The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation

Xia, Enhua; Tong, Wei; Hou, Yan; An, Yanlin; Chen, Linbo; Wu, Qiong; Liu, Yunlong; Li, Jingling; Li, Fangdong; Li, Ruopei; Li, Penghui; Zhao, Hongxing; Ge, Ruoheng; Huang, Jin; Mallano, Ali Inayat; Zhang, Yanrui; Liu, Shengrui; Deng, Wei‐Wei; Song, Chuankui; Zhang, Zhaoliang; Zhao, Jian; Shu, Wei; Zhang, Zhengzhu; Xia, Tao; Wei, Chaoling; Wan, Xiaochun

doi:10.1016/j.molp.2020.04.010

Cited by 274 publications

(288 citation statements)

References 81 publications

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“…This disparity may result from differences in the reference population. The present population comprised mainly composed of Japanese accessions, whereas those of previous studies 31,34 comprised mainly Chinese accessions. In cross-pollinated species, such as tea plants, LD may decay as a result of extreme genetic drift during domestication and breeding during evolution [35][36][37][38] .…”

Section: Discussionmentioning

confidence: 79%

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Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants

Yamashita

Uchida

Tanaka

et al. 2020

Sci Rep

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Effectively using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genome-wide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The present GP, based on genome-wide SNPs, and six models produced moderate prediction accuracy values (r) for the levels of most catechins, represented by ( −)-epigallocatechin gallate (r = 0.32–0.41) and caffeine (r = 0.44–0.51), but low r values for free amino acids and chlorophylls. Integrated analysis of GWAS and GP detected potential candidate genes for each metabolite using 80–160 top-ranked SNPs that resulted in the maximum cumulative prediction value. Applying GPs and GWASs to tea accession traits will contribute to genomics-assisted tea breeding.

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Section: Discussionmentioning

confidence: 79%

“…Genotyping using the latest chromosome-scale genome and linkage disequilibrium (LD). Our previous study 28 detected SNPs in these tea accessions using a scaffold-scale reference genome 30 , but the latest chromosome-scale reference genome was published by Xia et al (2020) 31 . We re-detected SNPs using the chromosome-scale reference genome.…”

mentioning

confidence: 99%

Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants

Yamashita

Uchida

Tanaka

et al. 2020

Sci Rep

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“…Due to the limitations of sampling in India, we cannot rule out the possibility of other evolutionary scenarios, an evaluation of which will require a more comprehensive collection of samples. Although several studies related to tea genomics have recently been published 1,16,36,37 , considering the complex genome content and valuable contribution to both agriculture and health of tea, a future pangenome analysis will be essential for the tea research community.…”

Section: Discussionmentioning

confidence: 99%

Population sequencing enhances understanding of tea plant evolution

et al. 2020

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Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the ‘Longjing 43’ cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.

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“…Subsequently, the remaining clean reads were subjected to paired-end alignment against the tea plant reference genome (Xia et al, 2020) using Bowtie v2.3.4.3 (Langmead et al, 2009) with default parameters. The ddRAD sequencing generated raw reads has been deposited in the NCBI Sequence-Read Archive (SRA) database.…”

Section: Genotyping By Sequencing and Computational Processingmentioning

confidence: 99%

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

Hazra

Kumar

Sengupta

et al. 2020

Preprint

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Genotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ∼10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their ‘hybrid’ ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p < 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.

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The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation

Cited by 274 publications

References 81 publications

Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants

Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants

Population sequencing enhances understanding of tea plant evolution

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

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