Abstract: 【Objective】Skin thickness at 9 typical sites of the whole pig body were measured in Bamaxiang pig breed, one of the Chinese local miniature pig breeds. There are 46 candidate SNPs located in a major QTL affecting skin thickness on sus scrofa chromosome 7 (SSC7) were genotyped in the Bamaxiang pig population. One aim of this study is to make clear variation rule of skin thickness at different body sites in Bamaxiang pigs. The other aim is to verify the major QTL affecting skin thickness on SSC7 in Bamaxiang pig population by association study in a specific genomic region. Result of this study will contribute to further revealing the genetic mechanism of swine skin thickness in a larger pig population at whole genome level, and increase our understanding about pig skin. 【Method】A totle of 50 Bamaxiang pigs, including 27 females and 23 castrated males, were randomly selected from a Bamaxiang pig population consisting of 319 adult pigs, which were slaughtered at 300 days. The skin with 5 cm² area were cut from 9 body sites of cheek, shoulder, back, loin, rump, chest, belly, armpit and trotter. Skin thickness at these 9 different body sites were accurately measured using digital caliper. The difference of skin thickness between pairwise body sites and the difference between females and castrated males were tested using the basic statistic package of R language. Pairwise Pearson's correlation coefficients were calculated between skin thickness at different body sites, meanwhile their significant tests were done. A total of 46 SNPs located in the region from 34.5 to 36.2 Mb on SSC7 were selected and designed for genotyping on a SEQUENOM MassARRAY SNP Genotyping platform. Combined with the above phenotypes of skin thickness, association studies on the target candidate region were performed by a general mixed linear model using SNPasscoc package of R language. Based on the association results and biological function of genes, positional candidate genes were determined. 【Result】One-way analysis of variance showed that an extreme significant difference with a 2.95×10^-117 probability existed among skin thickness at 9 body sites in Bamaxiang pigs. The thickest body sites were loin and back with skin thickness of (5.15 ± 0.92) and (4.97 ± 0.85) mm, respectively, while the thinnest sites were belly and armpit with skin thickness of (1.77 ± 0.36) and (1.97 ± 0.68) mm, respectively. The body sites with skin thickness from thick to thin in turn were loin, back, shoulder, cheek, rump, trotter, chest, armpit and belly. Skin thickness of castrated male pig at armpit was significantly thinner than female pig with a 0.021 probability. When compared between other pairwise body sites, skin thickness had no significant differences. There was no significant correlation between skin thickness at belly and back, between belly and shoulder, and between belly and cheek. Other pairwise combinations had a significant positive correlation. Association analysis between skin thickness at 9 different body sites and the above candidate SNPs suggested that the major QTL on SSC7 affecting skin thickness was also identified in Bamaxiang pig population. Three most promising SNPs were worthy of being further focused on. SNP (chr7:34856565) showed most significant association with skin thickness at loin (P_cor = 5.15×10^-6), which was also the most significant site associated with skin thickness at shoulder (P_cor = 5.75×10^-6). SNP (chr7:35543837) was the most significant site associated with skin thickness at armpit (P_cor = 3.05×10^-5), at rump (P_cor = 0.010), at chest (P_cor = 0.013) and cheek (P_cor = 0.025), also was the second most significant site with shoulder. SNP (chr7:35573869) was the top significant site associated with back skin thickness (P_cor = 1.17×10^-5), and followed by SNPs (chr7:35543837 and chr7: 34856565). Based on nearest genes of top SNPs and their biological function, ANKS1A and HMGA1 were preliminarily suggested to be positional candidate genes possibly affecting skin thickness in pigs.  【Conclusion】It was the first time to measure skin thickness at 9 different body sites and report the variation rule of skin thickness along the whole body in Bamaxiang pig breed, one of the Chinese local miniature pig breed. Meanwhile the major QTL affecting skin thickness on SSC7 was verified in Bamaxiang pig population, it provided an important clue and base to reveal the genetic mechanism of pig skin thickness in future. ANKS1A and HMGA1 might be positional causal genes affecting skin thickness in pigs, and it needs further verification of biological functional test.

Key words: Bamaxiang pigs, skin thickness, candidate SNP sites, association study