Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep

Abstract

Fat-tail content of sheep breeds is varied and the molecular mechanisms regulating fat-tail development have not been well characterized. Aiming at better identifying the important candidate genes and their functional pathways contributing to fat deposition in the tail, a comparative transcriptome analysis was performed between fat- (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds using RNA-seq. The experiment was conducted on six male lambs (three lambs per each breed) at seven months of age. Four different combinations of aligners and statistical methods including Hisat2 + edgeR, Hisat2 + DESeq2, STAR + edgeR and STAR + DESeq2 were used to identify the differentially expressed genes (DEGs). The DEGs were selected for functional enrichment analysis and protein-protein interaction (PPI) network construction. Module analysis was also conducted to mine the functional sub-networks from the PPI network. In total, 264 genes including 80 up- and 184 down-regulated genes were identified as DEGs. The RNA-Seq results were validated by Q-RT-PCR. Functional analysis of DEGs and the module analysis of PPI network demonstrated that in addition to pathways affecting lipid metabolism, a series of enriched functional terms related to “response to interleukin”, “MAPK signaling pathways”, “Wnt signaling pathway”, “ECM-receptor interaction”, “regulation of actin cytoskeleton”, and “response to cAMP” might contribute to the deposition of fat in tails of sheep. Overall results using RNA-Seq analysis characterized important candidate genes involved in the fatty acid metabolism and regulation of fat deposition, suggesting novel insights into molecular aspects of fat-tail metabolism in sheep. Selected DEGs should be further investigated as potential markers associated with the fat-tail development in sheep breeds.

RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep

“…Our previous study showed that most of the differentially expressed genes up-regulated in Zel compared to Lori-Bakhtiari were involved in fatty acid oxidation pathways such as PPAR signaling pathway 3 . Likewise, most of the breed-specific SNPs identified in this study were characterized in Zel.…”

“…FABP4 is a small cytosolic protein that specifically transports long chain fatty acids to the sites of storage 75 . This gene was candidated for being relevant to fat deposition in our previous studies 3,11 . Also, the role of this gene in determining the fat content has been highlighted in mouse 76 , cattle 77 and pig 78 .…”

“…1), all of which were treated with the same protocols. Detailed information about the samples and the experimental design have been described previously 3 . Briefly, fat-tail tissues of the sheep were collected immediately after the animals were slaughtered at seven months of age (four Lori-Bakhtiari and four Zel sheep).…”

“…Lori-Bakhtiari and Zel. To clarify, these are two of over 28 Iranian sheep breeds 3,10 differing in many morphological features and phenotypes. Lori-Bakhtiari is one of the heaviest breeds in the south-western regions of Iran with a large fat-tail often hanging down the hocks.…”

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

“…Comparative transcriptome analysis is another efficient way used for identifying candidate causative genes that associated with distinct phenotypic differences between thin-and fat-tailed sheep breeds [56][57][58]. However, it presented little power to identify genetic factors that contribute to these phenotypic differences because the identified DEGs always reflect both cisand trans-acting regulatory variations [59].…”