Transcriptomic Data Reveal Sheep Intramuscular Fat Deposition-Associated LncRNAs and Their Associated Genes and Pathways

doi:10.7668/hbnxb.20195563

Abstract

Abstract:

Intramuscular fat deposition,as a key factor affecting meat quality(e.g.tenderness,flavor,and juiciness),is closely related to the regulation of lipogenesis and lipid metabolism by long non-coding RNA(lncRNA).Based on the previous finding that the intramuscular fat content of Tan sheep was significantly higher than that of Dorper sheep and Small-tailed Han sheep,the dorsal longest muscle of these three sheep breeds was used as the target,and differentially expressed mRNAs(DE mRNAs)and lncRNAs(DE lncRNAs)and their related pathways were screened by transcriptome sequencing,with the aim of revealing molecular mechanism of high intramuscular fat deposition in Tan sheep.The results showed:836 DE mRNAs and 832 DE lncRNAs were identified in the Small-tailed Han sheep vs.Tan sheep group;578 DE mRNAs and 700 DE lncRNAs were screened in the Dorper sheep vs.Tan sheep group.The intersection of the two groups fielded a total of 226 DE mRNAs and 308 DE lncRNAs.Target gene prediction for the 308 DE lncRNAs identified 1 475 potential targets,including 687 co_expression(co-expressed)target genes and 788 co_localization(co-localized)target genes.GO and KEGG enrichment analysis of DE mRNAs revealed fat deposition-related pathways such as regulation of actin cytoskeleton and prolactin signaling pathway,with genes like FGF14 and FGF9 were reported to participate in animal fat metabolism.Enrichment analysis of co-expressed and co-localized target genes identified fat metabolism-related pathways,including the cAMP signaling pathway,prolactin signaling pathway,and insulin signaling pathway.Further functional analysis screened key genes associated with fat metabolism(CREBBP,ATP1B3,PPP1R3C, and PIK3R1),which may play crucial regulatory roles in ovine intramuscular fat deposition.The qRT-PCR results of 6 randomly selected DE mRNAs and 6 randomly selected DE lncRNAs were consistent with transcriptome sequencing data.

Key words: Tan sheep, Intramuscular fat deposition, Transcriptome, lncRNA

CLC Number:

S826

WANG Dingxiang, LI Chenglong, GUO Chenhao, FENG Dengzhen, KANG Xiaolong. Transcriptomic Data Reveal Sheep Intramuscular Fat Deposition-Associated LncRNAs and Their Associated Genes and Pathways[J]. Acta Agriculturae Boreali-Sinica, 2025, 40(6): 202-212. doi: 10.7668/hbnxb.20195563.

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Figures/Tables 6

Tab.1 Primer information of mRNA and lncRNA

引物名称 Primer name	引物序列(5'—3') Primer sequence(5'—3')	产物长度/bp Product length	退火温度/℃ Tm
PRKAA2	F:AGCAGAGGTCTGGTTCCTCA	158	60
	R:AGGTGAGACAGAGGACGACA
FGF9	F:AGTGGACTCTACCTCGGCAT	158	60
	R:ACGTAGAACCTCCGTCCAGT
FGF2	F:ACTTTAAGGACCCCAAGCGG	170	60
	R:ACGGTTTGCACACACTCCTT
TNC	F:ATGGGGAGATACGGGGACAA	115	60
	R:TTCGGAAGTTGCTGGGTCTC
CRH	F:CTTCCTCCGCCTGGGTAAC	103	60
	R:CTTGTCCGGAGAAAGGCGAC
CASR	F:CTTTGCTGTGCTGGGCATTT	125	60
	R:AGAGCAGGGAGAAGAGGAGG
GAPDH	F:TCGGAGTGAACGGATTCGG	162	60
	R:TGATGACGAGCTTCCCGTTC
TCONS_00033873	F:GTGCCGCCTCTGTGAACTTG	143	60
	R:GGTGACTGCTCTTCTGCTTTCTG
TCONS_00128473	F:TCAGACACAACTTAGCGACTACAC	83	60
	R:AAGCCTCCACCACCTCCAAC
TCONS_00112422	F:GGCTACCTGATGCGAAGAACTG	100	60
	R:CATCCAACCATCTCATCCTCTGTC
TCONS_00153755	F:TCTGGCTTTGTTTGAAGGGTTGTG	75	60
	R:CACCACCACTCCGAGGAATCC
TCONS_00193487	F:CCTGAGTGACTGAACTGAACTGAAG	135	60
	R:GGAAGGACAGATGATGAAGCAGAC
TCONS_00150301	F:TTGTGATTCGCTCTCCTCTTGTTG	109	60
	R:ATTGCTGCTTCTGCCGTTACTG

Tab.2 Intramuscular fat content in three sheep breeds

品种 Breeds	肌内脂肪/% Intramuscular fat content
杜泊羊D	3.41±0.41b
滩羊 T	5.42±2.35a
小尾寒羊XH	2.09±0.82b

Fig.1 Venn and volcano plots of DE mRNAs and DE lncRNAs A,D show the Venn diagram of DE mRNAs and DE lncRNAs of the two groups TvsH & TvsD;B and C.Volcano plots of DE mRNAs from the TvsD and TvsH groups;E and F.Volcano plots of DE lncRNAs from the TvsD and TvsH groups.

Fig.2 GO and KEGG enrichment analysis of DE mRNAs A.GO enrichment analysis of DE mRNAs:1.Chromatin silencing,2.Protein deacetylation,3.Protein deacylation,4.Negative regulation of gene expression,epigenetic,5.Macromolecule deacylation,6.Membrane fusion,7.Membrane organization,8.Nicotianamine metabolic process,9.Nicotianamine biosynthetic process,10.Eukaryotic translation initiation factor 2 complex,11.Virion membrane,12.Ciliary base,13.Growth factor activity,14.Receptor binding,15.Molecular transducer activity,16.Protein binding,17.Extracellular ligand-gated ion channel activity,18.Histone deacetylase activity,19.NAD-dependent histone deacetylase activity,20.Deacetylase activity,21.Protein deacetylase activity,22.NAD-dependent protein deacetylase activity,23.Hydrolase activity,acting on carbon-nitrogen(but not peptide)bonds,in linear amides,24.Growth factor receptor binding,25.Cytokine receptor binding,26.Phosphatidylinositol phosphate kinase activity,27.Receptor activity,28.Nicotianamine synthase activity,29.Ligand-gated ion channel activity,30.Ligand-gated channel activity;B.KEGG enrichment analysis of DE mRNAs:1.Hedgehog signaling pathway,2.Morphine addiction,3.Circadian rhythm,4.Circadian entrainment,5.Retrograde endocannabinoid signaling,6.Nicotine addiction,7.Bacterial invasion of epithelial cells,8.GABA ergic synapse,9.Neuroactive ligand-receptor interaction,10.Long-term depression,11.Melanogenesis,12.Mucin type O-Glycan biosynthesis,13.Melanoma,14.Glutamatergic synapse,15.Oocyte meiosis,16.African trypanosomiasis,17.Regulation of actin cytoskeleton,18.HTLV-I infection,19.TGF-beta signaling pathway,20.Prolactin signaling pathway.

Fig.3 GO and KEGG enrichment analysis of DE lncRNAs A.GO enrichment analysis of co-expressed target genes for DE lncRNAs:1.Amine biosynthetic process,2.Cellular biogenic amine biosynthetic process,3.Polyamine metabolic process,4.Polyamine biosynthetic process,5.Cellular biogenic amine metabolic process,6.Cellular amine metabolic process,7.Ammonium ion metabolic process,8.Spermine biosynthetic process,9.Spermine metabolic process,10.Immune system process,11.Skeletal system development,12.Chondrocyte differentiation,13.Chondrocyte proliferation,14.Cartilage development,15.Connective tissue development,16.Regeneration,17.Tissue regeneration,18.Developmental growth,19.Immune response,20.Amine metabolic process,21.rRNA processing,22.rRNA metabolic process,23.Response to fungus,24.Phycobilisome,25.Plasma membrane protein complex,26.Ferric iron binding,27.Cytokine activity,28.G-protein coupled receptor binding,29.Chemokine activity,30.Chemokine receptor binding;B.KEGG enrichment analysis of co-expressed target genes for DE lncRNAs:1.Mineral absorption,2.Ribosome biogenesis in eukaryotes,3.Influenza A,4.Salmonella infection,5.Legionellosis,6.Amoebiasis,7.Rheumatoid arthritis,8.Bile secretion,9.NOD-like receptor signaling pathway,10.Ribosome,11.Herpes simplex infection,12.Cardiac muscle contraction,13.Prion diseases,14.Tyrosine metabolism,15.cAMP signaling pathway,16.Drug metabolism-other enzymes,17.Cysteine and methionine metabolism,18.Tryptophan metabolism,19.Adrenergic signaling in cardiomyocytes 20.Ether lipid metabolism;C.GO enrichment analysis of co-located target genes for DE lncRNAs:1.Monovalent inorganic cation transport,2.Cellular nitrogen compound biosynthetic process,3.Potassium ion transport,4.Aromatic compound biosynthetic process,5.Heterocycle biosynthetic process,6.Nuclear-transcribed mRNA catabolic process,nonsense-mediated decay,7.Organic cyclic compound biosynthetic process,8.Inorganic cation transmembrane transport,9.Cellular nitrogen compound metabolic process,10.Inorganic ion transmembrane transport,11.Macromolecule biosynthetic process,12.Nucleobase-containing compound biosynthetic process,13.Transcription,DNA-templated,14.Nucleic acid-templated transcription,15.Regulation of transcription,DNA-templated,16.Regulation of nucleic acid-templated transcription,17.Cellular macromolecule biosynthetic process,18.Gene expression,19.RNA biosynthetic process,20.Cation transmembrane transport,21.Proton-transporting two-sector ATPase complex,catalytic domain,22.Intracellular,23.Cell,24.Cell part,25.Phospholipase inhibitor activity,26.Lipase inhibitor activity,27.Inward rectifier potassium channel activity,28.Nucleic acid binding,29.Potassium ion transmembrane transporter activity,30.Voltage-gated potassium channel activity;D.KEGG enrichment analysis of co-located target genes for DE lncRNAs:1.Antigen processing and presentation,2.RIG-I-like receptor signaling pathway,3.Osteoclast differentiation,4.Platelet activation,5.Taste transduction,6.Cell adhesion molecules(CAMs),7.Ribosome,8.Endometrial cancer,9.Tuberculosis,10.Insulin signaling pathway,11.Glyoxylate and dicarboxylate metabolism,12.Herpes simplex infection,13.Influenza A,14.GnRH signaling pathway,15.Gastric acid secretion,16.Thyroid cancer,17.Neurotrophin signaling pathway,18.Circadian rhythm,19.Prolactin signaling pathway,20.Hepatitis C.

Fig.4 qRT-PCR validation of DE mRNAs and DE lncRNAs

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