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

Yaokun Li,Yi Ding,Linsen Zan,Jiuzhou Song,Chunping Zhao,Yanghua He,José A Carrillo,Yung-Fu Chang

doi:10.1371/journal.pone.0116437

Yaokun Li, Yi Ding + Show 6 more

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https://doi.org/10.1371/journal.pone.0116437

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Abstract

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.

Highlights

As the integral part of food production system, cattle make valuable contributions to the diversity of human food supply, and play a main role in nutrient recycling and still constitute a significant work force in some countries
Our analysis demonstrated that most of the pathways enriched with the differentially expressed genes were related to cell development and biosynthesis
Among the top 10 differentially expressed genes (DEGs), DSG1 is related to embryonic, organ and organismal development; RSPO3 is related to abnormal morphology and organismal death

Summary

Introduction

As the integral part of food production system, cattle make valuable contributions to the diversity of human food supply, and play a main role in nutrient recycling and still constitute a significant work force in some countries. The increment of meat production is critical for the years to come, the improvement in composition and quality of the beef is essential. With regard to the perceived divergence in nutritional quality between grass-fed and grain-fed cattle, growing consumers were interested in grass-fed beef products due to the decreasing fatty acid content [3]. Studies on lamb suggested that the meat from concentrate feeding was more tender and juicer than the grass-fed lambs; the carcass was heavier, with more fatty and less liver flavor in animals from concentrate diets [5]. Numerous studies have demonstrated higher concentration of vitamin E in the meat of grass-fed cattle compared with products from concentrate diets [8,9,10]

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