Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing

PLoS One. 2016 Mar 10;11(3):e0151424. doi: 10.1371/journal.pone.0151424. eCollection 2016.

Abstract

Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Camellia sinensis / genetics*
  • Genes, Plant*
  • Genome-Wide Association Study*
  • High-Throughput Nucleotide Sequencing*
  • Polymorphism, Single Nucleotide*

Grant support

This work received financial support from the Major Project of the Chinese National Program for Fundamental Research and Development (2012CB722903), the Science and Technology Project of AnHui Province (13Z03012) and the Tea Genome Project of AnHui Province, China grants to Xiao-Chun Wan, the Program for Changjiang Scholars and Innovative Research Team in University (IRT1101) grants to Zhengzhu Zhang, the National Natural Science Foundation of China (31300578), the Collegiate Natural Science Foundation of Anhui Province (KJ2013Z078), and the Academic backbone cultivation project of Anhui Agricultural University (2014XKPY-34) grants to Hua Yang. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. BGI-Shenzhen provided support in the form of salaries for Jian-Bo Jian, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of these authors are articulated in the ‘author contributions’ section.