GSE122349
Identification of genes related with carcass fatness in pigs based on RNA-seq results
Purpose: RNA-seq method was applied to select genes expressed in fat tissue and pinpointed genes potentially associated with fatness traits in pigs. Methods: The RNA-seq analysis was performed on fat tissue collected from 16 Pulawska pigs (8 pigs per two groups - with high and low backfat thickness) maintained at the same environmental and feeding condition. The total RNA was isolated using by TriReagent and 300ng was used to  cDNA libraries preparation.  The NGS sequencing was performed on HiScan SQ (Illumina) in 90 single-end cycles. The quantifying transcript abundances was made using the RSEM supported by STAR aligner. The raw reads were aligned to the Sus scrofa reference genome. Differentially expressed genes were detected by DESeq2. The RNA-seq results were validated using by qPCR. Results: In the group of pigs characterized by thicker subcutaneous fat, 166 genes with increased expression were identified, including genes involved in biological processes associated with negative regulation of long-chain fatty acid transport (GO: 0010748) (IRS2, THBS1, AKT2), regulation of metabolic lipids ( GO: 0019216) (EEF1A2, IRS2, ACACA, SIK1, ADGRF5, IDH1, FGF2, PDE3B, FASN, AKT2, CYR61, CHD9, ME1, SCD), cellular response to hormonal stimuli (GO: 0032870) (IRS2, ACACA, SIK1 , GHR, NR4A1, PDE3B, PTGER2, AKT2, AACS, ADCY6, KAT2B, RHOQ, FOS). Genes involved in the signaling pathway responsible for the activation of gene expression by SREBF (R-SSC-2426168) (ACACA, FASN, CHD9, SCD ) and the insulin signaling pathway also were identified (RHOQ, SOCS3, IRS2, AKT2, PDE3B, PYGM, FASN, ACACA). Conclusions: The presented results allowed to pinpointed the interesting, candidate genes related with fat content in carcasses in pigs, which can be analyzed in future in the term of using in breeding practice as genetic markers.  The study was financed from funds of the project -BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016. Overall design: The subcutaneous fat transcriptome sequencing was performed for 16 samples collected form Pulawska breed, using Illumina HiScan SQ in 90 single-end cycles and in 4 technical repetitions.