Identification of Novel Genes and Variations Associated to Glycolytic Potential Based on Pig Model

In livestock, glycolytic potential (GP) is a critical indicator for evaluating the meat quality. To date, two major genes protein kinase AMP-activated γ3 non-catalytic subunit gene (PRKAG3) and phosphorylase kinase catalytic subunit gamma 1(PHKG1), and corresponding cause mutations influencing GP have been confirmed in pigs. Therefore, the aim of this study to identify the novel candidate genes and variations related to GP-related traits using a four-hybrid pig model [Pietrain (P)× Duroc (D)] ×[(Landrace) ×(Yorkshire)]. We totally constructed six RNA-seq libraries using longissimus dorsi (LD) muscles, and each library contained two higher GP (H) or two lower GP (L) individuals. A total of 525, 698 and 135 differentially expressed genes (DEGs) were identified between H11 vs L11, H9 vs L9, and H5 vs L5 groups using PossionDis method, respectively. Notably, we found 97 non-redundant DEGs were mapped to GP related QTLs from three paired comparison groups. Moreover, 69 DEGs were identified between H (H11, H9 and H5) and L (L11, L9 and L5) groups using NOIseq method. Additionally, 1,076 potential specific SNPs were figured out between H and L groups, and approximately 40 large Indels with a length ≥ 5bp were identified in each sequencing library. In conclusion, our data provide foundation for further confirming the key genes and the functional mutations affecting GP-related traits in pigs, and also pave the way for elucidating the underling molecular regulatory mechanisms of glycogen metabolism in future study. Moreover, this study might provide valuable information for study on human glycogen storage diseases.

• Publication year

  2018

• Venue

  bioRxiv

• Publication date

  2018-07-11

• Fields of study

  Agricultural and Food Sciences, Biology

• Identifiers
  DOI 10.1101/367581
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

• The effect of oil plants supplementation in pig diet on quality and nutritive value of pork meat

  2017cited by this paper
• Revealing new candidate genes for reproductive traits in pigs: combining Bayesian GWAS and functional pathways

  2016cited by this paper
• RNA-seq analysis reveals new candidate genes for drip loss in a Pietrain × Duroc × Landrace × Yorkshire population.

  2016influential reference
• Identification of candidate genes associated with porcine meat color traits by genome-wide transcriptome analysis

  2016influential reference
• StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

  2015influential reference
• A founder AGL mutation causing glycogen storage disease type IIIa in Inuit identified through whole-exome sequencing: a case series

  2015cited by this paper
• The relationship of pork longissimus muscle pH to mitochondrial respiratory activities, meat quality and muscle structure.

  2015cited by this paper
• HISAT: a fast spliced aligner with low memory requirements

  2015influential reference
• Genome-wide association analyses for meat quality traits in Chinese Erhualian pigs and a Western Duroc × (Landrace × Yorkshire) commercial population

  2015cited by this paper
• rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

  2014influential reference
• CXCR3, CXCL10 and type 1 diabetes.

  2014cited by this paper
• A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle

  2014influential reference
• Relationship Between Glycolytic Potential and Meat Quality of Duroc Pigs with Consideration of Carcass Chilling System / Związek potencjału glikolitycznego z cechami jakości mięsa tuczników rasy Duroc, z uwzględnieniem systemu chłodzenia tusz

  2013cited by this paper
• Quality of meat and meat products produced from southern European pig breeds.

  2012cited by this paper
• Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

  2012influential reference
• Fast gapped-read alignment with Bowtie 2

  2012influential reference
• INAUGURAL ARTICLE by a Recently Elected Academy Member:Strong signatures of selection in the domestic pig genome

  2012cited by this paper
• Liver transcriptome profile in pigs with extreme phenotypes of intramuscular fatty acid composition

  2012influential reference
• Exploring the gonad transcriptome of two extreme male pigs with RNA-seq

  2011influential reference
• A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing

  2011influential reference
• RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

  2011influential reference
• Differential expression in RNA-seq: a matter of depth.

  2011influential reference
• Whole-genome resequencing reveals loci under selection during chicken domestication

  2010cited by this paper
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

  2010cited by this paper
• Screening 52 single nucleotide polymorphisms for extreme value of glycolytic potential and drip loss in pigs.

  2010cited by this paper
• Mitochondrial respiratory activity in porcine longissimus muscle fibers of different pig genetics in relation to their meat quality.

  2010cited by this paper
• The expression of genes PKM2 and CAST in the muscle tissue of pigs differentiated by glycolytic potential and drip loss, with reference to the genetic group.

  2010cited by this paper
• Effects of feeding and rearing systems on growth, carcass composition and meat quality in pigs.

  2008cited by this paper
• Rate and extent of pH decline affect proteolysis of cytoskeletal proteins and water-holding capacity in pork.

  2007cited by this paper
• Relationships between longissimus glycolytic potential and swine growth performance, carcass traits, and pork quality.

  2003cited by this paper
• A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth, and feed intake traits

  2000cited by this paper
• A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle.

  2000influential reference
• Double muscling in cattle due to mutations in the myostatin gene.

  1997cited by this paper
• A deletion in the bovine myostatin gene causes the double–muscled phenotype in cattle

  1997cited by this paper
• The significance of digital gene expression profiles.

  1997influential reference
• Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia.

  1991cited by this paper
• Pork of low technological quality with a normal rate of muscle pH fall in the immediate post-mortem period: The case of the Hampshire breed.

  1985cited by this paper

• No citing papers are available for this paper.