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Lou W, Zhang H, Luo H, Chen Z, Shi R, Guo X, Zou Y, Liu L, Brito LF, Guo G, Wang Y. Corrigendum to “Genetic analyses of blood β-hydroxybutyrate predicted from milk infrared spectra and its association with longevity and female reproductive traits in Holstein cattle” (J. Dairy Sci. 105:3269–3281). J Dairy Sci 2023; 106:3051. [PMID: 37003636 DOI: 10.3168/jds.2023-106-4-3051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Affiliation(s)
- W Lou
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H Zhang
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H Luo
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Z Chen
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - R Shi
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; Animal Breeding and Genomics Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - X Guo
- Center of Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - Y Zou
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - L F Brito
- Department of Animal Science, Purdue University, West Lafayette, IN 47907
| | - G Guo
- Beijing Sunlon Livestock Development Company Limited, Beijing, 10029, China
| | - Y Wang
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
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Fonseca Brito L, Tödter S, Kottlau J, Cermann K, Spier A, Petersen E, Schäfer I, Twerenbold R, Aepfelbacher M, Lütgehetmann M, Stahl FR. Performance of an interferon-γ release assay-based test for cell-mediated immunity to SARS-CoV-2. Front Immunol 2023; 14:1069968. [PMID: 36875076 PMCID: PMC9978494 DOI: 10.3389/fimmu.2023.1069968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
In search for immunological correlates of protection against acute coronavirus disease 2019 (COVID-19) there is a need for high through-put assays for cell-mediated immunity (CMI) to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We established an interferon-γ release assay -based test for detection of CMI against SARS-CoV-2 spike (S) or nucleocapsid (NC) peptides. Blood samples obtained from 549 healthy or convalescent individuals were measured for interferon-γ (IFN-γ) production after peptide stimulation using a certified chemiluminescence immunoassay. Test performance was calculated applying cutoff values with the highest Youden indices in receiver-operating-characteristics curve analysis and compared to a commercially available serologic test. Potential confounders and clinical correlates were assessed for all test systems. 522 samples obtained from 378 convalescent in median 298 days after PCR-confirmed SARS-CoV-2 infection and 144 healthy control individuals were included in the final analysis. CMI testing had a sensitivity and specificity of up to 89% and 74% for S peptides and 89% and 91% for NC peptides, respectively. High white blood cell counts correlated negatively with IFN-γ responses but there was no CMI decay in samples obtained up to one year after recovery. Severe clinical symptoms at time of acute infection were associated with higher measures of adaptive immunity and reported hair loss at time of examination. This laboratory-developed test for CMI to SARS-CoV-2 NC peptides exhibits excellent test performance, is suitable for high through-put routine diagnostics, and should be evaluated for clinical outcome prediction in prospective pathogen re-exposure.
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Affiliation(s)
- Luís Fonseca Brito
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Virus-Host-Interaction, Leibniz Institute of Virology, Hamburg, Germany
| | - Silvia Tödter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julian Kottlau
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathrin Cermann
- Institute of Microbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anthea Spier
- Institute of Microbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elina Petersen
- Department of Cardiology, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Population Health Research Department, University Heart and Vascular Center, Hamburg, Germany
| | - Ines Schäfer
- Department of Cardiology, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Population Health Research Department, University Heart and Vascular Center, Hamburg, Germany
| | - Raphael Twerenbold
- Department of Cardiology, University Heart and Vascular Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Population Health Research Department, University Heart and Vascular Center, Hamburg, Germany.,German Center for Cardiovascular Research (DZHK) Partner Site Hamburg-Kiel-Lübeck, Hamburg, Germany
| | - Martin Aepfelbacher
- Institute of Microbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Microbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Felix R Stahl
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Virus-Host-Interaction, Leibniz Institute of Virology, Hamburg, Germany
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Lou W, Zhang H, Luo H, Chen Z, Shi R, Guo X, Zou Y, Liu L, Brito LF, Guo G, Wang Y. Genetic analyses of blood β-hydroxybutyrate predicted from milk infrared spectra and its association with longevity and female reproductive traits in Holstein cattle. J Dairy Sci 2022; 105:3269-3281. [PMID: 35094854 DOI: 10.3168/jds.2021-20389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 11/16/2021] [Indexed: 11/19/2022]
Abstract
Ketosis is one of the most prevalent and complex metabolic disorders in high-producing dairy cows and usually detected through analyses of β-hydroxybutyrate (BHB) concentration in blood. Our main objectives were to evaluate genetic parameters for blood BHB predicted based on Fourier-transform mid-infrared spectra from 5 to 305 d in milk, and estimate the genetic relationships of blood BHB with 7 reproduction traits and 6 longevity traits in Holstein cattle. Predicted blood BHB records of 11,609 Holstein cows (after quality control) were collected from 2016 to 2019 and used to derive 4 traits based on parity number, including predicted blood BHB in all parities (BHBp), parity 1 (BHB1), parity 2 (BHB2), and parity 3+ (BHB3). Single- and multitrait repeatability models were used for estimating genetic parameters for the 4 BHB traits. Random regression test-day models implemented via Bayesian inference were used to evaluate the daily genetic feature of BHB variability. In addition, genetic correlations were calculated for the 4 BHB traits with reproduction and longevity traits. The heritability estimates of BHBp, BHB1, BHB2, and BHB3 ranged from 0.100 ± 0.026 (± standard error) to 0.131 ± 0.023. The BHB in parities 1 to 3+ were highly genetically correlated and ranged from 0.788 (BHB1 and BHB2) to 0.911 (BHB1 and BHB3). The daily heritability of BHBp ranged from 0.069 to 0.195, higher for the early and lower for the later lactation periods. A similar trend was observed for BHB1, BHB2, and BHB3. There are low direct genetic correlations between BHBp and selected reproductive performance and longevity traits, which ranged from -0.168 ± 0.019 (BHBp and production life) to 0.157 ± 0.019 (BHBp and age at first calving) for the early lactation stage (5 to 65 d). These direct genetic correlations indicate that cows with higher BHBp (greater likelihood of having ketosis) in blood usually have shorter production life (-0.168 ± 0.019). Cows with higher fertility and postpartum recovery, such as younger age at first calving (0.157 ± 0.019) and shorter interval from calving to first insemination in heifer (0.111 ± 0.006), usually have lower BHB concentration in the blood. Furthermore, the direct genetic correlations change across parity and lactation stage. In general, our results suggest that selection for lower predicted BHB in early lactation could be an efficient strategy for reducing the incidence of ketosis as well as indirectly improving reproductive and longevity performance in Holstein cattle.
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Affiliation(s)
- W Lou
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H Zhang
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - H Luo
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Z Chen
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - R Shi
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China; Animal Breeding and Genomics Group, Wageningen University & Research, PO Box 338, 6700 AH Wageningen, the Netherlands
| | - X Guo
- Center of Quantitative Genetics and Genomics, Aarhus University, Tjele, 8830, Denmark
| | - Y Zou
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - L Liu
- Beijing Dairy Cattle Center, Beijing, 100192, China
| | - L F Brito
- Department of Animal Science, Purdue University, West Lafayette, IN 47907
| | - G Guo
- Beijing Sunlon Livestock Development Company Limited, Beijing, 10029, China
| | - Y Wang
- National Engineering Laboratory of Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs (MARA); College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Martins R, Brito LF, Machado PC, Pinto LFB, Silva MR, Schenkel FS, Pedrosa VB. Genome-wide association study and pathway analysis for carcass fatness in Nellore cattle measured by ultrasound. Anim Genet 2021; 52:730-733. [PMID: 34370325 DOI: 10.1111/age.13129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2021] [Indexed: 12/16/2022]
Abstract
Identifying genes or genomic regions influencing carcass-quality traits such as fatness (FTN) is essential to optimize the genetic selection processes in beef cattle. The aim of this study was to identify genomic regions associated with FTN in Nellore cattle as well as to elucidate the metabolic pathways related to the phenotypic expression. Ultrasound-based measurements of FTN were collected in 11 750 animals, with 39 903 animals in the pedigree file. Additionally, 1440 animals were genotyped using the GGP-indicus 35K SNP panel, which contained 33 623 SNPs after quality control. Twenty genes related to FTN were found on 11 chromosomes, explaining 12.96% of the total additive genetic variance. Gene ontology revealed seven genes: NR1L2, PKD2, GSK3β, EXT1, RAD51B, SORCS1 and DPH6, associated with important processes related to FTN. In addition, novel candidate genes (MAATS1, LYPD1, CDK5RAP2, RAD51B, c13H2Oorf96 and TRAPPC11) were detected and could provide further knowledge to uncover genetic regions associated to carcass fatness in beef cattle.
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Affiliation(s)
- R Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - L F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - P C Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - L F B Pinto
- Department of Animal Sciences, Federal University of Bahia, Av. Adhemar de Barros s/n, Ondina, Salvador, BA, 40170-115, Brazil
| | - M R Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guarapes, SP, 16700-000, Brazil
| | - F S Schenkel
- Animal and Poultry Science Department, Centre for Genetic Improvement of Livestock, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - V B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
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Brito LF, Bedere N, Douhard F, Oliveira HR, Arnal M, Peñagaricano F, Schinckel AP, Baes CF, Miglior F. Review: Genetic selection of high-yielding dairy cattle toward sustainable farming systems in a rapidly changing world. Animal 2021; 15 Suppl 1:100292. [PMID: 34294547 DOI: 10.1016/j.animal.2021.100292] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 11/28/2022] Open
Abstract
The massive improvement in food production, as a result of effective genetic selection combined with advancements in farming practices, has been one of the greatest achievements of modern agriculture. For instance, the dairy cattle industry has more than doubled milk production over the past five decades, while the total number of cows has been reduced dramatically. This was achieved mainly through the intensification of production systems, direct genetic selection for milk yield and a limited number of related traits, and the use of modern technologies (e.g., artificial insemination and genomic selection). Despite the great betterment in production efficiency, strong drawbacks have occurred along the way. First, across-breed genetic diversity reduced dramatically, with the worldwide use of few common dairy breeds, as well as a substantial reduction in within-breed genetic diversity. Intensive selection for milk yield has also resulted in unfavorable genetic responses for traits related to fertility, health, longevity, and environmental sensitivity. Moving forward, the dairy industry needs to continue refining the current selection indexes and breeding goals to put greater emphasis on traits related to animal welfare, health, longevity, environmental efficiency (e.g., methane emission and feed efficiency), and overall resilience. This needs to be done through the definition of criteria (traits) that (a) represent well the biological mechanisms underlying the respective phenotypes, (b) are heritable, and (c) can be cost-effectively measured in a large number of animals and as early in life as possible. The long-term sustainability of the dairy cattle industry will also require diversification of production systems, with greater investments in the development of genetic resources that are resilient to perturbations occurring in specific farming systems with lesser control over the environment (e.g., organic, agroecological, and pasture-based, mountain-grazing farming systems). The conservation, genetic improvement, and use of local breeds should be integrated into the modern dairy cattle industry and greater care should be taken to avoid further genetic diversity losses in dairy cattle populations. In this review, we acknowledge the genetic progress achieved in high-yielding dairy cattle, closely related to dairy farm intensification, that reaches its limits. We discuss key points that need to be addressed toward the development of a robust and long-term sustainable dairy industry that maximize animal welfare (fundamental needs of individual animals and positive welfare) and productive efficiency, while also minimizing the environmental footprint, inputs required, and sensitivity to external factors.
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Affiliation(s)
- L F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA.
| | - N Bedere
- INRAE, Institut Agro, PEGASE, 35 590 Saint-Gilles, France
| | - F Douhard
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France
| | - H R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - M Arnal
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet Tolosan, France; Institut de l'Elevage, Chemin de Borde Rouge, 31 326 Castanet-Tolosan cedex, France
| | - F Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53 706, USA
| | - A P Schinckel
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47 907, USA
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3 000, Switzerland
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
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Novo LC, Gondo A, Gomes RC, Fernandes Junior JA, Ribas MN, Brito LF, Laureano MMM, Araújo CV, Menezes GRO. Genetic parameters for performance, feed efficiency, and carcass traits in Senepol heifers. Animal 2021; 15:100160. [PMID: 33546982 DOI: 10.1016/j.animal.2020.100160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 11/25/2022] Open
Abstract
Improving feed efficiency is a key breeding goal in the beef cattle industry. In this study, we estimated the genetic parameters for feed efficiency and carcass traits in Senepol cattle raised in tropical regions. Various indicators of feed efficiency [gain to feed ratio (G:F), feed conversion ratio (FCR), residual weight gain (RG), residual intake and body weight gain (RIG), and residual feed intake (RFI)] as well as growth [final BW, average daily gain (ADG), and DM intake (DMI)], and carcass [rib-eye area (REA), backfat thickness (BF), intramuscular fat score, and carcass conformation score] traits were included in the study. After data editing, records from 1 393 heifers obtained between 2009 and 2018 were used for the analyses. We fitted an animal model that included contemporary group (animals from the same farm that were evaluated in the same test season) as the fixed effect, and a linear effect of animal age at the beginning of the test as a covariate; in addition to random direct additive genetic and residual effects. The (co)variance components were estimated by Bayesian inference in uni- and bivariate analyses. Our results showed that feed efficiency indicators derived from residual variables such as RG, RIG, and RFI can be improved through genetic selection (h2 = 0.14 ± 0.06, 0.13 ± 0.06, and 0.20 ± 0.08, respectively). Variables calculated as ratios such as G:F and FCR were more influenced by environmental factors (h2 = 0.08 ± 0.05 and 0.09 ± 0.05), and were, therefore, less suitable for use in breeding programs. The traits with the greatest and impact on genetic progress in feed efficiency were ADG, REA, and BF. The traits with the greatest and least impact on growth and carcass traits were RG and RFI, respectively. Selection for feed efficiency will result in distinct overall effects on the growth and carcass traits of Senepol heifers. Direct selection for lower RFI may reduce DMI and increase carcass fatness at the finishing stage, but it might also result in reduced growth and muscle deposition. Residual BW gain is associated with the highest weight gain and zero impact on REA and BF, however, it is linked to higher feed consumption. Thus, the most suitable feed efficiency indicator was RIG, as it promoted the greatest decrease in feed intake concomitant with faster growth, with a similar impact on carcass traits when compared to the other feed efficiency indicators.
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Affiliation(s)
- L C Novo
- Research and Study Center for Animal Breeding, Federal University of Mato Grosso, 1200 Alexandre Ferronato Av, Sinop, Mato Grosso 78555-000, Brazil
| | - A Gondo
- EMBRAPA, Rádio Maia Av. 830, Campo Grande, Mato Grosso do Sul 79106-550, Brazil
| | - R C Gomes
- EMBRAPA, Rádio Maia Av. 830, Campo Grande, Mato Grosso do Sul 79106-550, Brazil
| | | | - M N Ribas
- INTERGADO LTDA, 1463 Rio Paranagua Street, Contagem, Minas Gerais 32280-300, Brazil
| | - L F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN 47907, USA
| | - M M M Laureano
- Research and Study Center for Animal Breeding, Federal University of Mato Grosso, 1200 Alexandre Ferronato Av, Sinop, Mato Grosso 78555-000, Brazil
| | - C V Araújo
- Research and Study Center for Animal Breeding, Federal University of Mato Grosso, 1200 Alexandre Ferronato Av, Sinop, Mato Grosso 78555-000, Brazil
| | - G R O Menezes
- EMBRAPA, Rádio Maia Av. 830, Campo Grande, Mato Grosso do Sul 79106-550, Brazil.
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Schultz EB, Santana TEZ, Silva FF, Garcia AO, Oliveira HR, Rodrigues MT, Brito LF. Short communication: Genetic parameter estimates for caprine arthritis encephalitis in dairy goats. J Dairy Sci 2020; 103:6407-6411. [PMID: 32331882 DOI: 10.3168/jds.2019-17740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 02/20/2020] [Indexed: 01/14/2023]
Abstract
Caprine arthritis encephalitis (CAE) is a chronic disease caused by a retrovirus from the Lentivirus genus. No effective vaccines or treatments exist, and therefore genetic selection for CAE resistance might be a feasible alternative. To our best knowledge, no other studies have investigated the genetic architecture of CAE resistance in dairy goats. In this context, this study was designed to estimate genetic parameters for CAE infection in Alpine and Saanen goats using a Bayesian threshold model. A total of 542 adult goats (and >3-generation pedigree), which were group-housed in a population with high CAE prevalence, were tested based on a serological infection assessment test (negative = 1 or positive = 2) and used for this study. Genetic parameters were estimated using the BLUPF90 family programs. There was considerable genetic variability for CAE resistance, and pedigree-based heritability was significantly different from zero (0.026 < heritability < 0.128). Our findings indicate that the prevalence of CAE in goat herds can be reduced or eliminated through direct genetic selection for CAE resistance in addition to proper management strategies.
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Affiliation(s)
- E B Schultz
- Departament of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - T E Z Santana
- Departament of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - F F Silva
- Departament of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - A O Garcia
- Departament of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - H R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - M T Rodrigues
- Departament of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-900, Brazil
| | - L F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Freitas PHF, Oliveira HR, Silva FF, Fleming A, Schenkel FS, Miglior F, Brito LF. Short communication: Time-dependent genetic parameters and single-step genome-wide association analyses for predicted milk fatty acid composition in Ayrshire and Jersey dairy cattle. J Dairy Sci 2020; 103:5263-5269. [PMID: 32307163 DOI: 10.3168/jds.2019-17820] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/28/2020] [Indexed: 12/27/2022]
Abstract
Milk fat content and fatty acid (FA) composition have great economic value to the dairy industry as they are directly associated with taste and chemical-physical characteristics of milk and dairy products. In addition, consumers' choices are not only based on the nutritional aspects of food, but also on products known to promote better health. Milk FA composition is also related to the metabolic status and physiological stages of cows and thus can also be used as indicator for other novel traits of interest (e.g., metabolic diseases and methane yield). Genetic selection is a promising alternative to manipulate milk FA composition. In this study, we aimed to (1) estimate time-dependent genetic parameters for 5 milk FA groups (i.e., short-chain, medium-chain, long-chain, saturated, and unsaturated) predicted based on milk mid-infrared spectroscopy, for Canadian Ayrshire and Jersey breeds, and (2) conduct a time-dependent, single-step genome-wide association study to identify genomic regions, candidate genes, and metabolic pathways associated with milk FA. We analyzed 31,709 test-day records of 9,648 Ayrshire cows from 268 herds, and 34,341 records of 11,479 Jersey cows from 883 herds. The genomic database contained a total of 2,330 Ayrshire and 1,019 Jersey animals. The average daily heritability ranged from 0.18 (long-chain FA) to 0.34 (medium-chain FA) in Ayrshire, and from 0.25 (long-chain and unsaturated FA) to 0.52 (medium-chain and saturated FA) in Jersey. Important genomic regions were identified in Bos taurus autosomes BTA3, BTA5, BTA12, BTA13, BTA14, BTA16, BTA18, BTA20, and BTA21. The proportion of the variance explained by 20 adjacent SNP ranged from 0.71% (saturated FA) to 1.11% (long-chain FA) in Ayrshire, and from 0.70% (unsaturated FA) to 3.09% (medium-chain FA) in Jersey cattle. Important candidate genes and pathways were also identified, such as the PTK2 and TRAPPC9 genes, associated with milk fat percentage, and HMGCS, FGF10, and C6 genes, associated with fertility traits and immune response. Our findings on the genetic parameters and candidate genes contribute to a better understanding of the genetic architecture of milk FA composition in Ayrshire and Jersey dairy cattle.
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Affiliation(s)
- P H F Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Sciences, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - H R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F F Silva
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - A Fleming
- Lactanet Canada, Guelph, Ontario, N1K 1E5, Canada
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - L F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Oliveira HR, Lourenco DAL, Masuda Y, Misztal I, Tsuruta S, Jamrozik J, Brito LF, Silva FF, Cant JP, Schenkel FS. Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle. J Dairy Sci 2019; 102:9995-10011. [PMID: 31477296 DOI: 10.3168/jds.2019-16821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/08/2019] [Indexed: 11/19/2022]
Abstract
Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression.
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Affiliation(s)
- H R Oliveira
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - Y Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - S Tsuruta
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - J Jamrozik
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - L F Brito
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F F Silva
- Department of Animal Sciences, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - J P Cant
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
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10
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Oliveira HR, Cant JP, Brito LF, Feitosa FLB, Chud TCS, Fonseca PAS, Jamrozik J, Silva FF, Lourenco DAL, Schenkel FS. Genome-wide association for milk production traits and somatic cell score in different lactation stages of Ayrshire, Holstein, and Jersey dairy cattle. J Dairy Sci 2019; 102:8159-8174. [PMID: 31301836 DOI: 10.3168/jds.2019-16451] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/13/2019] [Indexed: 12/16/2022]
Abstract
We performed genome-wide association analyses for milk, fat, and protein yields and somatic cell score based on lactation stages in the first 3 parities of Canadian Ayrshire, Holstein, and Jersey cattle. The genome-wide association analyses were performed considering 3 different lactation stages for each trait and parity: from 5 to 95, from 96 to 215, and from 216 to 305 d in milk. Effects of single nucleotide polymorphisms (SNP) for each lactation stage, trait, parity, and breed were estimated by back-solving the direct breeding values estimated using the genomic best linear unbiased predictor and single-trait random regression test-day models containing only the fixed population average curve and the random genomic curves. To identify important genomic regions related to the analyzed lactation stages, traits, parities and breeds, moving windows (SNP-by-SNP) of 20 adjacent SNP explaining more than 0.30% of total genetic variance were selected for further analyses of candidate genes. A lower number of genomic windows with a relatively higher proportion of the explained genetic variance was found in the Holstein breed compared with the Ayrshire and Jersey breeds. Genomic regions associated with the analyzed traits were located on 12, 8, and 15 chromosomes for the Ayrshire, Holstein, and Jersey breeds, respectively. Especially for the Holstein breed, many of the identified candidate genes supported previous reports in the literature. However, well-known genes with major effects on milk production traits (e.g., diacylglycerol O-acyltransferase 1) showed contrasting results among lactation stages, traits, and parities of different breeds. Therefore, our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the analyzed traits across breeds, parities, and lactation stages. Further functional studies are needed to validate our findings in independent populations.
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Affiliation(s)
- H R Oliveira
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil.
| | - J P Cant
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F L B Feitosa
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - T C S Chud
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - J Jamrozik
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Canadian Dairy Network (CDN), Guelph, Ontario, N1K 1E5, Canada
| | - F F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock (CGIL), Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Oliveira HR, Brito LF, Lourenco DAL, Silva FF, Jamrozik J, Schaeffer LR, Schenkel FS. Invited review: Advances and applications of random regression models: From quantitative genetics to genomics. J Dairy Sci 2019; 102:7664-7683. [PMID: 31255270 DOI: 10.3168/jds.2019-16265] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/02/2019] [Indexed: 12/23/2022]
Abstract
An important goal in animal breeding is to improve longitudinal traits; that is, traits recorded multiple times during an individual's lifetime or physiological cycle. Longitudinal traits were first genetically evaluated based on accumulated phenotypic expression, phenotypic expression at specific time points, or repeatability models. Until now, the genetic evaluation of longitudinal traits has mainly focused on using random regression models (RRM). Random regression models enable fitting random genetic and environmental effects over time, which results in higher accuracy of estimated breeding values compared with other statistical approaches. In addition, RRM provide insights about temporal variation of biological processes and the physiological implications underlying the studied traits. Despite the fact that genomic information has substantially contributed to increase the rates of genetic progress for a variety of economically important traits in several livestock species, less attention has been given to longitudinal traits in recent years. However, including genomic information to evaluate longitudinal traits using RRM is a feasible alternative to yield more accurate selection and culling decisions, because selection of young animals may be based on the complete pattern of the production curve with higher accuracy compared with the use of traditional parent average (i.e., without genomic information). Moreover, RRM can be used to estimate SNP effects over time in genome-wide association studies. Thus, by analyzing marker associations over time, regions with higher effects at specific points in time are more likely to be identified. Despite the advances in applications of RRM in genetic evaluations, more research is needed to successfully combine RRM and genomic information. Future research should provide a better understanding of the temporal variation of biological processes and their physiological implications underlying the longitudinal traits.
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Affiliation(s)
- H R Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G2W1, Canada; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F F Silva
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, 36570-000, Brazil
| | - J Jamrozik
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - L R Schaeffer
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G2W1, Canada
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G2W1, Canada.
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12
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Guarini AR, Sargolzaei M, Brito LF, Kroezen V, Lourenco DAL, Baes CF, Miglior F, Cole JB, Schenkel FS. Estimating the effect of the deleterious recessive haplotypes AH1 and AH2 on reproduction performance of Ayrshire cattle. J Dairy Sci 2019; 102:5315-5322. [PMID: 30954262 DOI: 10.3168/jds.2018-15366] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 02/18/2019] [Indexed: 11/19/2022]
Abstract
The effects of 2 deleterious recessive haplotypes on reproduction performance of Ayrshire cattle, Ayrshire Haplotype 1 (AH1) and Ayrshire Haplotype 2 (AH2), were investigated in Canadian Ayrshire cattle. We calculated their phenotypic effects on stillbirth (SB) rate and 56-d nonreturn rate (NRR) by estimating the interaction of service sire carrier status with maternal grandsire carrier status using the official Canadian evaluation models for those 2 traits. The interaction term included 9 subclasses for the 3 possible statuses of each bull: haplotype carrier, noncarrier, or not genotyped. For AH1, 394 carriers and 1,433 noncarriers were available, whereas 313 carriers and 1,543 noncarriers were available for the AH2 haplotype. The number of matings considered for SB was 34,312 for heifers (first parity) and 115,935 for cows (later parities). For NRR, 49,479 matings for heifers and 160,528 for cows were used to estimate the haplotype effects. We observed a negative effect of AH1 on SB rates, which was 2.0% higher for matings of AH1-carrier sires to dams that had an AH1-carrier sire; this effect was found for both heifers and cows. However, AH1 had small, generally nonsignificant effects on NRR. The AH2 haplotype had a substantial negative effect on NRR, with 5.1% more heifers and 4.0% more cows returning to service, but the effects on SB rates were inconsistent and mostly small effects. Our results validate the harmful effects of AH1 and AH2 on reproduction traits in the Canadian Ayrshire population. This information will be of great interest for the dairy industry, allowing producers to make mating decisions that would reduce reproductive losses.
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Affiliation(s)
- A R Guarini
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Select Sires Inc., Plain City, OH 43064
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - V Kroezen
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Canadian Dairy Network, Guelph, Ontario N1K 1E5, Canada
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Services, USDA, Beltsville, MD 20705
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Fleming A, Baes CF, Martin AAA, Chud TCS, Malchiodi F, Brito LF, Miglior F. Symposium review: The choice and collection of new relevant phenotypes for fertility selection. J Dairy Sci 2019; 102:3722-3734. [PMID: 30712934 DOI: 10.3168/jds.2018-15470] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 12/02/2018] [Indexed: 12/17/2022]
Abstract
In dairy production, high fertility contributes to herd profitability by achieving greater production and maintaining short calving intervals. Improved management practices and genetic selection have contributed to reversing negative trends in dairy cow fertility, but further progress is still required. Phenotypes included in current genetic evaluations are largely interval and binary traits calculated from insemination and calving date records. Several indicator traits such as calving, health, variation in body condition score, and longevity traits also apply to genetic improvement of fertility. Several fertility traits are included in the selection indices of many countries, but for improved selection, the development of novel phenotypes that more closely describe the physiology of reproduction and limit management bias could be more effective. Progesterone-based phenotypes can be determined from milk samples to describe the heritable interval from calving to corpus luteum activity, as well as additional measures of cow cyclicity. A fundamental component of artificial insemination practices is the observation of estrus. Novel phenotypes collected on estrous activity could be used to select for cows clearly displaying heat, as those cows are more likely to be inseminated at the right time and therefore have greater fertility performance. On-farm technologies, including in-line milk testing and activity monitors, may allow for phenotyping novel traits on large numbers of animals. Additionally, selection for improved fertility using traditional traits could benefit from refined and accurate recording and implementation of parameters such as pregnancy confirmation and reproductive management strategy, to differentiate embryonic or fetal loss, and to ensure selection for reproductive capability without producer intervention. Opportunities exist to achieve genetic improvement of reproductive efficiency in cattle using novel phenotypes, which is required for long-term sustainability of the dairy cattle population and industry.
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Affiliation(s)
- A Fleming
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada.
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A A A Martin
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Animal Breeding and Genomics Centre, Wageningen University and Research, Wageningen, 6708PB, the Netherlands
| | - T C S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F Malchiodi
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Semex Alliance, Guelph, ON, N1H 6J2, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
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14
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Guarini AR, Lourenco DAL, Brito LF, Sargolzaei M, Baes CF, Miglior F, Misztal I, Schenkel FS. Genetics and genomics of reproductive disorders in Canadian Holstein cattle. J Dairy Sci 2018; 102:1341-1353. [PMID: 30471913 DOI: 10.3168/jds.2018-15038] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/29/2018] [Indexed: 01/25/2023]
Abstract
In Canada, reproductive disorders known to affect the profitability of dairy cattle herds have been recorded by producers on a voluntary basis since 2007. Previous studies have shown the feasibility of using producer-recorded health data for genetic evaluations. Despite low heritability estimates and limited availability of phenotypic information, sufficient genetic variation has been observed for those traits to indicate that genetic progress, although slow, can be achieved. Pedigree- and genomic-based analyses were performed on producer-recorded health data of reproductive disorders, including retained placenta (RETP), metritis (METR), and cystic ovaries (CYST) using traditional BLUP and single-step genomic BLUP. Genome-wide association studies and functional analyses were carried out to unravel significant genomic regions and biological pathways, and to better understand the genetic mechanisms underlying RETP, METR, and CYST. Heritability estimates (posterior standard deviation in parentheses) were 0.02 (0.003), 0.01 (0.004), and 0.02 (0.003) for CYST, METR, and RETP, respectively. A moderate to strong genetic correlation of 0.69 (0.102) was found between METR and RETP. Averaged over all traits, sire proof reliabilities increased by approximately 11 percentage points with the incorporation of genomic data using a multiple-trait linear model. Biological pathways and associated genes underlying the studied traits were identified and will contribute to a better understanding of the biology of these 3 health disorders in dairy cattle.
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Affiliation(s)
- A R Guarini
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - D A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; The Semex Alliance, Guelph, ON, Canada N1H 6J2
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1; Canadian Dairy Network, Guelph, ON, Canada N1K 1E5
| | - I Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens 30602
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G 2W1.
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15
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Mallikarjunappa S, Sargolzaei M, Brito LF, Meade KG, Karrow NA, Pant SD. Short communication: Uncovering quantitative trait loci associated with resistance to Mycobacterium avium ssp. paratuberculosis infection in Holstein cattle using a high-density single nucleotide polymorphism panel. J Dairy Sci 2018; 101:7280-7286. [PMID: 29753465 DOI: 10.3168/jds.2018-14388] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) is the etiological agent of Johne's disease in cattle. Johne's disease is a disease of significant economic, animal welfare, and public health concern around the globe. Therefore, understanding the genetic architecture of resistance to MAP infection has great relevance to advance genetic selection methods to breed more resistant animals. The objectives of this study were to perform a genome-wide association study of previously analyzed 50K genotypes now imputed to a high-density single nucleotide polymorphism panel (777K), aiming to validate previously reported associations and potentially identify additional single nucleotide polymorphisms associated with antibody response to MAP infection. A principal component regression-based genome-wide association study revealed 15 putative quantitative trait loci (QTL) associated with the MAP infection phenotype (serum or milk ELISA tests) on 9 different chromosomes (Bos taurus autosomes 5, 6, 7, 10, 14, 15, 16, 20, and 21). These results validated previous findings and identified new QTL on Bos taurus autosomes 15, 16, 20, and 21. The positional candidate genes NLRP3, IFi47, TRIM41, TNFRSF18, and TNFRSF4 lying within these QTL were identified. Further functional validation of these genes is now warranted to investigate their roles in regulating the immune response and, consequently, cattle resistance to MAP infection.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Graham Centre for Agricultural Innovation, NSW DPI and Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia; Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland, C15 PW93; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Ontario, Canada; The Semex Alliance, Guelph, Ontario, N1H 6J2, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - K G Meade
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland, C15 PW93
| | - N A Karrow
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Ontario, Canada
| | - S D Pant
- Graham Centre for Agricultural Innovation, NSW DPI and Charles Sturt University, Locked Bag 588, Wagga Wagga, NSW 2678, Australia.
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16
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Id-Lahoucine S, Casellas J, Fonseca P, Miglior F, Sargolzaei M, Brito LF, Miller SP, Schenkel FS, Asselstine VH, Chesnais JP, Lohuis M, Medrano JF, Cánovas A. 24 Unravelling Genomic Regions with Transmission Ratio Distortion: Identification of Candidate Lethal Alleles in Cattle. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - J Casellas
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - P Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - F Miglior
- Canadian Dairy Network, Guelph, ON, Canada
| | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - V H Asselstine
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | | | - J F Medrano
- Department of Animal Science, University of California, Davis, CA
| | - A Cánovas
- University of Guelph, Guelph, ON, Canada
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17
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Fonseca PADS, Id-Lahoucine S, Casellas J, Miglior F, Reverter A, Fortes MR, Nguyen LT, Porto-Neto LR, Sargolzaei M, Brito LF, Miller SP, Schenkel FS, Lohuis M, Medrano JF, Canovas A. 25 Functional Characterization of Genes Mapped in Transmission Ratio Distortion Regions of the Bovine Genome Affecting Reproduction. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - S Id-Lahoucine
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - J Casellas
- Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - F Miglior
- Canadian Dairy Network, Guelph, ON, Canada
| | | | - M R Fortes
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, St Lucia, Australia
| | - L T Nguyen
- The University of Queensland, School of Chemistry and Molecular Biosciences, St Lucia, Australia
| | | | - M Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - L F Brito
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - J F Medrano
- Department of Animal Science, University of California, Davis, CA
| | - A Canovas
- University of Guelph, Guelph, ON, Canada
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Martin P, Barkema HW, Brito LF, Narayana SG, Miglior F. Symposium review: Novel strategies to genetically improve mastitis resistance in dairy cattle. J Dairy Sci 2018; 101:2724-2736. [PMID: 29331471 DOI: 10.3168/jds.2017-13554] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 11/27/2017] [Indexed: 01/27/2023]
Abstract
Mastitis is a disease of major economic importance to the dairy cattle sector because of the high incidence of clinical mastitis and prevalence of subclinical mastitis and, consequently, the costs associated with treatment, production losses, and reduced animal welfare. Disease-recording systems compiling data from a large number of farms are still not widely implemented around the world; thus, selection for mastitis resistance is often based on genetically correlated indicator traits such as somatic cell count (SCC), udder depth, and fore udder attachment. However, in the past years, several countries have initiated collection systems of clinical mastitis, based on producers recording data in most cases. The large data sets generated have enabled researchers to assess incidence of this disease and to investigate the genetic background of clinical mastitis itself, as well as its relationships with other traits of interest to the dairy industry. The genetic correlations between clinical mastitis and its previous proxies were estimated more accurately and confirmed the strong relationship of clinical mastitis with SCC and udder depth. New traits deriving from SCC were also studied, with the most relevant findings being associated with mean somatic cell score (SCS) in early lactation, standard deviation of SCS, and excessive test-day SCC pattern. Genetic correlations between clinical mastitis and other economically important traits indicated that selection for mastitis resistance would also improve resistance against other diseases and enhance both fertility and longevity. However, milk yield remains negatively correlated with clinical mastitis, emphasizing the importance of including health traits in the breeding objectives to achieve genetic progress for all important traits. These studies enabled the establishment of new genetic and genomic evaluation models, which are more efficient for selection to mastitis resistance. Further studies that are potential keys for future improvement of mastitis resistance are deep investigation of the bacteriology of mastitis, identification of novel indicator traits and tools for selection, and development of a larger female reference population to improve reliability of genomic evaluations. These cutting-edge studies will result in a better understanding of the genetic background of mastitis resistance and enable a more accurate phenotyping and genetic selection to improve mastitis resistance, and consequently, animal welfare and industry profitability.
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Affiliation(s)
- P Martin
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1.
| | - H W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, Canada, T2N 1N4
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - S G Narayana
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1; Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Dr. NW, Calgary, Alberta, Canada, T2N 1N4
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, Canada, N1G 2W1; Canadian Dairy Network, Guelph, Ontario, Canada, N1K 1E5
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Xu Q, Wang YC, Liu R, Brito LF, Kang L, Yu Y, Wang DS, Wu HJ, Liu A. Differential gene expression in the peripheral blood of Chinese Sanhe cattle exposed to severe cold stress. Genet Mol Res 2017; 16:gmr-16-02-gmr.16029593. [PMID: 28653738 DOI: 10.4238/gmr16029593] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Livestock is an important food resource for the inhabitants of cold regions, such as northern Asia and alpine regions, where agriculture is limited. In these regions, cold stress largely affects livestock production, thereby reducing the productivity and survival of animals. Despite the importance of breeding cold-tolerant animals, few studies have investigated the effects of cold stress on cattle. Furthermore, whether severe cold stress alters gene expression or affects molecular genetic mechanisms remains unknown. Thus, we investigated gene expression changes in the peripheral blood samples of the Chinese Sanhe cattle exposed to severe cold. A total of 193 genes were found to exhibit significant alteration in expression (P < 0.05; fold change > 1.3), with 107 genes showing upregulation and 86 showing downregulation after cold exposure. The differences in the expression of 10 selected genes were further validated by real-time qRT-PCR. Further analyses showed that these differentially expressed genes (DEGs) were predominantly associated with important biological pathways and gene networks, such as lipid metabolism and cell death and survival, which are potentially associated with severe cold-stress resistance. Identification and description of these cold stress-induced DEGs might lead to the discovery of novel blood biomarkers that could be used to assess cold-stress resistance in cattle. To our knowledge, this is the first genomic evidence of differences in the transcript expression pattern in cattle exposed to severe cold stress. Our findings provide insights on the potential molecular mechanisms underlying cold-stress response in cattle.
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Affiliation(s)
- Q Xu
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia, Moguai Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia, China
| | - Y C Wang
- Key Laboratory of Agricultural Animal Genetics and Breeding National Engineering, Laboratory for Animal Breeding, College of Animal Science and Technology, , , China
| | - R Liu
- Key Laboratory of Agricultural Animal Genetics and Breeding National Engineering, Laboratory for Animal Breeding, College of Animal Science and Technology, , , China
| | - L F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, , , Canada
| | - L Kang
- Xiertala Cattle Breeding Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia, Moguai Farm, Hailaer Farm Buro, Hailaer, Inner Mongolia, China
| | - Y Yu
- Key Laboratory of Agricultural Animal Genetics and Breeding National Engineering, Laboratory for Animal Breeding, College of Animal Science and Technology, , , China
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Silva FG, Brito LF, Torres RA, Ribeiro Júnior JI, Oliveira HR, Caetano GC, Rodrigues MT. Factors that influence the test day milk yield and composition. Genet Mol Res 2013; 12:1522-32. [PMID: 23765958 DOI: 10.4238/2013.13.5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The objective of this research was to study the factors that influence the test day milk yield (TDMY) and percentages of protein, fat, lactose, and total dry extract obtained on test day. We evaluated 110,732 weekly milk production records from 1496 goats and 19,271 monthly milk constituent records from 1245 Alpine and Saanen goats, which were collected from 1997 to 2010 in the goat sector at Universidade Federal de Viçosa. To ensure greater record reliability, only lactation data with kidding order between 1 to 6, type of kidding data including 0 to 3 kids, milk control years after 1997, and genetic groupings other than types 7 or 9 were considered, due to the relative lack of information recorded for some classes of these factors. Data in which the reported milk days were less than 7 or greater than 315 were also eliminated. Goats aged greater than 300 days at calving and those aged less than 6 years at control were considered in this study. Milk production was higher in the dry season in comparison to the rainy season. Genetic grouping did not influence all traits in both breedings. The TDMY tended to increase along with increasing age of the goats at kidding, while the opposite trend was observed relative to kidding order. Factors that significantly influenced all of the studied traits varied, and the factors that significantly influenced each trait were altered between the relationship of Alpine and Saanen breeds. Thus, the analysis of factors that influence traits to be evaluated in the herd under study is critical for defining the best evaluation model.
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Affiliation(s)
- F G Silva
- Departamento de Zootecnia, Universidade Federal de Viçosa, Viçosa, MG, Brasil.
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Gábor G, Kastelic JP, Cook RB, Sasser RG, Brito LF, Csik JV, Coulter GH, Györkös I. Effects of GnRH treatment on scrotal surface temperatures in bulls. Can J Vet Res 2001; 65:60-3. [PMID: 11227197 PMCID: PMC1189644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Two experiments were conducted to characterize scrotal surface temperature (SST) in bulls treated with gonadotropin releasing hormone (GnRH). In Experiment 1, Angus bulls (n = 10, 18 mo, 597 kg) were given GnRH (400 ng/kg) or saline, IV. Bottom SST increased approximately 1.7 degrees C (P < 0.005) over time (0 to 90 min) at an ambient temperature of 5 degrees C. However, there was no significant effect of GnRH treatment and temperature increases were attributed to stress. When the experiment was repeated at an ambient temperature of 25 degrees C, SST was elevated prior to treatment, with no subsequent significant increase. Experiment 2 was conducted with Charolais bulls (n = 6, 12-14 mo, 517 kg) with an emphasis on minimizing stress. Bottom SST increased approximately 2 degrees C (P < 0.05) between 0 and 45 min after GnRH treatment, supporting the hypothesis that GnRH treatment increases SST in bulls. In conclusion, it was apparent that stress, high ambient temperatures, and GnRH treatment can all increase SST in bulls.
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Affiliation(s)
- G Gábor
- Research Institute for Animal Breeding and Nutrition, Herceghalom, Hungary
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