Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling

PLoS One. 2015 Aug 20;10(8):e0135978. doi: 10.1371/journal.pone.0135978. eCollection 2015.

Abstract

Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Age Factors
  • Animals
  • Breeding
  • DNA, Mitochondrial / metabolism
  • Energy Metabolism / genetics
  • Fats / analysis
  • Fats / metabolism
  • Fatty Acids / analysis
  • Fatty Acids / metabolism
  • Female
  • Gene Expression Profiling* / methods
  • Gene Expression Regulation, Developmental
  • Gene Ontology
  • Muscle, Skeletal / chemistry
  • Muscle, Skeletal / growth & development*
  • Muscle, Skeletal / metabolism
  • Phenotype
  • Real-Time Polymerase Chain Reaction
  • Swine / genetics
  • Swine / growth & development*

Substances

  • DNA, Mitochondrial
  • Fats
  • Fatty Acids

Grants and funding

The study was supported by the Sichuan Sci & Tech Support Program (No. 2013NZ0041), the earmarked fund for China Agriculture Research System (No. CARS-36-485 05B), the Chinese National Sci & Tech Support Program (No. 2013BAD20B07), and International Science & Technology Cooperation Program of China (2014DFA31260). Mabian Gold Liangshan Agricultural Development Co., Ltd. provided support in the form of a salary for author RY, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. LC Sciences provided support in the form of a salary for author YL, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section.