title: Identification of candidate genes associated with porcine meat color traits by genome-wide transcriptome analysis.
abstract: Meat color is considered to be the most important indicator of meat quality, however, the molecular mechanisms underlying traits related to meat color remain mostly unknown. In this study, to elucidate the molecular basis of meat color, we constructed six cDNA libraries from biceps femoris (Bf) and soleus (Sol), which exhibit obvious differences in meat color, and analyzed the whole-transcriptome differences between Bf (white muscle) and Sol (red muscle) using high-throughput sequencing technology. Using DEseq2 method, we identified 138 differentially expressed genes (DEGs) between Bf and Sol. Using DEGseq method, we identified 770, 810, and 476 DEGs in comparisons between Bf and Sol in three separate animals. Of these DEGs, 52 were overlapping DEGs. Using these data, we determined the enriched GO terms, metabolic pathways and candidate genes associated with meat color traits. Additionally, we mapped 114 non-redundant DEGs to the meat color QTLs via a comparative analysis with the porcine quantitative trait loci (QTL) database. Overall, our data serve as a valuable resource for identifying genes whose functions are critical for meat color traits and can accelerate studies of the molecular mechanisms of meat color formation.
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Bojiang
authors.initials: B
authors.lastname: Li
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Dong
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Pinghua
authors.initials: P
authors.lastname: Li
authors.affiliation: Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture, Key Lab of Agriculture Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Animal Science, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.|The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
authors.forename: Zhuqing
authors.initials: Z
authors.lastname: Ren
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Han
authors.initials: H
authors.lastname: Wang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Fengxiang
authors.initials: F
authors.lastname: Yu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Caibo
authors.initials: C
authors.lastname: Ning
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Kaiqing
authors.initials: K
authors.lastname: Liu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Wei
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Ruihua
authors.initials: R
authors.lastname: Huang
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Jie
authors.initials: J
authors.lastname: Chen
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wangjun
authors.initials: W
authors.lastname: Wu
authors.affiliation: Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Liu
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D003116:Color; D019295:Computational Biology; D005260:Female; D020869:Gene Expression Profiling; D015723:Gene Library; D016678:Genome; D008460:Meat; D018482:Muscle, Skeletal / Q000378:metabolism; D010641:Phenotype; D040641:Quantitative Trait Loci; D034421:Sus scrofa / Q000235:genetics*; D013552:Swine; D059467:Transcriptome