HapTea

Haplotype Database of Tea

Research • Genomics • Haplotypes

Introduction

Here we have generated Haplotype Database and Visualization of Haplotype from 369 combine VCF Dataset. The Data was downloaded for total 15 chromosome from NCBI (https://pubmed.ncbi.nlm.nih.gov/34601584/). Here 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. And Only polymorphic SNPs are extracted minor allele frequency threshold 0.05. LD value was calculated and based on that haplotypes were visualized.

Reference:

  1. Singh, N., Rawal, H. C., Angadi, U. B., Sharma, T. R., Singh, N. K., & Mondal, T. K. (2022). A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L.) Kuntze). Bioinformatics, 38(2), 318-324.
  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.