Transcriptome Analysis of the Adipose Tissue of Luchuan and Duroc Pigs

Abstract

Fat deposition is a crucial element in pig production that affects production efficiency, quality and consumer choices. In this study, Duroc pigs, a Western, famous lean pig breed, and Luchuan pigs, a Chinese, native obese pig breed, were used as animal materials. Transcriptome sequencing was used to compare the back adipose tissue of Duroc and Luchuan pigs, to explore the key genes regulating fat deposition. The results showed that 418 genes were highly expressed in the Duroc pig, and 441 genes were highly expressed in the Luchuan pig. In addition, the function enrichment analysis disclosed that the DEGs had been primarily enriched in lipid metabolism, storage and transport pathways. Furthermore, significant differences in the metabolic pathways of alpha-linolenic acid, linoleic acid and arachidonic acid explained the differences in the flavor of the two kinds of pork. Finally, the gene set enrichment analysis (GSEA) exposed that the difference in fat deposition between Duroc and Luchuan pigs may be due to the differential regulation of the metabolism pathway of fatty acid. Therefore, this study described the differential expression transcriptional map of adipose tissue of Duroc pig and Luchuan pig, identified the functional genes regulating pig fat deposition, and provided new hypotheses and references for further study of fat development.

Keywords: Duroc; Luchuan; fat deposition; lipid metabolism; meat quality; transcriptome.

Figure 1

Phenotype and characteristics of RNA-seq data. (A) Adipose tissue sections at 200× and 400× magnification. Quantification of the diameter and area of adipocytes. (B) Backfat thickness of Duroc and Luchuan. (C) PCA of samples. (D) The petal Venn diagram of the gene identified by RNA-seq. (E) Expression abundance correlation analysis between Duroc and Luchuan in RNA-seq. (F) Distribution of the mRNA abundance. The data are expressed as mean ± SD. **** p < 0.0001.

Figure 2

Identification of DEGs. (A) The statistical analysis of DEGs between Duroc and Luchuan adipose. (B) The volcano map of DEGs. The gene with p-value < 0.01 and log₂ Fold Change > 1 is marked in red; the gene with p-value < 0.01 and log₂ Fold Change < −1 is marked in blue. (C) Duroc and Luchuan adipose tissue can be clearly distinguished based on their transcriptome characteristics. The color key (from blue to red) of abundance value indicated low to high expression levels.

Figure 3

GO and KEGG analysis of DEGs for Duroc and Luchuan adipose. (A) GO analysis of DEGs. (B) KEGG summary graph showing the summary of the KEGG pathway. Different colors represent different KEGG A class categories. (C) Left: distribution of DEGs across chromosomes. Right: significantly enriched GO terms by DEGs in chromosome 12.

Figure 4

Functional gene screening and functional verification. (A) GSEA-KEGG analysis of the transcriptome. A pathway of positive enrichment score is up-regulated, whereas a pathway of negative enrichment score is down-regulated. (B) Gene expression heatmap of the fatty acid metabolic pathway. The color key (from blue to red) of abundance value indicated low to high expression levels. (C) Gene expression levels quantified by RNA-seq and RT-qPCR. HACD2, 3-hydroxyacyl-CoA dehydratase 2. HSD17B4, hydroxysteroid 17-beta dehydrogenase 4. The data are expressed as mean ± SD. * p < 0.05.