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Fowler SM, Kerr M, Hopkins DL, Schmidtke LM. Validation of Raman spectroscopic models to verify the origin of Australian beef grown under different production systems. Meat Sci 2024; 214:109522. [PMID: 38692014 DOI: 10.1016/j.meatsci.2024.109522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/21/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Verification of beef production systems and authentication of origin is becoming increasingly important as consumers base purchase decisions on a greater number of perceived values including the healthiness and environmental impact of products. Previously Raman spectroscopy has been explored as a tool to classify carcases from grass and grain fed cattle. Thus, the aim of the current study was to validate Partial Least Squares Discriminant Analysis (PLS-DA) models created using independent samples from carcases sampled from northern and southern Australian production systems in 2019, 2020 and 2021. Validation of the robustness of discrimination models was undertaken using spectral measures of fat from 585 carcases which were measured in 2022 using a Raman handheld device with a sample excised for fatty acid analysis. PLS-DA models were constructed and then employed to classify samples as either grass or grain fed in a two-class model. Overall, predictions were high with accuracies of up to 95.7% however, variation in the predictive ability was noted with models created for southern cattle yielding an accuracy of 73.2%. While some variation in fatty acids and therefore models can be attributed to differences in genetics, management and diet, the impact of duration of feeding is currently unknown and thus further work is warranted.
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Affiliation(s)
- Stephanie M Fowler
- Centre for Red Meat and Sheep Development, NSW Department of Primary Industries, Cowra, Australia; Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia.
| | - Matthew Kerr
- Centre for Red Meat and Sheep Development, NSW Department of Primary Industries, Cowra, Australia
| | - David L Hopkins
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia; ACT Australia, Canberra, Australia
| | - Leigh M Schmidtke
- Gulbali Institute, Charles Sturt University, Wagga Wagga, NSW, Australia
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2
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Young T, Laroche O, Walker SP, Miller MR, Casanovas P, Steiner K, Esmaeili N, Zhao R, Bowman JP, Wilson R, Bridle A, Carter CG, Nowak BF, Alfaro AC, Symonds JE. Prediction of Feed Efficiency and Performance-Based Traits in Fish via Integration of Multiple Omics and Clinical Covariates. BIOLOGY 2023; 12:1135. [PMID: 37627019 PMCID: PMC10452023 DOI: 10.3390/biology12081135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023]
Abstract
Fish aquaculture is a rapidly expanding global industry, set to support growing demands for sources of marine protein. Enhancing feed efficiency (FE) in farmed fish is required to reduce production costs and improve sector sustainability. Recognising that organisms are complex systems whose emerging phenotypes are the product of multiple interacting molecular processes, systems-based approaches are expected to deliver new biological insights into FE and growth performance. Here, we establish 14 diverse layers of multi-omics and clinical covariates to assess their capacities to predict FE and associated performance traits in a fish model (Oncorhynchus tshawytscha) and uncover the influential variables. Inter-omic relatedness between the different layers revealed several significant concordances, particularly between datasets originating from similar material/tissue and between blood indicators and some of the proteomic (liver), metabolomic (liver), and microbiomic layers. Single- and multi-layer random forest (RF) regression models showed that integration of all data layers provide greater FE prediction power than any single-layer model alone. Although FE was among the most challenging of the traits we attempted to predict, the mean accuracy of 40 different FE models in terms of root-mean square errors normalized to percentage was 30.4%, supporting RF as a feature selection tool and approach for complex trait prediction. Major contributions to the integrated FE models were derived from layers of proteomic and metabolomic data, with substantial influence also provided by the lipid composition layer. A correlation matrix of the top 27 variables in the models highlighted FE trait-associations with faecal bacteria (Serratia spp.), palmitic and nervonic acid moieties in whole body lipids, levels of free glycerol in muscle, and N-acetylglutamic acid content in liver. In summary, we identified subsets of molecular characteristics for the assessment of commercially relevant performance-based metrics in farmed Chinook salmon.
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Affiliation(s)
- Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
- The Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | | | | | - Matthew R. Miller
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | | | | | - Noah Esmaeili
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Ruixiang Zhao
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - John P. Bowman
- Tasmanian Institute of Agricultural Research, University of Tasmania, Hobart 7005, Australia
| | - Richard Wilson
- Central Science Laboratory, Research Division, University of Tasmania, Hobart 7001, Australia
| | - Andrew Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Chris G. Carter
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
- Blue Economy Cooperative Research Centre, Launceston 7250, Australia
| | - Barbara F. Nowak
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
| | - Andrea C. Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Science, School of Science, Private Bag 92006, Auckland 1142, New Zealand
| | - Jane E. Symonds
- Cawthron Institute, Nelson 7010, New Zealand
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart Private Bag 49, Hobart 7005, Australia
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Zhang H, Elolimy AA, Akbar H, Thanh LP, Yang Z, Loor JJ. Association of residual feed intake with peripartal ruminal microbiome and milk fatty acid composition during early lactation in Holstein dairy cows. J Dairy Sci 2022; 105:4971-4986. [DOI: 10.3168/jds.2021-21454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/08/2022] [Indexed: 11/19/2022]
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Miao Y, Fu C, Liao M, Fang F. Differences in Liver microRNA profiling in pigs with low and high
feed efficiency. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:312-329. [PMID: 35530409 PMCID: PMC9039951 DOI: 10.5187/jast.2022.e4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 01/09/2022] [Indexed: 11/21/2022]
Abstract
Feed cost is the main factor affecting the economic benefits of pig industry.
Improving the feed efficiency (FE) can reduce the feed cost and improve the
economic benefits of pig breeding enterprises. Liver is a complex metabolic
organ which affects the distribution of nutrients and regulates the efficiency
of energy conversion from nutrients to muscle or fat, thereby affecting feed
efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed
efficiency through the modulation of gene expression at the post-transcriptional
level. In this study, we analyzed miRNA profiling of liver tissues in High-FE
and Low-FE pigs for the purpose of identifying key miRNAs related to feed
efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel
miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were
co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly
differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of
which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes
and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs
indicated that the target genes of DE miRNAs were significantly enriched in
insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and
mammalian target of rapamycin signaling pathway. To verify the reliability of
sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse
transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs
were confirmed to be consistent with sequencing data. DE miRNA data indicated
that liver-specific miRNAs synergistically acted with mRNAs to improve feed
efficiency. The liver miRNAs expression analysis revealed the metabolic pathways
by which the liver miRNAs regulate pig feed efficiency.
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Affiliation(s)
- Yuanxin Miao
- College of Bioengineering,Jingchu
University of Technology, Jingmen 448000, Hubei, China
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Chuanke Fu
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Mingxing Liao
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Fang Fang
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
- National Center for International Research
on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong
Agricultural University, Wuhan 430070, China
- Corresponding author: Fang Fang, Key Laboratory of
Agricultural Animal Genetics, Breeding and Reproduction of Ministry of
Education, Huazhong Agricultural University, Wuhan 430070, China. Tel:
+86-278-728-2091, E-mail:
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Taussat S, Saintilan R, Krauss D, Maupetit D, Fouilloux MN, Renand G. Relationship between feed efficiency and slaughter traits of French Charolais bulls. J Anim Sci 2019; 97:2308-2319. [PMID: 30957842 DOI: 10.1093/jas/skz108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/02/2019] [Indexed: 11/12/2022] Open
Abstract
Improving feed efficiency is of interest to French beef producers so as to increase their profitability. To enable this improvement through selection, genetic correlations with production traits need to be quantified. The objective of this study was to estimate the genetic parameters for growth, feed efficiency (FE), and slaughter performance of young beef bulls of the French Charolais breed. Three feed efficiency criteria were calculated: residual feed intake (RFI), residual gain (RG), and ratio of FE. Data on feed intake, growth, and FE were available for 4,675 Charolais bulls tested in performance test stations and fed with pelleted diet. Between 1985 and 1989, 60 among 510 of these bulls were selected to procreate one generation of 1,477 progeny bulls which received the same pelleted diet at the experimental farm in Bourges. In addition to feed intake, growth, and FE traits, these terminal bulls also had slaughter traits of carcass yield, carcass composition, and weight of visceral organs collected. Genetic parameters were estimated using linear mixed animal models. Between performance test bulls and terminal bulls, the genetic correlation of RFI was 0.80 ± 0.18; it was 0.70 ± 0.21 for RG and 0.46 ± 0.20 for FE. For carcass traits, RFI was negatively correlated with carcass yield (-0.18 ± 0.14) and muscle content (-0.47 ± 0.14) and positively with fat content (0.48 ± 0.13). Conversely, RG and FE were positively correlated with carcass yield and muscle content and negatively with fat content. For the three FE criteria, efficient animals had leaner carcass. For visceral organs (as a proportion of empty body weight), RFI was genetically correlated with the proportions of the 5th quarter (0.51 ± 0.17), internal fat (0.36 ± 0.14), abomasum (0.46 ± 0.20), intestines (0.38 ± 0.17), liver (0.36 ± 0.16), and kidneys (0.73 ± 0.11). Conversely, RG and FE were negatively associated with these traits. The high-energy expenditure associated with the high-protein turnover in visceral organs may explain this opposite relationship between FE and the proportion of visceral organs. Selection for final weight and RFI increased growth and FE in progeny, and also improved carcass yield and muscle content in the carcass. To conclude, determinations of growth and feed intake in performance test stations are effective to select bulls to improve their growth, FE, and muscle content in carcass.
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Affiliation(s)
- Sébastien Taussat
- Allice, Paris, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Daniel Krauss
- UE0332 Domaine Expérimental Bourges-La Sapinière, INRA, Osmoy, France
| | - David Maupetit
- UE0332 Domaine Expérimental Bourges-La Sapinière, INRA, Osmoy, France
| | | | - Gilles Renand
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Magiri R, Lai K, Huang Y, Mutwiri G, Wilson HL. Innate immune response profiles in pigs injected with vaccine adjuvants polydi(sodium carboxylatoethylphenoxy)phosphazene (PCEP) and Emulsigen. Vet Immunol Immunopathol 2019; 209:7-16. [PMID: 30885308 DOI: 10.1016/j.vetimm.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 12/23/2022]
Abstract
Vaccines are formulated with adjuvants to enhance or direct antigen-specific immune responses against pathogens. However, the mechanisms of action (MOA) of adjuvants are not well understood and are under-investigated in large animal species. We have previously reported that injection of mice induced innate immune responses as indicated by increased cell recruitment and cytokine production at the site of injection with polyphosphazene (PCEP) adjuvant. In the present study, we evaluated whether PCEP induced similar innate immune responses in pigs. Piglets were injected with either PCEP or Emulsigen intradermally (I.D.) and the local cellular infiltration and cytokine production were evaluated at the site of injection and the draining lymph nodes. PCEP induced infiltration of macrophages, T and B cells, leucocytes and necrotic debris at the site of injection as well as PCEP-induced leucocyte infiltration in the draining lymph nodes. Emulsigen induced diffuse infiltration of leucocytes, macrophages, and lymphocytes at the site of injection as well as at the draining lymph nodes. PCEP induced significant production of interleukin IL-1β, and IL-13 at the site of injection and IL-1β, and IL-6 at the draining lymph nodes. Emulsigen promoted the production of IL-1β, IL-6, and IL-12 at the site of injection but not in the draining lymph nodes. No cytokines were detected in blood after injection of either adjuvant. Together, our data indicate that in pigs, the adjuvants PCEP and Emulsigen stimulate early innate immune responses at the injection site by creating an immunocompetent environment that may contribute to increased immunogenicity of the co-administered antigens.
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Affiliation(s)
- Royford Magiri
- Vaccinology & Immunotherapeutic Program, School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada; Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Ken Lai
- Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Yanyun Huang
- Prairie Diagnostic Services, 52 Campus Drive, Saskatoon, SK, Canada
| | - George Mutwiri
- Vaccinology & Immunotherapeutic Program, School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada; Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Heather L Wilson
- Vaccinology & Immunotherapeutic Program, School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada; Vaccine & Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.
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