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Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition
BACKGROUND: The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, tr...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941690/ https://www.ncbi.nlm.nih.gov/pubmed/29739312 http://dx.doi.org/10.1186/s12864-018-4747-1 |
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author | Li, Baojun Qiao, Liying An, Lixia Wang, Weiwei Liu, Jianhua Ren, Youshe Pan, Yangyang Jing, Jiongjie Liu, Wenzhong |
author_facet | Li, Baojun Qiao, Liying An, Lixia Wang, Weiwei Liu, Jianhua Ren, Youshe Pan, Yangyang Jing, Jiongjie Liu, Wenzhong |
author_sort | Li, Baojun |
collection | PubMed |
description | BACKGROUND: The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. RESULTS: Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM–receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated. CONCLUSIONS: This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4747-1) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5941690 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-59416902018-05-14 Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition Li, Baojun Qiao, Liying An, Lixia Wang, Weiwei Liu, Jianhua Ren, Youshe Pan, Yangyang Jing, Jiongjie Liu, Wenzhong BMC Genomics Research Article BACKGROUND: The level of fat deposition in carcass is a crucial factor influencing meat quality. Guangling Large-Tailed (GLT) and Small-Tailed Han (STH) sheep are important local Chinese fat-tailed breeds that show distinct patterns of fat depots. To gain a better understanding of fat deposition, transcriptome profiles were determined by RNA-sequencing of perirenal, subcutaneous, and tail fat tissues from both the sheep breeds. The common highly expressed genes (co-genes) in all the six tissues, and the genes that were differentially expressed (DE genes) between these two breeds in the corresponding tissues were analyzed. RESULTS: Approximately 47 million clean reads were obtained for each sample, and a total of 17,267 genes were annotated. Of the 47 highly expressed co-genes, FABP4, ADIPOQ, FABP5, and CD36 were the four most highly transcribed genes among all the known genes related to adipose deposition. FHC, FHC-pseudogene, and ZC3H10 were also highly expressed genes and could, thus, have roles in fat deposition. A total of 2091, 4233, and 4131 DE genes were identified in the perirenal, subcutaneous, and tail fat tissues between the GLT and STH breeds, respectively. Gene Ontology (GO) analysis showed that some DE genes were associated with adipose metabolism. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that PPAR signaling pathway and ECM-receptor interaction were specifically enriched. Four genes, namely LOC101102230, PLTP, C1QTNF7, and OLR1 were up-regulated and two genes, SCD and UCP-1, were down-regulated in all the tested tissues of STH. Among the genes involved in ECM–receptor interaction, the genes encoding collagens, laminins, and integrins were quite different depending on the depots or the breeds. In STH, genes such as LAMB3, RELN, TNXB, and ITGA8, were identified to be up regulated and LAMB4 was observed to be down regulated. CONCLUSIONS: This study unravels the complex transcriptome profiles in sheep fat tissues, highlighting the candidate genes involved in fat deposition. Further studies are needed to investigate the roles of the candidate genes in fat deposition and in determining the meat quality of sheep. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-018-4747-1) contains supplementary material, which is available to authorized users. BioMed Central 2018-05-08 /pmc/articles/PMC5941690/ /pubmed/29739312 http://dx.doi.org/10.1186/s12864-018-4747-1 Text en © The Author(s). 2018 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Li, Baojun Qiao, Liying An, Lixia Wang, Weiwei Liu, Jianhua Ren, Youshe Pan, Yangyang Jing, Jiongjie Liu, Wenzhong Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title | Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title_full | Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title_fullStr | Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title_full_unstemmed | Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title_short | Transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
title_sort | transcriptome analysis of adipose tissues from two fat-tailed sheep breeds reveals key genes involved in fat deposition |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5941690/ https://www.ncbi.nlm.nih.gov/pubmed/29739312 http://dx.doi.org/10.1186/s12864-018-4747-1 |
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