Simple SummaryThe Tunchang pig has characteristics such as tolerance of coarse feed, strong disease resistance, and delicious meat. In 2014, it was listed as one of the main populations of pigs in Hainan and included in the National Livestock and Poultry Genetic Resources Protection List. Protecting and developing the genetic resources of Tunchang pigs can effectively ensure the sustainable development of animal husbandry in Hainan Province. Whole-genome re-sequencing data were used to analyze the genetic diversity, population structure, and selection signals of Tunchang pigs. Compared to commercial pigs, Tunchang pigs have higher genetic diversity and are closer to indigenous Chinese breeds in terms of genetics. Through comprehensive analysis of multiple selection signals, candidate genes for meat quality, disease resistance, growth, and reproduction were identified.AbstractTunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV,CBR4,TNNT1,TNNT3,VPS13A,PLD3,SRFBP1, andSSPN), immune regulation (CD48,FBL,PTPRH,GNA14,LOX,SLAMF6,CALCOCO1,IRGC, andZNF667), growth and development (SYT5,PRX,PPP1R12C, andSMG9), reproduction (LGALS13andEPG5), vision (SLC9A8andKCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.