title: Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs.
abstract: BACKGROUND
  The growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina's Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds.
  
  
  RESULTS
  Muscle morphological changes indicate the importance of primary fiber formation from 30 to 40 dpc (days post coitus), and secondary fiber formation from 55 to 70 dpc. We screened 4,331 differentially expressed genes in TC and 2,259 in YK (log2 ratio >1 and probability >0.7). Cluster analysis showed different gene expression patterns between TC and YK pigs. The transcripts were annotated in terms of Gene Ontology related to muscle development. We found that the genes CXCL10, EIF2B5, PSMA6, FBXO32, and LOC100622249 played vital roles in the muscle regulatory networks in the TC breed, whereas the genes SGCD, ENG, THBD, AQP4, and BTG2 played dominant roles in the YK breed. These genes showed breed-specific and development-dependent differential expression patterns. Furthermore, 984 genes were identified in myogenesis. A heat map showed that significantly enriched pathways (FDR <0.05) had stage-specific functional regulatory mechanisms. Finally, the differentially expressed genes from our sequencing results were confirmed by real-time quantitative polymerase chain reaction.
  
  
  CONCLUSIONS
  This study detected many functional genes and showed differences in the molecular mechanisms of skeletal muscle development between TC and YK pigs. TC pigs showed slower muscle growth and more complicated genetic regulation than YK pigs. Many differentially expressed genes showed breed-specific expression patterns. Our data provide a better understanding of skeletal muscle developmental differences and valuable information for improving pork quality.
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. yuqiangzhao@hotmail.com.
authors.forename: Yuqiang
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. watterfall@126.com.
authors.forename: Ji
authors.initials: J
authors.lastname: Li
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. suemorley@126.com.
authors.forename: Huijing
authors.initials: H
authors.lastname: Liu
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. xiyu1988@163.com.
authors.forename: Yu
authors.initials: Y
authors.lastname: Xi
authors.affiliation: National Animal Husbandry Services Ministry of Agriculture, Beijing, PR China. kiko@vip.sina.com.
authors.forename: Ming
authors.initials: M
authors.lastname: Xue
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. whliu@mail.hzau.edu.cn.
authors.forename: Wanghong
authors.initials: W
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen, PR China. zhuangzhenhua@genomics.org.cn.
authors.forename: Zhenhua
authors.initials: Z
authors.lastname: Zhuang
authors.affiliation: Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture, Huazhong Agricultural University, Wuhan, PR China. leimg@mail.hzau.edu.cn.
authors.forename: Minggang
authors.initials: M
authors.lastname: Lei
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D053263:Gene Regulatory Networks; D016678:Genome; D024510:Muscle Development / Q000235:genetics; D018485:Muscle Fibers, Skeletal / Q000473:pathology; D018482:Muscle, Skeletal / Q000378:metabolism*; D012313:RNA / Q000032:analysis / Q000302:isolation & purification / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D013552:Swine / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D012313:RNA