Comparative muscle transcriptome of Mali and Hampshire breeds of pigs: a preliminary study.

Muscle development is an important priority of pig breeding programs. There is a considerable variation in muscularity between the breeds, but the regulation mechanisms of genes underlying myogenesis are still unclear. Transcriptome data from two breeds of pigs with divergent muscularity (Mali and Hampshire) were integrated with histology, immunofluorescence and meat yield to identify differences in myogenesis during the early growth phase. The muscle transcriptomics analysis revealed 17,721 common, 1413 and 1115 unique transcripts to Hampshire and Mali, respectively. This study identified 908 differentially expressed genes (p < 0.05; log2FC > ±1) in the muscle samples, of which 550 were upregulated and 358 were downregulated in Hampshire pigs, indicating differences in physiological process related to muscle function and development. Expression of genes related to myoblast fusion (MYMK), skeletal muscle satellite cell proliferation (ANGPT1, CDON) and growth factors (HGF, IGF1, IGF2) were higher in Hampshire than Mali, even though transcript levels of several other myogenesis-related genes (MYF6, MYOG, MSTN) were similar. The number of fibers per fascicle and the expression of myogenic marker proteins (MYOD1, MYOG and PAX7) were more in Hampshire as compared to Mali breed of pig, supporting results of transcriptome studies. The results suggest that differences in muscularity between breeds could be related to the regulation of myoblast fusion and myogenic activities. The present study will help to identify genes that could be explored for their utility in the selection of animals with different muscularities.

[1]  P. Saxena,et al.  Cell adhesion an important determinant of myogenesis and satellite cell activity. , 2021, Biochimica et biophysica acta. Molecular cell research.

[2]  F. Relaix,et al.  Master regulators of skeletal muscle lineage development and pluripotent stem cells differentiation , 2021, Cell regeneration.

[3]  Jiying Wang,et al.  Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development , 2021, BMC genomic data.

[4]  V. Gladyshev,et al.  A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription , 2021, Nature Communications.

[5]  Q. Zhang,et al.  Comparative genome-wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs. , 2020, Animal genetics.

[6]  M. Sarkar,et al.  Transcriptome profiling of different developmental stages of corpus luteum during the estrous cycle in pigs. , 2020, Genomics.

[7]  R. Varshney,et al.  Transcriptome Analysis Identified Coordinated Control of Key Pathways Regulating Cellular Physiology and Metabolism upon Aspergillus flavus Infection Resulting in Reduced Aflatoxin Production in Groundnut , 2020, Journal of fungi.

[8]  Meng Li,et al.  Comparative Transcriptome Analyses of Longissimus thoracis Between Pig Breeds Differing in Muscle Characteristics , 2020, Frontiers in Genetics.

[9]  D. Schaffer,et al.  β-Catenin signaling dynamics regulate cell fate in differentiating neural stem cells , 2020, Proceedings of the National Academy of Sciences.

[10]  Honglin Liu,et al.  Transcriptome analysis reveals the genetic basis of skeletal muscle glycolytic potential based on a pig model. , 2020, Gene.

[11]  D. Huylebroeck,et al.  Zeb2 Regulates Myogenic Differentiation in Pluripotent Stem Cells , 2020, International journal of molecular sciences.

[12]  Sally E. Johnson,et al.  Satellite cells and their regulation in livestock. , 2020, Journal of animal science.

[13]  G. Hoxhaj,et al.  The PI3K–AKT network at the interface of oncogenic signalling and cancer metabolism , 2019, Nature Reviews Cancer.

[14]  T. Shan,et al.  The regulatory role of Myomaker and Myomixer–Myomerger–Minion in muscle development and regeneration , 2019, Cellular and Molecular Life Sciences.

[15]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[16]  R. Gottardo,et al.  A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level , 2019, bioRxiv.

[17]  Lusheng Huang,et al.  A whole genome sequence association study of muscle fiber traits in a White Duroc×Erhualian F2 resource population , 2019, Asian-Australasian journal of animal sciences.

[18]  Bronwen L. Aken,et al.  An improved pig reference genome sequence to enable pig genetics and genomics research , 2019, bioRxiv.

[19]  E. Stehfest,et al.  Future global pig production systems according to the Shared Socioeconomic Pathways. , 2019, The Science of the total environment.

[20]  J. Vilo,et al.  g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) , 2019, Nucleic Acids Res..

[21]  J. Noguera,et al.  Comparing the mRNA expression profile and the genetic determinism of intramuscular fat traits in the porcine gluteus medius and longissimus dorsi muscles , 2019, BMC Genomics.

[22]  Jinzeng Yang,et al.  Differential Transcriptome Analysis of Early Postnatal Developing Longissimus Dorsi Muscle from Two Pig Breeds Characterized in Divergent Myofiber Traits and Fatness , 2019, Animal biotechnology.

[23]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[24]  M. Kozlov,et al.  Myomaker and Myomerger Work Independently to Control Distinct Steps of Membrane Remodeling during Myoblast Fusion. , 2018, Developmental cell.

[25]  K. Piórkowska,et al.  Examining the Genetic Background of Porcine Muscle Growth and Development Based on Transcriptome and miRNAome Data , 2018, International journal of molecular sciences.

[26]  Chonglong Wang,et al.  Identification of differentially expressed genes in longissimus dorsi muscle between Wei and Yorkshire pigs using RNA sequencing , 2018, Genes & Genomics.

[27]  J. Oprzadek,et al.  Breed-dependent microRNA expression in the primary culture of skeletal muscle cells subjected to myogenic differentiation , 2018, BMC Genomics.

[28]  Loren Miraglia,et al.  The microprotein Minion controls cell fusion and muscle formation , 2017, Nature Communications.

[29]  C. Stewart,et al.  Does skeletal muscle have an ‘epi’‐memory? The role of epigenetics in nutritional programming, metabolic disease, aging and exercise , 2016, Aging cell.

[30]  Kui Li,et al.  Comparison of skeletal muscle miRNA and mRNA profiles among three pig breeds , 2016, Molecular Genetics and Genomics.

[31]  H. Yeger,et al.  Multilabel immunofluorescence and antigen reprobing on formalin-fixed paraffin-embedded sections: novel applications for precision pathology diagnosis , 2016, Modern Pathology.

[32]  L. V. van Loon,et al.  Satellite cells in human skeletal muscle plasticity , 2015, Front. Physiol..

[33]  E. McNally,et al.  Membrane fusion in muscle development and repair. , 2015, Seminars in cell & developmental biology.

[34]  A. Blais.  Myogenesis in the genomics era. , 2015, Journal of molecular biology.

[35]  V. Moresi,et al.  Regulation of skeletal muscle development and homeostasis by gene imprinting, histone acetylation and microRNA. , 2015, Biochimica et biophysica acta.

[36]  F. Dilworth,et al.  A KAP1 phosphorylation switch controls MyoD function during skeletal muscle differentiation , 2015, Genes & development.

[37]  P. Le Roy,et al.  The Longissimus and Semimembranosus Muscles Display Marked Differences in Their Gene Expression Profiles in Pig , 2014, PloS one.

[38]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[39]  P. Rigby,et al.  Gene regulatory networks and transcriptional mechanisms that control myogenesis. , 2014, Developmental cell.

[40]  S. Joo,et al.  Control of fresh meat quality through manipulation of muscle fiber characteristics. , 2013, Meat science.

[41]  M. T. te Pas,et al.  Functional analysis of inter-individual transcriptome differential expression in pig longissimus muscle. , 2013, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.

[42]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[43]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[44]  Yu Xin Wang,et al.  Building muscle: molecular regulation of myogenesis. , 2012, Cold Spring Harbor perspectives in biology.

[45]  D. Lösel,et al.  Potential sources of early-postnatal increase in myofibre number in pig skeletal muscle , 2011, Histochemistry and Cell Biology.

[46]  Jiaqi Li,et al.  Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness , 2011, PloS one.

[47]  Y. Billon,et al.  Genetic parameters for residual feed intake in growing pigs, with emphasis on genetic relationships with carcass and meat quality traits. , 2007, Journal of animal science.

[48]  S. Cirera,et al.  Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR , 2007, BMC Molecular Biology.

[49]  Robert M. Stephens,et al.  DAVID Bioinformatics Resources : expanded annotation database and novel algorithms to better extract biology from large gene lists , 2007 .

[50]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[51]  C. Berri,et al.  Muscle fibre ontogenesis in farm animal species. , 2002, Reproduction, nutrition, development.

[52]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[53]  K. Piórkowska,et al.  A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits , 2018, Genetics and molecular biology.

[54]  G. Monin,et al.  Influence of breed and muscle metabolic type on muscle glycolytic potential and meat pH in pigs. , 1987, Meat science.