Table 1_Whole genome resequencing reveals genetic relationships and differences between three types of Hainan local pig breeds.xlsx

IntroductionHainan Island, a landmass separated from the Chinese mainland, is characterized by a tropical monsoon maritime climate with ample sunshine and rainfall. It features low-lying plains along the coast and a central mountainous core. These topographical and ecological conditions in the tropics have shaped the unique genetic characteristics of local pig breeds in Hainan. To date, the similarities and differences in the genetic characteristics of different pig breeds, especially pig breeds from different geographical regions, remain unclear.
MethodsWhole genome resequencing were applied to 25 Duntou (DT) pigs from the western, 17 Wuzhishan (WZS) pigs from the central, and 23 Wenchang (WC) pigs from the eastern part of Hainan Island. Among the different pig populations, genetic relationships were assessed through ADMIXTURE analysis, phylogenetic tree construction, and multidimensional scaling analysis. Subsequently, genetic differences were determined by identifying differentially selection regions (DSRs) and the candidate genes within these regions.
ResultsAfter quality control, 13,614,302 autosomal single nucleotide polymorphisms (SNPs) were used in the present study. The results revealed that DT and WZS pigs had closer genetic connections, whereas the genetic connection between WC and the other two pig breeds was relatively distant. Moreover, 1,174 selected genes from DSRs were identified between DT and WZS pigs, WZS and WC pigs, and DT and WC pigs, which included a number of important candidates associated with the growth properties of WZS pigs, and farrowing and fat deposition in WC pigs. The identified genes are able to serve as a scientific underpinning for the conservation and diversified utilization of these indigenous pig breeds.
DiscussionThis study provides a genome-wide view of the genetic structure of pig breeds from different geographical locations in Hainan. Our data may provide the molecular characteristics for the formation of these pig breeds, thus helping us better understand the origin and genetic differences of local pig breeds in Hainan.

引言
海南岛是与中国大陆隔海相望的岛屿，属热带季风海洋性气候，日照充足、降水丰沛。其沿海分布着低海拔平原，中部则为山地核心区域。这些热带地形与生态条件，塑造了海南地方猪种独特的遗传特征。迄今为止，不同猪种尤其是不同地理区域猪种的遗传特征异同尚未明确。

材料与方法
本研究对来自海南岛西部的25头屯头猪（Duntou，DT）、中部的17头五指山猪（Wuzhishan，WZS）以及东部的23头文昌猪（Wenchang，WC）开展全基因组重测序。通过ADMIXTURE分析、系统发育树构建与多维标度分析，评估不同猪群体间的遗传亲缘关系；随后通过鉴定选择性差异区域（differentially selected regions，DSRs）及其内的候选基因，解析群体间的遗传差异。

结果
经质量控制后，本研究共纳入13614302个常染色体单核苷酸多态性位点（single nucleotide polymorphisms，SNPs）进行分析。结果显示，屯头猪与五指山猪的遗传亲缘关系较近，而文昌猪与另外两个猪种的遗传亲缘关系相对较远。此外，在屯头猪与五指山猪、五指山猪与文昌猪、屯头猪与文昌猪的比较中，共鉴定得到1174个来自DSRs的候选基因，其中包含与五指山猪生长性能、文昌猪产仔性能及脂肪沉积相关的多个重要候选基因。上述鉴定得到的基因可为这些地方猪种的保护与多元化开发利用提供科学依据。

讨论
本研究全面解析了海南不同地理区域猪种的遗传结构。本研究所得数据可为阐释这些猪种的形成提供分子特征依据，进而助力我们更深入地理解海南地方猪种的起源与遗传差异。