基于全基因组重测序的白化茶树mSNP标记开发及验证

刘浩然; 张晨禹; 龚洋; 叶圆圆; 陈杰丹; 陈亮; 刘丁丁; 马春雷

doi:10.13305/j.cnki.jts.2023.01.003

茶叶科学 >

2023 , Vol. 43 >Issue 1: 27 - 39

DOI: https://doi.org/10.13305/j.cnki.jts.2023.01.003

研究报告

基于全基因组重测序的白化茶树mSNP标记开发及验证

刘浩然 ,
张晨禹 ,
龚洋 ,
叶圆圆 ,
陈杰丹 ,
陈亮 ,
刘丁丁 ,
马春雷

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1.中国农业科学院茶叶研究所/农业农村部特种经济动植物生物学与遗传育种重点实验室,浙江杭州 310008;
2.中国农业科学院研究生院,北京 100081

刘浩然,男,硕士研究生,主要从事茶树资源育种与遗传改良研究。

收稿日期: 2022-10-12

修回日期: 2022-11-24

网络出版日期: 2023-03-01

基金资助

国家重点研发计划课题（2021YFD1200203）、浙江省农业（茶树）新品种选育重大科技专项子课题（2021C02067-6-1）、中国农业科学院茶叶研究所基本科研业务费（1610212022009）、浙江省自然科学基金（LQ20C160010）

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Development and Application of Albinotea Plant mSNP Molecular Markers Based on Genome-wide Resequencing

LIU Haoran ,
ZHANG Chenyu ,
GONG Yang ,
YE Yuanyuan ,
CHEN Jiedan ,
CHEN Liang ,
LIU Dingding ,
MA Chunlei

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1. Tea Research Institute of the Chinese Academy of Agricultural Science/Key Laboratory of Biology, Genetics and Breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, P. R. China, Hangzhou 310008, China;
2. Graduate School of Chinese Academy of Agriculture Science, Beijing 100081, China

Received date: 2022-10-12

Revised date: 2022-11-24

Online published: 2023-03-01

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摘要

为探究白化茶树遗传变异信息及mSNP液相芯片在茶树种质资源鉴定中的可行性,利用全基因组重测序对18份白化茶树资源进行遗传多样性分析和突变位点检测。结果表明,基于全基因组水平的SNP标记可将18份白化茶树资源分为3类,且基本呈现出具有亲缘关系或地理位置接近的资源聚在一起的趋势;对重测序数据进行功能注释后发现,在18份白化茶树资源中存在17 056个共有非同义突变基因,其中14个叶绿素合成相关基因中存在98个错义突变位点。随后,基于前期获得的基因组变异信息开发了一套包含59个mSNP、222个SNP位点的液相芯片,利用该液相芯片检测13份茶树资源的基因型信息。结果表明,同一品种两两之间的遗传相似度在92%~98%,不同品种间的遗传相似度则在84%以下,表明该芯片可对18份白化茶树资源进行准确鉴别,研究结果可为mSNP液相芯片在茶树种质资源鉴定、分子标记辅助育种等方面的应用奠定基础。

关键词： 茶树; mSNP分子标记; 靶向测序基因型检测; 遗传多样性; 全基因组重测序

本文引用格式

刘浩然 , 张晨禹 , 龚洋 , 叶圆圆 , 陈杰丹 , 陈亮 , 刘丁丁 , 马春雷 . 基于全基因组重测序的白化茶树mSNP标记开发及验证[J]. 茶叶科学, 2023 , 43(1) : 27 -39 . DOI: 10.13305/j.cnki.jts.2023.01.003

Abstract

To explore the information of genetic variation in albino tea and the feasibility of the mSNP liquid chip in the identification of tea germplasm, we analyzed the genetic diversity and detected the mutation sites of 18 tea resources by genome resequencing. The results indicate that the 18 albino tea accessions could be divided into three groups based on genome-wide SNP markers, and the resources with genetic relationship or close geographical location tended to cluster together. Functional annotation of the resequencing data reveals 17 056 non-synonymous mutated genes in the 18 albino tea resources, of which 98 missense mutations were found in 14 chlorophyll synthesis related genes. Then, based on the genomic variation information obtained in the previous study, we developed a set of liquid chip containing 59 mSNP and 222 SNP sites for the first time, and used the liquid chip to detect the genotype information of 13 tea plants. The results show that the genetic similarity between pairs of the same cultivar was 92%-98%, and the genetic similarity between different cultivar was less than 84%, indicating that the chip could accurately identify 18 albino tea accessions. Our results laid a foundation for the application of mSNP liquid phase chip in the identification of tea germplasm resources and molecular marker-assisted breeding.

Key words： tea plant; mSNP; GBTS; genetic diversity; whole genome resequencing

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