Gene Mining and Genomics-assisted Breeding Empowered by the Pangenome of Tea Plant Camellia Sinensis

Overview

Journal Nat Plants

Specialties Biology
Genetics

Date 2023 Nov 27

PMID 38012346

Authors

Shuai Chen

Pengjie Wang

Weilong Kong

Kun Chai

Shengcheng Zhang

Jiaxin Yu

Yibin Wang

Mengwei Jiang

Wenlong Lei

Xiao Chen

Wenling Wang

Yingying Gao

Shenyang Qu

Fang Wang

Yinghao Wang

Qing Zhang

Mengya Gu

Kaixing Fang

Chunlei Ma

Weijiang Sun

Naixing Ye

Hualing Wu

Xingtan Zhang

Affiliations

Soon will be listed here.

Abstract

Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.

Citing Articles

Benchmarking, detection, and genotyping of structural variants in a population of whole-genome assemblies using the SVGAP pipeline.

Hu M, Wan P, Chen C, Tang S, Chen J, Wang L bioRxiv. 2025; .

PMID: 39975360 PMC: 11839052. DOI: 10.1101/2025.02.07.637096.

Restriction site-associated DNA sequencing (RAD-seq) of tea plant (Camellia sinensis) in Sichuan province, China, provides insights into free amino acid and polyphenol contents of tea.

Wang X, Sun M, Xiong Y, Liu X, Li C, Wang Y PLoS One. 2024; 19(12):e0314144.

PMID: 39636847 PMC: 11620369. DOI: 10.1371/journal.pone.0314144.

Deciphering the anthocyanin metabolism gene network in tea plant (Camellia sinensis) through structural equation modeling.

Xia P, Chen M, Chen L, Yang Y, Ma L, Bi P BMC Genomics. 2024; 25(1):1093.

PMID: 39548396 PMC: 11568573. DOI: 10.1186/s12864-024-11012-8.

Grapevine pangenome facilitates trait genetics and genomic breeding.

Liu Z, Wang N, Su Y, Long Q, Peng Y, Shangguan L Nat Genet. 2024; 56(12):2804-2814.

PMID: 39496880 PMC: 11631756. DOI: 10.1038/s41588-024-01967-5.

An enhancer-transposable element from purple leaf tea varieties underlies the transition from evergreen to purple leaf color.

Xie H, Zhu J, Wang H, Zhang L, Tong X, Huang F Plant Commun. 2024; 6(2):101176.

PMID: 39444159 PMC: 11897448. DOI: 10.1016/j.xplc.2024.101176.

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