1
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Sood V, Rodas-González A, Valente TS, Virtuoso MCS, Li C, Lam S, López-Campos Ó, Segura J, Basarab J, Juárez M. Genome-wide association study for primal cut lean traits in Canadian beef cattle. Meat Sci 2023; 204:109274. [PMID: 37437385 DOI: 10.1016/j.meatsci.2023.109274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 07/14/2023]
Abstract
This study identified genomic variants and underlying candidate genes related to the whole carcass and individual primal cut lean content in Canadian commercial crossbred beef cattle. Genotyping information of 1035 crossbred beef cattle were available alongside estimated and actual carcass lean meat yield and individual primal cut lean content in all carcasses. Significant fixed effects and covariates were identified and included in the animal model. Genome-wide association analysis were implemented using the weighted single-step genomic best linear unbiased prediction (WssGBLUP). A number of candidate genes identified linked to lean tissue production were unrelated to estimated lean meat yield and were specific to the actual lean traits. Among these, 41 genes were common for actual lean traits, on specific regions of BTA4, BTA13 and BTA25 indicating potential involvement in lean mass synthesis. Therefore, the results suggested the inclusion of primal cut lean traits as a selection objective in breeding programs with consideration of further functional studies of the identified genes could help in optimizing lean yield for maximal carcass value.
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Affiliation(s)
- Vipasha Sood
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Food and Human Nutritional Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Argenis Rodas-González
- Department of Animal Science, Faculty of Agricultural and Food Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marcos Claudio S Virtuoso
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada; Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Stephanie Lam
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Óscar López-Campos
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Jose Segura
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - John Basarab
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Manuel Juárez
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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2
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Pisello L, Sala G, Rueca F, Passamonti F, Pravettoni D, Ranciati S, Boccardo A, Bergero D, Forte C. An exploratory cross-sectional study of the impact of farm characteristics and calf management practices on morbidity and passive transfer of immunity in 202 Chianina beef-suckler calves. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1948806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lorenzo Pisello
- Dipartimento di Medicina Veterinaria, University of Perugia, Perugia, Italy
| | - Giulia Sala
- Dipartimento di Medicina Veterinaria, University of Milan, Lodi, Italy
| | - Fabrizio Rueca
- Dipartimento di Medicina Veterinaria, University of Perugia, Perugia, Italy
| | | | - Davide Pravettoni
- Dipartimento di Medicina Veterinaria, University of Milan, Lodi, Italy
| | - Saverio Ranciati
- Dipartimento di Scienze Statistiche Paolo Fortunati, University of Bologna, Bologna, Italy
| | - Antonio Boccardo
- Dipartimento di Medicina Veterinaria, University of Milan, Lodi, Italy
| | - Domenico Bergero
- Dipartimento di Scienze Veterinarie, University of Turin, Grugliasco, Italy
| | - Claudio Forte
- Dipartimento di Scienze Veterinarie, University of Turin, Grugliasco, Italy
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3
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Daghio M, Ciucci F, Buccioni A, Cappucci A, Casarosa L, Serra A, Conte G, Viti C, McAmmond BM, Van Hamme JD, Mele M. Correlation of Breed, Growth Performance, and Rumen Microbiota in Two Rustic Cattle Breeds Reared Under Different Conditions. Front Microbiol 2021; 12:652031. [PMID: 33995309 PMCID: PMC8117017 DOI: 10.3389/fmicb.2021.652031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/19/2021] [Indexed: 01/04/2023] Open
Abstract
The use of rustic cattle is desirable to face challenges brought on by climate change. Maremmana (MA) and Aubrac (AU) are rustic cattle breeds that can be successfully used for sustainable production. In this study, correlations between two rearing systems (feedlot and grazing) and the rumen microbiota, the lipid composition of rumen liquor (RL), and the growth performance of MA and AU steers were investigated. Bacterial community composition was characterized by high-throughput sequencing of 16S rRNA gene amplicons, and the RL lipid composition was determined by measuring fatty acid (FA) and the dimethyl acetal profiles. The main factor influencing bacterial community composition was the cattle breed. Some bacterial groups were positively correlated to average daily weight gain for the two breeds (i.e., Rikenellaceae RC9 gut group, Fibrobacter and Succiniclasticum in the rumen of MA steers, and Succinivibrionaceae UCG-002 in the rumen of AU steers); despite this, animal performance appeared to be influenced by short chain FAs production pathways and by the presence of H2 sinks that divert the H2 to processes alternative to the methanogenesis.
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Affiliation(s)
- Matteo Daghio
- Dipartimento di Scienze e Tecnologie Agrarie Alimentari Ambientali e Forestali, University of Florence, Florence, Italy
| | - Francesca Ciucci
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy
| | - Arianna Buccioni
- Dipartimento di Scienze e Tecnologie Agrarie Alimentari Ambientali e Forestali, University of Florence, Florence, Italy
| | - Alice Cappucci
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy.,Centro di Ricerche Agro-ambientali "E. Avanzi", University of Pisa, Pisa, Italy
| | - Laura Casarosa
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy
| | - Andrea Serra
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy.,Centro di Ricerche Agro-ambientali "E. Avanzi", University of Pisa, Pisa, Italy
| | - Giuseppe Conte
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy.,Centro di Ricerche Agro-ambientali "E. Avanzi", University of Pisa, Pisa, Italy
| | - Carlo Viti
- Dipartimento di Scienze e Tecnologie Agrarie Alimentari Ambientali e Forestali, University of Florence, Florence, Italy
| | - Breanne M McAmmond
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Jonathan D Van Hamme
- Department of Biological Sciences, Thompson Rivers University, Kamloops, BC, Canada
| | - Marcello Mele
- Dipartimento di Scienze Agrarie, Alimentari e Agro-ambientali, University of Pisa, Pisa, Italy.,Centro di Ricerche Agro-ambientali "E. Avanzi", University of Pisa, Pisa, Italy
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4
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Ben-Jemaa S, Senczuk G, Ciani E, Ciampolini R, Catillo G, Boussaha M, Pilla F, Portolano B, Mastrangelo S. Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle. Front Genet 2021; 12:675569. [PMID: 33995500 PMCID: PMC8113768 DOI: 10.3389/fgene.2021.675569] [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: 03/03/2021] [Accepted: 04/07/2021] [Indexed: 12/31/2022] Open
Abstract
The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.
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Affiliation(s)
- Slim Ben-Jemaa
- Laboratoire des Productions Animales et Fourragères, Institut National de la Recherche Agronomique de Tunisie, University of Carthage, Ariana, Tunisia
| | - Gabriele Senczuk
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Elena Ciani
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Gennaro Catillo
- Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), Centro di Ricerca Zootecnia e Acquacoltura, Lodi, Italy
| | - Mekki Boussaha
- INRAE, AgroParisTech, University of Paris Saclay, Saint Aubin, France
| | - Fabio Pilla
- Dipartimento di Agricoltura, Ambiente e Alimenti, University of Molise, Campobasso, Italy
| | - Baldassare Portolano
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
| | - Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Palermo, Italy
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5
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López-Pedrouso M, Lorenzo JM, Di Stasio L, Brugiapaglia A, Franco D. Quantitative proteomic analysis of beef tenderness of Piemontese young bulls by SWATH-MS. Food Chem 2021; 356:129711. [PMID: 33831824 DOI: 10.1016/j.foodchem.2021.129711] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/21/2021] [Accepted: 03/24/2021] [Indexed: 12/19/2022]
Abstract
Quantitative proteomic approach is a suitable way to tackle the beef tenderness. Ten aged-beef samples from Longissimus thoracis of Piemontese breed classified as tender (n = 5) and tough (n = 5) meat were evaluated using SWATH-MS and bioinformatic tools for the identification of the proteins and pathways most influencing tenderness variability. Between the two textural groups, proteomic changes were mainly caused by 43 differentially abundant proteins (DAPs) arranged in reference patterns as displayed by the heat map analysis. Most of these DAPs were associated with energy metabolism. From the functional proteomic analysis, two clusters of proteins, including ACO2, MDH1, MDH2 and CS in one cluster and FBP2, PFKL, LDHA, TPI1 and GAPDH/S in the other cluster, suggest gluconeogenesis, glycolysis and citrate cycle as key pathways for Piemontese breed beef tenderness. These findings contribute to a deeper insight into molecular pathways related to beef tenderness.
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Affiliation(s)
- María López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela 15872, Spain
| | - José M Lorenzo
- Centro Tecnológico de la Carne de Galicia, Rúa Galicia N° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, Ourense 32900, Spain; Área de Tecnología de los Alimentos, Facultad de Ciencias de Ourense, Universidad de Vigo, 32004 Ourense, Spain
| | - Liliana Di Stasio
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Alberto Brugiapaglia
- Department of Agricultural, Forest and Food Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Torino, Italy
| | - Daniel Franco
- Centro Tecnológico de la Carne de Galicia, Rúa Galicia N° 4, Parque Tecnológico de Galicia, San Cibrao das Viñas, Ourense 32900, Spain.
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6
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Sebastianelli M, Forte C, Galarini R, Gobbi M, Pistidda E, Moncada C, Cannizzo FT, Pezzolato M, Bozzetta E, Cenci-Goga BT, Manuali E. LC-MS/MS analyses of bile and histological analyses of thymus as diagnostic tools to detect low dose dexamethasone illicit treatment in beef cattle at slaughterhouse. Steroids 2020; 160:108671. [PMID: 32464136 DOI: 10.1016/j.steroids.2020.108671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Abstract
Dexamethasone (DXM) is a synthetic adrenal corticosteroid with anti-inflammatory properties used for therapeutic purposes in a wide range of pathologies and of the most common corticosteroids used for anabolic purposes in beef cattle. It is proven that DXM induces histological changes, traceable as increasing fatty infiltration of the thymus associated with a concurrent decrease of the cortex-medulla ratio, so the histological examination of the thymus gland has been established as an indirect morphological biomarker. The aim of the present study is to compare thymus histology and DXM concentrations in biological fluids collected at slaughterhouse after 1 month of DXM treatment. Our findings demonstrate that a low dosage of DXM administered to 12 months-old-Chianina beef cattle induces severe thymic atrophy with concurrent reduction of the cortex/medulla ratio, demonstrable even when DXM residues are not found in serum and urine samples. It is worth to note that, at the slaughterhouse, DXM residues are detectable in bile samples, indicating the ability of this biological fluid to bio-concentrate the administered drug if compared to serum and urine. Therefore, bile could be candidates as new liquid matrix for the screening programs planned to contrast the illegal use of anabolic substances.
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Affiliation(s)
- Martina Sebastianelli
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", 06126 - Perugia, Italy
| | - Claudio Forte
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", 06126 - Perugia, Italy.
| | - Roberta Galarini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", 06126 - Perugia, Italy.
| | - Marco Gobbi
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", 06126 - Perugia, Italy.
| | - Elisabetta Pistidda
- Igiene degli allevamenti e delle Produzioni Zootecniche, Azienda Sanitaria Locale Umbria 1, 06121 - Perugia, Italy.
| | - Claudia Moncada
- Igiene degli allevamenti e delle Produzioni Zootecniche, Azienda Sanitaria Locale Umbria 1, 06121 - Perugia, Italy.
| | | | - Marzia Pezzolato
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 - Torino, Italy.
| | - Elena Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, 10154 - Torino, Italy.
| | | | - Elisabetta Manuali
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche "Togo Rosati", 06126 - Perugia, Italy.
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7
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Arhondakis S, Milanesi M, Castrignanò T, Gioiosa S, Valentini A, Chillemi G. Evidence of distinct gene functional patterns in GC-poor and GC-rich isochores in Bos taurus. Anim Genet 2020; 51:358-368. [PMID: 32069522 DOI: 10.1111/age.12917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2020] [Indexed: 01/10/2023]
Abstract
Vertebrate genomes are mosaics of megabase-size DNA segments with a fairly homogeneous base composition, called isochores. They are divided into five families characterized by different guanine-cytosine (GC) levels and linked to several functional and structural properties. The increased availability of fully sequenced genomes allows the investigation of isochores in several species, assessing their level of conservation across vertebrate genomes. In this work, we characterized the isochores in Bos taurus using the ARS-UCD1.2 genome version. The comparison of our results with the well-studied human isochores and those of other mammals revealed a large conservation in isochore families, in number, average GC levels and gene density. Exceptions to the established increase in gene density with the increase in isochores (GC%) were observed for the following gene biotypes: tRNA, small nuclear RNA, small nucleolar RNA and pseudogenes that have their maximum number in H2 and H1 isochores. Subsequently, we assessed the ontology of all gene biotypes looking for functional classes that are statistically over- or under-represented in each isochore. Receptor activity and sensory perception pathways were significantly over-represented in L1 and L2 (GC-poor) isochores. This was also validated for the horse genome. Our analysis of housekeeping genes confirmed a preferential localization in GC-rich isochores, as reported in other species. Finally, we assessed the SNP distribution of a bovine high-density SNP chip across the isochores, finding a higher density in the GC-rich families, reflecting a potential bias in the chip, widely used for genetic selection and biodiversity studies.
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Affiliation(s)
- S Arhondakis
- Bioinformatics and Computational Science (BioCoS), Boniali 11-19, Chania, 73134, Crete, Greece
| | - M Milanesi
- Department of Support, Production and Animal Health, School of Veterinary Medicine, São Paulo State University, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil.,International Atomic Energy Agency Collaborating Centre on Animal Genomics and Bioinformatics, 16050-680 R. Clóvis Pestana 793 - Dona Amelia, Araçatuba, SP, Brazil
| | - T Castrignanò
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - S Gioiosa
- SCAI - Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - A Valentini
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy
| | - G Chillemi
- Department for Innovation in Biological, Agro-food and Forest Systems, DIBAF, University of Tuscia, via S. Camillo de Lellis s.n.c, 01100, Viterbo, Italy.,Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, IBIOM, CNR, Bari, Italy
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8
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Qi K, Men X, Wu J, Xu Z. Rearing pattern alters porcine myofiber type, fat deposition, associated microbial communities and functional capacity. BMC Microbiol 2019; 19:181. [PMID: 31387544 PMCID: PMC6683424 DOI: 10.1186/s12866-019-1556-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 07/26/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The Chinese believe that the meat of pigs reared in the past with free range tastes better than that of the pigs reared indoor on a large scale today. Gastrointestinal microflora is closely associated with the main factor of meat flavour, including fibre characteristics and lipid metabolism. Our method in this study involved different raising patterns within the semi free-grazing farm (FF) or indoor feeding farm (DF), the measurement of fat deposition and myofiber type by paraffin section and reverse transcription polymerase chain reaction and the identification of microbiome and functional capacities associated with meat quality through metagenomic sequencing. RESULTS Results showed that the fat area in muscle and adipose tissue and the myofiber density significantly increased in the pigs of the FF group. The relative abundance of bacteria associated with lipid metabolism, such as g_Oscillibacter, in the feces of the FF group was higher than that in DF group, and the relative abundance of some bacteria with probiotic function, including g_Lactobacillus and g_Clostridium, was lower than that in DF group. The abundance of g_Clostridium was significantly positively correlated with the intramuscular fat area, whereas health-related bacteria, such as g_Butyricicoccus, g_Eubacterium, g_Phascolarctobacterium and g_Oribacterium, was significantly negatively correlated with abdominal fat area, myofiber density and adipose triglyceride lipase (ATGL) mRNA expression. KEGG analysis showed that pigs raised in semi free-grazing farm can activate the pathway of inosine monophosphate (IMP) biosynthesis, glycolysis/gluconeogenesis and alanine, aspartate and glutamate metabolism. CONCLUSIONS Free range feeding improves meat quality by changing the fibre type, myofiber density and metabolic pathways related to flavour amino acids, IMP or glycolysis/gluconeogenesis in muscle. However, prolonged feeding cycle increases fat deposition and associated microbial communities.
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Affiliation(s)
- Keke Qi
- Institute of Animal Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Jianggan, Hangzhou, 310021 People’s Republic of China
| | - Xiaoming Men
- Institute of Animal Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Jianggan, Hangzhou, 310021 People’s Republic of China
| | - Jie Wu
- Institute of Animal Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Jianggan, Hangzhou, 310021 People’s Republic of China
| | - Ziwei Xu
- Institute of Animal Science, Zhejiang Academy of Agricultural Sciences, 145 Shiqiao Road, Jianggan, Hangzhou, 310021 People’s Republic of China
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9
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Refoyo-Martínez A, da Fonseca RR, Halldórsdóttir K, Árnason E, Mailund T, Racimo F. Identifying loci under positive selection in complex population histories. Genome Res 2019; 29:1506-1520. [PMID: 31362936 PMCID: PMC6724678 DOI: 10.1101/gr.246777.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 07/23/2019] [Indexed: 12/24/2022]
Abstract
Detailed modeling of a species’ history is of prime importance for understanding how natural selection operates over time. Most methods designed to detect positive selection along sequenced genomes, however, use simplified representations of past histories as null models of genetic drift. Here, we present the first method that can detect signatures of strong local adaptation across the genome using arbitrarily complex admixture graphs, which are typically used to describe the history of past divergence and admixture events among any number of populations. The method—called graph-aware retrieval of selective sweeps (GRoSS)—has good power to detect loci in the genome with strong evidence for past selective sweeps and can also identify which branch of the graph was most affected by the sweep. As evidence of its utility, we apply the method to bovine, codfish, and human population genomic data containing panels of multiple populations related in complex ways. We find new candidate genes for important adaptive functions, including immunity and metabolism in understudied human populations, as well as muscle mass, milk production, and tameness in specific bovine breeds. We are also able to pinpoint the emergence of large regions of differentiation owing to inversions in the history of Atlantic codfish.
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Affiliation(s)
- Alba Refoyo-Martínez
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
| | - Rute R da Fonseca
- Centre for Macroecology, Evolution and Climate, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copehnagen 2100, Denmark
| | - Katrín Halldórsdóttir
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland
| | - Einar Árnason
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík 107, Iceland.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark
| | - Fernando Racimo
- Lundbeck GeoGenetics Centre, The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1350, Denmark
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10
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Moridi M, Hosseini Moghaddam SH, Mirhoseini SZ, Bionaz M. Transcriptome analysis showed differences of two purebred cattle and their crossbreds. ITALIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1080/1828051x.2018.1482800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Misagh Moridi
- Department of Animal Sciences, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | | | - Massimo Bionaz
- Department of Animal and Rangeland Sciences, Oregon State University, Corvallis, OR, USA
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11
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Transcriptomic and metabolomic responses induced in the livers of growing pigs by a short-term intravenous infusion of sodium butyrate. Animal 2018; 12:2318-2326. [PMID: 29458450 DOI: 10.1017/s1751731118000174] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Previous studies showed that butyrate played benefit roles in the health and metabolism of animals. However, little information on the effects of butyrate on the metabolism of piglets at the extraintestinal level is available. The present study investigated transcriptomic and metabolomic responses in the livers of pigs to evaluate the effects of intravenous sodium butyrate (SB) on the body's metabolism at the extraintestinal level. A total of 12 Duroc×Landrace×Large White growing barrows (60 days of age) fitted with jugular vein cannula were randomly allocated to either the SB group or the control (CO) group. Pigs in the SB group were intravenously infused with 10 ml SB (200 mmol/l) for 7 days, whereas pigs in the CO group were treated with the same amount of saline. The livers of pigs were collected for gene expression and metabolome analyses. The RNA sequencing (RNA-Seq) analysis showed that the mRNA expression of Acyl-CoA synthetase long-chain family member 1 (ACSL1), carnitine palmitoyltransferase 1A (CPT1A), acetyl-CoA acyltransferase 2 (ACAA2) and phosphoenolpyruvate carboxykinase 1 (PCK1) were downregulated (Q<0.05), whereas fatty acid binding protein 1 (FABP1) and cytochrome P450 family 7 subfamily A member 1 (CYP7A1) were upregulated (P<0.05) by SB treatment, indicating a decrease in fatty acid oxidation and gluconeogenesis and an increase in fatty acid transportation and cholesterol metabolism. Gas chromatography-mass spectrometry analysis showed that raffinose was enriched in the SB group compared with the CO group, indicating a decrease in metabolism of galactose. Moreover, SB treatment significantly decreased the concentration of blood cholesterol. The results suggest that a short-term intravenous infusion of SB could modulate hepatic lipid metabolism by decreasing fatty acid oxidation and increasing fatty acid transportation and cholesterol metabolism.
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