ICAR-National Institute for Plant Biotechnology
Pusa, New Delhi
ICAR-Indian Agricultural Statistics Research Institute
New Delhi -110012
Tea HapMap |
Introduction | |
| Here we have generated first HapMap of tea genome. RNA seq data was downloaded for a total of 369 tea accessions from National Genomics Data Center, BGI (Project ID: CRA001438; https://bigd.big.ac.cn/search?dbId=gsa&q=CRA001438) and EMBL-EBI (Project ID: PRJNA222497; https://www.ebi.ac.uk/ena/data/view/PRJNA222497). Tea polymorphisms were determined from these 369 taxa by mapping data against reference genome of tea (CSS_V1.2) (https://github.com/JiedanChen/TeaGenomeData) with mapping quality threshold 30. | |
| Reference: | |
| 1. Yang H, Wei CL, Liu HW, et al. Genetic Divergence between Camellia sinensis and Its Wild Relatives Revealed via Genome-Wide SNPs from RAD Sequencing. PLoS One. 2016;11(3):e0151424. | |
| 2. Niu S, Song Q, Koiwa H, et al. Genetic diversity, linkage disequilibrium, and population structure analysis of the tea plant (Camellia sinensis) from an origin center, Guizhou plateau, using genome-wide SNPs developed by genotyping-by-sequencing.BMC Plant Biol. 2019;19(1):328. | |
ICAR-National Institute for Plant Biotechnology Pusa, New Delhi |
ICAR-Indian Agricultural Statistics Research Institute New Delhi -110012 |