Breed, Diet, and Interaction Effects on Adipose Tissue Transcriptome in Iberian and Duroc Pigs Fed Different Energy Sources

Abstract

In this study, we analyzed the effects of breed, diet energy source, and their interaction on adipose tissue transcriptome in growing Iberian and Duroc pigs. The study comprised 29 Iberian and 19 Duroc males, which were kept under identical management conditions except the nutritional treatment. Two isoenergetic diets were used with 6% high oleic sunflower oil (HO) or carbohydrates (CH) as energy sources. All animals were slaughtered after 47 days of treatment at an average live weight of 51.2 kg. Twelve animals from each breed (six fed each diet) were employed for ham subcutaneous adipose tissue RNA-Seq analysis. The data analysis was performed using two different bioinformatic pipelines. We detected 837 and 1456 differentially expressed genes (DEGs) according to breed, depending on the pipeline. Due to the strong effect of breed on transcriptome, the effect of the diet was separately evaluated in the two breeds. We identified 207 and 57 DEGs depending on diet in Iberian and Duroc pigs, respectively. A joint analysis of both effects allowed the detection of some breed–diet interactions on transcriptome, which were inferred from RNA-Seq and quantitative PCR data. The functional analysis showed the enrichment of functions related to growth and tissue development, inflammatory response, immune cell trafficking, and carbohydrate and lipid metabolism, and allowed the identification of potential regulators. The results indicate different effects of diet on adipose tissue gene expression between breeds, affecting relevant biological pathways.

Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds

“…IGF2 was found significantly overexpressed in BI (log2 FC = −0.884, p < 0.05) despite their leaner phenotype which indicates that fat deposition is regulated at other levels. This result is in agreement with previous studies that found IGF2 overexpression in leaner Duroc when compared to the fatter Iberian pig genotype [52].…”

“…Similar to what was found in a recent study [52] that compared the transcriptome of animals with distinct tissue distribution (Iberian vs. Duroc), a set of genes that play an important role in growth and development was, within our dataset, consistently found overexpressed in BI, the breed with the highest lean muscle tissue deposition. Those genes included IGF2 (log2 FC = −0.884, q < 0.05), FOS (log2 FC = −1.087, q < 0.05) and FOSB (log2 FC = −2.028, q < 0.01).…”

“…As in other studies with the Iberian pig breed [52,68,69], genetically similar to AL, compared to the leaner Duroc and Landrace breeds, LEP gene was found significantly overexpressed in the AL pig (log2 FC = 1.376, q < 0.05). This is in agreement with its recognized fatter phenotype and, very similar to the IB breed, suggesting the development of leptin resistance [27,52].…”

“…Moreover, PCK1 has been found to regulate free fatty acid reesterification and glyceroneogenesis in white adipose tissue [64]. Contrarily to what was found in another study using Iberian when compared to Duroc pigs [52], PCK1 gene was found significantly overexpressed in BI (log2 FC = −1.959, q < 0.05) which suggest that in BI the path of gluconeogenesis/glyceroneogenesis pathway is favoured. A single nucleotide polymorphism c.A2456C in the PCK1 gene has been reported to favour higher intramuscular deposition and better meat quality in pigs muscle [65].…”

“…GC content ranged from 49 to 56%. Resulting trimmed paired-end reads were mapped to the reference genome Sscrofa11.1 with a consistent alignment rate of 97% using HISAT2 over all samples, which is higher than most previous pig transcriptome studies [47][48][49][50][51][52] and is probably due to an improved annotated reference genome.…”