Integrative Analysis of Transcriptomic and Lipidomic Profiles Reveals a Differential Subcutaneous Adipose Tissue Mechanism among Ningxiang Pig and Berkshires, and Their Offspring

SIMPLE SUMMARY: Understanding differential mechanisms of the subcutaneous adipose tissue between indigenous breeds and modern pig breeds is important. After transcriptome sequencing and liposome detection of the subcutaneous adipose tissue in Ningxiang pigs, Berkshires and F(1) offspring, we retrieved differentially expressed genes (DEGs) and significantly changed lipids (SCLs) in different groups. Integrative analysis of transcriptomic and lipidomic profiles and KEGG annotation revealed that the difference in fat deposition among Ningxiang pig, Berkshires, and F(1) offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This study identified the key genes and lipids and also provided insights into selection for backfat thickness and the fat composition of adipose tissue for pig breeding. ABSTRACT: Adipose tissue composition contributes greatly to the quality and nutritional value of meat. Transcriptomic and lipidomic techniques were used to investigate the molecular mechanisms of the differences in fat deposition in Ningxiang pigs, Berkshires and F(1) offspring. Transcriptomic analysis identified 680, 592, and 380 DEGs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F(1) offspring, and Ningxiang pigs vs. F(1) offspring. The lipidomic analysis screened 423, 252, and 50 SCLs in comparisons of Ningxiang pigs vs. Berkshires, Berkshires vs. F(1) offspring, and Ningxiang pigs vs. F(1) offspring. Lycine, serine, and the threonine metabolism pathway, fatty acid biosynthesis and metabolism-related pathways were significantly enriched in comparisons of Berkshires vs. Ningxiang pigs and Berkshires vs. F(1) offspring. The DEGs (PHGDH, LOC110256000) and the SCLs (phosphatidylserines) may have a great impact on the glycine, serine, and the threonine metabolism pathway. Moreover, the DEGs (FASN, ACACA, CBR4, SCD, ELOV6, HACD2, CYP3A46, CYP2B22, GPX1, and GPX3) and the SCLs (palmitoleic acid, linoleic acid, arachidonic acid, and icosadienoic acid) play important roles in the fatty acid biosynthesis and metabolism of fatty acids. Thus, the difference in fat deposition among Ningxiang pig, Berkshires, and F(1) offspring may be caused by differences in the expression patterns of key genes in multiple enriched KEGG pathways. This research revealed multiple lipids that are potentially available biological indicators and screened key genes that are potential targets for molecular design breeding. The research also explored the molecular mechanisms of the difference in fat deposition among Ningxiang pig, Berkshires, and F(1) pigs, and provided an insight into selection for backfat thickness and the fat composition of adipose tissue for future breeding strategies.