scholarly journals Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Shengrui Liu ◽  
Yanlin An ◽  
Wei Tong ◽  
Xiuju Qin ◽  
Lidia Samarina ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Genetic Research ◽  
Distribution Patterns ◽  
Genetic Variations ◽  
Tea Plant ◽  
Plant Genome ◽  
Nucleotide Polymorphisms ◽  
Indel Markers ◽  
Genome Wide ◽  
Caffeine Biosynthesis

Abstract Background Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on 46 tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

scholarly journals Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

2019 ◽  
Author(s):  
Shengrui Liu ◽  
Yanlin An ◽  
Wei Tong ◽  
Xiuju Qin ◽  
Lidia Samarina ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Genetic Research ◽  
Distribution Patterns ◽  
Genetic Variations ◽  
Tea Plant ◽  
Plant Genome ◽  
Nucleotide Polymorphisms ◽  
Indel Markers ◽  
Genome Wide ◽  
Caffeine Biosynthesis

Abstract Background: Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results: In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion: The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

scholarly journals Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

2019 ◽  
Author(s):  
Shengrui Liu ◽  
Yanlin An ◽  
Wei Tong ◽  
Xiuju Qin ◽  
Lidia Samarina ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Camellia Sinensis ◽  
Genetic Research ◽  
Genetic Variations ◽  
Tea Plant ◽  
Plant Genome ◽  
Nucleotide Polymorphisms ◽  
Indel Markers ◽  
Genome Wide ◽  
Caffeine Biosynthesis

Abstract Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. In this study, we investigated the genome-wide genetic variation between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. The identified genome-wide genetic variation and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

scholarly journals Characterization of genome-wide genetic variation between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetics research

2019 ◽  
Author(s):  
Shengrui Liu ◽  
Yanlin An ◽  
Wei Tong ◽  
Xiuju Qin ◽  
Lidia Samarina ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Camellia Sinensis ◽  
Distribution Patterns ◽  
Tea Plant ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Genetics Research ◽  
Indel Markers ◽  
Genome Wide ◽  
Caffeine Biosynthesis

Abstract Single nucleotide polymorphisms (SNPs) and Insertions/Deletions (InDels) are the major genetic variations and distributed extensively across the plant whole genome. Few investigations of these variations, however, have been performed in the long-lived perennial tea plant. Here, we have investigated the genome-wide genetic variation between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, generating 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting informative with an average 4.02 of the number of alleles ( Na ) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the content of catechin/caffeine between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. The identified genome-wide genetic variation and newly-developed InDel markers will provide a valuable resource for tea plant genetics and genomics studies, especially those SNPs/InDels within catechin/caffeine biosynthesis-related genes can be served as pivotal candidates for elucidating the molecular mechanism of catechin/caffeine biosynthesis.

scholarly journals Genome-Wide Identification of CsATGs in Tea Plant and the Involvement of CsATG8e in Nitrogen Utilization

2020 ◽  
Vol 21 (19) ◽  
pp. 7043
Author(s):  
Wei Huang ◽  
Dan-Ni Ma ◽  
Hong-Ling Liu ◽  
Jie Luo ◽  
Pu Wang ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Woody Species ◽  
Nutrient Utilization ◽  
Tea Plant ◽  
Plant Genome ◽  
Wild Type ◽  
Genome Wide ◽  
A Genome ◽  
Phosphorus And Potassium ◽  
Stage 1

Nitrogen (N) is a macroelement with an indispensable role in the growth and development of plants, and tea plant (Camellia sinensis) is an evergreen perennial woody species with young shoots for harvest. During senescence or upon N stress, autophagy has been shown to be induced in leaves, involving a variety of autophagy-related genes (ATGs), which have not been characterized in tea plant yet. In this study, a genome-wide survey in tea plant genome identified a total of 80 Camellia Sinensis autophagy-related genes, CsATGs. The expression of CsATG8s in the tea plant showed an obvious increase from S1 (stage 1) to S4 (stage 4), especially for CsATG8e. The expression levels of AtATGs (Arabidopsis thaliana) and genes involved in N transport and assimilation were greatly improved in CsATG8e-overexpressed Arabidopsis. Compared with wild type, the overexpression plants showed earlier bolting, an increase in amino N content, as well as a decrease in biomass and the levels of N, phosphorus and potassium. However, the N level was found significantly higher in APER (aerial part excluding rosette) in the overexpression plants relative to wild type. All these results demonstrated a convincing function of CsATG8e in N remobilization and plant development, indicating CsATG8e as a potential gene for modifying plant nutrient utilization.

scholarly journals Genome-Wide Analysis Reveals Stress and Hormone Responsive Patterns of JAZ Family Genes in Camellia Sinensis

2020 ◽  
Vol 21 (7) ◽  
pp. 2433 ◽  
Author(s):  
Jiazhi Shen ◽  
Zhongwei Zou ◽  
Hongqing Xing ◽  
Yu Duan ◽  
Xujun Zhu ◽  
...  
Keyword(s):  
Camellia Sinensis ◽  
Abiotic Stresses ◽  
Synergistic Effects ◽  
Tea Plant ◽  
Plant Genome ◽  
Pcr Analysis ◽  
Limited Information ◽  
Genome Database ◽  
Recombinant Cells ◽  
Genome Wide

JAZ (Jasmonate ZIM-domain) proteins play pervasive roles in plant development and defense reaction. However, limited information is known about the JAZ family in Camellia sinensis. In this study, 12 non-redundant JAZ genes were identified from the tea plant genome database. Phylogenetic analysis showed that the 12 JAZ proteins belong to three groups. The cis-elements in promoters of CsJAZ genes and CsJAZ proteins interaction networks were also analyzed. Quantitative RT–PCR analysis showed that 7 CsJAZ genes were preferentially expressed in roots. Furthermore, the CsJAZ expressions were differentially induced by cold, heat, polyethylene glycol (PEG), methyl jasmonate (MeJA), and gibberellin (GA) stimuli. The Pearson correlations analysis based on expression levels showed that the CsJAZ gene pairs were differentially expressed under different stresses, indicating that CsJAZs might exhibit synergistic effects in response to various stresses. Subcellular localization assay demonstrated that CsJAZ3, CsJAZ10, and CsJAZ11 fused proteins were localized in the cell nucleus. Additionally, the overexpression of CsJAZ3, CsJAZ10, and CsJAZ11 in E. coli enhanced the growth of recombinant cells under abiotic stresses. In summary, this study will facilitate the understanding of the CsJAZ family in Camellia sinensis and provide new insights into the molecular mechanism of tea plant response to abiotic stresses and hormonal stimuli.

scholarly journals Genome-Wide Identification, Characterization and Function Analysis of Lineage-Specific Genes in the Tea Plant Camellia sinensis

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhizhu Zhao ◽  
Dongna Ma
Keyword(s):  
Camellia Sinensis ◽  
Function Analysis ◽  
Gc Content ◽  
Tea Plant ◽  
Pentose Phosphate ◽  
Specific Expression ◽  
Phenotypic Alteration ◽  
Genome Wide ◽  
The Rich ◽  
Lineage Specific Genes

Genes that have no homologous sequences with other species are called lineage-specific genes (LSGs), are common in living organisms, and have an important role in the generation of new functions, adaptive evolution and phenotypic alteration of species. Camellia sinensis var. sinensis (CSS) is one of the most widely distributed cultivars for quality green tea production. The rich catechins in tea have antioxidant, free radical elimination, fat loss and cancer prevention potential. To further understand the evolution and utilize the function of LSGs in tea, we performed a comparative genomics approach to identify Camellia-specific genes (CSGs). Our result reveals that 1701 CSGs were identified specific to CSS, accounting for 3.37% of all protein-coding genes. The majority of CSGs (57.08%) were generated by gene duplication, and the time of duplication occurrence coincide with the time of two genome-wide replication (WGD) events that happened in CSS genome. Gene structure analysis revealed that CSGs have shorter gene lengths, fewer exons, higher GC content and higher isoelectric point. Gene expression analysis showed that CSG had more tissue-specific expression compared to evolutionary conserved genes (ECs). Weighted gene co-expression network analysis (WGCNA) showed that 18 CSGs are mainly associated with catechin synthesis-related pathways, including phenylalanine biosynthesis, biosynthesis of amino acids, pentose phosphate pathway, photosynthesis and carbon metabolism. Besides, we found that the expression of three CSGs (CSS0030246, CSS0002298, and CSS0030939) was significantly down-regulated in response to both types of stresses (salt and drought). Our study first systematically identified LSGs in CSS, and comprehensively analyzed the features and potential functions of CSGs. We also identified key candidate genes, which will provide valuable assistance for further studies on catechin synthesis and provide a molecular basis for the excavation of excellent germplasm resources.

scholarly journals A brief overview of GWAS: discover genetic variations of diseases and phenotypes

2020 ◽  
Vol 185 ◽  
pp. 03014
Author(s):  
Zhiying Peng
Keyword(s):  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Variations ◽  
Nucleotide Polymorphisms ◽  
Information Discovery ◽  
Genome Wide ◽  
Whole Genomes ◽  
Statistical Analysis Method ◽  
History Of ◽  
Application Fields

GWAS, or Genome-wide association study, is a statistical analysis method to reveal specific genetic variations, usually single nucleotide polymorphisms, with particular phenotypes or diseases. The power to scan whole genomes from large scale samples made the method an efficient tool for information discovery. In the last decades, the application of GWAS has flourished, which benefited our understanding related to diseases, breeding and many other topics. In this review, we overviewed the history of GWAS, as well as different approaches to perform the analysis under different circumstances during different stages. Meanwhile, we also showed how different GWAS approaches benefited diverse research and application fields, and the potential limitations of the method.

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