Whole-Genome Resequencing Reveals the Genetic Diversity and Structure of a Collection of Yellow-Flowered Camellias in the United States

Yellow-flowered camellias are a sought-after rarity that has a narrow natural distribution in southern China and northern Vietnam. Belonging to the Camellia sect. Chrysantha Chang, many of the yellow-flowered camellia species are endangered. In this study, whole-genome resequencing (WGR) was applied to a collection of 25 yellow-flowered camellias in the United States of America to generate molecular markers and estimate genetic diversity. A total of 200,385,257 SNPs, 15,632,190 indels, 420,648 structural variations, and 9067 CNVs were identified among the 25 plants. There were 122 SNPs within the chalcone synthase (CHS) gene. Two groups of plants, C. nitidissima and hybrids, were distinctly separated from the other individuals. High within-population diversity and moderate among-population differentiation were found. Compared to the genetic diversity present in the native regions of yellow-flowered camellias, only a limited number of species have been introduced to the United States. The current study is the first report of whole-genome resequencing of yellow camellias and the first investigation of genetic diversity and structure of a collection of individuals from the U.S. This significant genomic resource shall have a meaningful impact on conservation and breeding, as well as on species identification and evolution studies. The genetic diversity information shall guide the efforts in breeding and the introduction of new species.