This study focuses on the Camellia sinensis (C. sinensis) population and aims to (i) identify single nucleotide polymorphisms (SNPs) on the genome level, (ii) investigate the genetic diversity and population structure, and (iii) characterize the linkage disequilibrium (LD) pattern to facilitate next genome-wide association mapping and marker-assisted selection.
We collected 415 tea accessions from the Origin Center and analyzed the genetic diversity, population structure and LD pattern using the genotyping-by-sequencing (GBS) approach. A total of 79,016 high-quality SNPs were identified; the polymorphism information content (PIC) and genetic diversity (GD) based on these SNPs showed a higher level of genetic diversity in cultivated type than in wild type. The 415 accessions were clustered into three groups by STRUCTURE software and confirmed using principal component analyses (PCA)-wild type, cultivated type, and admixed wild type. However, unweighted pair group method with arithmetic mean (UPGMA) trees indicated the accessions should be grouped into more clusters. Further analyses identified four groups, the Pure Wild Type, Admixed Wild Type, ancient landraces and modern landraces using STRUCTURE, and the results were confirmed by PCA and UPGMA tree method. A higher level of genetic diversity was detected in ancient landraces and Admixed Wild Type than that in the Pure Wild Type and modern landraces. The highest differentiation was between the Pure Wild Type and modern landraces. A relatively fast LD decay with a short range (kb) was observed, and the LD decays of four inferred populations were different.
This study is, to our knowledge, the first population genetic analysis of tea germplasm from the Origin Center, Guizhou Plateau, using GBS. The LD pattern, population structure and genetic differentiation of the tea population revealed by our study will benefit further genetic studies, germplasm protection, and breeding.
为了高效地保护和利用种质资源进行标记开发和育种，我们必须准确描述茶树群体的特征。本研究聚焦于茶树（C. sinensis）群体，旨在：(i) 在基因组水平上鉴定单核苷酸多态性（SNP）；(ii) 研究遗传多样性和群体结构；(iii) 描述连锁不平衡（LD）模式，以促进全基因组关联作图和标记辅助选择。
我们从起源中心收集了 415 份茶树样本，采用基因分型测序（GBS）方法分析遗传多样性、群体结构和 LD 模式。共鉴定出 79,016 个高质量 SNP；基于这些 SNP 的多态性信息含量（PIC）和遗传多样性（GD）显示，栽培型的遗传多样性水平高于野生型。STRUCTURE 软件将 415 份样本聚类为三组，并通过主成分分析（PCA）-野生型、栽培型和混生野生型进一步确认。然而，非加权对组平均法（UPGMA）树表明，样本应该分为更多的聚类。进一步的分析使用 STRUCTURE 鉴定出四个群体，分别为纯野生型、混生野生型、古老地方品种和现代地方品种，结果通过 PCA 和 UPGMA 树法得到了确认。古老地方品种和混生野生型的遗传多样性水平高于纯野生型和现代地方品种。纯野生型和现代地方品种之间的遗传分化最高。观察到 LD 快速衰减，范围较短（kb），且四个推断群体的 LD 衰减情况不同。
本研究是首次利用 GBS 对贵州高原起源中心茶树种质资源进行群体遗传分析。本研究揭示的茶树群体 LD 模式、群体结构和遗传分化将有助于进一步的遗传研究、种质保护和育种。
