Simple SummaryProtection of genetic diversity is important for the sustainable development of the animal industry. Due to the unique environment in Hainan Province, the local pig populations have excellent heat resistance and adaptability. Moreover, the meat quality of these pigs is excellent and very popular with the market. Analysis of the genetic composition of the population may provide valuable information for conservation and utilization of the breed. Therefore, in our study, we aimed to assess the genetic diversity and population structure of three Chinese indigenous pig populations in Hainan Province, and further identified candidate selection signatures based on whole-genome sequencing data. Our analysis shows that native Chinese pig populations are more diverse than commercial pigs. In addition, analysis of selection signatures revealed some candidate genes related to certain traits, such as stress resistance.AbstractIndigenous pig populations in Hainan Province live in tropical climate conditions and a relatively closed geographical environment, which has contributed to the formation of some excellent characteristics, such as heat tolerance, strong disease resistance and excellent meat quality. Over the past few decades, the number of these pig populations has decreased sharply, largely due to a decrease in growth rate and poor lean meat percentage. For effective conservation of these genetic resources (such as heat tolerance, meat quality and disease resistance), the whole-genome sequencing data of 78 individuals from 3 native Chinese pig populations, including Wuzhishan (WZS), Tunchang (TC) and Dingan (DA), were obtained using a 150 bp paired-end platform, and 25 individuals from two foreign breeds, including Landrace (LR) and Large White (LW), were downloaded from a public database. A total of 28,384,282 SNPs were identified, of which 27,134,233 SNPs were identified in native Chinese pig populations. Both genetic diversity statistics and linkage disequilibrium (LD) analysis indicated that indigenous pig populations displayed high genetic diversity. The result of population structure implied the uniqueness of each native Chinese pig population. The selection signatures were detected between indigenous pig populations and foreign breeds by using the population differentiation index (FST) method. A total of 359 candidate genes were identified, and some genes may affect characteristics such as immunity (IL-2,IL-21andZFYVE16), adaptability (APBA1), reproduction (FGF2,RNF17,ADAD1andHIPK4), meat quality (ABCA1,ADIG,TLE4andIRX5), and heat tolerance (VPS13A,HSPA4). Overall, the findings of this study will provide some valuable insights for the future breeding, conservation and utilization of these three Chinese indigenous pig populations.