Abstract
Simple SummaryThe genetic mechanisms that regulate biological processes, such as skeletal muscle development and growth, or intramuscular fat deposition, have attracted great interest, given their impact on production traits and meat quality. In this sense, a comparison of the transcriptome of skeletal muscle between phenotypically different pig breeds, or along growth, could be useful to improve the understanding of the molecular processes underlying the differences in muscle metabolism and phenotypic traits, potentially driving the identification of causal genes, regulators and metabolic pathways involved in their variability.This experiment was conducted to investigate the effects of developmental stage, breed, and diet energy source on the genome-wide expression, meat quality traits, and tissue composition of biceps femoris muscle in growing pure Iberian and Duroc pigs. The study comprised 59 Iberian (IB) and 19 Duroc (DU) animals, who started the treatment at an average live weight (LW) of 19.9 kg. The animals were kept under identical management conditions and fed two diets with different energy sources (6% high oleic sunflower oil or carbohydrates). Twenty-nine IB animals were slaughtered after seven days of treatment at an average LW of 24.1 kg, and 30 IB animals plus all the DU animals were slaughtered after 47 days at an average LW of 50.7 kg. The main factors affecting the muscle transcriptome were age, with 1832 differentially expressed genes (DEGs), and breed (1055 DEGs), while the effect of diet on the transcriptome was very small. The results indicated transcriptome changes along time in Iberian animals, being especially related to growth and tissue development, extracellular matrix (ECM) composition, and cytoskeleton organization, with DEGs affecting relevant functions and biological pathways, such as myogenesis. The breed also affected functions related to muscle development and cytoskeleton organization, as well as functions related to solute transport and lipid and carbohydrate metabolism. Taking into account the results of the two main comparisons (age and breed effects), we can postulate that the Iberian breed is more precocious than the Duroc breed, regarding myogenesis and muscle development, in the studied growing stage.
Highlights
Pig meat is widely consumed worldwide and comprises one of the main sources of protein for human nutrition
The two breed groups did not differ in body weight at the end of the experimental period (51.2 kg vs. 50.2 kg in the Duroc and Iberian pigs, respectively, p-value = 0.6). This is in agreement with the findings reported by Ayuso et al, 2016 [4], who found no difference between purebred Iberian and Duroc crossbreeds (IB × Du) in the growing period, after a smaller birth weight was observed in the purebred animals, indicating catch-up growth in the early growing stages of Iberian animals, which is compatible with the activation of growth functions and pathways in the muscle transcriptome of Iberian animals reported here
In order to assess the technical validation in high-throughput transcriptomic studies, we calculated the correlation coefficient (CCC) coefficient, and it is interesting to highlight that a value of 0.80 was obtained, which supports a considerable general relationship between the RNA-Seq and Quantitative PCR (qPCR) expression values [35]
Summary
Pig meat is widely consumed worldwide and comprises one of the main sources of protein for human nutrition. The Iberian pig traditional production system is a good example of a sustainable system [3], based on the ad libitum intake of natural resources in a characteristic extensive system (“montanera”) This breed is characterized by high residual feed intake and a peculiar fatty acid (FA) profile [1], with a high concentration of monounsaturated fatty acids (MUFA), which leads to distinctive organoleptic and technological characteristics of its meat and markedly influences the excellent quality of its dry-cured products. These characteristics are due to its genetic predisposition [4,5] and the traditional production system
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