Single Nucleotide Polymorphisms and Insertion/Deletion Variation Analysis of Octoploid and Decaploid Tropical Oil Tea Camellia Populations Based on Whole-Genome Resequencing
Jiaming Song,
Xin Zhao,
Bo Lin,
Shihui Zhang,
Hanggui Lai,
Feifei Chen,
Dongyi Huang,
Jinping Liu,
Haiyan Hu,
Jian Wang,
Wenqiang Wu,
Xiaolong Huang
Affiliations
Jiaming Song
Forestry Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China
Xin Zhao
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Bo Lin
Forest Seed and Seedling General Station of Hainan Province, Haikou 570203, China
Shihui Zhang
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Hanggui Lai
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Feifei Chen
Forestry Research Institute, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou 571100, China
Dongyi Huang
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Jinping Liu
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Haiyan Hu
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Jian Wang
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Wenqiang Wu
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Xiaolong Huang
School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan Engineering Research Center for Tropical Oil Tea Camellia, Hainan University, Sanya 572000, China
Oil tea camellia (Camellia spp.) is an important woody oil crop with a high nutritional and economic value. Whole-genome resequencing (WGR) technology can provide an in-depth understanding of the genetic background of this plant as well as a reference for breeding research, germplasm resource conservation, and genetic modification. In this study, we analyzed SNP and InDel variations in 49 individual oil tea camellia germplasm samples collected from five populations located in three provinces of China: Hainan, Guangdong and Guangxi. The samples were analyzed through WGR after the ploidy of the samples was determined through flow cytometry. A total of 239,441,603 high-quality single nucleotide polymorphisms (SNPs) and 23,510,374 high-quality insertion/deletion variation sites (InDels) were obtained. The distribution of SNPs and InDels in different functional regions differed significantly, with a high density of variations in non-coding regions, such as intergenic regions and introns, and a relatively low density of variations in coding regions. Transition was the main type of SNP variation. A population genetic diversity analysis revealed that the sampled oil tea camellia populations exhibited a high genetic diversity and extensive genetic variation. The genetic diversity of the oil tea camellia populations in the Hainan region was higher than inland regions. This study also determined the genetic diversity of and variations between octoploid and decaploid oil tea camellia in the tropics and between Hainan-based and inland oil tea camellia. Such findings provide a reference for the conservation of germplasm resources and the genetic modification of oil tea camellia.
