Fan Li, Zongliang He, Yinglin Lu, Jing Zhou, Heng Cao, Xingyu Zhang, Hongjie Ji, Kunpeng Lv, Debing Yu, Minli Yu
{"title":"通过转录组分析鉴定鸭胸肌发育差异的相关差异基因","authors":"Fan Li, Zongliang He, Yinglin Lu, Jing Zhou, Heng Cao, Xingyu Zhang, Hongjie Ji, Kunpeng Lv, Debing Yu, Minli Yu","doi":"10.5713/ab.23.0505","DOIUrl":null,"url":null,"abstract":"Objective\nThe objective of this study was to identify candidate genes that play im-portant roles in skeletal muscle development in ducks.\n\n\nMethods\nIn 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.\n\n\nResults\nA 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.\n\n\nConclusion\nThis study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.","PeriodicalId":2,"journal":{"name":"ACS Applied Bio Materials","volume":"169 ","pages":""},"PeriodicalIF":4.6000,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Identification of relevant differential genes to the divergent devel-opment of pectoral muscle in ducks by transcriptomic analysis.\",\"authors\":\"Fan Li, Zongliang He, Yinglin Lu, Jing Zhou, Heng Cao, Xingyu Zhang, Hongjie Ji, Kunpeng Lv, Debing Yu, Minli Yu\",\"doi\":\"10.5713/ab.23.0505\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Objective\\nThe objective of this study was to identify candidate genes that play im-portant roles in skeletal muscle development in ducks.\\n\\n\\nMethods\\nIn 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.\\n\\n\\nResults\\nA 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.\\n\\n\\nConclusion\\nThis study provided information of molecular mechanisms underlying the developmental differences in skeletal muscles between specialized duck lines.\",\"PeriodicalId\":2,\"journal\":{\"name\":\"ACS Applied Bio Materials\",\"volume\":\"169 \",\"pages\":\"\"},\"PeriodicalIF\":4.6000,\"publicationDate\":\"2024-04-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"ACS Applied Bio Materials\",\"FirstCategoryId\":\"97\",\"ListUrlMain\":\"https://doi.org/10.5713/ab.23.0505\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"MATERIALS SCIENCE, BIOMATERIALS\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"ACS Applied Bio Materials","FirstCategoryId":"97","ListUrlMain":"https://doi.org/10.5713/ab.23.0505","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"MATERIALS SCIENCE, BIOMATERIALS","Score":null,"Total":0}
Identification of relevant differential genes to the divergent devel-opment of pectoral muscle in ducks by transcriptomic analysis.
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.
期刊介绍:
ACS Applied Bio Materials is an interdisciplinary journal publishing original research covering all aspects of biomaterials and biointerfaces including and beyond the traditional biosensing, biomedical and therapeutic applications.
The journal is devoted to reports of new and original experimental and theoretical research of an applied nature that integrates knowledge in the areas of materials, engineering, physics, bioscience, and chemistry into important bio applications. The journal is specifically interested in work that addresses the relationship between structure and function and assesses the stability and degradation of materials under relevant environmental and biological conditions.