title: Transcriptome analysis of mRNA and miRNA in skeletal muscle indicates an important network for differential Residual Feed Intake in pigs.
abstract: Feed efficiency (FE) can be measured by feed conversion ratio (FCR) or residual feed intake (RFI). In this study, we measured the FE related phenotypes of 236 castrated purebred Yorkshire boars, and selected 10 extreme individuals with high and low RFI for transcriptome analysis. We used RNA-seq analyses to determine the differential expression of genes and miRNAs in skeletal muscle. There were 99 differentially expressed genes identified (q ≤ 0.05). The down-regulated genes were mainly involved in mitochondrial energy metabolism, including FABP3, RCAN, PPARGC1 (PGC-1A), HK2 and PRKAG2. The up-regulated genes were mainly involved in skeletal muscle differentiation and proliferation, including IGF2, PDE7A, CEBPD, PIK3R1 and MYH6. Moreover, 15 differentially expressed miRNAs (|log2FC| ≥ 1, total reads count ≥ 20, p ≤ 0.05) were identified. Among them, miR-136, miR-30e-5p, miR-1, miR-208b, miR-199a, miR-101 and miR-29c were up-regulated, while miR-215, miR-365-5p, miR-486, miR-1271, miR-145, miR-99b, miR-191 and miR-10b were down-regulated in low RFI pigs. We conclude that decreasing mitochondrial energy metabolism, possibly through AMPK - PGC-1A pathways, and increasing muscle growth, through IGF-1/2 and TGF-β signaling pathways, are potential strategies for the improvement of FE in pigs (and possibly other livestock). This study provides new insights into the molecular mechanisms that determine RFI and FE in pigs.
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Lu
authors.initials: L
authors.lastname: Jing
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Hou
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Hui
authors.initials: H
authors.lastname: Wu
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Yuanxin
authors.initials: Y
authors.lastname: Miao
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Xinyun
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Cao
authors.affiliation: Division of Nutritional Sciences, University of Nottingham, School of Biosciences, Loughborough, Leics. LE12 5RD, United Kingdom.
authors.forename: John Michael
authors.initials: JM
authors.lastname: Brameld
authors.affiliation: Division of Nutritional Sciences, University of Nottingham, School of Biosciences, Loughborough, Leics. LE12 5RD, United Kingdom.
authors.forename: Tim
authors.initials: T
authors.lastname: Parr
authors.affiliation: Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
authors.forename: Shuhong
authors.initials: S
authors.lastname: Zhao
mesh_terms: D055372:AMP-Activated Protein Kinases / Q000378:metabolism; D000821:Animal Feed; D000818:Animals; D016000:Cluster Analysis; D015536:Down-Regulation; D004734:Energy Metabolism / Q000235:genetics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D007334:Insulin-Like Growth Factor I / Q000378:metabolism; D007335:Insulin-Like Growth Factor II / Q000378:metabolism; D008297:Male; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D008928:Mitochondria / Q000378:metabolism; D024510:Muscle Development; D018482:Muscle, Skeletal / Q000378:metabolism*; D010641:Phenotype; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D013552:Swine; D014157:Transcription Factors / Q000378:metabolism; D016212:Transforming Growth Factor beta / Q000235:genetics; D015854:Up-Regulation
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger; D014157:Transcription Factors; D016212:Transforming Growth Factor beta; C111264:peroxisome-proliferator-activated receptor-gamma coactivator-1; D007334:Insulin-Like Growth Factor I; D007335:Insulin-Like Growth Factor II; D055372:AMP-Activated Protein Kinases