Genomic analyses of agronomic traits in tea plants and related Camellia species

The genus <i>Camellia</i> contains three types of domesticates that meet various needs of ancient humans: the ornamental <i>C. japonica</i>, the edible oil-producing <i>C. oleifera</i>, and the beverage-purposed tea plant <i>C. sinensis</i>. The genomic drivers of the functional diversification of <i>Camellia</i> domesticates remain unknown. Here, we present the genomic variations of 625 <i>Camellia</i> accessions based on a new genome assembly of <i>C. sinensis</i> var. <i>assamica</i> ('YK10'), which consists of 15 pseudo-chromosomes with a total length of 3.35 Gb and a contig N50 of 816,948 bp. These accessions were mainly distributed in East Asia, South Asia, Southeast Asia, and Africa. We profiled the population and subpopulation structure in tea tree <i>Camellia</i> to find new evidence for the parallel domestication of <i>C. sinensis</i> var. <i>assamica</i> (CSA) and <i>C. sinensis</i> var. <i>sinensis</i> (CSS). We also identified candidate genes associated with traits differentiating CSA, CSS, oilseed <i>Camellia</i>, and ornamental <i>Camellia</i> cultivars. Our results provide a unique global view of the genetic diversification of <i>Camellia</i> domesticates and provide valuable resources for ongoing functional and molecular breeding research.