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Zhou X, Li C, He Z, Liu H, Wang M, He J. Metabolomics Profiling of Serum and Urine from Chuanzang Black Pigs with Different Residual Feed Intake. Animals (Basel) 2024; 14:2323. [PMID: 39199856 PMCID: PMC11350911 DOI: 10.3390/ani14162323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 08/06/2024] [Accepted: 08/10/2024] [Indexed: 09/01/2024] Open
Abstract
This study was conducted to evaluate associations of blood variables and urine variables with different residual feed intakes (RFIs) in growing Chuanzang black (CB) pigs. A total of 228 growing CB boars from 99 days were used. The same basal diet was offered ad libitum and individual feed intake and body weight were measured over a period of 181 d. The CB pigs were categorized based on their residual feed intake values, with six individuals each from the high and low ends selected and divided into two groups: the low residual feed intake group (LS) and the high residual feed intake group (HS). Serum and urine samples were collected at the end of the experiment for determination of metabolomics profiling. Results showed that there were significantly different metabolites in serum and urine of different RFI groups (fold-change, FC > 2.0 or FC < 0.5, and p < 0.05), and 21 metabolites were identified in serum and 61 in urine. Cluster analysis showed that 20 metabolites were up-regulated and one metabolite was down-regulated in serum; 44 metabolites were up-regulated and 17 metabolites were down-regulated in urine. Kyoto Encyclopedia of Genes and Genomes analysis showed that the differential metabolites of serum were enriched in linoleic acid metabolism, and the differential metabolites of urine were enriched in steroid hormone biosynthesis, taurine and hypotaurine metabolism, and primary bile acid biosynthesis. The correlations between serum metabolites and urine metabolites indicated a significant positive correlation between all fatty acyls in serum metabolites and L-glutamate in urine. However, no compelling genetic or blood biomarkers have been found to explain the differences in RFI, suggesting multiple approaches to effective feed use in pigs. This study provides new insights into the subsequent assessment of RFI by metabolomics profiling, as well as the development of novel feed additives for the factors that will facilitate future research directions in CB pigs.
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Affiliation(s)
| | | | | | | | | | - Jian He
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China; (X.Z.); (C.L.); (Z.H.); (H.L.); (M.W.)
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Fernandes AC, Reverter A, Keogh K, Alexandre PA, Afonso J, Palhares JCP, Cardoso TF, Malheiros JM, Bruscadin JJ, de Oliveira PSN, Mourão GB, de Almeida Regitano LC, Coutinho LL. Transcriptional response to an alternative diet on liver, muscle, and rumen of beef cattle. Sci Rep 2024; 14:13682. [PMID: 38871745 PMCID: PMC11176196 DOI: 10.1038/s41598-024-63619-2] [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: 12/05/2023] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Feed cost represents a major economic determinant within cattle production, amounting to an estimated 75% of the total variable costs. Consequently, comprehensive approaches such as optimizing feed utilization through alternative feed sources, alongside the selection of feed-efficient animals, are of great significance. Here, we investigate the effect of two diets, traditional corn-grain fed and alternative by-product based, on 14 phenotypes related to feed, methane emission and production efficiency and on multi-tissue transcriptomics data from liver, muscle, and rumen wall, derived from 52 Nellore bulls, 26 on each diet. To this end, diets were contrasted at the level of phenotype, gene expression, and gene-phenotype network connectivity. As regards the phenotypic level, at a P value < 0.05, significant differences were found in favour of the alternative diet for average daily weight gain at finishing, dry matter intake at finishing, methane emission, carcass yield and subcutaneous fat thickness at the rib-eye muscle area. In terms of the transcriptional level of the 14,776 genes expressed across the examined tissues, we found 487, 484, and 499 genes differentially expressed due to diet in liver, muscle, and rumen, respectively (P value < 0.01). To explore differentially connected phenotypes across both diet-based networks, we focused on the phenotypes with the largest change in average number of connections within diets and tissues, namely methane emission and carcass yield, highlighting, in particular, gene expression changes involving SREBF2, and revealing the largest differential connectivity in rumen and muscle, respectively. Similarly, from examination of differentially connected genes across diets, the top-ranked most differentially connected regulators within each tissue were MEOX1, PTTG1, and BASP1 in liver, muscle, and rumen, respectively. Changes in gene co-expression patterns suggest activation or suppression of specific biological processes and pathways in response to dietary interventions, consequently impacting the phenotype. The identification of genes that respond differently to diets and their associated phenotypic effects serves as a crucial stepping stone for further investigations, aiming to build upon our discoveries. Ultimately, such advancements hold the promise of improving animal welfare, productivity, and sustainability in livestock farming.
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Affiliation(s)
- Anna Carolina Fernandes
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Antonio Reverter
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Kate Keogh
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
- Animal and Bioscience Research Department, Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, Ireland
| | - Pâmela Almeida Alexandre
- CSIRO Agriculture & Food, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, QLD, 4067, Australia
| | - Juliana Afonso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | | | - Tainã Figueiredo Cardoso
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
| | - Jessica Moraes Malheiros
- Brazilian Agricultural Research Corporation, Embrapa Pecuária Sudeste, São Carlos, São Paulo, Brazil
- Beef Cattle Research Center, Animal Science Institute (IZ), Sertãozinho, São Paulo, Brazil
| | - Jennifer Jessica Bruscadin
- Center of Biological and Health Sciences, Federal University of São Carlos, São Carlos, São Paulo, Brazil
| | | | - Gerson Barreto Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil
| | | | - Luiz Lehmann Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brazil.
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Linck Moroni J, Tsoi S, Wenger II, Plastow GS, Dyck MK. Placental Transcriptome Analysis in Connection with Low Litter Birth Weight Phenotype (LBWP) Sows. Genes (Basel) 2024; 15:703. [PMID: 38927639 PMCID: PMC11203121 DOI: 10.3390/genes15060703] [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: 04/07/2024] [Revised: 05/16/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
It is possible to identify sub-populations of sows in every pig herd that consistently give birth to low birth weight (BW) piglets, irrespective of the litter size. A previous study from our group demonstrated that placental development is a main factor affecting the litter birth weight phenotype (LBWP) in sows, thereby impacting the BW of entire litters, but the biological and molecular pathways behind this phenomenon are largely unknown. The aim of this study was to investigate the differential gene expression in placental tissues at day 30 of gestation between low LBWP (LLBWP) vs. high LBWP (HLBWP) sows from a purebred Large White maternal line. Using mRNA sequencing, we found 45 differentially expressed genes (DEGs) in placental tissues of LLBWP and HLBWP sows. Furthermore, (GO) enrichment of upregulated DEGs predicted that there were two biological processes significantly related to cornification and regulation of cell population proliferation. To better understand the molecular interaction between cell proliferation and cornification, we conducted transcriptional factor binding site (TFBS) prediction analysis. The results indicated that a highly significant TFBS was located at the 5' upstream of all four upregulated genes (CDSN, DSG3, KLK14, KRT17), recognized by transcription factors EGR4 and FOSL1. Our findings provide novel insight into how transcriptional regulation of two different biological processes interact in placental tissues of LLBWP sows.
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Affiliation(s)
| | | | | | | | - Michael K. Dyck
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada; (J.L.M.); (S.T.); (I.I.W.); (G.S.P.)
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dos Santos CA, Eler JP, Oliveira ECDM, Espigolan R, Giacomini G, Ferraz JBS, Paim TDP. Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation. PLoS One 2024; 19:e0301937. [PMID: 38662691 PMCID: PMC11045132 DOI: 10.1371/journal.pone.0301937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Genomic regions related to tropical adaptability are of paramount importance for animal breeding nowadays, especially in the context of global climate change. Moreover, understanding the genomic architecture of these regions may be very relevant for aiding breeding programs in choosing the best selection scheme for tropical adaptation and/or implementing a crossbreeding scheme. The composite MONTANA TROPICAL® population was developed by crossing cattle of four different biological types to improve production in harsh environments. Pedigree and genotype data (51962 SNPs) from 3215 MONTANA TROPICAL® cattle were used to i) characterize the population structure; ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to each selected region. The population structure based on principal components had a weak relationship with the genetic contribution of the different biological types. Clustering analyses (ADMIXTURE) showed different clusters according to the number of generations within the composite population. Considering results of both selection signatures approaches, we identified only one consensus region on chromosome 20 (35399405-40329703 bp). Genes in this region are related to immune function, regulation of epithelial cell differentiation, and cell response to ionizing radiation. This region harbors the slick locus which is related to slick hair and epidermis anatomy, both of which are related to heat stress adaptation. Also, QTLs in this region were related to feed intake, milk yield, mastitis, reproduction, and slick hair coat. The signatures of selection detected here arose in a few generations after crossbreeding between contrasting breeds. Therefore, it shows how important this genomic region may be for these animals to thrive in tropical conditions. Further investigations on sequencing this region can identify candidate genes for animal breeding and/or gene editing to tackle the challenges of climate change.
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Affiliation(s)
- Camila Alves dos Santos
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
| | - Joanir Pereira Eler
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | | | - Rafael Espigolan
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Gabriela Giacomini
- Associação Internacional de criadores de Montana, Mogi Mirim, São Paulo, Brazil
| | - José Bento Sterman Ferraz
- Departamento de Zootecnia, Faculdade de Zootecnia e Engenharia de alimentos, Universidade de São Paulo, Pirassununga, São Paulo, Brazil
| | - Tiago do Prado Paim
- Programa de Pós-graduação em Zootecnia, Instituto Federal de Ciência, Educação e Tecnologia Goiano, Rio Verde, Goiás, Brazil
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Cheng X, Du X, Liang Y, Degen AA, Wu X, Ji K, Gao Q, Xin G, Cong H, Yang G. Effect of grape pomace supplement on growth performance, gastrointestinal microbiota, and methane production in Tan lambs. Front Microbiol 2023; 14:1264840. [PMID: 37840727 PMCID: PMC10569316 DOI: 10.3389/fmicb.2023.1264840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Grape pomace (GP), a by-product in wine production, is nutritious and can be used as a feed ingredient for ruminants; however, its role in shaping sheep gastrointestinal tract (GIT) microbiota is unclear. We conducted a controlled trial using a randomized block design with 10 Tan lambs fed a control diet (CD) and 10 Tan lambs fed a pelleted diet containing 8% GP (dry matter basis) for 46 days. Rumen, jejunum, cecum, and colon bacterial and archaeal composition were identified by 16S rRNA gene sequencing. Dry matter intake (DMI) was greater (p < 0.05) in the GP than CD group; however, there was no difference in average daily gain (ADG, p < 0.05) and feed conversion ratio (FCR, p < 0.05) between the two groups. The GP group had a greater abundance of Prevotella 1 and Prevotella 7 in the rumen; of Sharpe, Ruminococcaceae 2, and [Ruminococcus] gauvreauii group in the jejunum; of Ruminococcaceae UCG-014 and Romboutsia in the cecum, and Prevotella UCG-001 in the colon; but lesser Rikenellaceae RC9 gut group in the rumen and cecum, and Ruminococcaceae UCG-005 and Ruminococcaceae UCG-010 in the colon than the CD group. The pathways of carbohydrate metabolism, such as L-rhamnose degradation in the rumen, starch and glycogen degradation in the jejunum, galactose degradation in the cecum, and mixed acid fermentation and mannan degradation in the colon were up-graded; whereas, the pathways of tricarboxylic acid (TCA) cycle VIII, and pyruvate fermentation to acetone in the rumen and colon were down-graded with GP. The archaeal incomplete reductive TCA cycle was enriched in the rumen, jejunum, and colon; whereas, the methanogenesis from H2 and CO2, the cofactors of methanogenesis, including coenzyme M, coenzyme B, and factor 420 biosynthesis were decreased in the colon. The study concluded that a diet including GP at 8% DM did not affect ADG or FCR in Tan lambs. However, there were some potential benefits, such as enhancing propionate production by microbiota and pathways in the GIT, promoting B-vitamin production in the rumen, facilitating starch degradation and amino acid biosynthesis in the jejunum, and reducing methanogenesis in the colon.
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Affiliation(s)
- Xindong Cheng
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xia Du
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanping Liang
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Abraham Allan Degen
- Desert Animal Adaptations and Husbandry, Wyler Department of Dryland Agriculture, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Xiukun Wu
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Kaixi Ji
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiaoxian Gao
- Ningxia Feed Engineering Technology Research Center, Ningxia University, Yinchuan, China
| | - Guosheng Xin
- Ningxia Feed Engineering Technology Research Center, Ningxia University, Yinchuan, China
| | - Haitao Cong
- Shandong Huakun Rural Revitalization Institute Co., Ltd., Jinan, China
| | - Guo Yang
- Key Laboratory of Stress Physiology and Ecology of Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
- Yellow River Estuary Tan Sheep Institute of Industrial Technology, Dongying, China
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6
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Li X, Yang B, Dong Z, Geng D, Wang C, Guo Q, Jiang Y, Chen G, Chang G, Bai H. Growth performance, carcass traits, meat quality, and blood variables of small-sized meat ducks with different feed efficiency phenotypes. Poult Sci 2023; 102:102818. [PMID: 37354613 PMCID: PMC10404786 DOI: 10.1016/j.psj.2023.102818] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/26/2023] Open
Abstract
The study investigated the effects of feed efficiency (residual feed intake, RFI and residual intake and gain, RIG) on the production performance of small-sized meat ducks. Ninety ducks with intermediate and extreme (high and low) RFI values were selected from 1,083 male ducks of similar body weight, and the 3 groups were then redivided according to RIG. For both efficiency measures, the feed conversion ratio (FCR) and average daily feed intake (ADFI) of efficient ducks were significantly lower than those of inefficient ducks (P < 0.05), while the residual body weight gain (RG) was significantly higher in efficient ducks (P < 0.05). Inefficient-RFI animals showed greater skin fat yield (P < 0.05), but no other differences in carcass traits were observed (P > 0.05). RIG had positive effects on the pH1 value of the breast muscle (P < 0.05), but feed efficiency did not affect the other meat quality traits (P > 0.05). With regard to blood biochemical parameters, efficient ducks had significantly lower triglycerides (TG) (P < 0.05). Correlation analysis demonstrated that RFI was positively correlated with average daily feed intake and feed conversion ratio (P < 0.05), while RIG exhibited a strong negative correlation with both (P < 0.05). The average daily body weight gain was positively correlated with RIG (P < 0.05). RIG had a positive effect on the pH1 value of the breast muscle (P < 0.05). Furthermore, triglyceride and high-density lipoprotein cholesterol levels correlated with both efficiency classifications (P < 0.05). Overall, the efficiency measures did not affect the carcass and meat quality of small-sized meat ducks but could identify ducks with lower feed consumption and fast growth.
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Affiliation(s)
- Xiaofan Li
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Baolong Yang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhaoqi Dong
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Dandan Geng
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Chenxiao Wang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Qixin Guo
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guohong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China; Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China.
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Mota LFM, Santos SWB, Júnior GAF, Bresolin T, Mercadante MEZ, Silva JAV, Cyrillo JNSG, Monteiro FM, Carvalheiro R, Albuquerque LG. Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits. BMC Genomics 2022; 23:424. [PMID: 35672696 PMCID: PMC9172108 DOI: 10.1186/s12864-022-08671-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08671-w.
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Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Tiago Bresolin
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Josineudson A V Silva
- National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.,School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu - SP, 18618-681, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Fábio M Monteiro
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil. .,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.
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8
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Hummel GL, Austin K, Cunningham-Hollinger HC. Comparing the maternal-fetal microbiome of humans and cattle: a translational assessment of the reproductive, placental, and fetal gut microbiomes. Biol Reprod 2022; 107:371-381. [PMID: 35412586 DOI: 10.1093/biolre/ioac067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/23/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
An analysis of sites within the maternal reproductive microbiome that potentially contribute to fetal gut microbial colonization, with a special focus on the comparison between humans and cattle.
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Affiliation(s)
- Gwendolynn L Hummel
- Department of Animal and Veterinary Science, University of Wyoming, Laramie, WY, 82071
| | - Kathleen Austin
- Department of Animal and Veterinary Science, University of Wyoming, Laramie, WY, 82071
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9
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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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10
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Wang B, Wang S, Ding M, Lu H, Wu H, Li Y. Quercetin Regulates Calcium and Phosphorus Metabolism Through the Wnt Signaling Pathway in Broilers. Front Vet Sci 2022; 8:786519. [PMID: 35155643 PMCID: PMC8828646 DOI: 10.3389/fvets.2021.786519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/22/2021] [Indexed: 12/22/2022] Open
Abstract
This study intended to explore the effect and mechanism of different doses of dietary quercetin on calcium and phosphorus metabolism to provide an experimental basis for preventing leg disease in broilers. A total of 480 1-day-old healthy Arbor Acre broilers were randomly allotted into four groups (0, 0.02, 0.04, 0.06%) for 42 days. Compared with control, 0.06% quercetin significantly increased the unit weight and the relative weight of tibia in broilers (P < 0.05). Meanwhile, phosphorus content and bone mineral density (BMD) were significantly increased by 0.06% dietary quercetin supplementation in tibia (P < 0.05). Ash of tibia was significantly increased by 0.04 and 0.06% quercetin in broilers (P < 0.05). In addition, 0.06% quercetin significantly increased the content of serum calcium-binding protein (CB), estradiol (E2), osteocalcin (OC), alkaline phosphatase (ALP), and calcitonin (CT) (P < 0.05); 0.04% quercetin significantly increased 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3) (P < 0.05) content in serum of broilers. The content of serum parathyroid (PTH) was significantly decreased by 0.02 and 0.06% quercetin (P < 0.05) in broilers. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the Wnt signaling pathway was a key signaling pathway of calcium and phosphorus metabolism in broilers which was significantly regulated by quercetin. The differentially expressed genes (DEGs) from transcriptome sequencing were validated with real-time quantitative PCR (RT-qPCR). In conclusion, 0.06% dietary quercetin supplementation improved calcium and phosphorus metabolism by regulating the Wnt signaling pathway in broilers.
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11
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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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12
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Dervishi E, Reimert I, van der Zande LE, Mathur P, Knol EF, Plastow GS. Relationship between indirect genetic effects for growth, environmental enrichment, coping style and sex with the serum metabolome profile of pigs. Sci Rep 2021; 11:23377. [PMID: 34862433 PMCID: PMC8642533 DOI: 10.1038/s41598-021-02814-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Including Indirect Genetic Effects (IGE) in breeding programs to reduce aggression in group housed animals has been proposed. However, the effect of selection for IGE for growth on animal metabolism and physiology is unknown. The purpose of this study was twofold: (1) To investigate the effects of this new breeding method along with two housing (barren and straw), coping style (high and low resisters) and sex (female and castrated males) options on the metabolome profile of pigs. (2) To identify and map biological processes associated with a regrouping test at 9 weeks of age. We used Nuclear Magnetic Resonance to quantify 49 serum metabolites at week 8, 9 and 22. Also, we quantified 3 catecholamines (tyramine, epinephrine, phenylethylamine) and serotonin and three water soluble vitamins (B2, B5 and B7). Overall, no significant differences were observed between negative and positive IGE animals. The magnitude of change (delta) of many metabolites as a response to the regrouping test was significantly affected by IGE, especially that of the amino acids (P < 0.05), being greater in positive IGE pigs. The regrouping test was associated with alteration in glycine, serine and threonine metabolism. In conclusion positive and negative IGE animals respond differently to the regrouping test.
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Affiliation(s)
- Elda Dervishi
- Livestock Gentec, University of Alberta, 116 St and 85 Ave, Edmonton, AB, T6G 2R3, Canada.
| | - Inonge Reimert
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Lisette E van der Zande
- Adaptation Physiology Group, Department of Animal Sciences, Wageningen University and Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Pramod Mathur
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Egbert F Knol
- Topigs Norsvin Research Center B.V, 6640 AA, Beuningen, The Netherlands
| | - Graham S Plastow
- Livestock Gentec, University of Alberta, 116 St and 85 Ave, Edmonton, AB, T6G 2R3, Canada
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13
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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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14
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Xiao C, Deng J, Zeng L, Sun T, Yang Z, Yang X. Transcriptome Analysis Identifies Candidate Genes and Signaling Pathways Associated With Feed Efficiency in Xiayan Chicken. Front Genet 2021; 12:607719. [PMID: 33815460 PMCID: PMC8010316 DOI: 10.3389/fgene.2021.607719] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Feed efficiency is an important economic factor in poultry production, and the rate of feed efficiency is generally evaluated using residual feed intake (RFI). The molecular regulatory mechanisms of RFI remain unknown. Therefore, the objective of this study was to identify candidate genes and signaling pathways related to RFI using RNA-sequencing for low RFI (LRFI) and high RFI (HRFI) in the Xiayan chicken, a native chicken of the Guangxi province. Chickens were divided into four groups based on FE and sex: LRFI and HRFI for males and females, respectively. We identified a total of 1,015 and 742 differentially expressed genes associated with RFI in males and females, respectively. The 32 and 7 Gene Ontology (GO) enrichment terms, respectively, identified in males and females chiefly involved carbohydrate, amino acid, and energy metabolism. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 11 and 5 significantly enriched signaling pathways, including those for nutrient metabolism, insulin signaling, and MAPK signaling, respectively. Protein-protein interaction (PPI) network analysis showed that the pathways involving CAT, ACSL1, ECI2, ABCD2, ACOX1, PCK1, HSPA2, and HSP90AA1 may have an effect on feed efficiency, and these genes are mainly involved in the biological processes of fat metabolism and heat stress. Gene set enrichment analysis indicated that the increased expression of genes in LRFI chickens was related to intestinal microvilli structure and function, and to the fat metabolism process in males. In females, the highly expressed set of genes in the LRFI group was primarily associated with nervous system and cell development. Our findings provide further insight into RFI regulation mechanisms in chickens.
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Affiliation(s)
- Cong Xiao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jixian Deng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Linghu Zeng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tiantian Sun
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Zhuliang Yang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Xiurong Yang
- College of Animal Science and Technology, Guangxi University, Nanning, China
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15
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Yang L, Wang X, He T, Xiong F, Chen X, Chen X, Jin S, Geng Z. Association of residual feed intake with growth performance, carcass traits, meat quality, and blood variables in native chickens. J Anim Sci 2020; 98:5821583. [PMID: 32303739 DOI: 10.1093/jas/skaa121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/16/2020] [Indexed: 12/27/2022] Open
Abstract
Improving feed efficiency is a primary goal in poultry breeding strategies. Residual feed intake (RFI) in chickens typically calculated during the growing period is a measure of feed efficiency that is independent of the level of production. The objective of this study was to evaluate phenotypic correlations of growth performance, carcass traits, meat quality, and blood variables with RFI in growing native chickens. A total of 1,008 chickens were selected for the experiment to derive RFI. After the RFI measurement period of 42 d, 25 chickens with low RFI values, 25 chickens with medium RFI values, and 25 chickens with high RFI values were selected. The RFI was significantly positively correlated with feed conversion ratio and average daily feed intake, while it was not significantly correlated with initial body weight (BW), final BW, average daily body weight gain, and metabolic BW0.75. The abdominal fat weight and yield of high RFI group were significantly greater than those of medium and low RFI groups, and the abdominal fat yield was significantly positively correlated with RFI. Moreover, the plasma insulin-like growth factor 1 (IGF-1) content of low RFI group was significantly greater than those of high and medium RFI groups. The plasma concentrations of adrenocorticotropic hormone, triiodothyronine (T3), and cortisol of high RFI birds were significantly greater than that of low RFI birds. RFI was significantly positively correlated with plasma concentrations of T3 and cortisol, while it was significantly negatively correlated with plasma concentration of IGF-1. In addition, the serum levels of glucose and triglyceride of high RFI birds were significantly lower than that of low RFI birds. The serum low-density lipoprotein cholesterol (LDL-C) content of high RFI group was significantly greater than that of medium and low RFI groups, and it was significantly positively correlated with RFI. Our data suggested that selection of chickens with low RFI values may be beneficial to reduce fat deposition in native chickens without affecting the meat quality. Circulating IGF-1, T3, cortisol, and LDL-C concentrations can be used as indirect selection indicators of feed efficiency in native chickens. The effect of IGF-1, T3, cortisol, and LDL-C on feed efficiency of native chickens should be carefully examined and validated in future breeding programs.
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Affiliation(s)
- Lei Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Xiaolong Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Tingting He
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Fengliang Xiong
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China
| | - Xianzhen Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Xingyong Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, P.R. China.,Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei, P.R. China
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16
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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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17
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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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18
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Zhang Y, Li F, Chen Y, Wu H, Meng Q, Guan LL. Metatranscriptomic Profiling Reveals the Effect of Breed on Active Rumen Eukaryotic Composition in Beef Cattle With Varied Feed Efficiency. Front Microbiol 2020; 11:367. [PMID: 32231647 PMCID: PMC7082318 DOI: 10.3389/fmicb.2020.00367] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/19/2020] [Indexed: 01/09/2023] Open
Abstract
Exploring the compositional characteristics of rumen eukaryotic community can expand our understanding of their role in rumen function and feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen eukaryotic community (protozoa and fungi) in beef cattle (n = 48) of three breeds [Angus (AN), Charolais (CH), and Kinsella Composite (KC)] and with divergent residual feed intake (RFI). The composition of active rumen eukaryotic microbiota was evaluated based on enriched 18S rRNAs from the metatranscriptomic datasets. At the phylum level, a total of four protozoal taxa (Ciliophora, Parabasalia, unclassified SAR, and unclassified Alveolata), six fungal taxa (Neocallimastigomycota, Basidiomycota, unclassified Fungi, Mucoromycota, Ascomycota, and Chytridiomycota), and one sister group of kingdom Fungi (unclassified Opisthokonta) were detected with relative abundances higher than 0.01% and in at least 50% of animals within each breed. Among these, Ciliophora, Parabasalia, unclassified Opisthokonta, and Neocallimastigomycota were the top four active eukaryotic phyla. At the genus level, a total of 8 ciliated protozoa, 5 flagellated protozoa, 5 anaerobic fungi, and 10 aerobic fungi taxa were detected, with unclassified Trichostomatia, Tetratrichomonas, unclassified Neocallimastigaceae, and Pleurotus being the most predominant taxa of ciliated protozoa, flagellated protozoa, anaerobic fungi, and aerobic fungi, respectively. Differential abundance analysis revealed that breed had a significant effect on the phylogenetic lineages of rumen eukaryotes, and seven fungal taxa were more abundant (linear discriminant analysis score > 2 with P < 0.05) in the rumen of KC steers than in the rumen of AN and CH steers. Although principal coordinate analysis (PCoA) revealed that the ruminal active eukaryotic profiles were not distinguishable between high- and low-RFI groups, the diversity indices, including Faith’s phylogenetic diversity (PD), observed operational taxonomic units (OTUs), and Shannon index of rumen eukaryotes were higher in low-RFI steers than those in high-RFI steers. Meanwhile, the abundance of genus Entodinium and the kingdom Fungi was higher in low-RFI steers than that in high-RFI steers. This information on active rumen eukaryotic microbiota and identified differential abundance of taxa between high- and low-RFI animals suggests the possibility of improving feed efficiency through altering rumen eukaryotic microbiota.
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Affiliation(s)
- Yawei Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Fuyong Li
- 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
| | - Hao Wu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qingxiang Meng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Le Luo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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19
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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: 17] [Impact Index Per Article: 3.4] [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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Host transcriptome and microbiome interaction modulates physiology of full-sibs broilers with divergent feed conversion ratio. NPJ Biofilms Microbiomes 2019; 5:24. [PMID: 31552140 PMCID: PMC6754422 DOI: 10.1038/s41522-019-0096-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022] Open
Abstract
Efficient livestock production relies on effective conversion of feed into body weight gain (BWG). High levels of feed conversion are especially important in production of broiler chickens, birds reared for meat, where economic margins are tight. Traits associated with improved broiler growth and feed efficiency have been subjected to intense genetic selection, but measures such as feed conversion ratio (FCR) remain variable, even between full siblings (sibs). Non-genetic factors such as the composition and function of microbial populations within different enteric compartments have been recognized to influence FCR, although the extent of interplay between hosts and their microbiomes is unclear. To examine host–microbiome interactions we investigated variation in the composition and functions of host intestinal-hepatic transcriptomes and the intestinal microbiota of full-sib broilers with divergent FCR. Progeny from 300 broiler families were assessed for divergent FCR set against shared genetic backgrounds and exposure to the same environmental factors. The seven most divergent full-sib pairs were chosen for analysis, exhibiting marked variation in transcription of genes as well as gut microbial diversity. Examination of enteric microbiota in low FCR sibs revealed variation in microbial community structure and function with no difference in feed intake compared to high FCR sibs. Gene transcription in low and high FCR sibs was significantly associated with the abundance of specific microbial taxa. Highly intertwined interactions between host transcriptomes and enteric microbiota are likely to modulate complex traits like FCR and may be amenable to selective modification with relevance to improving intestinal homeostasis and health.
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Association analysis between feed efficiency and expression of key genes of the avTOR signaling pathway in meat-type ducks. Mol Biol Rep 2019; 46:3537-3544. [PMID: 31140048 DOI: 10.1007/s11033-019-04720-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/07/2019] [Indexed: 10/26/2022]
Abstract
Genes involved in the target of rapamycin (TOR) signaling pathway are implicated in nutrient translation, cell proliferation and differentiation, and anabolism, which can affect both growth and feed intake. However, the role of TOR signaling in the regulation of feed intake and feed efficiency in poultry is not clear. In the present study, a total of 1000 ducks, of similar initial weight, were chosen and transferred to individual cages to determine their residual feed intake (RFI) from the age of 21 to 42 days. Subsequently, 60 ducks, which were divided into high (HRFI) and low (LRFI) groups according to their RFI, were chosen to analyze the TOR signaling activities in the liver. The differential expression level of genes involved in the TOR signaling pathway was assayed by the real-time polymerase chain reaction. In the liver, the expression of AKT, avTOR, avLST8, and S6K1 was significantly higher in LRFI ducks than in HRFI ducks; avTOR and AKT were negatively associated with the feed conversion ratio and RFI. Furthermore, PI3K was moderately positively associated with AKT; AKT was strongly positively associated with PI3K, avTOR, avLST8, and S6K1; and avTOR was strongly positively associated with S6K1. In conclusion, the activation of avTOR signaling in the liver of LRFI ducks might be ascribed to higher energy state or more active nutrient transport (amino acids), or both, than those in the liver of HRFI ducks. The results of the present study indicate that AKT and avTOR of TOR signaling might be used as candidate genes to assess molecular regulation of feed efficiency.
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Fonseca LD, Eler JP, Pereira MA, Rosa AF, Alexandre PA, Moncau CT, Salvato F, Rosa-Fernandes L, Palmisano G, Ferraz JBS, Fukumasu H. Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle. Sci Rep 2019; 9:5364. [PMID: 30926873 PMCID: PMC6441086 DOI: 10.1038/s41598-019-41813-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.
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Affiliation(s)
- Leydiana D Fonseca
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Joanir P Eler
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Mikaele A Pereira
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Alessandra F Rosa
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Pâmela A Alexandre
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Cristina T Moncau
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Fernanda Salvato
- Institute of Biology, State University of Campinas, Campinas, 13083-862, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - José B S Ferraz
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil.
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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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Moraïs S, Mizrahi I. The Road Not Taken: The Rumen Microbiome, Functional Groups, and Community States. Trends Microbiol 2019; 27:538-549. [PMID: 30679075 DOI: 10.1016/j.tim.2018.12.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/28/2018] [Accepted: 12/19/2018] [Indexed: 02/07/2023]
Abstract
The rumen ecosystem represents a classic example of host-microbiome symbiosis. In this obligatory relationship, the host feeds on plant fibers that can only be degraded through a set of complex metabolic cascades, exclusively encoded in rumen-associated microbes. These various metabolic pathways are distributed across a multitude of microbial populations. Application of basic ecological principles to this ecosystem can contribute to profound understanding of the rules that shape it. Here, we discuss recent studies by examining the mapping between host attributes, rumen ecosystem composition, and functionality to propose simple, yet powerful concepts to guide the interpretation of microbiome data and enable a better understanding of how the system responds to perturbations.
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Affiliation(s)
- Sarah Moraïs
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, 8410501 Beer-Sheva, Israel.
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25
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Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency. BMC Bioinformatics 2018; 19:513. [PMID: 30558534 PMCID: PMC6296024 DOI: 10.1186/s12859-018-2553-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/30/2018] [Indexed: 02/05/2023] Open
Abstract
Background Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associated with high and low feed efficiency and their regulator genes in Danish Holstein and Jersey cows. RNA-sequencing data from Holstein and Jersey cows with high and low residual feed intake (RFI) and treated with two diets (low and high concentrate) were used. Approximately 26 million and 25 million pair reads were mapped to bovine reference genome for Jersey and Holstein breed, respectively. Subsequently, the gene count expressions data were analysed using a Weighted Gene Co-expression Network Analysis (WGCNA) approach. Functional enrichment analysis from Ingenuity® Pathway Analysis (IPA®), ClueGO application and STRING of these modules was performed to identify relevant biological pathways and regulatory genes. Results WGCNA identified two groups of co-expressed genes (modules) significantly associated with RFI and one module significantly associated with diet. In Holstein cows, the salmon module with module trait relationship (MTR) = 0.7 and the top upstream regulators ATP7B were involved in cholesterol biosynthesis, steroid biosynthesis, lipid biosynthesis and fatty acid metabolism. The magenta module has been significantly associated (MTR = 0.51) with the treatment diet involved in the triglyceride homeostasis. In Jersey cows, the lightsteelblue1 (MTR = − 0.57) module controlled by IFNG and IL10RA was involved in the positive regulation of interferon-gamma production, lymphocyte differentiation, natural killer cell-mediated cytotoxicity and primary immunodeficiency. Conclusion The present study provides new information on the biological functions in liver that are potentially involved in controlling feed efficiency. The hub genes and upstream regulators (ATP7b, IFNG and IL10RA) involved in these functions are potential candidate genes for the development of new biomarkers. However, the hub genes, upstream regulators and pathways involved in the co-expressed networks were different in both breeds. Hence, additional studies are required to investigate and confirm these findings prior to their use as candidate genes. Electronic supplementary material The online version of this article (10.1186/s12859-018-2553-z) contains supplementary material, which is available to authorized users.
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26
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Huws SA, Creevey CJ, Oyama LB, Mizrahi I, Denman SE, Popova M, Muñoz-Tamayo R, Forano E, Waters SM, Hess M, Tapio I, Smidt H, Krizsan SJ, Yáñez-Ruiz DR, Belanche A, Guan L, Gruninger RJ, McAllister TA, Newbold CJ, Roehe R, Dewhurst RJ, Snelling TJ, Watson M, Suen G, Hart EH, Kingston-Smith AH, Scollan ND, do Prado RM, Pilau EJ, Mantovani HC, Attwood GT, Edwards JE, McEwan NR, Morrisson S, Mayorga OL, Elliott C, Morgavi DP. Addressing Global Ruminant Agricultural Challenges Through Understanding the Rumen Microbiome: Past, Present, and Future. Front Microbiol 2018; 9:2161. [PMID: 30319557 PMCID: PMC6167468 DOI: 10.3389/fmicb.2018.02161] [Citation(s) in RCA: 183] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/23/2018] [Indexed: 12/24/2022] Open
Abstract
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi, methanogenic archaea and phages. These microbes interact closely to breakdown plant material that cannot be digested by humans, whilst providing metabolic energy to the host and, in the case of archaea, producing methane. Consequently, ruminants produce meat and milk, which are rich in high-quality protein, vitamins and minerals, and therefore contribute to food security. As the world population is predicted to reach approximately 9.7 billion by 2050, an increase in ruminant production to satisfy global protein demand is necessary, despite limited land availability, and whilst ensuring environmental impact is minimized. Although challenging, these goals can be met, but depend on our understanding of the rumen microbiome. Attempts to manipulate the rumen microbiome to benefit global agricultural challenges have been ongoing for decades with limited success, mostly due to the lack of a detailed understanding of this microbiome and our limited ability to culture most of these microbes outside the rumen. The potential to manipulate the rumen microbiome and meet global livestock challenges through animal breeding and introduction of dietary interventions during early life have recently emerged as promising new technologies. Our inability to phenotype ruminants in a high-throughput manner has also hampered progress, although the recent increase in “omic” data may allow further development of mathematical models and rumen microbial gene biomarkers as proxies. Advances in computational tools, high-throughput sequencing technologies and cultivation-independent “omics” approaches continue to revolutionize our understanding of the rumen microbiome. This will ultimately provide the knowledge framework needed to solve current and future ruminant livestock challenges.
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Affiliation(s)
- Sharon A Huws
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Christopher J Creevey
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Linda B Oyama
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Stuart E Denman
- Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Milka Popova
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
| | - Rafael Muñoz-Tamayo
- UMR Modélisation Systémique Appliquée aux Ruminants, INRA, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Evelyne Forano
- UMR 454 MEDIS, INRA, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sinead M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Grange, Ireland
| | - Matthias Hess
- College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Ilma Tapio
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Hauke Smidt
- Department of Agrotechnology and Food Sciences, Wageningen, Netherlands
| | - Sophie J Krizsan
- Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - David R Yáñez-Ruiz
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Alejandro Belanche
- Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain
| | - Leluo Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Robert J Gruninger
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Tim A McAllister
- Lethbridge Research Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | | | - Rainer Roehe
- Scotland's Rural College, Edinburgh, United Kingdom
| | | | - Tim J Snelling
- The Rowett Institute, University of Aberdeen, Aberdeen, United Kingdom
| | - Mick Watson
- The Roslin Institute and the Royal (Dick) School of Veterinary Studies (R(D)SVS), University of Edinburgh, Edinburgh, United Kingdom
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Elizabeth H Hart
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Alison H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Nigel D Scollan
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Rodolpho M do Prado
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | - Eduardo J Pilau
- Laboratório de Biomoléculas e Espectrometria de Massas-Labiomass, Departamento de Química, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Graeme T Attwood
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Joan E Edwards
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, Netherlands
| | - Neil R McEwan
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen, United Kingdom
| | - Steven Morrisson
- Sustainable Livestock, Agri-Food and Bio-Sciences Institute, Hillsborough, United Kingdom
| | - Olga L Mayorga
- Colombian Agricultural Research Corporation, Mosquera, Colombia
| | - Christopher Elliott
- Institute for Global Food Security, Queen's University of Belfast, Belfast, United Kingdom
| | - Diego P Morgavi
- Institute National de la Recherche Agronomique, UMR1213 Herbivores, Clermont Université, VetAgro Sup, UMR Herbivores, Clermont-Ferrand, France
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Izadnia HR, Tahmoorespur M, Bakhtiarizadeh MR, Nassiri M, Esmaeilkhanien S. Gene expression profile analysis of residual feed intake for Isfahan native chickens using RNA-SEQ data. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2018.1507625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
| | - Mojtaba Tahmoorespur
- Faculty of Agriculture, Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammadreza Nassiri
- Faculty of Agriculture, Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, Iran
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Abo-Ismail MK, Lansink N, Akanno E, Karisa BK, Crowley JJ, Moore SS, Bork E, Stothard P, Basarab JA, Plastow GS. Development and validation of a small SNP panel for feed efficiency in beef cattle. J Anim Sci 2018; 96:375-397. [PMID: 29390120 DOI: 10.1093/jas/sky020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022] Open
Abstract
The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.
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Affiliation(s)
- M K Abo-Ismail
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt
| | - N Lansink
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - E Akanno
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - B K Karisa
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J J Crowley
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Canadian Beef Breeds Council, Calgary, AB, Canada
| | - S S Moore
- Centre for Animal Science, University of Queensland, St Lucia, Australia
| | - E Bork
- Rangeland Research Institute, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - P Stothard
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J A Basarab
- Alberta Agriculture and Forestry, Lacombe Research Centre, Lacombe, AB, Canada
| | - G S Plastow
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
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29
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Asher A, Shabtay A, Cohen-Zinder M, Aharoni Y, Miron J, Agmon R, Halachmi I, Orlov A, Haim A, Tedeschi LO, Carstens GE, Johnson KA, Brosh A. Consistency of feed efficiency ranking and mechanisms associated with inter-animal variation among growing calves. J Anim Sci 2018; 96:990-1009. [PMID: 29385602 PMCID: PMC6093583 DOI: 10.1093/jas/skx045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
This study investigated the possible mechanisms for explaining interanimal variation in efficiency of feed utilization in intact male Holstein calves. Additionally, we examined whether the feed efficiency (FE) ranking of calves (n = 26) changed due to age and/or diet quality. Calves were evaluated during three periods (P1, P2, and P3) while fed a high-quality diet (calculated mobilizable energy [ME] of 11.8 MJ/kg DM) during P1 and P3, and a low-quality diet (calculated ME of 7.7 MJ/kg DM) during P2. The study periods were 84, 119, and 127 d, respectively. Initial ages of the calves in P1, P2, and P3 were 7, 11, and 15 mo, respectively, and initial body weight (BW) were 245, 367, and 458 kg, respectively. Individual dry matter intake (DMI), average daily gain (ADG), diet digestibility, and heat production (HP) were measured in all periods. The measured FE indexes were: residual feed intake (RFI), the gain-to-feed ratio (G:F), residual gain (RG), residual gain and intake (RIG), the ratio of HP-to-ME intake (HP/MEI), and residual heat production (RHP). For statistical analysis, animals' performance data in each period, were ranked by RFI, and categorized into high-, medium-, and low-RFI groups (H-RFI, M-RFI, and L-RFI). RFI was not correlated with in vivo digestibility, age, BW, BCS, or ADG in all three periods. The L-RFI group had lowest DMI, MEI, HP, retained energy (RE), and RE/ADG. Chemical analysis of the longissimus dorsi muscle shows that the L-RFI group had a higher percentage of protein and a lower percentage of fat compared to the H-RFI group. We suggested that the main mechanism separating L- from H-RFI calves is the protein-to-fat ratio in the deposited tissues. When efficiency was related to kg/day (DMI and ADG) and not to daily retained energy, the selected efficient L-RFI calves deposited more protein and less fat per daily gain than less efficient H-RFI calves. However, when the significant greater heat increment and maintenance energy requirement of protein compared to fat deposition in tissue were considered, we could not exclude the hypothesis that variation in efficiency is partly explained by efficient energy utilization. The ranking classification of calves to groups according to their RFI efficiency was independent of diet quality and age.
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Affiliation(s)
- A Asher
- Northern R&D, MIGAL, Galilee Technology Center, Kiryat Shmona, Israel
| | - A Shabtay
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - M Cohen-Zinder
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - Y Aharoni
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - J Miron
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - R Agmon
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - I Halachmi
- Institute of Agricultural Engineering, ARO, Bet-Dagan, Israel
| | - A Orlov
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
| | - A Haim
- University of Haifa, Israeli Center for Interdisciplinary Research in Chronobiology, Haifa, Israel
| | - L O Tedeschi
- Texas A&M University, Department of Animal Science, College Station
| | - G E Carstens
- Texas A&M University, Department of Animal Science, College Station
| | - K A Johnson
- Washington State University, Department of Animal Science, Pullman
| | - A Brosh
- Institute of Animal Science, ARO, Beef Cattle Section, Newe Yaar Resarch Center, Ramat Yishay, Israel
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Meale SJ, Morgavi DP, Cassar-Malek I, Andueza D, Ortigues-Marty I, Robins RJ, Schiphorst AM, Migné C, Pétéra M, Laverroux S, Graulet B, Boudra H, Cantalapiedra-Hijar G. Exploration of Biological Markers of Feed Efficiency in Young Bulls. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:9817-9827. [PMID: 29058420 DOI: 10.1021/acs.jafc.7b03503] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The efficiency with which ruminants convert feed to desirable products is difficult to measure under normal commercial settings. We explored the use of potential biological markers from easily obtainable samples, that is, blood, hair, and feces, to characterize potential causes of divergent efficiency when considered as residual feed intake (RFI) or feed conversion efficiency (FCE). A total of 54 Charolais bulls, 20 in period 1 and 34 in period 2, were examined for individual dry matter intake (DMI) and growth. Bulls were offered a diet of 70:30 wrapped grass silage to concentrate for 99 d. At the conclusion of the test period, blood samples were collected for the determination of vitamins B2 and B6, and plasma used for the determination of metabolites, natural isotopic 15N abundance (15N NIA, expressed as δ15N ‰) and fractionation (Δ15Nplasma proteins-diet and Δ13Cplasma proteins-diet) and near-infrared spectroscopy (NIRS). Feces were analyzed by NIRS. Bulls were slaughtered at 15-17 months of age and carcass characteristics determined. Bulls were ranked according to RFI with extremes (SD ± 0.5; n = 31) classified as either efficient (Neg-RFI) or inefficient (Pos-RFI). Extreme bulls were then classified for FCE (high vs low FCE), changing the groups. Pos-RFI bulls consumed 14% more feed than Neg-RFI bulls for the same level of weight gain. Low FCE bulls tended to eat more, but had lower weight gains than high FCE bulls. No differences were detected in carcass conformation, fat scores, hot carcass weight, or dressing percentage. Yet, heart and bladder weights were heavier in Pos-RFI, and rumen weight tended to be heavier in Pos-RFI bulls. RFI did not affect bulk 15N or 13C fractionation. A negative correlation was observed between FCE and Δ15Nplasma proteins-diet. Inefficient bulls (Pos-RFI) had higher δ15N in glycine compared to Neg-RFI bulls. Similarly, metabolomic analysis showed a tendency for concentrations of glycine and sarcosine to be elevated in Pos-RFI bulls, whereas aspartic acid and carnosine tended to be elevated, and serine tended to be lower in High FCE. Among vitamins, only flavin adenine dinucleotide concentration was higher in the blood of bulls with High FCE. These results suggest that the two feed efficiency metrics differ in the underlying mechanisms of metabolism, where RFI is driven by differences in the energetic requirements of visceral organs and the extent of AA catabolism.
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Affiliation(s)
- Sarah J Meale
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Diego P Morgavi
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Isabelle Cassar-Malek
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Donato Andueza
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Isabelle Ortigues-Marty
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Richard J Robins
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes, France
| | - Anne-Marie Schiphorst
- Elucidation of Biosynthesis by Isotopic Spectrometry Group, CEISAM, CNRS-University of Nantes UMR6230 , B.P. 92208, F-44322 Nantes, France
| | | | | | - Sophie Laverroux
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Benoit Graulet
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
| | - Hamid Boudra
- Université Clermont Auvergne, INRA , VetAgro Sup, UMR Herbivores, F-63122 Saint-Genès-Champanelle, France
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Dai P, Luan S, Lu X, Luo K, Kong J. Comparative transcriptome analysis of the Pacific White Shrimp (Litopenaeus vannamei) muscle reveals the molecular basis of residual feed intake. Sci Rep 2017; 7:10483. [PMID: 28874698 PMCID: PMC5585345 DOI: 10.1038/s41598-017-10475-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 08/10/2017] [Indexed: 01/29/2023] Open
Abstract
Feed efficiency is an economically important trait in genetic improvement programs of L. vannamei. Residual feed intake (RFI), an ideal measure of feed efficiency, is the difference between observed feed intake and expected feed requirement predicted from maintenance and production. Exploring the molecular basis of RFI is essential to facilitate the genetic breeding of feed efficiency in L. vannamei. However, few studies have been reported in this aspect. In this study, we sequenced muscle transcriptomes of a high-efficiency group, a low-efficiency group and a control group originating from two families, and compared the gene expression patterns between each extreme group and the control group. A total of 383 differentially expressed genes were identified, most of which were involved in cell proliferation, growth and signaling, glucose homeostasis, energy and nutrients metabolism. Functional enrichment analysis of these genes revealed 13 significantly enriched biological pathways, including signaling pathways such as PI3K-Akt signaling pathway, AMPK signaling pathway and mTOR signaling pathway, as well as some important pathways such as ubiquitin mediated proteolysis, cell cycle, pentose phosphate pathway and glycolysis/gluconeogenesis. These genes and pathways provide initial insight into the molecular mechanisms driving the feed efficiency in L. vannamei.
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Affiliation(s)
- Ping Dai
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Sheng Luan
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Xia Lu
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Kun Luo
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China
| | - Jie Kong
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266235, China.
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Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle. Appl Environ Microbiol 2017; 83:AEM.00061-17. [PMID: 28235871 DOI: 10.1128/aem.00061-17] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 02/15/2017] [Indexed: 12/14/2022] Open
Abstract
Exploring compositional and functional characteristics of the rumen microbiome can improve the understanding of its role in rumen function and cattle feed efficiency. In this study, we applied metatranscriptomics to characterize the active rumen microbiomes of beef cattle with different feed efficiencies (efficient, n = 10; inefficient, n = 10) using total RNA sequencing. Active bacterial and archaeal compositions were estimated based on 16S rRNAs, and active microbial metabolic functions including carbohydrate-active enzymes (CAZymes) were assessed based on mRNAs from the same metatranscriptomic data sets. In total, six bacterial phyla (Proteobacteria, Firmicutes, Bacteroidetes, Spirochaetes, Cyanobacteria, and Synergistetes), eight bacterial families (Succinivibrionaceae, Prevotellaceae, Ruminococcaceae, Lachnospiraceae, Veillonellaceae, Spirochaetaceae, Dethiosulfovibrionaceae, and Mogibacteriaceae), four archaeal clades (Methanomassiliicoccales, Methanobrevibacter ruminantium, Methanobrevibacter gottschalkii, and Methanosphaera), 112 metabolic pathways, and 126 CAZymes were identified as core components of the active rumen microbiome. As determined by comparative analysis, three bacterial families (Lachnospiraceae, Lactobacillaceae, and Veillonellaceae) tended to be more abundant in low-feed-efficiency (inefficient) animals (P < 0.10), and one archaeal taxon (Methanomassiliicoccales) tended to be more abundant in high-feed-efficiency (efficient) cattle (P < 0.10). Meanwhile, 32 microbial metabolic pathways and 12 CAZymes were differentially abundant (linear discriminant analysis score of >2 with a P value of <0.05) between two groups. Among them, 30 metabolic pathways and 11 CAZymes were more abundant in the rumen of inefficient cattle, while 2 metabolic pathways and 1 CAZyme were more abundant in efficient animals. These findings suggest that the rumen microbiomes of inefficient cattle have more diverse activities than those of efficient cattle, which may be related to the host feed efficiency variation.IMPORTANCE This study applied total RNA-based metatranscriptomics and showed the linkage between the active rumen microbiome and feed efficiency (residual feed intake) in beef cattle. The data generated from the current study provide fundamental information on active rumen microbiome at both compositional and functional levels, which serve as a foundation to study rumen function and its role in cattle feed efficiency. The findings that the active rumen microbiome may contribute to variations in feed efficiency of beef cattle highlight the possibility of enhancing nutrient utilization and improve cattle feed efficiency through modification of rumen microbial functions.
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Olivieri BF, Mercadante MEZ, Cyrillo JNDSG, Branco RH, Bonilha SFM, de Albuquerque LG, Silva RMDO, Baldi F. Genomic Regions Associated with Feed Efficiency Indicator Traits in an Experimental Nellore Cattle Population. PLoS One 2016; 11:e0164390. [PMID: 27760167 PMCID: PMC5070821 DOI: 10.1371/journal.pone.0164390] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/23/2016] [Indexed: 01/18/2023] Open
Abstract
The objective of this study was to identify genomic regions and metabolic pathways associated with dry matter intake, average daily gain, feed efficiency and residual feed intake in an experimental Nellore cattle population. The high-density SNP chip (Illumina High-Density Bovine BeadChip, 777k) was used to genotype the animals. The SNP markers effects and their variances were estimated using the single-step genome wide association method. The (co)variance components were estimated by Bayesian inference. The chromosome segments that are responsible for more than 1.0% of additive genetic variance were selected to explore and determine possible quantitative trait loci. The bovine genome Map Viewer was used to identify genes. In total, 51 genomic regions were identified for all analyzed traits. The heritability estimated for feed efficiency was low magnitude (0.13±0.06). For average daily gain, dry matter intake and residual feed intake, heritability was moderate to high (0.43±0.05; 0.47±0.05, 0.18±0.05, respectively). A total of 8, 17, 14 and 12 windows that are responsible for more than 1% of the additive genetic variance for dry matter intake, average daily gain, feed efficiency and residual feed intake, respectively, were identified. Candidate genes GOLIM4, RFX6, CACNG7, CACNG6, CAPN8, CAPN2, AKT2, GPRC6A, and GPR45 were associated with feed efficiency traits. It was expected that the response to selection would be higher for residual feed intake than for feed efficiency. Genomic regions harboring possible QTL for feed efficiency indicator traits were identified. Candidate genes identified are involved in energy use, metabolism protein, ion transport, transmembrane transport, the olfactory system, the immune system, secretion and cellular activity. The identification of these regions and their respective candidate genes should contribute to the formation of a genetic basis in Nellore cattle for feed efficiency indicator traits, and these results would support the selection for these traits.
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Affiliation(s)
- Bianca Ferreira Olivieri
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil
| | - Maria Eugênia Zerlotti Mercadante
- Instituto de Zootecnia, Centro Avançado de Pesquisa Tecnológica do Agronegócio de Bovinos de Corte, Rodovia Carlos Tonanni, km 94, CEP 14.174-000, Sertãozinho, SP, Brazil
| | | | - Renata Helena Branco
- Instituto de Zootecnia, Centro Avançado de Pesquisa Tecnológica do Agronegócio de Bovinos de Corte, Rodovia Carlos Tonanni, km 94, CEP 14.174-000, Sertãozinho, SP, Brazil
| | - Sarah Figueiredo Martins Bonilha
- Instituto de Zootecnia, Centro Avançado de Pesquisa Tecnológica do Agronegócio de Bovinos de Corte, Rodovia Carlos Tonanni, km 94, CEP 14.174-000, Sertãozinho, SP, Brazil
| | - Lucia Galvão de Albuquerque
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil
| | - Rafael Medeiros de Oliveira Silva
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil
| | - Fernando Baldi
- Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, Via de acesso Prof. Paulo Donato Castellane, s/no, CEP 14884-900 Jaboticabal, SP, Brazil
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de Almeida Santana MH, Junior GAO, Cesar ASM, Freua MC, da Costa Gomes R, da Luz E Silva S, Leme PR, Fukumasu H, Carvalho ME, Ventura RV, Coutinho LL, Kadarmideen HN, Ferraz JBS. Copy number variations and genome-wide associations reveal putative genes and metabolic pathways involved with the feed conversion ratio in beef cattle. J Appl Genet 2016; 57:495-504. [PMID: 27001052 DOI: 10.1007/s13353-016-0344-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/20/2016] [Accepted: 03/02/2016] [Indexed: 10/22/2022]
Abstract
The use of genome-wide association results combined with other genomic approaches may uncover genes and metabolic pathways related to complex traits. In this study, the phenotypic and genotypic data of 1475 Nellore (Bos indicus) cattle and 941,033 single nucleotide polymorphisms (SNPs) were used for genome-wide association study (GWAS) and copy number variations (CNVs) analysis in order to identify candidate genes and putative pathways involved with the feed conversion ratio (FCR). The GWAS was based on the Bayes B approach analyzing genomic windows with multiple regression models to estimate the proportion of genetic variance explained by each window. The CNVs were detected with PennCNV software using the log R ratio and B allele frequency data. CNV regions (CNVRs) were identified with CNVRuler and a linear regression was used to associate CNVRs and the FCR. Functional annotation of associated genomic regions was performed with the Database for Annotation, Visualization and Integrated Discovery (DAVID) and the metabolic pathways were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG). We showed five genomic windows distributed over chromosomes 4, 6, 7, 8, and 24 that explain 12 % of the total genetic variance for FCR, and detected 12 CNVRs (chromosomes 1, 5, 7, 10, and 12) significantly associated [false discovery rate (FDR) < 0.05] with the FCR. Significant genomic regions (GWAS and CNV) harbor candidate genes involved in pathways related to energetic, lipid, and protein metabolism. The metabolic pathways found in this study are related to processes directly connected to feed efficiency in beef cattle. It was observed that, even though different genomic regions and genes were found between the two approaches (GWAS and CNV), the metabolic processes covered were related to each other. Therefore, a combination of the approaches complement each other and lead to a better understanding of the FCR.
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Affiliation(s)
- Miguel Henrique de Almeida Santana
- Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark.,Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | | | | | - Mateus Castelani Freua
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Rodrigo da Costa Gomes
- Empresa Brasileira de Pesquisa Agropecuária, CNPGC/EMBRAPA, BR 262 km 4, 79002-970, Campo Grande, Brazil
| | - Saulo da Luz E Silva
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Paulo Roberto Leme
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Heidge Fukumasu
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Minos Esperândio Carvalho
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
| | - Ricardo Vieira Ventura
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil.,University of Guelph, 50 Stone Road East, Guelph, Ontario, N1G 2W1, Canada
| | - Luiz Lehmann Coutinho
- Escola Superior de Agricultura Luiz de Queiroz, University of São Paulo, 13418-900, Piracicaba, Brazil
| | - Haja N Kadarmideen
- Faculty of Health and Medical Sciences, University of Copenhagen, Grønnegårdsvej 7, 1870, Frederiksberg, Denmark
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, University of São Paulo, Duque de Caxias Norte, 225, 13635-900, Pirassununga, Brazil
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Sgorlon S, Fanzago M, Sandri M, Gaspardo B, Stefanon B. Association of Index of Welfare and Metabolism with the Genetic Merit of Holstein and Simmental Cows After the Peak of Lactation. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2015.3841] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
| | - Marta Fanzago
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Italy
| | - Misa Sandri
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Italy
| | - Brigitta Gaspardo
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Italy
| | - Bruno Stefanon
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Italy
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36
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Yi G, Yuan J, Bi H, Yan W, Yang N, Qu L. In-Depth Duodenal Transcriptome Survey in Chickens with Divergent Feed Efficiency Using RNA-Seq. PLoS One 2015; 10:e0136765. [PMID: 26418546 PMCID: PMC4721924 DOI: 10.1371/journal.pone.0136765] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 08/07/2015] [Indexed: 12/19/2022] Open
Abstract
Since the feed cost is a major determinant of profitability in poultry industry, how to improve feed efficiency through genetic selection is an intriguing subject for breeders and producers. As a more suitable indicator assessing feed efficiency, residual feed intake (RFI) is defined as the difference between observed and expected feed intake based on maintenance and growth. However, the genetic mechanisms responsible for RFI in chickens are still less well appreciated. In this study, we investigated the duodenal transcriptome architecture of extreme RFI phenotypes in the six brown-egg dwarf hens (three per group) using RNA sequencing technology. Among all mapped reads, an average of 75.62% fell into annotated exons, 5.50% were located in introns, and the remaining 18.88% were assigned to intergenic regions. In total, we identified 41 promising candidate genes by differential expression analysis between the low and high RFI groups. Furthermore, qRT-PCR assays were designed for 10 randomly chosen genes, and nine (90.00%) were successfully validated. Functional annotation analyses revealed that these significant genes belong to several specific biological functions related to digestibility, metabolism and biosynthesis processes as well as energy homeostasis. We also predicted 253 intergenic coding transcripts, and these transcripts were mainly involved in fundamental biological regulation and metabolism processes. Our findings provided a pioneering exploration of biological basis underlying divergent RFI using RNA-Seq, which pinpoints promising candidate genes of functional relevance, is helpful to guide future breeding strategies to optimize feed efficiency and assists in improving the current gene annotation in chickens.
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Affiliation(s)
- Guoqiang Yi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jingwei Yuan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huijuan Bi
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- * E-mail:
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37
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de Oliveira PSN, Cesar ASM, do Nascimento ML, Chaves AS, Tizioto PC, Tullio RR, Lanna DPD, Rosa AN, Sonstegard TS, Mourao GB, Reecy JM, Garrick DJ, Mudadu MA, Coutinho LL, Regitano LCA. Identification of genomic regions associated with feed efficiency in Nelore cattle. BMC Genet 2014; 15:100. [PMID: 25257854 PMCID: PMC4198703 DOI: 10.1186/s12863-014-0100-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 09/10/2014] [Indexed: 01/17/2023] Open
Abstract
Background Feed efficiency is jointly determined by productivity and feed requirements, both of which are economically relevant traits in beef cattle production systems. The objective of this study was to identify genes/QTLs associated with components of feed efficiency in Nelore cattle using Illumina BovineHD BeadChip (770 k SNP) genotypes from 593 Nelore steers. The traits analyzed included: average daily gain (ADG), dry matter intake (DMI), feed-conversion ratio (FCR), feed efficiency (FE), residual feed intake (RFI), maintenance efficiency (ME), efficiency of gain (EG), partial efficiency of growth (PEG) and relative growth rate (RGR). The Bayes B analysis was completed with Gensel software parameterized to fit fewer markers than animals. Genomic windows containing all the SNP loci in each 1 Mb that accounted for more than 1.0% of genetic variance were considered as QTL region. Candidate genes within windows that explained more than 1% of genetic variance were selected by putative function based on DAVID and Gene Ontology. Results Thirty-six QTL (1-Mb SNP window) were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 18, 19, 20, 21, 22, 24, 25 and 26 (UMD 3.1). The amount of genetic variance explained by individual QTL windows for feed efficiency traits ranged from 0.5% to 9.07%. Some of these QTL minimally overlapped with previously reported feed efficiency QTL for Bos taurus. The QTL regions described in this study harbor genes with biological functions related to metabolic processes, lipid and protein metabolism, generation of energy and growth. Among the positional candidate genes selected for feed efficiency are: HRH4, ALDH7A1, APOA2, LIN7C, CXADR, ADAM12 and MAP7. Conclusions Some genomic regions and some positional candidate genes reported in this study have not been previously reported for feed efficiency traits in Bos indicus. Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0100-0) contains supplementary material, which is available to authorized users.
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