Association mapping of caffeine content with TCS1 in tea plant and its related species.
Caffeine is the most abundant purine alkaloid in majority of tea plant and its related species. This purine alkaloid contributes to the important flavor and health attributes of tea. Tea caffeine synthase 1 (TCS1, EC 2.1.1.159/2.1.1.160) gene plays a crucial role in caffeine biosynthesis. The objective of this study was to investigate the genetic relationship between the TCS1 and caffeine content of tea plant and its related species using association mapping. We identified 87 single-nucleotide polymorphisms (SNPs, π = 0.00447) by resequencing the TCS1 locus of 44 tea accessions. Linkage disequilibrium (LD) analysis showed that LD did not extend over the entire gene (r(2) < 0.1, within 1000 bp). Two cleaved amplified polymorphism sequence (CAPS) markers were developed from sequence variations (SNP4318 and SNP6252). By association mapping, we identified SNP4318 associated with caffeine content in four environments, explaining 4.0%-7.7% of the phenotypic variance. We also validated the significant marker-trait associations in site-directed mutagenesis experiments. Examination of allelic variation and linkage disequilibrium by a candidate-gene-based approach can help to decipher the genetic basis of caffeine biosynthesis. Moreover, the SNP marker identified in this study can potentially be applied for future marker-assisted selection to improve tea quality.
Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, Zhejiang 310008, China.
Ji-Qiang
JQ
Jin
Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, Zhejiang 310008, China.
Ming-Zhe
MZ
Yao
Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, Zhejiang 310008, China.
Chun-Lei
CL
Ma
Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, Zhejiang 310008, China.
Jian-Qiang
JQ
Ma
Tea Research Institute of the Chinese Academy of Agricultural Sciences, National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, 9 South Meiling Road, Hangzhou, Zhejiang 310008, China. Electronic address: liangchen@mail.tricaas.com.
Liang
L
Chen
D002110:Caffeine / Q000096:biosynthesis*; D028241:Camellia sinensis / Q000201:enzymology* / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D060146:Ecotype; D020224:Expressed Sequence Tags; D005787:Gene Frequency / Q000235:genetics; D017343:Genes, Plant; D005819:Genetic Markers; D005838:Genotype; D060005:Genotyping Techniques; D015810:Linkage Disequilibrium / Q000235:genetics; D016297:Mutagenesis, Site-Directed; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011994:Recombinant Proteins / Q000378:metabolism; D015203:Reproducibility of Results; D013045:Species Specificity
D005819:Genetic Markers; D011994:Recombinant Proteins; D002110:Caffeine
Caffeine; Linkage disequilibrium mapping; Single-nucleotide polymorphism; Tea caffeine synthase; Tea plant