title: Comparison of skeletal muscle miRNA and mRNA profiles among three pig breeds.
abstract: The pig is an important source of animal protein, and is also an ideal model for human disease. There are significant differences in growth rate, muscle mass, and meat quality between different breeds. To understand the molecular mechanisms underlying porcine skeletal muscle phenotypes, we performed mRNA and miRNA profiling of muscle from three different breeds of pig, Landrace (lean-type), Tongcheng (obese-type), and Wuzhishan (mini-type) by Solexa sequencing. Forty-three genes and 106 miRNAs were differentially expressed between Landrace and Tongcheng pigs, 92 genes and 151 miRNAs were differentially expressed between Tongcheng and Wuzhishan pigs, and 145 genes and 156 miRNAs were differential expressed between Landrace and Wuzhishan pigs. Gene ontology analysis suggested that genes differentially expressed between Landrace and Tongcheng pigs were mainly involved in the biological processes of oxidative stress and muscle organ development. Meanwhile, for Tongcheng vs Wuzhishan and Landrace vs Wuzhishan pigs, the differentially expressed genes were involved in fatty acid metabolism, oxidative stress, muscle contraction, and muscle organ development, processes that are closely related to meat quality. To investigate the molecular mechanisms underlying meat quality diversity based on differentially expressed genes and miRNAs, interaction networks were constructed, according to target prediction results and integration analysis of up-regulated genes with down-regulated miRNAs or down-regulated genes with up-regulated miRNAs. Our findings identify candidate genes and miRNAs associated with muscle development and indicate their potential roles in muscle phenotype variance between different pig breeds. These results serve as a foundation for further studies on muscle development and molecular breeding.
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Xinhua
authors.initials: X
authors.lastname: Hou
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, People's Republic of China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Shiyun
authors.initials: S
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Chaoju
authors.initials: C
authors.lastname: Hua
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Rong
authors.initials: R
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Mu
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China. zhonglinqy_99@sina.com.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, People's Republic of China. zhonglinqy_99@sina.com.
authors.forename: Zhonglin
authors.initials: Z
authors.lastname: Tang
authors.affiliation: Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China.
authors.forename: Kui
authors.initials: K
authors.lastname: Li
mesh_terms: D000818:Animals; D001947:Breeding; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D050356:Lipid Metabolism / Q000235:genetics; D008460:Meat; D035683:MicroRNAs / Q000096:biosynthesis* / Q000235:genetics; D024510:Muscle Development / Q000235:genetics*; D018482:Muscle, Skeletal / Q000378:metabolism; D012333:RNA, Messenger / Q000096:biosynthesis* / Q000235:genetics; D034421:Sus scrofa / Q000235:genetics / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger
keywords: Pig; Skeletal muscles; Solexa sequencing; Transcriptome; miRNAs