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Keogh K, Kenny DA, Alexandre PA, Waters SM, McGovern E, McGee M, Reverter A. Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency. Anim Microbiome 2024; 6:52. [PMID: 39304935 DOI: 10.1186/s42523-024-00337-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 08/24/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis. RESULTS Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG. CONCLUSIONS Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia.
| | - David A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Pamela A Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Sinead M Waters
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, Galway, Ireland
| | - Emily McGovern
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
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Keogh K, McGee M, Kenny DA. Effect of breed and dietary composition on the miRNA profile of beef steers divergent for feed efficiency. Sci Rep 2024; 14:20046. [PMID: 39209905 PMCID: PMC11362461 DOI: 10.1038/s41598-024-70669-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Identifying and breeding cattle that are more feed efficient is of great benefit to beef production. Additionally, it is crucial that genes contributing to feed efficiency are robust across varying management settings including dietary source as well as being relevant across contrasting breeds of cattle. The aim of this study was to determine miRNAs that are contributing to the expression of residual feed intake (RFI) across two breeds and dietary sources. miRNA profiling was undertaken in Longissimus dorsi tissue of Charolais and Holstein-Friesian steers divergent for RFI phenotype following two contrasting consecutive diets (high-forage and high-concentrate). Ten miRNA were identified as differentially expressed (adj. P < 0.1) across the breed and diet contrasts examined. Of particular interest was the differential expression of miR-2419-5p and miR-2415-3p, both of which were up-regulated in the Low-RFI Charolais steers across each dietary phase. Pathway analysis of target mRNA genes of differentially expressed miRNA revealed enrichment (P < 0.05) for pathways including metabolic related pathways, insulin receptor signalling, adipogenesis as well as pathways related to skeletal muscle growth. These results provide insight into the skeletal muscle miRNAome of beef cattle and their potential molecular regulatory mechanisms relating to feed efficiency in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
| | - M McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - D A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
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Taiwo G, Morenikeji OB, Idowu M, Sidney T, Adekunle A, Cervantes AP, Peters S, Ogunade IM. Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes. BMC Genomics 2024; 25:245. [PMID: 38443809 PMCID: PMC10913640 DOI: 10.1186/s12864-024-10150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.
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Affiliation(s)
- Godstime Taiwo
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, 300 Campus Drive, 16701, Bradford, PA, USA.
| | - Modoluwamu Idowu
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Taylor Sidney
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Ajiboye Adekunle
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | | | - Sunday Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ibukun M Ogunade
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA.
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Keogh K, Kenny DA, Alexandre PA, McGee M, Reverter A. An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle. BMC Genomics 2024; 25:234. [PMID: 38438858 PMCID: PMC10910725 DOI: 10.1186/s12864-024-10151-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 02/21/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network. RESULTS Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts. CONCLUSIONS Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland.
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia.
| | - D A Kenny
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - P A Alexandre
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia
| | - M McGee
- Livestock Systems Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - A Reverter
- Queensland Bioscience Precinct, CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, 4067, Brisbane, QLD, Australia
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Li H, Wang X, Vinsky M, Manafiazar G, Fitzsimmons C, Li L, Li C. Analyses of plasma metabolites using a high performance four-channel CIL LC-MS method and identification of metabolites associated with enteric methane emissions in beef cattle. PLoS One 2024; 19:e0299268. [PMID: 38427676 PMCID: PMC10906882 DOI: 10.1371/journal.pone.0299268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/06/2024] [Indexed: 03/03/2024] Open
Abstract
Reducing enteric methane (one greenhouse gas) emissions from beef cattle not only can be beneficial in reducing global warming, but also improve efficiency of nutrient utilization in the production system. However, direct measurement of enteric methane emissions on individual cattle is difficult and expensive. The objective of this study was to detect plasma metabolites that are associated with enteric methane emissions in beef cattle. Average enteric methane emissions (CH4) per day (AVG_DAILYCH4) for each individual cattle were measured using the GreenFeed emission monitoring (GEM) unit system, and beef cattle with divergent AVG_DAILYCH4 from Angus (n = 10 for the low CH4 group and 9 for the high CH4 group), Charolais (n = 10 for low and 10 for = high), and Kinsella Composite (n = 10 for low and 10 for high) populations were used for plasma metabolite quantification and metabolite-CH4 association analyses. Blood samples of these cattle were collected near the end of the GEM system tests and a high performance four-channel chemical isotope labeling (CIL) liquid chromatography (LC) mass spectrometer (MS) method was applied to identify and quantify concentrations of metabolites. The four-channel CIL LC-MS method detected 4235 metabolites, of which 1105 were found to be significantly associated with AVG_DAILYCH4 by a t-test, while 1305 were significantly associated with AVG_DAILYCH4 by a regression analysis at p<0.05. Both the results of the t-test and regression analysis revealed that metabolites that were associated with enteric methane emissions in beef cattle were largely breed-specific whereas 4.29% to 6.39% CH4 associated metabolites were common across the three breed populations and 11.07% to 19.08% were common between two breed populations. Pathway analyses of the CH4 associated metabolites identified top enriched molecular processes for each breed population, including arginine and proline metabolism, arginine biosynthesis, butanoate metabolism, and glutathione metabolism for Angus; beta-alanine metabolism, pyruvate metabolism, glycolysis / gluconeogenesis, and citrate cycle (TCA cycle) for Charolais; phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arginine biosynthesis, and arginine and proline metabolism for Kinsella Composite. The detected CH4 associated metabolites and enriched molecular processes will help understand biological mechanisms of enteric methane emissions in beef cattle. The detected CH4 associated plasma metabolites will also provide valuable resources to further characterize the metabolites and verify their utility as biomarkers for selection of cattle with reduced methane emissions.
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Affiliation(s)
- Hongwei Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
| | - Xiaohang Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Ghader Manafiazar
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Animal Science and Aquaculture, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, Alberta, Canada
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Lin C, Wang W, Zhang D, Huang K, Zhang Y, Li X, Zhao Y, Zhao L, Wang J, Zhou B, Cheng J, Xu D, Li W, Zhang X, Zheng W. Analysis of liver miRNA in Hu sheep with different residual feed intake. Front Genet 2023; 14:1113411. [PMID: 37928243 PMCID: PMC10620975 DOI: 10.3389/fgene.2023.1113411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Feed efficiency (FE), an important economic trait in sheep production, is indirectly assessed by residual feed intake (RFI). However, RFI in sheep is varied, and the molecular processes that regulate RFI are unclear. It is thus vital to investigate the molecular mechanism of RFI to developing a feed-efficient sheep. The miRNA-sequencing (RNA-Seq) was utilized to investigate miRNAs in liver tissue of 6 out of 137 sheep with extreme RFI phenotypic values. In these animals, as a typical metric of FE, RFI was used to distinguish differentially expressed miRNAs (DE_miRNAs) between animals with high (n = 3) and low (n = 3) phenotypic values. A total of 247 miRNAs were discovered in sheep, with four differentially expressed miRNAs (DE_miRNAs) detected. Among these DE_miRNAs, three were found to be upregulated and one was downregulated in animals with low residual feed intake (Low_RFI) compared to those with high residual feed intake (High_RFI). The target genes of DE_miRNAs were primarily associated with metabolic processes and biosynthetic process regulation. Furthermore, they were also considerably enriched in the FE related to glycolysis, protein synthesis and degradation, and amino acid biosynthesis pathways. Six genes were identified by co-expression analysis of DE_miRNAs target with DE_mRNAs. These results provide a theoretical basis for us to understand the sheep liver miRNAs in RFI molecular regulation.
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Affiliation(s)
- Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Kai Huang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaolong Li
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Liming Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Zheng
- Institute of Animal Husbandry Quality Standards, Xinjiang Academy of Animal Sciences, Urumqi, Xinjiang, China
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Yang C, Huang Z, Pan C, Wang S. Characterization of feed efficiency-related key signatures molecular in different cattle breeds. PLoS One 2023; 18:e0289939. [PMID: 37756351 PMCID: PMC10529570 DOI: 10.1371/journal.pone.0289939] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/30/2023] [Indexed: 09/29/2023] Open
Abstract
Feed efficiency is a major constraint in the beef industry and has a significant negative correlation with residual feed intake (RFI). RFI is widely used as a measure of feed efficiency in beef cattle and is independent of economic traits such as body weight and average daily gain. However, key traits with commonality or specificity among beef cattle breeds at the same level of RFI have not been reported. Accordingly, the present study hypothesized that signatures associated with feed efficiency would have commonality or specificity in the liver of cattle breeds at the same RFI level. By comparing and integrating liver transcriptome data, we investigated the critical signatures closely associated with RFI in beef cattle using weighted co-expression network analysis, consensus module analysis, functional enrichment analysis and protein network interaction analysis. The results showed that the consensus modules in Angus and Charolais cattle were negatively correlated, and four (turquoise, red, tan, yellow) were significantly positively correlated in Angus liver, while (turquoise, red) were significantly negatively correlated in Charolais liver. These consensus modules were found to be primarily involved in biological processes such as substance metabolism, energy metabolism and gene transcription, which may be one of the possible explanations for the difference in feed efficiency between the two beef breeds. This research also identified five key candidate genes, PLA2G12B, LCAT, MTTP, LCAT, ABCA1 and FADS1, which are closely associated with hepatic lipid metabolism. The present study has identified some modules, genes and pathways that may be the major contributors to the variation in feed efficiency among different cattle breeds, providing a new perspective on the molecular mechanisms of feed efficiency in beef cattle and a research basis for investigating molecular markers associated with feed efficiency in beef cattle.
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Affiliation(s)
- Chaoyun Yang
- College of Animal Science, Xichang University, Xichang City, Sichuan Province, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Zengwen Huang
- College of Animal Science, Xichang University, Xichang City, Sichuan Province, China
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
| | - Shuzhe Wang
- Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan City, Ningxia, China
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Mi H, Hu F, Gebeyew K, Cheng Y, Du R, Gao M, He Z, Tan Z. Genome wide transcriptome analysis provides bases on hepatic lipid metabolism disorder affected by increased dietary grain ratio in fattening lambs. BMC Genomics 2023; 24:364. [PMID: 37386405 DOI: 10.1186/s12864-023-09465-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The liver is a principal metabolic organ and has a major role in regulating lipid metabolism. With the development of rapidly fattening livestock in the modern breeding industry, the incidence of hepatic steatosis and accumulation in animals was significantly increased. However, the molecular mechanisms responsible for hepatic lipid metabolic disturbances in a high concentrate diet remain unclear. The objective of this study was to evaluate the effects of increasing concentrate level in a fattening lamb diet on biochemical indices, hepatic triglycerides (TG) concentration, and hepatic transcriptomic profiles. In the present study, 42 weaned lambs (about 3 ± 0.3 months old) were randomly assigned to the GN60 group (60% concentrate of dry matter, GN60, n = 21) or GN70 group (70% concentrate of dry matter, n = 21) for a 3-months feeding trial. RESULTS No difference was observed in the growth performance or plasma biochemical parameters between the GN60 group and the GN70 group. The hepatic TG concentration was higher in the GN70 group than GN60 group (P < 0.05). Hepatic transcriptomic analysis showed that there were 290 differentially expressed genes identified between GN60 and GN70 groups, with 125 genes up-regulated and 165 genes down-regulated in the GN70 group. The enriched Gene Ontology (GO) items and KEGG pathways and protein-protein interaction (PPI) network of differentially expressed genes (DEGs) revealed that the majority of enriched pathways were related to lipid metabolism. Further analysis revealed that the fatty acid synthesis was up-regulated, while fatty acid transport, oxidation, and TG degradation were down-regulated in the GN70 group when compared with the GN60 group. CONCLUSIONS These results indicated that GN70 induced excess lipid deposition in the liver of lambs during the fattening period, with high synthesis rates and low degradation rates of TG. The identified mechanisms may help understand hepatic metabolism in lambs with a high concentrate diet and provide insight into decreasing the risk of liver metabolism disorder in animals.
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Affiliation(s)
- Hui Mi
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Hu
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kefyalew Gebeyew
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Cheng
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruiping Du
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia, 010031, China
| | - Min Gao
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, Inner Mongolia, 010031, China
| | - Zhixiong He
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Keogh K, McKenna C, Waters SM, Porter RK, Fitzsimons C, McGee M, Kenny DA. Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake. Sci Rep 2023; 13:9034. [PMID: 37270611 DOI: 10.1038/s41598-023-35661-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is necessary for the accurate identification of feed efficient animals and will underpin accelerated genetic improvement of the trait. The aim of this study was to determine genes and biological processes contributing to RFI across varying breed type and dietary sources in skeletal muscle tissue. Residual feed intake was calculated in Charolais and Holstein-Friesian steers across multiple dietary phases (phase-1: high concentrate (growing-phase); phase-2: zero-grazed grass (growing-phase); phase-3: high concentrate (finishing-phase). Steers divergent for RFI within each breed and dietary phase were selected for muscle biopsy collection, and muscle samples subsequently subjected to RNAseq analysis. No gene was consistently differentially expressed across the breed and diet types examined. However, pathway analysis revealed commonality across breeds and diets for biological processes including fatty acid metabolism, immune function, energy production and muscle growth. Overall, the lack of commonality of individual genes towards variation in RFI both within the current study and compared to the published literature, suggests other genomic features warrant further evaluation in relation to RFI.
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Affiliation(s)
- Kate Keogh
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - Clare McKenna
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Sinead M Waters
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - Richard K Porter
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Claire Fitzsimons
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Teagasc, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, Co. Meath, C15 PW93, Ireland.
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10
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Transcriptome profile analysis identifies candidate genes of feed utilization in Dorper and Small Tail Han Crossbred sheep. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Taiwo G, Idowu MD, Wilson M, Pech-Cervantes A, Estrada-Reyes ZM, Ogunade IM. Residual Feed Intake in Beef Cattle Is Associated With Differences in Hepatic mRNA Expression of Fatty Acid, Amino Acid, and Mitochondrial Energy Metabolism Genes. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2022.828591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We evaluated the mRNA expression of genes involved in hepatic fatty acid, amino acid, and mitochondrial energy metabolism in crossbred beef steers with divergent low and high residual feed intake (RFI). Low-RFI beef steers (n = 8; RFI = - 1.93 kg/d) and high-RFI beef steers (n = 8; RFI = + 2.01kg/d) were selected from a group of 56 growing crossbred beef steers (average BW = 261 ± 18.5 kg) fed a high-forage total mixed ration after a 49-d performance testing period. At the end of the 49-d performance testing period, liver biopsies were collected from the low-RFI and high-RFI beef steers for RNA extraction and cDNA synthesis. The mRNA expression of 84 genes each related to fatty acid metabolism, amino acid metabolism, and mitochondrial energy metabolism were analyzed using pathway-focused PCR-based arrays. The mRNA expression of 8 genes (CRAT, SLC27A5, SLC27A2, ACSBG2, ACADL, ACADSB, ACAA1, and ACAA2) involved fatty acid transport and β-oxidation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI, compared to high-RFI steers. Among those involved in amino acid metabolism, hepatic mRNA expression of a gene encoding for aminoadipate aminotransferase, an enzyme related to lysine degradation, was downregulated (FC = -5.45, FDR = 0.01) in low-RFI steers, whereas those of methionine adenosyltransferase I and aspartate aminotransferase 2, which both link amino acid and lipid metabolism, were upregulated (FC ≥ 2.0, FDR ≤ 0.05). Two mitochondrial energy metabolism genes (UQCRC1 and ATP5G1) involved in ATP synthesis via oxidative phosphorylation were upregulated (FC ≥ 2.0, FDR ≤ 0.05) in low-RFI beef steers, compared to high-RFI beef steers. The results of this study demonstrated that low-RFI beef steers exhibit upregulation of molecular mechanisms related to fatty acid transport, fatty acid β-oxidation, and mitochondrial ATP synthesis, which suggest that low-RFI beef steers have enhanced metabolic capacity to maximize capture of energy and nutrients from feeds consumed.
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12
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Proteomic analysis of adipose tissue revealing differentially abundant proteins in highly efficient mid-lactating dairy cows. Sci Rep 2022; 12:9721. [PMID: 35697844 PMCID: PMC9192684 DOI: 10.1038/s41598-022-13964-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 05/31/2022] [Indexed: 11/26/2022] Open
Abstract
The improvement of nutrient utilization efficiency in dairy cows represents an important task in view of the current rising demand for animal products and sustainable resource usage. In this perspective, the identification of appropriate markers to identify the most efficient animals for dairy production becomes a crucial factor. Residual feed intake (RFI), which represents the difference between predicted and actual intake, is used to define the efficiency of cows. In this study, subcutaneous adipose tissue (AT) was collected from five high efficient (HEF) and five low efficient (LEF) mid-lactation Holstein dairy cows, that represented subgroups of the 20% lowest RFI values (HEF) and highest 20% RFI values (LEF), out of a cohort of 155 cows that were examined for feed efficiency at the individual dairy barn at Volcani Institute, Israel. Adipose samples were examined for proteomic analysis by nano-LC/MS–MS and gene expression by RT-PCR. A total of 101 differential proteins (P ≤ 0.05 and fold change ± 1.5) and two protein networks related to feed efficiency were found between HEF and LEF cows. Among the enriched top canonical pathways, FAT10 signaling, EIF2 signaling, Sirtuin signaling, Acute phase response signaling, Protein ubiquitination and mTOR signaling pathways were related to feed efficiency in AT. Furthermore, abundance of transferrin (TF; FC = 78.35, P = 0.02) enriched pathways, including mTOR signaling, LXR/RXR and FXR/RXR activation was found in AT of HEF cows. Relative mRNA expression of RBM39, which is involved in energy metabolism, was decreased in AT of HEF versus LEF. The relationship found between the AT proteins and/or metabolic pathways and the feed efficiency demonstrates that AT may reflect metabolic adaptations to high efficiency, and suggests that these proteins together with their metabolic mechanisms are suitable candidates as biomarkers to identify efficient cows for dairy production.
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13
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Taiwo GA, Idowu M, Denvir J, Cervantes AP, Ogunade IM. Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis. Front Vet Sci 2022; 9:848027. [PMID: 35518641 PMCID: PMC9062580 DOI: 10.3389/fvets.2022.848027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/08/2022] [Indexed: 11/19/2022] Open
Abstract
We applied whole blood transcriptome analysis and gene set enrichment analysis to identify pathways associated with divergent selection for low or high RFI in beef cattle. A group of 56 crossbred beef steers (average BW = 261 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake (RFI). After RFI determination, whole blood samples were collected from beef steers with the lowest RFI (most efficient; low-RFI; n = 8) and highest RFI (least efficient; high-RFI; n = 8). Prior to RNA extraction, whole blood samples collected were composited for each steer. Sequencing was performed on an Illumina NextSeq2000 equipped with a P3 flow. Gene set enrichment analysis (GSEA) was used to analyze differentially expressed gene sets and pathways between the two groups of steers. Results of GSEA revealed pathways associated with metabolism of proteins, cellular responses to external stimuli, stress, and heat stress were differentially inhibited (false discovery rate (FDR) < 0.05) in high-RFI compared to low-RFI beef cattle, while pathways associated with binding and uptake of ligands by scavenger receptors, scavenging of heme from plasma, and erythrocytes release/take up oxygen were differentially enriched (FDR < 0.05) in high-RFI, relative to low-RFI beef cattle. Taken together, our results revealed that beef steers divergently selected for low or high RFI revealed differential expressions of genes related to protein metabolism and stress responsiveness.
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Affiliation(s)
- Godstime A Taiwo
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV, United States
| | - Modoluwamu Idowu
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV, United States
| | - James Denvir
- Department of Medicine, Surgery, and Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV, United States
| | - Andres Pech Cervantes
- Agricultural Research Station, Fort Valley State University, Fort Valley, GA, United States
| | - Ibukun M Ogunade
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV, United States
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14
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Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
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Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
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15
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Taiwo G, Idowu M, Collins S, Sidney T, Wilson M, Pech-Cervantes A, Ogunade IM. Chemical Group-Based Metabolome Analysis Identifies Candidate Plasma Biomarkers Associated With Residual Feed Intake in Beef Steers. FRONTIERS IN ANIMAL SCIENCE 2022. [DOI: 10.3389/fanim.2021.783314] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We applied chemical group-based metabolomics to identify blood metabolic signatures associated with residual feed intake in beef cattle. A group of 56 crossbred growing beef steers (average BW = 261.3 ± 18.5 kg) were adapted to a high-forage total mixed ration in a confinement dry lot equipped with GrowSafe intake nodes for period of 49 d to determine their residual feed intake classification (RFI). After RFI determination, weekly blood samples were collected three times from beef steers with the lowest RFI [most efficient (HFE); n = 8] and highest RFI and least-efficient [least efficient (LFE); n = 8]. Plasma was prepared by centrifugation and composited for each steer. Metabolome analysis was conducted using a chemical isotope labeling (CIL)/liquid chromatography–mass spectrometry, which permitted the analysis of metabolites containing amine/phenol-, carboxylic acid-, and carbonyl-chemical groups, which are metabolites associated with metabolisms of amino acids, fatty acids, and carbohydrates, respectively. A total number of 495 amine/phenol-containing metabolites were detected and identified; pathway analysis of all these metabolites showed that arginine biosynthesis and histidine metabolism were enriched (P < 0.10) in HFE, relative to LFE steers. Biomarker analyses of the amine/phenol-metabolites identified methionine, 5-aminopentanoic acid, 2-aminohexanedioic acid, and 4-chlorolysine as candidate biomarkers of RFI [false discovery rate ≤ 0.05; Area Under the Curve (AUC) > 0.90]. A total of 118 and 330 metabolites containing carbonyl- and carboxylic acid-chemical groups, respectively were detected and identified; no metabolic pathways associated with these metabolites were altered and only one candidate biomarker (methionine sulfoxide) was identified. These results identified five candidate metabolite biomarkers of RFI in beef cattle which are mostly associated with amino acid metabolism. Further validation using a larger cohort of beef cattle of different genetic pedigree is required to confirm these findings.
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16
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Identifying the key genes and functional enrichment pathways associated with feed efficiency in cattle. Gene 2022; 807:145934. [PMID: 34478820 DOI: 10.1016/j.gene.2021.145934] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/21/2021] [Accepted: 08/27/2021] [Indexed: 12/22/2022]
Abstract
Residual feed intake (RFI) is a measurement of feed efficiency, and is inversely correlated with feed efficiency. The differentially expressed genes (DEGs) associated with RFI vary substantially among studies, posing great challenges in finding the RFI-related marker genes. This study attempted to resolve this issue by integrating and comparing the multiple transcriptome sequencing data associated with RFI in the cattle liver, using differential, functional enrichment, protein-protein interaction (PPI) network, weighted co-expression network (WGCNA), and gene set enrichment analyses (GSEA) to identify the candidate genes and functional enrichment pathways that are closely associated with RFI. Four candidate genes namely SHC1, GPX4, ACADL, and IGF1 were identified and validated as the marker genes for RFI. Four functional enrichment pathways, namely the fatty acid metabolism, sugar metabolism, energy metabolism, and protein ubiquitination were also found to be closely related to RFI. This study identified several genes and signaling pathways with shared characteristics, which will provide new insights into the molecular mechanisms related to the regulation of feed efficiency, and provide basis for molecular markers related to feed efficiency in beef cattle.
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17
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Artegoitia VM, Newman JW, Foote AP, Shackelford SD, King DA, Wheeler TL, Lewis RM, Freetly HC. Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits. Sci Rep 2022; 12:231. [PMID: 34997076 PMCID: PMC8742028 DOI: 10.1038/s41598-021-04049-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 12/14/2021] [Indexed: 11/25/2022] Open
Abstract
The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.
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Affiliation(s)
- Virginia M Artegoitia
- USDA, ARS, Western Human Nutrition Research Center, 430 West Health Sciences Drive, Davis, CA, 95616, USA. .,USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA. .,Animal Science, University Nebraska, Lincoln, NE, 68583, USA.
| | - J W Newman
- USDA, ARS, Western Human Nutrition Research Center, 430 West Health Sciences Drive, Davis, CA, 95616, USA
| | - A P Foote
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA.,Animal Science, Oklahoma State University, Stillwater, OK, 74078, USA
| | - S D Shackelford
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - D A King
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - T L Wheeler
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - R M Lewis
- Animal Science, University Nebraska, Lincoln, NE, 68583, USA
| | - H C Freetly
- USDA, ARS, Meat Animal Research Center, Clay Center, NE, 68933, USA
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18
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Fonseca PADS, Caldwell T, Mandell I, Wood K, Cánovas A. Genome-wide association study for meat tenderness in beef cattle identifies patterns of the genetic contribution in different post-mortem stages. Meat Sci 2022; 186:108733. [PMID: 35007800 DOI: 10.1016/j.meatsci.2022.108733] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/01/2022] [Accepted: 01/03/2022] [Indexed: 12/13/2022]
Abstract
The beef tenderization process during the post-mortem period is one of the most important sensorial attributes and it is well-established. The aim of this study was to identify the genetic contribution pattern to meat tenderness at 7-(LMD7), 14-(LMD14), and 21-(LMD21) days post-mortem. The heritabilities for LMD7 (0.194), LMD14 (0.142) and LMD21 (0.048) are well established in the population evaluated here. However, its genetic contribution in terms of genomic candidate regions is still poorly understood. Tenderness was measured in the Longissiums thoracis using Warner-Bratzler shear force in the three post-mortem periods. A total of 4323 crossbred beef cattle were phenotyped and genotyped using the Illumina BovineSNP50K. The percentage of the total genetic variance was estimated using the weighted single-step genomic best linear unbiased prediction method. The main candidate windows for LMD7 were associated with proteolysis of myofibrillar structures and the weakening endomysium and perimysium. Candidate windows for LMD14 and LMD21 were mapped in bovine QTLs for body composition, height and growth. Results presented herein highlight, the largest contribution of proteolysis related processes before 14-days post-mortem and body composition characteristics in later stages for meat tenderness.
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Affiliation(s)
- Pablo Augusto de Souza Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tim Caldwell
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Ira Mandell
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Katharine Wood
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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19
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Li J, Mukiibi R, Wang Y, Plastow GS, Li C. Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle. BMC Genomics 2021; 22:823. [PMID: 34781903 PMCID: PMC8591823 DOI: 10.1186/s12864-021-08064-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. RESULTS Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10-5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. CONCLUSIONS This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.
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Affiliation(s)
- Jiyuan Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Yining Wang
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada
| | - Graham S Plastow
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
| | - Changxi Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada.
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20
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Yang C, Han L, Li P, Ding Y, Zhu Y, Huang Z, Dan X, Shi Y, Kang X. Characterization and Duodenal Transcriptome Analysis of Chinese Beef Cattle With Divergent Feed Efficiency Using RNA-Seq. Front Genet 2021; 12:741878. [PMID: 34675965 PMCID: PMC8524388 DOI: 10.3389/fgene.2021.741878] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Residual feed intake (RFI) is an important measure of feed efficiency for agricultural animals. Factors associated with cattle RFI include physiology, dietary factors, and the environment. However, a precise genetic mechanism underlying cattle RFI variations in duodenal tissue is currently unavailable. The present study aimed to identify the key genes and functional pathways contributing to variance in cattle RFI phenotypes using RNA sequencing (RNA-seq). Six bulls with extremely high or low RFIs were selected for detecting differentially expressed genes (DEGs) by RNA-seq, followed by conducting GO, KEGG enrichment, protein-protein interaction (PPI), and co-expression network (WGCNA, n = 10) analysis. A total of 380 differentially expressed genes was obtained from high and low RFI groups, including genes related to energy metabolism (ALDOA, HADHB, INPPL1), mitochondrial function (NDUFS1, RFN4, CUL1), and feed intake behavior (CCK). Two key sub-networks and 26 key genes were detected using GO analysis of DEGs and PPI analysis, such as TPM1 and TPM2, which are involved in mitochondrial pathways and protein synthesis. Through WGCNA, a gene network was built, and genes were sorted into 27 modules, among which the blue (r = 0.72, p = 0.03) and salmon modules (r = -0.87, p = 0.002) were most closely related with RFI. DEGs and genes from the main sub-networks and closely related modules were largely involved in metabolism; oxidative phosphorylation; glucagon, ribosome, and N-glycan biosynthesis, and the MAPK and PI3K-Akt signaling pathways. Through WGCNA, five key genes, including FN1 and TPM2, associated with the biological regulation of oxidative processes and skeletal muscle development were identified. Taken together, our data suggest that the duodenum has specific biological functions in regulating feed intake. Our findings provide broad-scale perspectives for identifying potential pathways and key genes involved in the regulation of feed efficiency in beef cattle.
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Affiliation(s)
- Chaoyun Yang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Liyun Han
- Ningxia Agriculture Reclamation Helanshan Diary Co.Ltd., Yinchuan, China
| | - Peng Li
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yanling Ding
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Zhu
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Zengwen Huang
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Xingang Dan
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Yuangang Shi
- School of Agriculture, Ningxia University, Yinchuan, China
| | - Xiaolong Kang
- School of Agriculture, Ningxia University, Yinchuan, China
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21
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Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
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Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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22
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McKenna C, Keogh K, Porter RK, Waters SM, Cormican P, Kenny DA. An examination of skeletal muscle and hepatic tissue transcriptomes from beef cattle divergent for residual feed intake. Sci Rep 2021; 11:8942. [PMID: 33903612 PMCID: PMC8076192 DOI: 10.1038/s41598-021-87842-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/08/2021] [Indexed: 12/27/2022] Open
Abstract
The selection of cattle with enhanced feed efficiency is of importance with regard to reducing feed costs in the beef industry. Global transcriptome profiling was undertaken on liver and skeletal muscle biopsies from Simmental heifers and bulls divergent for residual feed intake (RFI), a widely acknowledged feed efficiency phenotype, in order to identify genes that may be associated with this trait. We identified 5 genes (adj. p < 0.1) to be differentially expressed in skeletal muscle between high and low RFI heifers with all transcripts involved in oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (adj. p < 0. 1) were differentially expressed in liver tissue between high and low RFI bulls with differentially expressed genes related to amino and nucleotide metabolism as well as endoplasmic reticulum protein processing. No genes were identified as differentially expressed in either heifer liver or bull muscle analyses. Results from this study show that the molecular control of RFI in young cattle is modified according to gender, which may be attributable to differences in physiological maturity between heifers and bulls of the same age. Despite this we have highlighted a number of genes that may hold potential as molecular biomarkers for RFI cattle.
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Affiliation(s)
- Clare McKenna
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland.,School of Biochemistry & Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Kate Keogh
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - Richard K Porter
- School of Biochemistry & Immunology, Trinity College Dublin, Dublin 2, D02 R590, Ireland
| | - Sinead M Waters
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - Paul Cormican
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Teagasc Grange, Dunsany, C15 PW93, Co. Meath, Ireland.
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23
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Zhang X, Paalvast Y, Wang Y, Rensen PCN, Groen AK. A hierarchical dynamic model used for investigating feed efficiency and its relationship with hepatic gene expression in APOE*3-Leiden.CETP mice. Physiol Rep 2021; 9:e14832. [PMID: 33932122 PMCID: PMC8087979 DOI: 10.14814/phy2.14832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Feed efficiency (FE) is an important trait for livestock and humans. While the livestock industry focuses on increasing FE, in the current obesogenic society it is more of interest to decrease FE. Hence, understanding mechanisms involved in the regulation of FE and particularly how it can be decreased would help tremendously in counteracting the obesity pandemic. However, it is difficult to accurately measure or calculate FE in humans. In this study, we aimed to address this challenge by developing a hierarchical dynamic model based on humanized mouse data. METHODS We analyzed existing experimental data derived from 105 APOE*3-Leiden.CETP (E3L.CETP) mice fed a high-fat high-cholesterol (HFHC) diet for 1 (N = 20), 2 (N = 19), 3 (N = 20), and 6 (N = 46) month. We developed an ordinary differential equation (ODE) based model to estimate the FE based on the longitudinal data of body weight and food intake. Since the liver plays an important role in maintaining metabolic homeostasis, we evaluated associations between FE and hepatic gene expression levels. Depending on the feeding duration, we observed different relationships between FE and hepatic gene expression levels. RESULTS After 1-month feeding of HFHC diet, we observed that FE was associated with vitamin A metabolism, arachidonic acid metabolism, and the PPAR signaling pathway. After 3- and 6-month feeding of HFHC diet, we observed that FE was associated most strongly with expression levels of Spink1 and H19, genes involved in cell proliferation and glucose metabolism, respectively. CONCLUSIONS In conclusion, our analysis suggests that various biological processes such as vitamin A metabolism, hepatic response to inflammation, and cell proliferation associate with FE at different stages of diet-induced obesity.
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Affiliation(s)
- Xiang Zhang
- Department of Experimental Vascular MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Human and Animal PhysiologyWageningen UniversityWageningenThe Netherlands
- Theoretical Biology and BioinformaticsUtrecht UniversityUtrechtThe Netherlands
| | - Yared Paalvast
- Department of PediatricsUniversity Medical Center GroningenGroningenThe Netherlands
| | - Yanan Wang
- Department of PediatricsUniversity Medical Center GroningenGroningenThe Netherlands
- Department of MedicineDivision of EndocrinologyLeiden University Medical CenterLeidenThe Netherlands
- Einthoven Laboratory for Experimental Vascular MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Patrick C. N. Rensen
- Department of MedicineDivision of EndocrinologyLeiden University Medical CenterLeidenThe Netherlands
- Einthoven Laboratory for Experimental Vascular MedicineLeiden University Medical CenterLeidenThe Netherlands
| | - Albert K. Groen
- Department of Experimental Vascular MedicineAmsterdam University Medical CenterUniversity of AmsterdamAmsterdamThe Netherlands
- Department of PediatricsUniversity Medical Center GroningenGroningenThe Netherlands
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24
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Giráldez F, Santos N, Santos A, Valdés C, López S, Andrés S. Fattening lambs with divergent residual feed intakes and weight gains: Unravelling mechanisms driving feed efficiency. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2021.114821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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25
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Plasma Carboxyl-Metabolome Is Associated with Average Daily Gain Divergence in Beef Steers. Animals (Basel) 2021; 11:ani11010067. [PMID: 33401431 PMCID: PMC7824440 DOI: 10.3390/ani11010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 11/17/2022] Open
Abstract
We applied an untargeted metabolomics technique to analyze the plasma carboxyl-metabolome of beef steers with divergent average daily gain (ADG). Forty-eight newly weaned Angus crossbred beef steers were fed the same total mixed ration ad libitum for 42 days. On day 42, the steers were divided into two groups of lowest (LF: n = 8) and highest ADG (HF: n = 8), and blood samples were obtained from the two groups for plasma preparation. Relative quantification of carboxylic-acid-containing metabolites in the plasma samples was determined using a metabolomics technique based on chemical isotope labeling liquid chromatography mass spectrometry. Metabolites that differed (fold change (FC) ≥ 1.2 or ≤ 0.83 and FDR ≤ 0.05) between LF and HF were identified using a volcano plot. Metabolite set enrichment analysis (MSEA) of the differential metabolites was done to determine the metabolic pathways or enzymes that were potentially altered. In total, 328 metabolites were identified. Volcano plot analysis revealed 43 differentially abundant metabolites; several short chain fatty acids and ketone bodies had greater abundance in HF steers. Conversely, several long chain fatty acids were greater in LF steers. Five enzymatic pathways, such as fatty acyl CoA elongation and fatty-acid CoA ligase were altered based on MSEA. This study demonstrated that beef steers with divergent ADG had altered plasma carboxyl-metabolome, which is possibly caused by altered abundances and/or activities of enzymes involved in fatty acid oxidation and biosynthesis in the liver.
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26
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Li J, Akanno EC, Valente TS, Abo-Ismail M, Karisa BK, Wang Z, Plastow GS. Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle. Front Genet 2020; 11:538600. [PMID: 33193612 PMCID: PMC7542097 DOI: 10.3389/fgene.2020.538600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolites, substrates or products of metabolic processes, are involved in many biological functions, such as energy metabolism, signaling, stimulatory and inhibitory effects on enzymes and immunological defense. Metabolomic phenotypes are influenced by combination of genetic and environmental effects allowing for metabolome-genome-wide association studies (mGWAS) as a powerful tool to investigate the relationship between these phenotypes and genetic variants. The objectives of this study were to estimate genomic heritability and perform mGWAS and in silico functional enrichment analyses for a set of plasma metabolites in Canadian crossbred beef cattle. Thirty-three plasma metabolites and 45,266 single nucleotide polymorphisms (SNPs) were available for 475 animals. Genomic heritability for all metabolites was estimated using genomic best linear unbiased prediction (GBLUP) including genomic breed composition as covariates in the model. A single-step GBLUP implemented in BLUPF90 programs was used to determine SNP P values and the proportion of genetic variance explained by SNP windows containing 10 consecutive SNPs. The top 10 SNP windows that explained the largest genetic variation for each metabolite were identified and mapped to detect corresponding candidate genes. Functional enrichment analyses were performed on metabolites and their candidate genes using the Ingenuity Pathway Analysis software. Eleven metabolites showed low to moderate heritability that ranged from 0.09 ± 0.15 to 0.36 ± 0.15, while heritability estimates for 22 metabolites were zero or negligible. This result indicates that while variations in 11 metabolites were due to genetic variants, the majority are largely influenced by environment. Three significant SNP associations were detected for betaine (rs109862186), L-alanine (rs81117935), and L-lactic acid (rs42009425) based on Bonferroni correction for multiple testing (family wise error rate <0.05). The SNP rs81117935 was found to be located within the Catenin Alpha 2 gene (CTNNA2) showing a possible association with the regulation of L-alanine concentration. Other candidate genes were identified based on additive genetic variance explained by SNP windows of 10 consecutive SNPs. The observed heritability estimates and the candidate genes and networks identified in this study will serve as baseline information for research into the utilization of plasma metabolites for genetic improvement of crossbred beef cattle.
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Affiliation(s)
- Jiyuan Li
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Everestus C Akanno
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tiago S Valente
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, Ethology and Animal Ecology Research Group, São Paulo State University, Jaboticabal, Brazil
| | - Mohammed Abo-Ismail
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, College of Agriculture, Food and Environmental Sciences, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Brian K Karisa
- Ministry of Agriculture and Forestry, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
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27
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Mukiibi R, Johnston D, Vinsky M, Fitzsimmons C, Stothard P, Waters SM, Li C. Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes. Sci Rep 2020; 10:19309. [PMID: 33168877 PMCID: PMC7653039 DOI: 10.1038/s41598-020-73885-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/08/2020] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules involved in regulation of multiple biological processes through modulating expression of their target genes. Here we employed RNAseq to profile liver tissue miRNAome of 60 steers from Angus, Charolais, and Kinsella Composite (KC) populations. Of these animals, 36 animals (n = 12 for each breed) were utilized to identify differentially expressed (DE) miRNAs between animals with high (n = 6) or low (n = 6) phenotypic values of residual feed intake (RFI), a common measurement of feed efficiency. At a threshold of fold-change > 1.5 and P-value < 0.05, we detected 12 (7 up- and 5 downregulated in low-RFI animals), 18 (12 up- and 6 downregulated), and 13 (8 up- and 5 downregulated) DE miRNAs for Angus, Charolais, and KC steers, respectively. Most of the DE miRNAs were breed specific, with bta-miR-449a and bta-miR-AB-2 being differentially expressed in all three breeds. The predicted target genes of the identified DE miRNA are mainly involved in cell cycle, cell death and survival, cell signaling, cellular growth and proliferation, protein trafficking, cell morphology, cell-to-cell signaling and interaction, cellular development, molecular transport, post-translational modification, as well as nutrient metabolism (lipids, carbohydrates, protein and amino acid). Our results provide insights into the bovine hepatic miRNAome and their potential roles in molecular regulation of RFI in beef cattle.
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Affiliation(s)
- Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Dayle Johnston
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Michael Vinsky
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.
- Lacombe Research and Development Centre, Lacombe, Agriculture and Agri-Food Canada, Alberta, T4L 1W1, Canada.
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28
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Alexandre PA, Reverter A, Berezin RB, Porto-Neto LR, Ribeiro G, Santana MHA, Ferraz JBS, Fukumasu H. Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. Genes (Basel) 2020; 11:genes11090997. [PMID: 32854445 PMCID: PMC7565090 DOI: 10.3390/genes11090997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.
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Affiliation(s)
- Pâmela A. Alexandre
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
- Correspondence: ; Tel.: +61-7-32142453
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
| | - Roberta B. Berezin
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Laercio R. Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
| | - Gabriela Ribeiro
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Miguel H. A. Santana
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil;
| | - José Bento S. Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Heidge Fukumasu
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
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29
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Xu C, Wang X, Zhuang Z, Wu J, Zhou S, Quan J, Ding R, Ye Y, Peng L, Wu Z, Zheng E, Yang J. A Transcriptome Analysis Reveals that Hepatic Glycolysis and Lipid Synthesis Are Negatively Associated with Feed Efficiency in DLY Pigs. Sci Rep 2020; 10:9874. [PMID: 32555275 PMCID: PMC7303214 DOI: 10.1038/s41598-020-66988-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 06/01/2020] [Indexed: 12/25/2022] Open
Abstract
Feed efficiency (FE) is an important trait in the porcine industry. Therefore, understanding the molecular mechanisms of FE is vital for the improvement of this trait. In this study, 6 extreme high-FE and 6 low-FE pigs were selected from 225 Duroc × (Landrace × Yorkshire) (DLY) pigs for transcriptomic analysis. RNA-seq analysis was performed to determine differentially expressed genes (DEGs) in the liver tissues of the 12 individuals, and 507 DEGs were identified between high-FE pigs (HE- group) and low-FE pigs (LE- group). A gene ontology (GO) enrichment and pathway enrichment analysis were performed and revealed that glycolytic metabolism and lipid synthesis-related pathways were significantly enriched within DEGs; all of these DEGs were downregulated in the HE- group. Moreover, Weighted gene co-expression analysis (WGCNA) revealed that oxidative phosphorylation, thermogenesis, and energy metabolism-related pathways were negatively related to HE- group, which might result in lower energy consumption in higher efficiency pigs. These results implied that the higher FE in the HE- group may be attributed to a lower glycolytic, energy consumption and lipid synthesizing potential in the liver. Furthermore, our findings suggested that the inhibition of lipid synthesis and glucose metabolic activity in the liver may be strategies for improving the FE of DLY pigs.
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Affiliation(s)
- Cineng Xu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Xingwang Wang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhanwei Zhuang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Jie Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Shenping Zhou
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Jianping Quan
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Rongrong Ding
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Yong Ye
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Longlong Peng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Zhenfang Wu
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China
| | - Enqin Zheng
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.
| | - Jie Yang
- College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangdong, P.R. China.
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30
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Sun HZ, Zhao K, Zhou M, Chen Y, Guan LL. Landscape of multi-tissue global gene expression reveals the regulatory signatures of feed efficiency in beef cattle. Bioinformatics 2020; 35:1712-1719. [PMID: 30329014 DOI: 10.1093/bioinformatics/bty883] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/01/2018] [Accepted: 10/16/2018] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Feed efficiency is an important trait for sustainable beef production that is regulated by the complex biological process, but the mode of action behinds it has not been clearly defined. Here, we aimed to elucidate the regulatory mechanisms of this trait through studying the landscape of the genome-wide gene expression of rumen, liver, muscle and backfat tissues, the key ones involved in the energy metabolism. RESULTS The transcriptome of 189 samples across four tissues from 48 beef steers with varied feed efficiency were generated using Illumina HiSeq4000. The analysis of global gene expression profiles of four tissues, functional analysis of tissue-shared and -unique genes, co-expressed network construction of tissue-shared genes, weighted correlations analysis between gene modules and feed efficiency-related traits in each tissue were performed. Among four tissues, the transcriptome of muscle tissue was distinctive from others, while those of rumen and backfat tissues were similar. The associations between co-expressed genes and feed efficiency related traits at single or all tissues level exhibited that the gene expression in the rumen, liver, muscle and backfat were the most correlated with feed conversion ratio, dry matter intake, average daily gain and residual feed intake, respectively. The 19 overlapped genes identified from the strongest module-trait relationships in four tissues are potential generic gene markers for feed efficiency. AVAILABILITY AND IMPLEMENTATION The distribution of gene expression data can be accessed at https://www.cattleomics.com/transcriptome. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hui-Zeng Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Ke Zhao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Food Quality and Safety, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xian, China
| | - Mi Zhou
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yanhong Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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31
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de Lima AO, Koltes JE, Diniz WJS, de Oliveira PSN, Cesar ASM, Tizioto PC, Afonso J, de Souza MM, Petrini J, Rocha MIP, Cardoso TF, Neto AZ, Coutinho LL, Mourão GB, Regitano LCA. Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses. Front Genet 2020; 11:189. [PMID: 32194642 PMCID: PMC7064723 DOI: 10.3389/fgene.2020.00189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.
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Affiliation(s)
- Andressa O de Lima
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Wellison J S Diniz
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Juliana Afonso
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Juliana Petrini
- Exact Sciences Institute, Federal University of Alfenas, Alfenas, Brazil
| | - Marina I P Rocha
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Tainã F Cardoso
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Empresa Brazileira de Pesquisa Agropecuária, Campinas, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
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Zhang F, Wang Y, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits. BMC Genomics 2020; 21:36. [PMID: 31931702 PMCID: PMC6956504 DOI: 10.1186/s12864-019-6362-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/02/2019] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) on residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) were conducted in a population of 7573 animals from multiple beef cattle breeds based on 7,853,211 imputed whole genome sequence variants. The GWAS results were used to elucidate genetic architectures of the feed efficiency related traits in beef cattle. RESULTS The DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants followed a scaled inverse chi-squared distribution to a greater extent. With a threshold of P-value < 1.00E-05, 16, 72, 88, and 116 lead DNA variants on multiple chromosomes were significantly associated with RFI, DMI, ADG, and MWT, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on DMI, ADG, and MWT were found on chromosomes 6, 14 and 20. On average, missense, 3'UTR, 5'UTR, and other regulatory region variants exhibited larger allele substitution effects in comparison to other functional classes. Intergenic and intron variants captured smaller proportions of additive genetic variance per DNA variant. Instead 3'UTR and synonymous variants explained a greater amount of genetic variance per DNA variant for all the traits examined while missense, 5'UTR and other regulatory region variants accounted for relatively more additive genetic variance per sequence variant for RFI and ADG, respectively. In total, 25 to 27 enriched cellular and molecular functions were identified with lipid metabolism and carbohydrate metabolism being the most significant for the feed efficiency traits. CONCLUSIONS RFI is controlled by many DNA variants with relatively small effects whereas DMI, ADG, and MWT are influenced by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory region and synonymous functional classes play a more important role per sequence variant in determining variation of the feed efficiency traits. The genetic architecture as revealed by the GWAS of the imputed 7,853,211 DNA variants will improve our understanding on the genetic control of feed efficiency traits in beef cattle.
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Affiliation(s)
- Feng Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, China.,Present Address: Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi, China
| | - Yining Wang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Liuhong Chen
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - John Basarab
- Alberta Agriculture and Forestry, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada. .,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
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Lindholm-Perry AK, Freetly HC, Oliver WT, Rempel LA, Keel BN. Genes associated with body weight gain and feed intake identified by meta-analysis of the mesenteric fat from crossbred beef steers. PLoS One 2020; 15:e0227154. [PMID: 31910243 PMCID: PMC6946124 DOI: 10.1371/journal.pone.0227154] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/11/2019] [Indexed: 12/12/2022] Open
Abstract
Mesenteric fat is a visceral fat depot that increases with cattle maturity and can be influenced by diet. There may be a relationship between the accumulation of mesenteric fat and feed efficiency in beef cattle. The purpose of this study was to identify genes that may be differentially expressed in steers with high and low BW gain and feed intake. RNA-Seq was used to evaluate the transcript abundance of genes in the mesenteric fat from a total of 78 steers collected over 5 different cohorts. A meta-analysis was used to identify genes involved with gain, feed intake or the interaction of both phenotypes. The interaction analysis identified 11 genes as differentially expressed. For the main effect of gain, a total of 87 differentially expressed genes (DEG) were identified (PADJ<0.05), and 24 were identified in the analysis for feed intake. Genes identified for gain were involved in functions and pathways including lipid metabolism, stress response/protein folding, cell proliferation/growth, axon guidance and inflammation. The genes for feed intake did not cluster into pathways, but some of the DEG for intake had functions related to inflammation, immunity, and/or signal transduction (JCHAIN, RIPK1, LY86, SPP1, LYZ, CD5, CD53, SRPX, and NF2). At PADJ<0.1, only 4 genes (OLFML3, LOC100300716, MRPL15, and PUS10) were identified as differentially expressed in two or more cohorts, highlighting the importance of evaluating the transcriptome of more than one group of animals and incorporating a meta-analysis. This meta-analysis has produced many mesenteric fat DEG that may be contributing to gain and feed intake in cattle.
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Affiliation(s)
- Amanda K. Lindholm-Perry
- Agricultural Research Service, United States Department of Agriculture, United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
- * E-mail:
| | - Harvey C. Freetly
- Agricultural Research Service, United States Department of Agriculture, United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - William T. Oliver
- Agricultural Research Service, United States Department of Agriculture, United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Lea A. Rempel
- Agricultural Research Service, United States Department of Agriculture, United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
| | - Brittney N. Keel
- Agricultural Research Service, United States Department of Agriculture, United States Meat Animal Research Center, Clay Center, Nebraska, United States of America
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Zhang D, Zhang X, Li F, Li C, La Y, Mo F, Li G, Zhang Y, Li X, Song Q, Zhao Y, Wang W. Transcriptome Analysis Identifies Candidate Genes and Pathways Associated With Feed Efficiency in Hu Sheep. Front Genet 2019; 10:1183. [PMID: 31798641 PMCID: PMC6878960 DOI: 10.3389/fgene.2019.01183] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
In the genetic improvement of livestock and poultry, residual feed intake (RFI) is an important economic trait. However, in sheep, the genetic regulatory mechanisms of RFI are unclear. In the present study, we measured the feed efficiency (FE)-related phenotypes of 137 male Hu lambs, and selected six lambs with very high (n = 3) and very low (n = 3) RFI values and analyzed their liver transcriptomes. A total of 101 differentially expressed genes were identified, of which 40 were upregulated and 61 were downregulated in the low-RFI group compared with that in the high-RFI group. The downregulated genes were mainly concentrated in immune function pathways, while the upregulated genes were mainly involved in energy metabolism pathways. Two differentially expressed genes, ADRA2A (encoding adrenoceptor alpha 2A) and RYR2 (ryanodine receptor 2), were selected as candidate genes for FE and subjected to single nucleotide polymorphism scanning and association analysis. Two synonymous mutations, ADRA2A g.1429 C > A and RYR2 g.1117 A > C, were detected, which were both significantly associated with the feed conversion rate. These findings provide a deeper understanding of the molecular mechanisms regulating FE, and reveal key genes and genetic variants that could be used to genetically improve FE in sheep.
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Affiliation(s)
- Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co. Ltd., Minqin, China
| | - Fadi Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co. Ltd., Minqin, China.,The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongfu La
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Futao Mo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Guoze Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
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Mukiibi R, Vinsky M, Keogh K, Fitzsimmons C, Stothard P, Waters SM, Li C. Liver transcriptome profiling of beef steers with divergent growth rate, feed intake, or metabolic body weight phenotypes1. J Anim Sci 2019; 97:4386-4404. [PMID: 31583405 PMCID: PMC6827404 DOI: 10.1093/jas/skz315] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
Average daily gain (ADG) and daily dry matter intake (DMI) are key determinants of beef industry profitability. These traits together with metabolic body weight (MWT) are combined as component traits to calculate residual feed intake (RFI), a common measure of feed efficiency in beef cattle. Recently, there have been significant efforts towards molecular genetic characterization of RFI through transcriptomic studies in different breeds and tissues. However, molecular mechanisms of RFI component traits still remain predominately unexplored. Therefore, in the current study, we investigated the hepatic transcriptomic profiles and their associations with ADG, DMI, and MWT in Angus, Charolais, and Kinsella Composite (KC) populations through global RNAseq analyses. In each population and for each trait, 12 steers with extreme phenotypes (n = 6 low and n = 6 high) were analyzed for differential gene expression. These animals were from 20 beef steers of each Angus, Charolais, and KC breed population that were initially selected for a transcriptome study of RFI. At a false discovery rate <0.05 and fold change >1.5, we identified 123, 102, and 78 differentially expressed (DE) genes between high- and low-ADG animals of Angus, Charolais, and KC populations, respectively. For DMI, 108, 180, and 156 DE genes were identified between high- and low-DMI from Angus, Charolais, and KC populations, respectively, while for MWT, 80, 82, and 84 genes were differentially expressed between high- and low-MWT animals in Angus, Charolais, and KC populations, respectively. The identified DE genes were largely breed specific (81.7% for ADG, 82.7% for DMI, and 83% for MWT), but were largely involved in the same biological functions across the breeds. Among the most enriched biological functions included metabolism of major nutrients (lipids, carbohydrates, amino acids, vitamins, and minerals), small molecule biochemistry, cellular movement, cell morphology, and cell-to-cell signaling and interaction. Notably, we identified multiple DE genes that are involved in cholesterol biosynthesis, and immune response pathways for the 3 studied traits. Thus, our findings present potential molecular genetic mechanisms and candidate genes that influence feed intake, growth, and MWT of beef cattle.
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Affiliation(s)
- Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Kate Keogh
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Carolyn Fitzsimmons
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Teagasc, Grange, Dunsany, County Meath, Ireland
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
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Ramayo-Caldas Y, Mármol-Sánchez E, Ballester M, Sánchez JP, González-Prendes R, Amills M, Quintanilla R. Integrating genome-wide co-association and gene expression to identify putative regulators and predictors of feed efficiency in pigs. Genet Sel Evol 2019; 51:48. [PMID: 31477014 PMCID: PMC6721172 DOI: 10.1186/s12711-019-0490-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/19/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Feed efficiency (FE) has a major impact on the economic sustainability of pig production. We used a systems-based approach that integrates single nucleotide polymorphism (SNP) co-association and gene-expression data to identify candidate genes, biological pathways, and potential predictors of FE in a Duroc pig population. RESULTS We applied an association weight matrix (AWM) approach to analyse the results from genome-wide association studies (GWAS) for nine FE associated and production traits using 31K SNPs by defining residual feed intake (RFI) as the target phenotype. The resulting co-association network was formed by 829 SNPs. Additive effects of this SNP panel explained 61% of the phenotypic variance of RFI, and the resulting phenotype prediction accuracy estimated by cross-validation was 0.65 (vs. 0.20 using pedigree-based best linear unbiased prediction and 0.12 using the 31K SNPs). Sixty-eight transcription factor (TF) genes were identified in the co-association network; based on the lossless approach, the putative main regulators were COPS5, GTF2H5, RUNX1, HDAC4, ESR1, USP16, SMARCA2 and GTF2F2. Furthermore, gene expression data of the gluteus medius muscle was explored through differential expression and multivariate analyses. A list of candidate genes showing functional and/or structural associations with FE was elaborated based on results from both AWM and gene expression analyses, and included the aforementioned TF genes and other ones that have key roles in metabolism, e.g. ESRRG, RXRG, PPARGC1A, TCF7L2, LHX4, MAML2, NFATC3, NFKBIZ, TCEA1, CDCA7L, LZTFL1 or CBFB. The most enriched biological pathways in this list were associated with behaviour, immunity, nervous system, and neurotransmitters, including melatonin, glutamate receptor, and gustation pathways. Finally, an expression GWAS allowed identifying 269 SNPs associated with the candidate genes' expression (eSNPs). Addition of these eSNPs to the AWM panel of 829 SNPs did not improve the accuracy of genomic predictions. CONCLUSIONS Candidate genes that have a direct or indirect effect on FE-related traits belong to various biological processes that are mainly related to immunity, behaviour, energy metabolism, and the nervous system. The pituitary gland, hypothalamus and thyroid axis, and estrogen signalling play fundamental roles in the regulation of FE in pigs. The 829 selected SNPs explained 61% of the phenotypic variance of RFI, which constitutes a promising perspective for applying genetic selection on FE relying on molecular-based prediction.
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Affiliation(s)
- Yuliaxis Ramayo-Caldas
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Emilio Mármol-Sánchez
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Maria Ballester
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Juan Pablo Sánchez
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
| | - Rayner González-Prendes
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marcel Amills
- grid.7080.fDepartment of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSCIC-IRTA-UAB-UB, Campus de LA Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
- grid.7080.fDepartament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Raquel Quintanilla
- 0000 0001 1943 6646grid.8581.4Animal Breeding and Genetics Program, Institute for Research and Technology in Food and Agriculture (IRTA), Torre Marimon, 08140 Caldes de Montbui, Spain
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Jin S, Xu Y, Zang H, Yang L, Lin Z, Li Y, Geng Z. Expression of genes related to lipid transport in meat-type ducks divergent for low or high residual feed intake. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:416-423. [PMID: 31480135 PMCID: PMC7054623 DOI: 10.5713/ajas.19.0284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/19/2019] [Indexed: 12/17/2022]
Abstract
Objective This study examined the effects of divergence in residual feed intake (RFI) on expression profiles of key genes related to lipid transport in the liver and duodenal epithelium and their associations with feed efficiency traits in meat-type ducks. Methods A total of 1,000 male ducks with similar body weight (1,042.1±87.2 g) were used in this study, and their individual RFI was calculated from 21 to 42 d of age. Finally, the 10 highest RFI (HRFI) and 10 lowest RFI (LRFI) ducks were chosen for examining the expression of key genes related to lipid transport in the liver and duodenal epithelium using quantitative polymerase chain reaction. Results In the liver, expression levels of albumin (ALB), CD36 molecule (CD36), fatty acid hydroxylase domain containing 2 (FAXDC2), and choline kinase alpha (CHKA) were significantly higher in LRFI ducks than in HRFI ducks (p<0.01); negative correlations (p<0.05) between expression levels of ALB, CD36, FAXDC2, and CHKA and RFI were detected in the liver. Additionally, ALB expression was strongly positively correlated (p<0.05) with CD36, FAXDC2, CHKA, and apolipoprotein H (APOH) expression in the liver. In duodenal epithelium, we found that mRNA levels of ALB, CD36, FAXDC2, and APOH were significantly higher in LRFI ducks than in HRFI ducks (p<0.01); RFI was strongly negatively correlated (p<0.05) with ALB, FAXDC2, and APOH expression, while ALB expression was strongly positively correlated with APOH expression (p<0.01) in duodenal epithelium. Furthermore, expression levels of both ALB and FAXDC2 genes were significantly associated with feed conversion ratio and RFI in both liver and duodenal epithelium (p<0.05). Conclusion Our findings therefore suggest that ALB and FAXDC2 genes might be used as potential gene markers designed to improve feed efficiency in future meat-type duck breeding programs.
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Affiliation(s)
- Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.,Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei 230036, China
| | - Yuan Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.,Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei 230036, China
| | - He Zang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.,Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei 230036, China
| | - Lei Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.,Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei 230036, China
| | - Zhiqiang Lin
- Huangshan Qiangying Duck Breeding Co. Ltd., Huangshan 245461, China
| | - Yongsheng Li
- Huangshan Qiangying Duck Breeding Co. Ltd., Huangshan 245461, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China.,Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei 230036, China
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Higgins MG, Kenny DA, Fitzsimons C, Blackshields G, Coyle S, McKenna C, McGee M, Morris DW, Waters SM. The effect of breed and diet type on the global transcriptome of hepatic tissue in beef cattle divergent for feed efficiency. BMC Genomics 2019; 20:525. [PMID: 31242854 PMCID: PMC6593537 DOI: 10.1186/s12864-019-5906-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 06/17/2019] [Indexed: 01/07/2023] Open
Abstract
Background Feed efficiency is an important economic and environmental trait in beef production, which can be measured in terms of residual feed intake (RFI). Cattle selected for low-RFI (feed efficient) have similar production levels but decreased feed intake, while also emitting less methane. RFI is difficult and expensive to measure and is not widely adopted in beef production systems. However, development of DNA-based biomarkers for RFI may facilitate its adoption in genomic-assisted breeding programmes. Cattle have been shown to re-rank in terms of RFI across diets and age, while also RFI varies by breed. Therefore, we used RNA-Seq technology to investigate the hepatic transcriptome of RFI-divergent Charolais (CH) and Holstein-Friesian (HF) steers across three dietary phases to identify genes and biological pathways associated with RFI regardless of diet or breed. Results Residual feed intake was measured during a high-concentrate phase, a zero-grazed grass phase and a final high-concentrate phase. In total, 322 and 33 differentially expressed genes (DEGs) were identified across all diets for CH and HF steers, respectively. Three genes, GADD45G, HP and MID1IP1, were differentially expressed in CH when both the high-concentrate zero-grazed grass diet were offered. Two canonical pathways were enriched across all diets for CH steers. These canonical pathways were related to immune function. Conclusions The absence of common differentially expressed genes across all dietary phases and breeds in this study supports previous reports of the re-ranking of animals in terms of RFI when offered differing diets over their lifetime. However, we have identified biological processes such as the immune response and lipid metabolism as potentially associated with RFI divergence emphasising the previously reported roles of these biological processes with respect to RFI. Electronic supplementary material The online version of this article (10.1186/s12864-019-5906-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marc G Higgins
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland.,Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Claire Fitzsimons
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland.,Present address: Department of Agriculture, Fisheries and the Marine, Celbridge, Co. Kildare, Ireland
| | - Gordon Blackshields
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Séan Coyle
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Clare McKenna
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre Teagasc, Grange, Dunsany, Co. Meath, Ireland.
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Vigors S, O'Doherty JV, Bryan K, Sweeney T. A comparative analysis of the transcriptome profiles of liver and muscle tissue in pigs divergent for feed efficiency. BMC Genomics 2019; 20:461. [PMID: 31170913 PMCID: PMC6555042 DOI: 10.1186/s12864-019-5740-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 04/26/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The improvement of feed efficiency is a key economic goal within the pig production industry. The objective of this study was to examine transcriptomic differences in both the liver and muscle of pigs divergent for feed efficiency, thus improving our understanding of the molecular mechanisms influencing feed efficiency and enabling the identification of candidate biomarkers. Residual feed intake (RFI) was calculated for two populations of pigs from two different farms of origin/genotype. The 6 most efficient (LRFI) and 6 least efficient (HRFI) animals from each population were selected for further analysis of Longissimus Dorsi muscle (n = 22) and liver (n = 23). Transcriptomic data were generated from liver and muscle collected post-slaughter. RESULTS The transcriptomic data segregated based on the RFI value of the pig rather than genotype/farm of origin. A total of 6463 genes were identified as being differentially expressed (DE) in muscle, while 964 genes were identified as being DE in liver. Genes that were commonly DE between muscle and liver (n = 526) were used for the multi-tissue analysis. These 526 genes were associated with protein targeting to membrane, extracellular matrix organisation and immune function. In the muscle-only analysis, genes associated with RNA processing, protein synthesis and energy metabolism were down regulated in the LRFI animals while in the liver-only analysis, genes associated with cell signalling and lipid homeostasis were up regulated in the LRFI animals. CONCLUSIONS Differences in the transcriptome segregated on pig RFI value rather than the genotype/farm of origin. Multi-tissue analysis identified that genes associated with GO terms protein targeting to membrane, extracellular matrix organisation and a range of terms relating to immune function were over represented in the differentially expressed genes of both liver and muscle.
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Affiliation(s)
- Stafford Vigors
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - John V O'Doherty
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Kenneth Bryan
- School of Agriculture & Food Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Torres Sweeney
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
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40
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Pareek CS, Sachajko M, Jaskowski JM, Herudzinska M, Skowronski M, Domagalski K, Szczepanek J, Czarnik U, Sobiech P, Wysocka D, Pierzchala M, Polawska E, Stepanow K, Ogłuszka M, Juszczuk-Kubiak E, Feng Y, Kumar D. Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq. Vet Sci 2019; 6:vetsci6020036. [PMID: 30934933 PMCID: PMC6631511 DOI: 10.3390/vetsci6020036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/16/2019] [Accepted: 03/26/2019] [Indexed: 12/26/2022] Open
Abstract
Global gene expression in liver transcriptome varies among cattle breeds. The present investigation was aimed to identify the differentially expressed genes (DEGs), metabolic gene networks and metabolic pathways in bovine liver transcriptome of young bulls. In this study, we comparatively analyzed the bovine liver transcriptome of dairy (Polish Holstein Friesian (HF); n = 6), beef (Hereford; n = 6), and dual purpose (Polish-Red; n = 6) cattle breeds. This study identified 895, 338, and 571 significant (p < 0.01) differentially expressed (DE) gene-transcripts represented as 745, 265, and 498 hepatic DE genes through the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-HF versus Polish-Red breeds comparisons, respectively. By combining all breeds comparisons, 75 hepatic DE genes (p < 0.01) were identified as commonly shared among all the three breed comparisons; 70, 160, and 38 hepatic DE genes were commonly shared between the following comparisons: (i) Polish-Red versus Hereford and Polish-HF versus Hereford; (ii) Polish-Red versus Hereford and Polish-HF versus Polish-Red; and (iii) Polish-HF versus Hereford and Polish-HF versus Polish-Red, respectively. A total of 440, 82, and 225 hepatic DE genes were uniquely observed for the Polish-Red versus Hereford, Polish-HF versus Hereford, and Polish-Red versus Polish-HF comparisons, respectively. Gene ontology (GO) analysis identified top-ranked enriched GO terms (p < 0.01) including 17, 16, and 31 functional groups and 151, 61, and 140 gene functions that were DE in all three breed liver transcriptome comparisons. Gene network analysis identified several potential metabolic pathways involved in glutamine family amino-acid, triglyceride synthesis, gluconeogenesis, p38MAPK cascade regulation, cholesterol biosynthesis (Polish-Red versus Hereford); IGF-receptor signaling, catecholamine transport, lipoprotein lipase, tyrosine kinase binding receptor (Polish-HF versus Hereford), and PGF-receptor binding, (Polish-HF versus Polish-Red). Validation results showed that the relative expression values were consistent to those obtained by RNA-seq, and significantly correlated between the quantitative reverse transcription PCR (RT-qPCR) and RNA-seq (Pearson’s r > 0.90). Our results provide new insights on bovine liver gene expressions among dairy versus dual versus beef breeds by identifying the large numbers of DEGs markers submitted to NCBI gene expression omnibus (GEO) accession number GSE114233, which can serve as useful genetic tools to develop the gene assays for trait-associated studies as well as, to effectively implement in genomics selection (GS) cattle breeding programs in Poland.
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Affiliation(s)
- Chandra Shekhar Pareek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mateusz Sachajko
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Jedrzej M Jaskowski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Magdalena Herudzinska
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Mariusz Skowronski
- Centre of Veterinary Sciences, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Krzysztof Domagalski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Joanna Szczepanek
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, 87-100 Torun, Poland.
| | - Urszula Czarnik
- Faculty of Animal Bio-engineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland.
| | - Przymeslaw Sobiech
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Dominika Wysocka
- Faculty of Veterinary Medicine, University of Warmia and Mazury in Olsztyn, 10719 Olsztyn, Poland.
| | - Mariusz Pierzchala
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Ewa Polawska
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Kamila Stepanow
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Magdalena Ogłuszka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzębiec, Poland.
| | - Edyta Juszczuk-Kubiak
- Faculty of Veterinary Medicine, Warsaw University of Life Sciences, 02-787 Warsaw, Poland.
| | - Yaping Feng
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08 854, USA.
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Alexandre PA, Naval-Sanchez M, Porto-Neto LR, Ferraz JBS, Reverter A, Fukumasu H. Systems Biology Reveals NR2F6 and TGFB1 as Key Regulators of Feed Efficiency in Beef Cattle. Front Genet 2019; 10:230. [PMID: 30967894 PMCID: PMC6439317 DOI: 10.3389/fgene.2019.00230] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/04/2019] [Indexed: 11/20/2022] Open
Abstract
Systems biology approaches are used as strategy to uncover tissue-specific perturbations and regulatory genes related to complex phenotypes. We applied this approach to study feed efficiency (FE) in beef cattle, an important trait both economically and environmentally. Poly-A selected RNA of five tissues (adrenal gland, hypothalamus, liver, skeletal muscle and pituitary) of eighteen young bulls, selected for high and low FE, were sequenced (Illumina HiSeq 2500, 100 bp, pared-end). From the 17,354 expressed genes considering all tissues, 1,335 were prioritized by five selection categories (differentially expressed, harboring SNPs associated with FE, tissue-specific, secreted in plasma and key regulators) and used for network construction. NR2F6 and TGFB1 were identified and validated by motif discovery as key regulators of hepatic inflammatory response and muscle tissue development, respectively, two biological processes demonstrated to be associated with FE. Moreover, we indicated potential biomarkers of FE, which are related to hormonal control of metabolism and sexual maturity. By using robust methodologies and validation strategies, we confirmed the main biological processes related to FE in Bos indicus and indicated candidate genes as regulators or biomarkers of superior animals.
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Affiliation(s)
- Pâmela A. Alexandre
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Marina Naval-Sanchez
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Laercio R. Porto-Neto
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - José Bento S. Ferraz
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
| | - Antonio Reverter
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Brisbane, QLD, Australia
| | - Heidge Fukumasu
- Department of Veterinary Medicine, College of Animal Sciences and Food Engineering, University of São Paulo, Pirassununga, Brazil
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