Understanding the role of myoglobin content in Iberian pigs fattened in an extensive system through analysis of the transcriptome profile

Abstract

Meat color is the first perceived sensory feature and one of the most important quality traits. Myoglobin is the main pigment in meat, giving meat its characteristic cherry-red color, highly appreciated by the consumers. In the current study, we used the RNA-seq technique to characterize the longissimus dorsi muscle transcriptome in two groups of Iberian pigs with divergent breeding values for myoglobin content. As a result, we identified 57 differentially expressed genes and transcripts (DEGs). Moreover, we have validated the RNA-seq expression of a set of genes by quantitative PCR (qPCR). Functional analyses revealed an enrichment of DEGs in biological processes related to oxidation (HBA1), lipid metabolism (ECH1, PLA2G10, PLD2), inflammation (CHST1, CD209, PLA2G10), and immune system (CD209, MX2, LGALS3, LGALS9). The upstream analysis showed a total of five transcriptional regulatory factors and eight master regulators that could moderate the expression of some DEGs, highlighting SPI1 and MAPK1, since they regulate the expression of DEGs involved in immune defense and inflammatory processes. Iberian pigs with high myoglobin content also showed higher expression of the HBA1 gene and both molecules, myoglobin and hemoglobin, have been described as having a protective effect against oxidative and inflammatory processes. Therefore, the HBA1 gene is a very promising candidate gene to harbor polymorphisms underlying myoglobin content, whereby further studies should be carried out for its potential use in an Iberian pig selection program.

Keywords: Iberian pig; RNA-seq; myoglobin content; transcriptome and functional analysis.

FIGURE 1

Volcano plot of differentially expressed genes (DEGs) and transcripts of High myoglobin group vs. Low myoglobin group. Red dots indicate DEGs with q‐value <0.10 and |Log₂ fold change| > 0.58. Grey dots are non‐significant genes

FIGURE 2

Network of protein‐protein interactions predicted with string database. Same color nodes sharing multiple edges are grouped in the same cluster

FIGURE 3

Gene network 1: dermatological diseases and conditions, immunological disease, organismal injury and abnormalities. Genes upregulated and downregulated in the High myoglobin group are represented in green and red colors respectively

FIGURE 4

Gene network 2: cell cycle, gene expression, lipid metabolism. Genes upregulated and downregulated in the High myoglobin group are represented in green and red colors respectively

FIGURE 5

Master regulator effects network predicted in Iberian pigs fattened in an open‐air free‐range system. In the upper tier is SPI1 (predicted to be activated, blue color). In the middle, there are the genes whose expression changes in response to the activation of SPI1 (green upregulated for the High myoglobin group). Dashed lines between SPI1 and differentially expressed genes represent the interactions, predicted to be activated (blue lines) or predicted to be inhibited (orange lines). In the lower tier, the expected phenotypic activate function (adhesion of immune cells, blue color) is shown