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Identification of relevant differential genes to the divergent devel-opment of pectoral muscle in ducks by transcriptomic analysis |
Fan Li1 
, Zongliang He2
, Yinglin Lu1
, Jing Zhou1
, Heng Cao1
, Xingyu Zhang1
, Hongjie Ji2
, Kunpeng Lv2
, Debing Yu1,*
, Minli Yu1,*
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1Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, 210095 Jiangsu, China
2Nanjing Institute of Animal Husbandry and Poultry Science, Nanjing 210036 Jiangsu, China |
Correspondence:
Debing Yu, Tel: +86-25-84395036, Fax: +86-25-84395036, Email: yuminli@njau.edu.cn
Minli Yu, Tel: +86-25-84395036, Fax: +86-25-84395036, Email: yuminli@njau.edu.cn
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Received: 1 December 2023 • Revised: 12 January 2024 • Accepted: 26 January 2024 |
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| Abstract |
Objective
The objective of this study was to identify candidate genes that play im-portant roles in skeletal muscle development in ducks.
Methods
In this study, we investigated the transcriptional sequencing of embryonic pectoral muscles from two specialized line LCA and LCC ducks which were devel-oped from Liancheng White ducks (female) and Cherry Valley ducks (male) F6 hybrid population. In addition, prediction of target genes for the differentially expressed mRNAs was conducted and the enriched gene ontology (GO) terms and Kyoto En-cyclopedia of Genes and Genomes (KEGG) signaling pathways were further analyzed. Finally, a protein-to-protein interaction (PPI) network was analyzed by using the tar-get genes to gain insights into their potential functional association.
Results
A total of 1428 differentially expressed genes (DEGs) with 762 being up-regulated genes and 666 being down-regulated genes in pectoral muscle of LCA and LCC ducks identified by RNA-seq (p < 0.05). Meanwhile, 23 GO terms in the down-regulated genes and 75 GO terms in up-regulated genes were significantly en-riched (p < 0.05). Furthermore, the top 5 most enriched pathways were ECM-receptor interaction, fatty acid degradation, pyruvate degradation, PPAR signaling pathway, and glycolysis/gluconeogenesis. Finally, the candidate genes including Integrin b3 (Itgb3), Pyruvate kinase M1/2 (Pkm), Insulin-like growth factor 1 (Igf1), glu-cose-6-phosphate isomerase（Gpi）, GABA type A receptor-associated protein-like 1(Gabarapl1), and Thyroid hormone receptor beta (Thrb) showed the most expression difference, and then were selected to verification by qRT-PCR. The result of qRT-PCR was consistent with that of transcriptome sequencing.
Conclusion
This study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.
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| Keywords:
Ducks; Gene Expression; Myofiber Characteristics; Skeletal Muscles; Transcriptomics |
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