Genome-wide association study of tea plant based on SLAF-seq revealed SNP variations regulating timing of bud flush

IF 1.6 Q3 GENETICS & HEREDITY

Plant Gene Pub Date : 2025-04-03 DOI:10.1016/j.plgene.2025.100511

Xiaozeng Mi , Dahe Qiao , Yanlin An , Chun Yang , Kaiqin Lin , Congling Peng , Juan Chen

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引用次数: 0

Abstract

As one of the most important agronomic traits of the tea plant (Camellia sinensis), the timing of bud flush (TBF) affects the sales price of tea beverages. Here, we performed specific-locus amplified fragment (SLAF) sequencing and genome-wide association study (GWAS) analysis on 200 offspring of natural hybridization from the ‘Qianmei 601’. A total of 796,294 SLAF tags and 2,324,211 single-nucleotide polymorphisms (SNPs) were obtained by sequencing. The 200 tea germplasms were clustered into four groups by population structure, principal component analysis (PCA) and phylogenetic tree analysis. GWAS identified twelve SNPs loci that were significantly associated with TBF traits. Seven candidate genes associated with TBF were subsequently identified by scanning in the regions within 1 Mb SNP loci. In addition, we found that two candidate genes (ARP and WRKY) were highly expressed in individuals with early TBF. Interestingly, cloning and sequencing of the ARP gene revealed C-G variants between the early and late TBF individuals. Our results provide a theoretical basis for early TBF breeding and functional gene analysis in tea plants.

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基于slf -seq的茶树全基因组关联研究揭示了调节花蕾绽放时间的SNP变异

作为茶树（Camellia sinensis）最重要的农艺性状之一，花蕾开花时间（TBF）影响着茶饮料的销售价格。本研究对“前美601”自然杂交的200个后代进行了SLAF测序和全基因组关联分析（GWAS）。测序共获得796,294个SLAF标签和2,324,211个单核苷酸多态性（snp）。通过群体结构分析、主成分分析和系统发育树分析，将200份茶叶种质资源聚为4个类群。GWAS鉴定出12个与TBF性状显著相关的snp位点。随后，通过扫描1个 Mb SNP位点内的区域，确定了7个与TBF相关的候选基因。此外，我们发现两个候选基因（ARP和WRKY）在早期TBF个体中高表达。有趣的是，ARP基因的克隆和测序显示，早期和晚期TBF个体之间存在C-G变异。研究结果为茶树TBF的早期选育和功能基因分析提供了理论依据。

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来源期刊

Plant Gene Agricultural and Biological Sciences-Plant Science

CiteScore

4.50

自引率

0.00%

发文量

审稿时长

51 days

期刊介绍： Plant Gene publishes papers that focus on the regulation, expression, function and evolution of genes in plants, algae and other photosynthesizing organisms (e.g., cyanobacteria), and plant-associated microorganisms. Plant Gene strives to be a diverse plant journal and topics in multiple fields will be considered for publication. Although not limited to the following, some general topics include: Gene discovery and characterization, Gene regulation in response to environmental stress (e.g., salinity, drought, etc.), Genetic effects of transposable elements, Genetic control of secondary metabolic pathways and metabolic enzymes. Herbal Medicine - regulation and medicinal properties of plant products, Plant hormonal signaling, Plant evolutionary genetics, molecular evolution, population genetics, and phylogenetics, Profiling of plant gene expression and genetic variation, Plant-microbe interactions (e.g., influence of endophytes on gene expression; horizontal gene transfer studies; etc.), Agricultural genetics - biotechnology and crop improvement.