Identification of the Genetic Basis for the Large-tailed Phenotypic Trait in Han Sheep Through Integrated mRNA and miRNA Analysis of Tail Fat Tissue Samples

Abstract

Background: While evolution has led certain breeds of sheep to exhibit large tails composed of fatty tissue, the genetic basis for this fatty large-tailed phenotypic trait remains to be defined in breeds of Han sheep. Here, we employed a high-throughput sequencing approach to identify mRNAs and microRNAs (miRNAs) that were differentially expressed in tail fat tissue samples from large-tailed Han (LTH) and small-tailed Han (STH) sheep in order to identify key genetic determinants of the large-tailed phenotype.Results: In total, we identified 521 mRNAs (237 upregulated, 284 downregulated) and 14 miRNAs (6 upregulated, 8 downregulated) that were differentially expressed between these two sheep breeds. Predictive analytical database tools were subsequently utilized to identify 2,409 putative targets of these differentially expressed miRNAs (DEMs), including 65 which were among the list of differentially expressed genes (DEGs) identified in the present study. By specifically focusing on predicted DEM/DEG pairs with appropriate regulatory directionality, we identified DIRF, HSD17B12, LPL, APOBR, INSIGI, THRSP, ACSL5, FAAH, ACSS2, APOA1, ACLY, and ACSM3 through mRNA analyses and ACSL4, FTO, FGF8, IGF2, GNPDA2, LIPG, PRKAA2, ELOVL7, SOAT2, and SIRT1 through miRNA analyses as candidate genes which may regulate fat deposition and fatty acid metabolism in the adipose tissue from the tails of Han sheep. Conclusion: Together, our data provide insight into the potential genetic basis for the large-tailed phenotype of LTH sheep, suggesting that it may be attributable to specific DEMs and DEGs that regulate one another and thereby control lipid metabolism. These data provide a basis for future research regarding the role of these genes in ovine tail fat deposition, and offer preliminary perspectives on the molecular mechanisms governing the fatty large-tailed phenotype in LTH sheep.

Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat

“…Among these DETs, 21 DETs are differentially expressed lncRNAs, including 14 known lncRNAs and seven novel lncRNAs. The correlation between differentially expressed lncRNAs and DETs which transcribed from tail fat related candidate genes, including diacylglycerol O-acyltransferase 2 ( DGAT2 ) ( Bakhtiarizadeh & Alamouti, 2020 ), acetyl-CoA carboxylase alpha ( ACACA ) ( Bakhtiarizadeh & Alamouti, 2020 ; Bakhtiarizadeh & Salami, 2019 ), ATP citrate lyase ( ACLY ) ( Bakhtiarizadeh & Alamouti, 2020 ), fatty acid synthase ( FASN ) ( Bakhtiarizadeh & Alamouti, 2020 ), stearoyl-CoA desaturase ( SCD ) ( Kang et al, 2017a ), and acyl-CoA synthetase short chain family member 2 ( ACSS2 ) ( Guangli et al, 2020 ), was investigated. The result suggests that 20 out of 21 lncRNAs (except lncRNA ENSOART00020017088) were significantly correlated with at least one transcripts ( Fig.…”

“…Four DETs, 11.689.28, 11.689.18, 11.689.14, and 11.660.12, were transcribed from ACLY . ACSS2 and ACLY have been identified as candidate genes related to tail fat deposition in sheep ( Bakhtiarizadeh & Alamouti, 2020 ; Guangli et al, 2020 ). Cytosolic acetyl CoA (Ac-CoA), the central precursor for lipid biosynthesis in mammals, is produced by ACLY from mitochondria-derived citrate or by ACSS2 from acetate ( Vysochan et al, 2017 ).…”

Peer Review #1 of "Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat (v0.1)"

“…Four DETs,11.689.28,11.689.18,11.689.14 and 11.660.12, were transcribed from ACLY. ACSS2 and ACLY have been identified as candidate genes related to tail fat deposition in sheep (Bakhtiarizadeh & Alamouti 2020;Guangli et al 2020). Cytosolic acetyl CoA (Ac-CoA), the central precursor for lipid biosynthesis in mammals, is produced by ACLY from mitochondriaderived citrate or by ACSS2 from acetate (Vysochan et al 2017).…”

Peer Review #2 of "Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat (v0.1)"

“…Among these DETs, 21 DETs are differentially expressed lncRNAs, including 14 known lncRNAs and seven novel lncRNAs. The correlation between differentially expressed lncRNAs and DETs which transcribed from tail fat related candidate genes, including diacylglycerol O-acyltransferase 2 (DGAT2) (Bakhtiarizadeh & Alamouti 2020), acetyl-CoA carboxylase alpha (ACACA) (Bakhtiarizadeh & Alamouti 2020;, ATP citrate lyase (ACLY) (Bakhtiarizadeh & Alamouti 2020), fatty acid synthase (FASN) (Bakhtiarizadeh & Alamouti 2020), stearoyl-CoA desaturase (SCD) (Kang et al 2017a), and acyl-CoA synthetase short chain family member 2 (ACSS2) (Guangli et al 2020), was investigated. The result suggests that 20 out of 21 lncRNAs (except lncRNA ENSOART00020017088) were significantly correlated with at least one transcripts (Fig.…”