Identification of Selection Signatures and Loci Associated with Important Economic Traits in Yunan Black and Huainan Pigs
Author:
Han Yachun1, Tan Tao1, Li Zixin2, Ma Zheng1, Lan Ganqiu2, Liang Jing2ORCID, Li Kui1, Bai Lijing1
Affiliation:
1. Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China 2. College of Animal Science & Technology, Guangxi University, Nanning 530003, China
Abstract
Henan Province is located in central China and rich in domestic pig populations; Huainan (HN) pigs are one of three Henan indigenous breeds with great performance, including early maturation, strong disease resistance and high meat quality. Yunan (YN) black pigs are a typical, newly cultivated breed, synthesized between HN pigs and American Duroc, and are subjected to selection for important traits, such as fast growth and excellent meat quality. However, the genomic differences, selection signatures and loci associated with important economic traits in YN black pigs and HN pigs are still not well understood. In this study, based on high-density SNP chip analysis of 159 samples covering commercial DLY (Duroc × Landrace × Large White) pigs, HN pigs and YN black pigs, we performed a comprehensive analysis of phylogenetic relationships and genetic diversity among the three breeds. Furthermore, we used composite likelihood ratio tests (CLR) and F-statistics (Fst) to identify specific signatures of selection associated with important economic traits and potential candidate genes. We found 147 selected regions (top 1%) harboring 90 genes based on genetic differentiation (Fst) in the YN-DLY group. In the HN-DLY group, 169 selected regions harbored 58 genes. In the YN-HN group, 179 selected regions harbored 77 genes. In addition, the QTLs database with the most overlapping regions was associated with triglyceride level, number of mummified pigs, hemoglobin and loin muscle depth for YN black pigs, litter size and intramuscular fat content for HN pigs, and humerus length, linolenic acid content and feed conversion ratio mainly in DLY pigs. Of note, overlapping 14 tissue-specific promoters’ annotation with the top Fst 1% selective regions systematically demonstrated the muscle-specific and hypothalamus-specific regulatory elements in YN black pigs. Taken together, these results contribute to an accurate knowledge of crossbreeding, thus benefitting the evaluation of production performance and improving the genome-assisted breeding of other important indigenous pig in the future.
Funder
the National Key R&D Program of China The National Natural Science Foundation of China
Subject
Genetics (clinical),Genetics
Reference50 articles.
1. Briggs, H.M. (1969). Modern Breeds of Livestock Hardcover, Collier Macmillan Ltd. 2. (2011). Animal Genetic Resources in China: Pigs, China Agriculture Press. 3. Detection of Selection Signatures in Chinese Landrace and Yorkshire Pigs Based on Genotyping-by-Sequencing Data;Wang;Front. Genet.,2018 4. Ma, Y., Zhang, H., Zhang, Q., and Ding, X. (2014). Identification of selection footprints on the X chromosome in pig. PLoS ONE, 9. 5. Xu, J., Ruan, Y., Sun, J., Shi, P., Huang, J., Dai, L., Xiao, M., and Xu, H. (2022). Association analysis of PRKAA2 and MSMB polymorphisms and growth traits of Xiangsu hybrid pigs. Genes, 14.
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