Longissimus dorsi transcriptome analysis of purebred and crossbred Iberian pigs differing in muscle characteristics

Abstract

Background: The two main genetic types in Iberian pig production show important phenotypic differences in growth, fattening and tissue composition since early developmental stages. The objective of this work was the evaluation of muscle transcriptome profile in piglets of both genetic types, in order to identify genes, pathways and regulatory factors responsible for their phenotypic differences. Contemporary families coming from pure Iberian pigs (IB) or from crossing with Duroc boars (DU×IB) were generated. Piglets (14 from each genetic type) were slaughtered at weaning (28 days) and longissimus dorsi was sampled for composition and gene expression studies. RNA was obtained and hybridized to Affymetrix Porcine Genechip expression arrays.

Results: Loin muscle chemical composition showed significant differences between genetic types in intramuscular fat content (6.1% vs. 4.3% in IB and DUxIB animals, respectively, P = 0.009) and in saturated (P = 0.019) and monounsaturated fatty acid proportions (P = 0.044). The statistical analysis of gene expression data allowed the identification of 256 differentially expressed (DE) genes between genetic types (FDR < 0.10), 102 upregulated in IB and 154 upregulated in DU×IB. Transcript differences were validated for a subset of DE genes by qPCR. We observed alteration in biological functions related to extracellular matrix function and organization, cellular adhesion, muscle growth, lipid metabolism and proteolysis. Candidate genes with known effects on muscle growth were found among the DE genes upregulated in DU×IB. Genes related to lipid metabolism and proteolysis were found among those upregulated in IB. Regulatory factors (RF) potentially involved in the expression differences were identified by calculating the regulatory impact factors. Twenty-nine RF were found, some of them with known relationship with tissue development (MSTN, SIX4, IRX3), adipogenesis (CEBPD, PPARGC1B), or extracellular matrix processes (MAX, MXI1). Correlation among the expression of these RF and DE genes show relevant differences between genetic types.

Conclusion: These results provide valuable information about genetic mechanisms determining the phenotypic differences on growth and meat quality between the genetic types studied, mainly related to the development and function of the extracellular matrix and also to some metabolic processes as proteolysis and lipid metabolism. Transcription factors and regulatory mechanisms are proposed for these altered biological functions.

Figure 1

Functional categorization analysis with IPA. Canonical pathways significantly enriched in the three sets of genes are shown (P < 0.05): A) Genes DE between both genetic types; B) Genes upregulated in IB; C) Genes upregulated in DU×IB. Signaling pathways are indicated with dark bars and metabolic pathways with light bars.

Figure 2

Gene network 1: Cellular Development, Cellular Growth and Proliferation, Embryonic Development (score 51). Molecules are represented as nodes and the biological relationships between nodes are represented as edges. Genes upregulated in IB are indicated in red and the ones upregulated in DU×IB are shown in green.

Figure 3

Gene network 2: Connective Tissue Disorders, Dermatological Diseases and Conditions, Cellular Assembly and Organization (score 47). Molecules are represented as nodes and the biological relationships between nodes are represented as edges. Genes upregulated in IB are indicated in red and the ones upregulated in DU×IB are shown in green.

Figure 4

Gene network 3: Protein Degradation, Protein Synthesis, Cell Morphology (score 41). Molecules are represented as nodes and the biological relationships between nodes are represented as edges. Genes upregulated in IB are indicated in red and the ones upregulated in DU×IB are shown in green.