A comparison of transcriptomic patterns measured in the skin of Chinese fine and coarse wool sheep breeds

Abstract

We characterised wool traits, and skin gene expression profiles of fine wool Super Merino (SM) and coarse wool Small Tail Han (STH) sheep. SM sheep had a significantly higher total density of wool follicles, heavier fleeces, finer fibre diameter, and increased crimp frequency, staple length and wool grease (lanolin) production. We found 435 genes were expressed at significantly different levels in the skin of the two breeds (127 genes more highly in SM and 308 genes more highly in STH sheep). Classification of the genes more highly expressed in SM sheep revealed numerous lipid metabolic genes as well as genes encoding keratins, keratin-associated proteins, and wool follicle stem cell markers. In contrast, mammalian epidermal development complex genes and other genes associated with skin cornification and muscle function were more highly expressed in STH sheep. Genes identified in this study may be further evaluated for inclusion in breeding programs, or as targets for therapeutic or genetic interventions, aimed at altering wool quality or yield. Expression of the lipid metabolic genes in the skin of sheep may be used as a novel trait with the potential to alter the content or properties of lanolin or the fleece.

Figure 1

Histological analysis of fixed and hematoxylin-eosin stained skin tissue from Super Merino and Small Tail Han sheep shown at 40 × magnification. Representative primary wool follicles are indicated with stars and arrows indicate the secondary wool follicles. (A) Cross section SM sheep. (A’) Transverse section of SM sheep. (B) Cross section STH sheep. (B’) Transverse section of STH sheep.

Figure 2

Hormone levels determined by ELISA in blood sampled from Super Merino and Small Tail Han sheep during Autumn. No significant differences were detected between the sheep breeds.

Figure 3

The skin development gene expression correlation network determined by application of IPA methodology. The pathways identified result from a set of genes expressed at higher levels in the Super Merino sheep and shown in green. Genes more highly expressed in Small Tail Han sheep are shown in red.

Figure 4

The type I interferon pathway gene network predicted by IPA analysis. Genes shown in green were more highly expressed in the Super Merino sheep. The pathway contained many interferon induced genes which may serve in an antiviral response, including IFI6, IFI27, ISG15, RSAD2, Mx1, Mx2, and IFITM3. Genes more highly expressed in STH sheep are shown in red.

Figure 5

The correlation network of lipid metabolism genes found to be enriched in Super Merino (SM) sheep. Key fatty acid metabolic genes identified include fatty acid synthesis genes (ELOVL1, 3, 4), a carnitine carrier involved in transfer of fatty acids to the mitochondrion (SLC25A20), and many fatty acid metabolic enzymes (fatty acid 2-hydroxylase gene (FA2H), acyl-CoA dehydrogenase family member 9 gene (ACAD9), membrane bound O-acyltransferase domain containing 7 gene (MBOAT7), and perilipin 2, and 4 genes (PLIN2 and 4)). The network also contained genes involved in cholesterol metabolism in SM sheep (Squalene epoxidase gene (SQLE) and 3-hydroxy-3-methylglutaryl-CoA reductase gene (HMGCR) and the 24-dehydrocholesterol reductase gene (DHCR24)), the ceramide synthase 4 gene (CERS4) involved in production of a constituent of the integral hair lipid, and genes related to synthesis of triacylglyceride (STRA6, CRABPI, RDH12, DGAT2L6) and wax esters (AWAT1) respectively.

Figure 6

The comparison of transcript expression in terms of fold change as measured by RNA-sequencing and quantitative PCR (qPCR).