Integration of Transcriptome and Whole Genomic Resequencing Data to Identify Key Genes Affecting Swine Fat Deposition

Abstract

Fat deposition is highly correlated with the growth, meat quality, reproductive performance and immunity of pigs. Fatty acid synthesis takes place mainly in the adipose tissue of pigs; therefore, in this study, a high-throughput massively parallel sequencing approach was used to generate adipose tissue transcriptomes from two groups of Songliao black pigs that had opposite backfat thickness phenotypes. The total number of paired-end reads produced for each sample was in the range of 39.29–49.36 millions. Approximately 188 genes were differentially expressed in adipose tissue and were enriched for metabolic processes, such as fatty acid biosynthesis, lipid synthesis, metabolism of fatty acids, etinol, caffeine and arachidonic acid and immunity. Additionally, many genetic variations were detected between the two groups through pooled whole-genome resequencing. Integration of transcriptome and whole-genome resequencing data revealed important genomic variations among the differentially expressed genes for fat deposition, for example, the lipogenic genes. Further studies are required to investigate the roles of candidate genes in fat deposition to improve pig breeding programs.

Putative positive role of inflammatory genes in fat deposition supported by altered gene expression in purified human adipocytes and preadipocytes from lean and obese adipose tissues

“…By constructing three mouse models with adipocyte (AC)-speci cally attenuated in ammatory responses, Asterholm et al [22] showed that proper AT remodeling and expansion are executed by in ammatory responses at the level of ACs, so that reduced or impaired local in ammatory responses in the AC cause pathogenic obesity-related conditions, such as hepatic steatosis or metabolic dysfunction due to ectopic lipid accumulation [23,24]. Interestingly, a recent AT-derived RNA-seq analysis of pigs showed that pigs with thicker backfat tended to express signi cantly lower levels of immune and in ammatory genes than pigs with thinner back fat, which indicates that expression of high in ammatory genes may be associated with lower fat accumulation in AT [25]. Few studies have addressed the positive role of the in ammatory response which may have a role in fat deposition in lean individuals, although fat cell differentiation and fat deposition must be regulated appropriately to maintain healthy fat homeostasis.…”

Putative Positive Role of Inflammatory Genes in Fat Deposition Supported by Altered Gene Expression in Purified Human Adipocytes and Preadipocytes From Lean and Obese Adipose Tissues

“…Baranova et al (2005) reported a paradoxical decrease in the expression of pro-angiogenic genes, which is another gene class that is expected to increase in obese individuals [29]. Moreover, a recent AT-derived RNA-seq analysis of pigs showed that pigs with thicker back fat tend to express signi cantly lower levels of immune and in ammatory genes than pigs with thinner back fat, indicating that the expression of high in ammatory genes may be associated with lower fat accumulation in AT [30].…”

Molecular cloning of SLC35D3 and analysis of its role during porcine intramuscular preadipocyte differentiation

“…Pigs have long served as models in biomedical research because of their similarity to humans with regard to body size, physiological conditions, eating patterns, and fat deposition [1][2][3][4]. Pig breeds do vary in fat deposition and are characterized by differences in intramuscular fat content and backfat thickness.…”