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Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle

Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, w...

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Autores principales: Li, Yaokun, Carrillo, José A., Ding, Yi, He, YangHua, Zhao, Chunping, Zan, Linsen, Song, Jiuzhou
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475051/
https://www.ncbi.nlm.nih.gov/pubmed/26090810
http://dx.doi.org/10.1371/journal.pone.0116437
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author Li, Yaokun
Carrillo, José A.
Ding, Yi
He, YangHua
Zhao, Chunping
Zan, Linsen
Song, Jiuzhou
author_facet Li, Yaokun
Carrillo, José A.
Ding, Yi
He, YangHua
Zhao, Chunping
Zan, Linsen
Song, Jiuzhou
author_sort Li, Yaokun
collection PubMed
description Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle.
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spelling pubmed-44750512015-06-30 Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle Li, Yaokun Carrillo, José A. Ding, Yi He, YangHua Zhao, Chunping Zan, Linsen Song, Jiuzhou PLoS One Research Article Beef represents a major diet component and one of the major sources of protein in human. The beef industry in the United States is currently undergoing changes and is facing increased demands especially for natural grass-fed beef. The grass-fed beef obtained their nutrients directly from pastures, which contained limited assimilable energy but abundant amount of fiber. On the contrary, the grain-fed steers received a grain-based regime that served as an efficient source of high-digestible energy. Lately, ruminant animals have been accused to be a substantial contributor for the green house effect. Therefore, the concerns from environmentalism, animal welfare and public health have driven consumers to choose grass-fed beef. Rumen is one of the key workshops to digest forage constituting a critical step to supply enough nutrients for animals’ growth and production. We hypothesize that rumen may function differently in grass- and grain-fed regimes. The objective of this study was to find the differentially expressed genes in the ruminal wall of grass-fed and grain-fed steers, and then explore the potential biopathways. In this study, the RNA Sequencing (RNA-Seq) method was used to measure the gene expression level in the ruminal wall. The total number of reads per sample ranged from 24,697,373 to 36,714,704. The analysis detected 342 differentially expressed genes between ruminal wall samples of animals raised under different regimens. The Fisher’s exact test performed in the Ingenuity Pathway Analysis (IPA) software found 16 significant molecular networks. Additionally, 13 significantly enriched pathways were identified, most of which were related to cell development and biosynthesis. Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis. Our results provided valuable insights into the molecular mechanisms resulting in the phenotype difference between grass-fed and grain-fed cattle. Public Library of Science 2015-06-19 /pmc/articles/PMC4475051/ /pubmed/26090810 http://dx.doi.org/10.1371/journal.pone.0116437 Text en © 2015 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Li, Yaokun
Carrillo, José A.
Ding, Yi
He, YangHua
Zhao, Chunping
Zan, Linsen
Song, Jiuzhou
Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title_full Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title_fullStr Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title_full_unstemmed Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title_short Ruminal Transcriptomic Analysis of Grass-Fed and Grain-Fed Angus Beef Cattle
title_sort ruminal transcriptomic analysis of grass-fed and grain-fed angus beef cattle
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475051/
https://www.ncbi.nlm.nih.gov/pubmed/26090810
http://dx.doi.org/10.1371/journal.pone.0116437
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