title: Transcriptome analysis revealed chimeric RNAs, single nucleotide polymorphisms and allele-specific expression in porcine prenatal skeletal muscle.
abstract: Prenatal skeletal muscle development genetically determines postnatal muscle characteristics such as growth and meat quality in pigs. However, the molecular mechanisms underlying prenatal skeletal muscle development remain unclear. Here, we performed the first genome-wide analysis of chimeric RNAs, single nuclear polymorphisms (SNPs) and allele-specific expression (ASE) in prenatal skeletal muscle in pigs. We identified 14,810 protein coding genes and 163 high-confidence chimeric RNAs expressed in prenatal skeletal muscle. More than 94.5% of the chimeric RNAs obeyed the canonical GT/AG splice rule and were trans-splicing events. Ten and two RNAs were aligned to human and mouse chimeric transcripts, respectively. We detected 106,457 high-quality SNPs (6,955 novel), which were mostly (89.09%) located within QTLs for production traits. The high proportion of non-exonic SNPs revealed the incomplete annotation status of the current swine reference genome. ASE analysis revealed that 11,300 heterozygous SNPs showed allelic imbalance, whereas 131 ASE variants were located in the chimeric RNAs. Moreover, 4 ASE variants were associated with various economically relevant traits of pigs. Taken together, our data provide a source for studies of chimeric RNAs and biomarkers for pig breeding, while illuminating the complex transcriptional events underlying prenatal skeletal muscle development in mammals.
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China.
authors.forename: Yalan
authors.initials: Y
authors.lastname: Yang
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China.
authors.forename: Zhonglin
authors.initials: Z
authors.lastname: Tang
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.
authors.forename: Xinhao
authors.initials: X
authors.lastname: Fan
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.
authors.forename: Kui
authors.initials: K
authors.lastname: Xu
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.
authors.forename: Yulian
authors.initials: Y
authors.lastname: Mu
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.
authors.forename: Rong
authors.initials: R
authors.lastname: Zhou
authors.affiliation: The State Key Laboratory for Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China.|Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, P.R.China.
authors.forename: Kui
authors.initials: K
authors.lastname: Li
mesh_terms: D000483:Alleles; D000818:Animals; D001835:Body Weight / Q000235:genetics; D001947:Breeding; D005091:Exons / Q000235:genetics; D005260:Female; D018507:Gene Expression Regulation, Developmental; D059014:High-Throughput Nucleotide Sequencing; D008297:Male; D058977:Molecular Sequence Annotation; D024510:Muscle Development / Q000235:genetics; D009124:Muscle Proteins / Q000096:biosynthesis / Q000235:genetics*; D018482:Muscle, Skeletal / Q000196:embryology / Q000378:metabolism*; D050506:Mutant Chimeric Proteins / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D012326:RNA Splicing; D012333:RNA, Messenger / Q000032:analysis* / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D034421:Sus scrofa / Q000235:genetics*; D059467:Transcriptome
chemical_list: D009124:Muscle Proteins; D050506:Mutant Chimeric Proteins; D012333:RNA, Messenger