title: Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq).
abstract: Genetic maps are important tools in plant genomics and breeding. The present study reports the large-scale discovery of single nucleotide polymorphisms (SNPs) for genetic map construction in tea plant. We developed a total of 6,042 valid SNP markers using specific-locus amplified fragment sequencing (SLAF-seq), and subsequently mapped them into the previous framework map. The final map contained 6,448 molecular markers, distributing on fifteen linkage groups corresponding to the number of tea plant chromosomes. The total map length was 3,965 cM, with an average inter-locus distance of 1.0 cM. This map is the first SNP-based reference map of tea plant, as well as the most saturated one developed to date. The SNP markers and map resources generated in this study provide a wealth of genetic information that can serve as a foundation for downstream genetic analyses, such as the fine mapping of quantitative trait loci (QTL), map-based cloning, marker-assisted selection, and anchoring of scaffolds to facilitate the process of whole genome sequencing projects for tea plant.
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Jian-Qiang
authors.initials: JQ
authors.lastname: Ma
authors.affiliation: Biomarker Technologies Co Ltd, Beijing, China.
authors.forename: Long
authors.initials: L
authors.lastname: Huang
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Chun-Lei
authors.initials: CL
authors.lastname: Ma
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Ji-Qiang
authors.initials: JQ
authors.lastname: Jin
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Chun-Fang
authors.initials: CF
authors.lastname: Li
authors.affiliation: Biomarker Technologies Co Ltd, Beijing, China.
authors.forename: Rong-Kai
authors.initials: RK
authors.lastname: Wang
authors.affiliation: Biomarker Technologies Co Ltd, Beijing, China.
authors.forename: Hong-Kun
authors.initials: HK
authors.lastname: Zheng
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Ming-Zhe
authors.initials: MZ
authors.lastname: Yao
authors.affiliation: National Center for Tea Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, Zhejiang, China; Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, Zhejiang, China.
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
mesh_terms: D028241:Camellia sinensis / Q000235:genetics*; D002874:Chromosome Mapping; D008040:Genetic Linkage; D018745:Genome, Plant; D060005:Genotyping Techniques; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D017422:Sequence Analysis, DNA / Q000379:methods