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

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, w...

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Bibliographic Details
Published in:PloS one 2015-08, Vol.10 (8), p.e0135978-e0135978
Main Authors: Shen, Linyuan, Luo, Jia, Du, Jingjing, Liu, Chendong, Wu, Xiaoqian, Pu, Qiang, Fu, Yuhua, Tang, Qianzi, Liu, Yuanrui, Li, Qiang, Yang, Runlin, Li, Xuewei, Tang, Guoqing, Jiang, Yanzhi, Li, Mingzhou, Zhang, Shunhua, Zhu, Li
Format: Article
Language:English
Subjects:
Age Factors
Animal growth
Animal models
Animal sciences
Animals
Asymptotic properties
Breeding
Cloning
DNA, Mitochondrial - metabolism
Energy metabolism
Energy Metabolism - genetics
Fats - analysis
Fats - metabolism
Fatty acid composition
Fatty acids
Fatty Acids - analysis
Fatty Acids - metabolism
Feeds
Female
Gene expression
Gene Expression Profiling - methods
Gene Expression Regulation, Developmental
Gene Ontology
Genes
Genetic analysis
Genetic diversity
Genomics
Growth curves
Growth rate
Hogs
Immune system
Indigenous animals
Laboratories
Meat
Meat quality
Metabolism
MicroRNAs
Muscle, Skeletal - chemistry
Muscle, Skeletal - growth & development
Muscle, Skeletal - metabolism
Muscles
Oils & fats
Phenotype
Phenotypes
Quantitative trait loci
Real-Time Polymerase Chain Reaction
RNA polymerase
Studies
Swine
Swine - genetics
Swine - growth & development
Transcription
Zoology
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0135978