Development and Utilization of High-Density Genome-Wide SNP Array for Tea Plants

Tea is a popular beverage with a high nutritional and economic value. Tea plants are diploid and have 15 pairs of homologous chromosomes, containing the entire genetic information of its genome. Despite the past publication of the data for a number of tea genomes, it is still difficult to identify novel germplasm resources and breeding new cultivars in an effective manner. Here, we present a 200 K tea single nucleotide polymorphism (SNP) array to improve the efficiency of tea plant genotyping. The re-sequencing data in our previous study was used for SNP identification of the array, and a total of 179,970 unique and informative SNPs were obtained in the SNP array. A set of 142 tea cultivars from different provinces of China and an F1 population of 'Longjing 43 (LJ43)' and 'Baihaozao (BHZ)' with 327 individuals were genotyped. Our SNP array data showed that tea plants are domesticated polyphyletically, with Southwest China as the domestication center of the Camellia sinensis var. assamica (CSA) population and the East of China as the domestication center of the C. sinensis var. sinensis (CSS) population. These results indicate the importance of SNP array for forward genetic research in tea plants.