Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle

Li, Yaokun; Carrillo, José A.; Ding, Yi; He, Yanghua; Zhao, Chunping; Liu, Jianan; Liu, George E.; Liu, Zan; Song, Jiuzhou

doi:10.1371/journal.pone.0135670

Cited by 12 publications

(11 citation statements)

References 39 publications

(36 reference statements)

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“…The RNA extraction, cDNA synthesis, library preparation, transcriptome sequencing, and raw data were carried out from our reported protocols [29][30][31]. We employed FastQC v.0.11.2 (https://www.bioinformatics.…”

Section: Rna Sequencing and Analysismentioning

confidence: 99%

“…Grass-fed beef may contain less total fat than grain-fed beef, but a lot more omega-3 fatty acids and conjugated linoleic acid [26][27][28]. In our previous studies, the alterations in divergences in free fatty acids, lipid levels, and gene expression patterns have been observed between grass-fed and grain-fed Angus cattle [29][30][31]. However, information on the possible mechanism on mitochondrial function and metabolism between the grass-fed and grain-fed is lacking.…”

Section: Introductionmentioning

confidence: 97%

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Diet induced the change of mtDNA copy number and metabolism in Angus cattle

Bai

Carrillo

et al. 2020

J Animal Sci Biotechnol

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Background: Grass-fed and grain-fed Angus cattle differ in the diet regimes. However, the intricate mechanisms of different beef quality and other phenotypes induced by diet differences are still unclear. Diet affects mitochondrial function and dynamic behavior in response to changes in energy demand and supply. In this study, we examined the mtDNA copy number, mitochondria-related genes expression, and metabolic biomarkers in grass-fed and grainfed Angus cattle. Results: We found that the grass-fed group had a higher mtDNA copy number than the grain-fed group. Among different tissues, the mtDNA copy number was the highest in the liver than muscle, rumen, and spleen. Based on the transcriptome of the four tissues, a lower expression of mtDNA-encoded genes in the grass-fed group compared to the grain-fed group was discovered. For the mitochondria-related nuclear genes, however, most of them were significantly down-regulated in the muscle of the grass-fed group and up-regulated in the other three tissues. In which, COX6A2, POLG2, PPIF, DCN, and NDUFA12, involving in ATP synthesis, mitochondrial replication, transcription, and maintenance, might contribute to the alterations of mtDNA copy number and gene expression. Meanwhile, 40 and 23 metabolic biomarkers were identified in the blood and muscle of the grain-fed group compared to a grass-fed group, respectively. Integrated analysis of the altered metabolites and gene expression revealed the high expression level of MDH1 in the grain-fed group might contribute to the mitochondrial NADH oxidation and spermidine metabolism for adapting the deletion mtDNA copy number. Conclusions: Overall, the study may provide further deep insight into the adaptive and regulatory modulations of the mitochondrial function in response to different feeding systems in Angus cattle.

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Section: Rna Sequencing and Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Diet induced the change of mtDNA copy number and metabolism in Angus cattle

Bai

Carrillo

et al. 2020

J Animal Sci Biotechnol

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“…The spleen is the largest lymphatic organ in the body, plays a critical role in the immune system [43], and contains many immune cells, including B cells, T cells, natural killer (NK) cells, and macrophages [16]. In the spleen tissues, 1530 DEGs were detected from which 135 GO terms and 15 KEGG pathways were annotated by GO and KEGG pathway enrichment analysis, respectively.…”

Section: Discussionmentioning

confidence: 99%

Comparative Analysis of the Liver and Spleen Transcriptomes between Holstein and Yunnan Humped Cattle

Chen

Zeng

Shi

et al. 2019

Animals

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Simple SummaryCattle are important agricultural animals that provide essential sources of meat, milk, fertilizer for crops, clothing, and animal traction for human use, and the demand for these products has increased in recent years. There are existing differences in disease resistance between different cattle breeds. However, the genetic basis underlying disease resistance differences is poorly understood and requires further investigation. In this study, many immune- and disease-relevant genes and pathways were identified between Holstein and Yunnan humped cattle using RNA-sequencing. The novel findings regarding the genetic basis underlying disease resistance differences between zebu cattle and taurine cattle will provide a scientific basis and key technical support for disease-resistant breeding of domestic cattle, and thus have important social and economic significance.AbstractPrevious studies have shown that Yunnan humped cattle have higher disease resistance than pure taurine cattle, such as Holsteins. However, there exists limited information about the molecular genetic basis underlying disease resistance differences between them. The objective of this study was to compare differentially expressed genes (DEGs) in the liver and spleen tissues of Holstein and Yunnan humped cattle through comparative transcriptome analysis, using RNA-sequencing. In total, 1564 (647 up- and 917 down-regulated genes) and 1530 (716 up- and 814 down-regulated genes) DEGs were obtained in the liver and spleen tissues of Holstein and Yunnan humped cattle comparison groups, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the DEGs were mainly associated with the RIG-I signaling pathway, immune responses, major histocompatibility complex (MHC) class I protein complex and complement activation, human T-cell lymphotropic virus type-I (HTLV-I) infection. Some genes related to immune function, such as C1QB, CD55, MASP2, C4BPA, MAVS, NOD2, and CD46, were up-regulated in Yunnan humped cattle, while C2, SERPING1, SERPINE1, TIRAP, TLR2, and TLR6 were down-regulated. The expression levels of 11 selected DEGs, analyzed by quantitative reverse-transcription polymerase chain reaction (RT-qPCR), were consistent with the deep sequencing results by RNA-sequencing. Our results will provide a scientific basis and key technical support for disease-resistant breeding of domestic cattle.

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“…After weaning, the calves were randomly assigned to either grass or grain-fed style to reach market weight and get slaughtered. Our previous studies using the same animals already pointed out several advantages of the grass-fed method over the grain-fed method [16,17]. In this study, we would like to probe further from the aspect of the gut bacteria to explore the potential roles of bacteria in the jejunum and their relationships with bile acids to in uence cattle metabolism.…”

Section: Introductionmentioning

confidence: 97%

Diet-induced Changes in Bacterial Communities in the Jejunum and Their Associations with Bile Acids in Angus Beef Cattle

Liu

Cai

et al. 2020

Preprint

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Background: The small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate bacterial composition and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the influence of diets on jejunal bacterial communities and examined its relationships with bile acids. Here, we examined the impact of grain- and grass-based diets on jejunal and fecal bacterial communities’ composition and investigated possible association of bacterial features with bile acids.Results: We demonstrated that the influences of diets on intestinal bacteria can be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was documented in feces of grass-fed cattle comparing to grain-fed cattle. Top 20 important genera identified with random forest analysis on fecal bacterial community can be good candidates for microbial biomarkers. Moreover, the jejunal bacteria of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and bacteria signatures predictive of bile acids were identified, indicative of the potential association of bacterial features with bile acids.Conclusions: The findings from this study provided novel insights into the relationships between jejunal bacteria and bile acids under different diets in Angus beef cattle. Our results should help us gain a better understanding of potential health benefits of grass-fed beef.

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Transcriptomic Profiling of Spleen in Grass-Fed and Grain-Fed Angus Cattle

Cited by 12 publications

References 39 publications

Diet induced the change of mtDNA copy number and metabolism in Angus cattle

Diet induced the change of mtDNA copy number and metabolism in Angus cattle

Comparative Analysis of the Liver and Spleen Transcriptomes between Holstein and Yunnan Humped Cattle

Diet-induced Changes in Bacterial Communities in the Jejunum and Their Associations with Bile Acids in Angus Beef Cattle

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