ORIGINAL RESEARCH article
Front. Vet. Sci.
Sec. Livestock Genomics
Volume 12 - 2025 | doi: 10.3389/fvets.2025.1544321
Whole genome resequencing reveals genetic relationships and differences between three types of Hainan local pig breeds
Provisionally accepted
- 1Sanya Institute of Nanjing Agricultural University, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- 2Dongfang City Comprehensive Administrative Law Enforcement Bureau, Dongfang, China
- 3Dazhang Jiaxing Pig Farm, Dongfang, China
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Hainan 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 breeds from different geographical regions, remain unclear. To shed light on this issue, 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 were selected to discover genetic relationships and differences using whole genome resequencing. After 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, 1,174selected genes from differentially selected regions (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. Overall, this 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.
Keywords: Duntou, Wuzhishan, Wenchang, pig, Resequencing, Genetic structure, Selection signal
Received: 12 Dec 2024; Accepted: 28 Apr 2025.
Copyright: © 2025 Yan, Chen, Zhao, Chen and Zhang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Jie Chen, Sanya Institute of Nanjing Agricultural University, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
Lifan Zhang, Sanya Institute of Nanjing Agricultural University, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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