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Fong A, Rochus CM, Shandilya UK, Muniz MMM, Sharma A, Schenkel FS, Karrow NA, Baes CF. The role of interleukin-10 receptor alpha (IL10Rα) in Mycobacterium avium subsp. paratuberculosis infection of a mammary epithelial cell line. BMC Genom Data 2024; 25:58. [PMID: 38867147 PMCID: PMC11167801 DOI: 10.1186/s12863-024-01234-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Johne's disease is a chronic wasting disease caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease is highly contagious and MAP infection in dairy cattle can eventually lead to death. With no available treatment for Johne's disease, genetic selection and improvements in management practices could help reduce its prevalence. In a previous study, the gene coding interleukin-10 receptor subunit alpha (IL10Rα) was associated with Johne's disease in dairy cattle. Our objective was to determine how IL10Rα affects the pathogenesis of MAP by examining the effect of a live MAP challenge on a mammary epithelial cell line (MAC-T) that had IL10Rα knocked out using CRISPR/cas9. The wild type and the IL10Rα knockout MAC-T cell lines were exposed to live MAP bacteria for 72 h. Thereafter, mRNA was extracted from infected and uninfected cells. Differentially expressed genes were compared between the wild type and the IL10Rα knockout cell lines. Gene ontology was performed based on the differentially expressed genes to determine which biological pathways were involved. RESULTS Immune system processes pathways were targeted to determine the effect of IL10Rα on the response to MAP infection. There was a difference in immune response between the wild type and IL10Rα knockout MAC-T cell lines, and less difference in immune response between infected and not infected IL10Rα knockout MAC-T cells, indicating IL10Rα plays an important role in the progression of MAP infection. Additionally, these comparisons allowed us to identify other genes involved in inflammation-mediated chemokine and cytokine signalling, interleukin signalling and toll-like receptor pathways. CONCLUSIONS Identifying differentially expressed genes in wild type and ILR10α knockout MAC-T cells infected with live MAP bacteria provided further evidence that IL10Rα contributes to mounting an immune response to MAP infection and allowed us to identify additional potential candidate genes involved in this process. We found there was a complex immune response during MAP infection that is controlled by many genes.
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Affiliation(s)
- Aisha Fong
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christina M Rochus
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
| | - Umesh K Shandilya
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Maria M M Muniz
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ankita Sharma
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Christine F Baes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3002, Switzerland.
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Lei Q, Zhang S, Wang J, Qi C, Liu J, Cao D, Li F, Han H, Liu W, Li D, Tang C, Zhou Y. Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken. Poult Sci 2024; 103:103705. [PMID: 38598913 DOI: 10.1016/j.psj.2024.103705] [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: 01/17/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.
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Affiliation(s)
- Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Wang
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dapeng Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Cunwei Tang
- Fujian Sunnzer Biological Technology Development Co. Ltd., 354100, Guang'ze, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China..
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Usai MG, Casu S, Sechi T, Salaris SL, Miari S, Mulas G, Cancedda MG, Ligios C, Carta A. Advances in understanding the genetic architecture of antibody response to paratuberculosis in sheep by heritability estimate and LDLA mapping analyses and investigation of candidate regions using sequence-based data. Genet Sel Evol 2024; 56:5. [PMID: 38200416 PMCID: PMC10777618 DOI: 10.1186/s12711-023-00873-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Paratuberculosis is a contagious and incurable disease that is caused by Mycobacterium avium subsp. paratuberculosis (MAP) with significant negative effects on animal welfare and farm profitability. Based on a large naturally infected flock over 12 years, we analyzed repeated enzyme-linked immunosorbent assay tests (ELISA), OvineSNP50 BeadChip genotypes and whole-genome sequences imputed from 56 influential animals. The main goals were to estimate the genetic parameters of proxy traits for resistance to MAP, identify genomic regions associated with the host's immune response against MAP and search for candidate genes and causative mutations through association and functional annotation analyses of polymorphisms identified by sequencing. RESULTS Two variables were derived from ELISA tests. The first, a binary variable, assessed the infection status of each animal over the entire productive life, while the second considered the level of antibody recorded over time. Very similar results were obtained for both variables. Heritability estimates of about 0.20 were found and a significant region capturing 18% and 13% of the genetic variance was detected on ovine chromosome 20 by linkage disequilibrium and linkage analysis on OvineSNP50 positions. Functional annotation and association analyses on the imputed sequence polymorphisms that were identified in this region were carried out. No significant variants showed a functional effect on the genes that mapped to this region, most of which belong to the major histocompatibility complex class II (MHC II). However, the conditional analysis led to the identification of two significant polymorphisms that can explain the genetic variance associated with the investigated genomic region. CONCLUSIONS Our results confirm the involvement of the host's genetics in susceptibility to MAP in sheep and suggest that selective breeding may be an option to limit the infection. The estimated heritability is moderate with a relevant portion being due to a highly significant region on ovine chromosome 20. The results of the combined use of sequence-based data and functional analyses suggest several genes belonging to the MHC II as the most likely candidates, although no mutations in their coding regions showed a significant association. Nevertheless, information from genotypes of two highly significant polymorphisms in the region can enhance the efficiency of selective breeding programs.
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Affiliation(s)
- Mario Graziano Usai
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sara Casu
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy.
| | - Tiziana Sechi
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sotero L Salaris
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Sabrina Miari
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | - Giuliana Mulas
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
| | | | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale Della Sardegna G. Pegreffi, 07100, Sassari, Italy
| | - Antonello Carta
- Research Unit Genetics and Biotechnology - Agris Sardegna, 07100, Sassari, Italy
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Badia-Bringué G, Canive M, Fernandez-Jimenez N, Lavín JL, Casais R, Blanco-Vázquez C, Vázquez P, Fernández A, Bilbao JR, Garrido JM, Juste RA, González-Recio O, Alonso-Hearn M. Summary-data based Mendelian randomization identifies gene expression regulatory polymorphisms associated with bovine paratuberculosis by modulation of the nuclear factor Kappa β (NF-κß)-mediated inflammatory response. BMC Genomics 2023; 24:605. [PMID: 37821814 PMCID: PMC10568764 DOI: 10.1186/s12864-023-09710-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified host genetic variants associated with paratuberculosis (PTB) susceptibility. Most of the GWAS-identified SNPs are in non-coding regions. Connecting these non-coding variants and downstream affected genes is a challenge and, up to date, only a few functional mutations or expression quantitative loci (cis-eQTLs) associated with PTB susceptibility have been identified. In the current study, the associations between imputed whole-genome sequence genotypes and whole RNA-Sequencing data from peripheral blood (PB) and ileocecal valve (ICV) samples of Spanish Holstein cows (N = 16) were analyzed with TensorQTL. This approach allowed the identification of 88 and 37 cis-eQTLs regulating the expression levels of 90 and 37 genes in PB and ICV samples, respectively (False discorey rate, FDR ≤ 0.05). Next, we applied summary-based data Mendelian randomization (SMR) to integrate the cis-eQTL dataset with GWAS data obtained from a cohort of 813 culled cattle that were classified according to the presence or absence of PTB-associated histopathological lesions in gut tissues. After multiple testing corrections (FDR ≤ 0.05), we identified two novel cis-eQTLs affecting the expression of the early growth response factor 4 (EGR4) and the bovine neuroblastoma breakpoint family member 6-like protein isoform 2 (MGC134040) that showed pleiotropic associations with the presence of multifocal and diffuse lesions in gut tissues; P = 0.002 and P = 0.017, respectively. While EGR4 acts as a brake on T-cell proliferation and cytokine production through interaction with the nuclear factor Kappa β (NF-κß), MGC134040 is a target gene of NF-κß. Our findings provide a better understanding of the genetic factors influencing PTB outcomes, confirm that the multifocal lesions are localized/confined lesions that have different underlying host genetics than the diffuse lesions, and highlight regulatory SNPs and regulated-gene targets to design future functional studies.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Bizkaia, Spain
| | - Maria Canive
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - José Luis Lavín
- Department of Applied Mathematics, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Rosa Casais
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Cristina Blanco-Vázquez
- Center of Animal Biotechnology, SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Asturias, Spain
| | - Patricia Vázquez
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Jose Ramón Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Biocruces-Bizkaia HRI, Leioa, Bizkaia, Spain
| | - Joseba M Garrido
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Ramón A Juste
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain
| | - Oscar González-Recio
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC, Madrid, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Derio, Bizkaia, Spain.
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Corbiere F, Guellouz D, Tasca C, Foures L, Dubaux E, Foucras G. Effects of Silirum ®-Based Vaccination Programs on Map Fecal Shedding and Serological Response in Seven French Dairy Herds. Animals (Basel) 2023; 13:ani13091569. [PMID: 37174606 PMCID: PMC10177616 DOI: 10.3390/ani13091569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/23/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
(1) Background: paratuberculosis is an important disease in ruminants, causing worldwide economic losses to the livestock industry. Although vaccination is known not to prevent transmission of the causative agent Mycobacterium avium subsp. paratuberculosis (Map), it is considered an effective tool for paratuberculosis in infected herds. The objectives of this controlled field study were to evaluate the effects of the whole-cell heat-killed Silirum® vaccine on Map fecal shedding and serological status in dairy herds infected with paratuberculosis. (2) Methods: The serological status (ELISA) and fecal shedding (qPCR) of 358 vaccinated cows were assessed over 3 years in 7 infected dairy herds in the Meuse department, France. Within each herd, cows from the last non-vaccinated birth cohort (n = 265) were used as controls. The probability and level of Map fecal shedding and the serological status were modeled using multivariable mixed general linear regression models. (3) Results: Overall, 34.7% of cows tested positive at least once on fecal qPCR, with significant differences between herds, but high shedding levels were observed in only 5.5% of cows. Compared to non-vaccinated seronegative cows, a statistically significant reduction in the probability of Map shedding was found only in cows vaccinated before 4 to 5 months of age that tested negative for Map antibodies throughout the study period (odds ratio = 0.5, 95% confidence interval: 0.3-0.9, p = 0.008), but no significant effect of vaccination on the amount of Map shedding could be evidenced. Finally, the younger the cows were when vaccinated, the less they tested positive on the serum ELISA. (4) Conclusions: a beneficial effect of vaccination on Map fecal shedding may exist in cows vaccinated before 4 to 5 months of age. The variability of the serum ELISA response in vaccinated cows remains to be investigated.
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Ingratta GG, Stempler A, Fernández B, Colavecchia SB, Jolly A, Minatel L, Paolicchi FA, Mundo SL. Early-stage findings in an experimental calf model infected with Argentinean isolates of Mycobacterium avium subsp. paratuberculosis. Vet Immunol Immunopathol 2023; 259:110595. [PMID: 37058952 DOI: 10.1016/j.vetimm.2023.110595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/30/2023] [Accepted: 04/10/2023] [Indexed: 04/16/2023]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is an important pathogen that causes granulomatous enteritis known as Johne's disease or paratuberculosis (PTB). In this study an experimental model of calves infected with Argentinean isolates of MAP for 180 days was used to provide more data of the early PTB stages. Calves were challenged by oral route with MAP strain IS900-RFLPA (MA; n = 3), MAP strain IS900-RFLPC (MC; n = 2) or mock infected (MI; n = 2), and response to infection was evaluated through peripheral cytokine expression, MAP tissue distribution and histopathological early-stage findings. Specific and varied levels of IFN-γ were only detected at 80 days post-infection in infected calves. These data indicate that specific IFN-γ is not a useful indicator for early detection of MAP infection in our calf model. At 110 days post-infection, TNF-α expression was higher than IL-10 in 4 of the 5 infected animals and a significant decrease of TNF-α expression was detected in infected vs. non-infected calves. All calves challenged were identified as infected by mesenteric lymph node tissue culture and real time IS900 PCR. In addition, for lymph nodes samples, the agreement between these techniques was almost perfect (κ = 0.86). Colonization of tissues and levels of tissue infection varied between individuals. Evidence of early MAP dissemination to extraintestinal tissues such as the liver was detected by culture in one animal (MAP strain IS900-RFLPA). In both groups microgranulomatous lesions were observed predominantly in the lymph nodes, with giant cells present only in the MA group. In summary, the findings described herein may indicate that local MAP strains induced specific immune responses with particularities that could suggest differences in their biological behavior. Further studies should be carried out in order to obtain an in-depth understanding of the influence of MAP strains in host-pathogen interactions and the outcome of disease.
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Affiliation(s)
- Giselle Gabriela Ingratta
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Stempler
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Bárbara Fernández
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina.
| | - Silvia Beatriz Colavecchia
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Ana Jolly
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonardo Minatel
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Patología, Av. San Martín 5285, C1417DSM Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando Alberto Paolicchi
- Instituto Nacional de Tecnología Agropecuaria (INTA), Estación Experimental Agropecuaria Balcarce, Laboratorio de Bacteriología, Ruta 226, Km 73.5, Balcarce B7620BEN, Provincia de Buenos Aires, Argentina; Universidad Nacional de Mar del Plata, Facultad de Ciencias Agrarias, Departamento de Producción Animal, Ruta 226, Km 73.5, Balcarce B7620BEN, Provincia de Buenos Aires, Argentina
| | - Silvia Leonor Mundo
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Inmunología, Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina; Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Instituto de Investigación y Tecnología en Reproducción Animal (INITRA), Av. Chorroarín 280, C1427CWO Ciudad Autónoma de Buenos Aires, Argentina
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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0339222. [PMID: 36445077 PMCID: PMC9769990 DOI: 10.1128/spectrum.03392-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M. avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.
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Sanchez MP, Tribout T, Fritz S, Guatteo R, Fourichon C, Schibler L, Delafosse A, Boichard D. New insights into the genetic resistance to paratuberculosis in Holstein cattle via single-step genomic evaluation. Genet Sel Evol 2022; 54:67. [PMID: 36243688 PMCID: PMC9569073 DOI: 10.1186/s12711-022-00757-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/24/2022] [Indexed: 11/10/2022] Open
Abstract
Background Bovine paratuberculosis, or Johne’s disease (JD), is a contagious and incurable disease caused by Mycobacterium avium subsp. paratuberculosis (MAP). It has adverse effects on animal welfare and is very difficult to control, leading to serious economic consequences. An important line of defense to this disease is host genetic resistance to MAP, which, when it will be more fully understood, could be improved through selective breeding. Using a large dataset of Holstein cows (161,253 animals including 56,766 cows with ELISA serological phenotypes and 12,431 animals with genotypes), we applied a single-step single nucleotide polymorphism (SNP) best linear unbiased prediction approach to investigate the genetic determinism underlying resistance to this disease (heritability estimate and identification of relevant genomic regions) and estimated genetic trends, reliability, and relative risk factors associated with genomic predictions. Results Resistance to JD was moderately heritable (0.14) and 16 genomic regions were detected that accounted for at least 0.05% of the breeding values variance (GV) in resistance to JD, and were located on chromosomes 1, 3, 5, 6, 7, 19, 20, 21, 23, 25, and 27, with the highest percentage of variance explained by regions on chromosomes 23 (0.36% GV), 5 (0.22% GV), 1 (0.14% GV), and 3 (0.13% GV). When estimated for the whole chromosomes, the autosomes with the largest overall contributions were chromosomes 3 (5.3% GV), 10 (4.8%), 23 (4.7%), 1 (3.6%), 7 (3.4%), 5 (2.9%), 12 (2.5%), 11 (2.2%), and 13 (2%). We estimated a slightly favorable genetic trend in resistance to JD over the last two decades, which can be explained by a low positive genetic correlation between resistance to JD and total merit index (+ 0.06). Finally, in a validation population of 907 cows, relatively reliable genomic predictions (reliability = 0.55) were obtained, which allowed the identification of cows at high risk of infection. Conclusions This study provides new insights into the genetic determinism of resistance to JD and shows that this trait can be predicted from SNP genotypes. It has led to the implementation of a single-step genomic evaluation that should rapidly become an effective tool for controlling paratuberculosis on French Holstein farms.
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Affiliation(s)
- Marie-Pierre Sanchez
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Thierry Tribout
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Sébastien Fritz
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,Eliance, 149 Rue de Bercy, 75012, Paris, France
| | | | | | | | | | - Didier Boichard
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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9
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Ros-Freixedes R, Johnsson M, Whalen A, Chen CY, Valente BD, Herring WO, Gorjanc G, Hickey JM. Genomic prediction with whole-genome sequence data in intensely selected pig lines. GENETICS SELECTION EVOLUTION 2022; 54:65. [PMID: 36153511 PMCID: PMC9509613 DOI: 10.1186/s12711-022-00756-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/05/2022] [Indexed: 12/03/2022]
Abstract
Background Early simulations indicated that whole-genome sequence data (WGS) could improve the accuracy of genomic predictions within and across breeds. However, empirical results have been ambiguous so far. Large datasets that capture most of the genomic diversity in a population must be assembled so that allele substitution effects are estimated with high accuracy. The objectives of this study were to use a large pig dataset from seven intensely selected lines to assess the benefits of using WGS for genomic prediction compared to using commercial marker arrays and to identify scenarios in which WGS provides the largest advantage. Methods We sequenced 6931 individuals from seven commercial pig lines with different numerical sizes. Genotypes of 32.8 million variants were imputed for 396,100 individuals (17,224 to 104,661 per line). We used BayesR to perform genomic prediction for eight complex traits. Genomic predictions were performed using either data from a standard marker array or variants preselected from WGS based on association tests. Results The accuracies of genomic predictions based on preselected WGS variants were not robust across traits and lines and the improvements in prediction accuracy that we achieved so far with WGS compared to standard marker arrays were generally small. The most favourable results for WGS were obtained when the largest training sets were available and standard marker arrays were augmented with preselected variants with statistically significant associations to the trait. With this method and training sets of around 80k individuals, the accuracy of within-line genomic predictions was on average improved by 0.025. With multi-line training sets, improvements of 0.04 compared to marker arrays could be expected. Conclusions Our results showed that WGS has limited potential to improve the accuracy of genomic predictions compared to marker arrays in intensely selected pig lines. Thus, although we expect that larger improvements in accuracy from the use of WGS are possible with a combination of larger training sets and optimised pipelines for generating and analysing such datasets, the use of WGS in the current implementations of genomic prediction should be carefully evaluated against the cost of large-scale WGS data on a case-by-case basis. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00756-0.
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10
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Alonso-Hearn M, Badia-Bringué G, Canive M. Genome-wide association studies for the identification of cattle susceptible and resilient to paratuberculosis. Front Vet Sci 2022; 9:935133. [PMID: 36172612 PMCID: PMC9510743 DOI: 10.3389/fvets.2022.935133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/22/2022] [Indexed: 12/18/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease or paratuberculosis (PTB), with important animal health and economic implications. There are no therapeutic strategies to control this disease, and vaccination with inactivated vaccines is limited in many countries because it can interfere with the intradermal test used for bovine tuberculosis detection. Thus, infected animals either get culled after a positive ELISA or fecal PCR result or die due to clinical disease. In this study, we review recent studies aimed to discover genetic markers which could help to identify and select cattle less susceptible and more resilient to PTB. In recent years, the genotyping and subsequent imputation to whole-genome sequence (WGS) has allowed the identification of single-nucleotide polymorphisms (SNPs), quantitative trait loci (QTL), and candidate genes in the Bos taurus genome associated with susceptibility to MAP infection. In most of these genome-wide association studies (GWAS), phenotypes were based on ante-mortem test results including serum ELISA, milk ELISA, and detection of MAP by fecal PCR and bacteriological culture. Cattle infected with MAP display lesions with distinct severity but the associations between host genetics and PTB-associated pathology had not been explored until very recently. On the contrary, the understanding of the mechanisms and genetic loci influencing pathogen resistance, and disease tolerance in asymptomatic individuals is currently very limited. The identification of long-time asymptomatic cattle that is able to resist the infection and/or tolerate the disease without having their health and milk production compromised is important for disease control and breeding purposes.
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11
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Kirkpatrick BW, Cooke ME, Frie M, Sporer KRB, Lett B, Wells SJ, Coussens PM. Genome-wide association analysis for susceptibility to infection by Mycobacterium avium ssp. paratuberculosis in US Holsteins. J Dairy Sci 2022; 105:4301-4313. [PMID: 35307176 DOI: 10.3168/jds.2021-21276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/27/2022] [Indexed: 12/19/2022]
Abstract
Paratuberculosis, or Johne's disease, is a chronic, granulomatous, gastrointestinal tract disease of cattle and other ruminants caused by the bacterium Mycobacterium avium subspecies paratuberculosis (MAP). Control of Johne's disease is based on programs of testing and culling animals positive for infection with MAP and concurrently modifying management to reduce the likelihood of infection. The current study was motivated by the hypothesis that genetic variation in host susceptibility to MAP infection can be dissected and quantifiable associations with genetic markers identified. Two separate GWAS analyses were conducted, the first using 897 genotyped Holstein artificial insemination sires with phenotypes derived from incidence of MAP infection among daughters based on milk ELISA testing records. The second GWAS analysis was a case-control design using US Holstein cows phenotyped for MAP infection by serum ELISA or fecal culture tests. Cases included cows positive for either serum ELISA, fecal culture, or both. Controls consisted of animals negative for all tests conducted. A total of 376 samples (70 cases and 306 controls) from a University of Minnesota Johne's management demonstration project and 184 samples (76 cases and 108 controls) from a Michigan State University study were used. Medium-density (sires) and high-density (cows) genotype data were imputed to full genome sequence for the analyses. Marker-trait associations were analyzed using the single-step (ss)GWAS procedure implemented in the BLUPF90 suite of programs. Evidence of significant genomic contributions for susceptibility to MAP infection were observed on multiple chromosomes. Results were combined across studies in a meta-analysis, and increased support for genomic regions on BTA7 and BTA21 were observed. Gene set enrichment analysis suggested pathways for antigen processing and presentation, antimicrobial peptides and natural killer cell-mediated cytotoxicity are relevant to variation in host susceptibility to MAP infection, among others. Genomic prediction was evaluated using a 5-fold cross-validation, and moderate correlations were observed between genomic breeding value predictions and daughter averages (∼0.43 to 0.53) for MAP infection in testing data sets. These results suggest that genomic selection against susceptibility to MAP infection is feasible in Holstein cattle.
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Affiliation(s)
- B W Kirkpatrick
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, Madison 53706.
| | - M E Cooke
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, Madison 53706
| | - M Frie
- Department of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing 48824
| | - K R B Sporer
- Department of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing 48824
| | - B Lett
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, 1675 Observatory Drive, Madison 53706
| | - S J Wells
- Department of Veterinary Population Medicine, University of Minnesota, 1365 Gortner Avenue, St. Paul 55108
| | - P M Coussens
- Department of Animal Science, Michigan State University, 474 S Shaw Ln, East Lansing 48824
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12
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Gu B, Sun R, Fang X, Zhang J, Zhao Z, Huang D, Zhao Y, Zhao Y. Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats. Animals (Basel) 2022; 12:ani12050548. [PMID: 35268118 PMCID: PMC8908837 DOI: 10.3390/ani12050548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats. Abstract Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.
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Affiliation(s)
- Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Deli Huang
- Tengda Animal Husbandry Co., Ltd., Chongqing 402360, China;
| | - Yuanping Zhao
- Dazu County Agriculture and Rural Committee, Chongqing 402360, China;
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
- Correspondence:
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13
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Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Gao X, Chen Y, Zhang L, Gao H, Li J, Xu L. Identification of Candidate Variants Associated With Bone Weight Using Whole Genome Sequence in Beef Cattle. Front Genet 2021; 12:750746. [PMID: 34912371 PMCID: PMC8667311 DOI: 10.3389/fgene.2021.750746] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Bone weight is critical to affect body conformation and stature in cattle. In this study, we conducted a genome-wide association study for bone weight in Chinese Simmental beef cattle based on the imputed sequence variants. We identified 364 variants associated with bone weight, while 350 of them were not included in the Illumina BovineHD SNP array, and several candidate genes and GO terms were captured to be associated with bone weight. Remarkably, we identified four potential variants in a candidate region on BTA6 using Bayesian fine-mapping. Several important candidate genes were captured, including LAP3, MED28, NCAPG, LCORL, SLIT2, and IBSP, which have been previously reported to be associated with carcass traits, body measurements, and growth traits. Notably, we found that the transcription factors related to MED28 and LCORL showed high conservation across multiple species. Our findings provide some valuable information for understanding the genetic basis of body stature in beef cattle.
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Affiliation(s)
- Qunhao Niu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianliu Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ling Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianzhen Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zezhao Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bo Zhu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yan Chen
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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14
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Crum TE, Schnabel RD, Decker JE, Taylor JF. Taurine and Indicine Haplotype Representation in Advanced Generation Individuals From Three American Breeds. Front Genet 2021; 12:758394. [PMID: 34733318 PMCID: PMC8558500 DOI: 10.3389/fgene.2021.758394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
Development of the American Breeds of beef cattle began in the 1920s as breeders and U. S. Experiment Station researchers began to create Bos taurus taurus × Bos taurus indicus hybrids using Brahman as the B. t. indicus source. By 1954, U.S. Breed Associations had been formed for Brangus (5/8 Angus × 3/8 Brahman), Beefmaster (½ Brahman × ¼ Shorthorn × ¼ Hereford), and Santa Gertrudis (5/8 Shorthorn × 3/8 Brahman). While these breeds were developed using mating designs expected to create base generation animals with the required genome contributions from progenitor breeds, each association has now registered advanced generation animals in which selection or drift may have caused the realized genome compositions to differ from initial expected proportions. The availability of high-density SNP genotypes for 9,161 Brangus, 3,762 Beefmaster, and 1,942 Santa Gertrudis animals allowed us to compare the realized genomic architectures of breed members to the base generation expectations. We used RFMix to estimate local ancestry and identify genomic regions in which the proportion of Brahman ancestry differed significantly from a priori expectations. For all three breeds, lower than expected levels of Brahman composition were found genome-wide, particularly in early-generation animals where we demonstrate that selection on beef production traits was likely responsible for the taurine enrichment. Using a proxy for generation number, we also contrasted the genomes of early- and advanced-generation animals and found that the indicine composition of the genome has increased with generation number likely due to selection on adaptive traits. Many of the most-highly differentiated genomic regions were breed specific, suggesting that differences in breeding objectives and selection intensities exist between the breeds. Global ancestry estimation is commonly performed in admixed animals to control for stratification in association studies. However, local ancestry estimation provides the opportunity to investigate the evolution of specific chromosomal segments and estimate haplotype effects on trait variation in admixed individuals. Investigating the genomic architecture of the American Breeds not only allows the estimation of indicine and taurine genome proportions genome-wide, but also the locations within the genome where either taurine or indicine alleles confer a selective advantage.
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Affiliation(s)
- Tamar E Crum
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States.,Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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15
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Guo J, Jiang R, Mao A, Liu GE, Zhan S, Li L, Zhong T, Wang L, Cao J, Chen Y, Zhang G, Zhang H. Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats. BMC Genomics 2021; 22:769. [PMID: 34706644 PMCID: PMC8555091 DOI: 10.1186/s12864-021-08089-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/14/2021] [Indexed: 12/01/2022] Open
Abstract
Background There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. Results We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. Conclusion Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08089-w.
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Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Rui Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ayi Mao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Siyuan Zhan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaxue Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Chen
- Nanjiang Yellow Goat Scientific Research Institute, Bazhong, 635600, China
| | - Guojun Zhang
- Nanjiang Yellow Goat Scientific Research Institute, Bazhong, 635600, China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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16
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Mallikarjunappa S, Brito LF, Pant SD, Schenkel FS, Meade KG, Karrow NA. Johne's Disease in Dairy Cattle: An Immunogenetic Perspective. Front Vet Sci 2021; 8:718987. [PMID: 34513975 PMCID: PMC8426623 DOI: 10.3389/fvets.2021.718987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/19/2021] [Indexed: 12/25/2022] Open
Abstract
Johne's disease (JD), also known as paratuberculosis, is a severe production-limiting disease with significant economic and welfare implications for the global cattle industry. Caused by infection with Mycobacterium avium subspecies paratuberculosis (MAP), JD manifests as chronic enteritis in infected cattle. In addition to the economic losses and animal welfare issues associated with JD, MAP has attracted public health concerns with potential association with Crohn's disease, a human inflammatory bowel disease. The lack of effective treatment options, such as a vaccine, has hampered JD control resulting in its increasing global prevalence. The disease was first reported in 1895, but in recognition of its growing economic impact, extensive recent research facilitated by a revolution in technological approaches has led to significantly enhanced understanding of the immunological, genetic, and pathogen factors influencing disease pathogenesis. This knowledge has been derived from a variety of diverse models to elucidate host-pathogen interactions including in vivo and in vitro experimental infection models, studies measuring immune parameters in naturally-infected animals, and by studies conducted at the population level to enable the estimation of genetic parameters, and the identification of genetic markers and quantitative trait loci (QTL) putatively associated with susceptibility or resistance to JD. The main objectives of this review are to summarize these recent developments from an immunogenetics perspective and attempt to extract the principal and common findings emerging from this wealth of recent information. Based on these analyses, and in light of emerging technologies such as gene-editing, we conclude by discussing potential future avenues for effectively mitigating JD in cattle.
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Affiliation(s)
- Sanjay Mallikarjunappa
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Sameer D Pant
- Graham Centre for Agricultural Innovation, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | - Kieran G Meade
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Niel A Karrow
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
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17
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Identification of loci associated with susceptibility to Mycobacterium avium subsp. paratuberculosis infection in Holstein cattle using combinations of diagnostic tests and imputed whole-genome sequence data. PLoS One 2021; 16:e0256091. [PMID: 34449805 PMCID: PMC8396740 DOI: 10.1371/journal.pone.0256091] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/29/2021] [Indexed: 12/16/2022] Open
Abstract
Bovine paratuberculosis (PTB) is a chronic inflammatory disease caused by Mycobacterium avium susbp. paratuberculosis (MAP). Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with susceptibility to bovine PTB. The main objective of this study was to identify quantitative trait loci (QTLs) associated with MAP infection in Spanish Holstein cows (N = 983) using combinations of diagnostic tests and imputed whole-genome sequence (WGS) data. The infection status of these animals was defined by three diagnostic methods including ELISA for MAP-antibodies detection, and tissue culture and PCR for MAP detection. The 983 cows included in this study were genotyped with the Bovine MD SNP50 Bead Chip, and the corresponding genotypes were imputed to WGS using the 1,000 Bull genomes reference population. In total, 33.77 million SNP variants per animal were identified across the genome. Linear mixed models were used to calculate the heritability (h2) estimates for each diagnostic test and test combinations. Next, we performed a case-control GWAS using the imputed WGS datasets and the phenotypes and combinations of phenotypes with h2 estimates > 0.080. After performing the GWAS, the test combinations that showed SNPs with a significant association (PFDR ≤ 0.05), were the ELISA-tissue PCR-tissue culture, ELISA-tissue culture, and ELISA-tissue PCR. A total of twelve quantitative trait loci (QTLs) highly associated with MAP infection status were identified on the Bos taurus autosomes (BTA) 4, BTA5, BTA11, BTA12, BTA14, BTA23, BTA24, and BTA28, and some of these QTLs were linked to immune-modulating genes. The identified QTLs on BTA23 spanning from 18.81 to 22.95 Mb of the Bos taurus genome overlapped with several QTLs previously found to be associated with PTB susceptibility, bovine tuberculosis susceptibility, and clinical mastitis. The results from this study provide more clues regarding the molecular mechanisms underlying susceptibility to PTB infection in cattle and might be used to develop national genetic evaluations for PTB in Spain.
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Yoshida GM, Yáñez JM. Increased accuracy of genomic predictions for growth under chronic thermal stress in rainbow trout by prioritizing variants from GWAS using imputed sequence data. Evol Appl 2021; 15:537-552. [PMID: 35505881 PMCID: PMC9046923 DOI: 10.1111/eva.13240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/01/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Through imputation of genotypes, genome‐wide association study (GWAS) and genomic prediction (GP) using whole‐genome sequencing (WGS) data are cost‐efficient and feasible in aquaculture breeding schemes. The objective was to dissect the genetic architecture of growth traits under chronic heat stress in rainbow trout (Oncorhynchus mykiss) and to assess the accuracy of GP based on imputed WGS and different preselected single nucleotide polymorphism (SNP) arrays. A total of 192 and 764 fish challenged to a heat stress experiment for 62 days were genotyped using a customized 1 K and 26 K SNP panels, respectively, and then, genotype imputation was performed from a low‐density chip to WGS using 102 parents (36 males and 66 females) as the reference population. Imputed WGS data were used to perform GWAS and test GP accuracy under different preselected SNP scenarios. Heritability was estimated for body weight (BW), body length (BL) and average daily gain (ADG). Estimates using imputed WGS data ranged from 0.33 ± 0.05 to 0.55 ± 0.05 for growth traits under chronic heat stress. GWAS revealed that the top five cumulatively SNPs explained a maximum of 0.94%, 0.86% and 0.51% of genetic variance for BW, BL and ADG, respectively. Some important functional candidate genes associated with growth‐related traits were found among the most important SNPs, including signal transducer and activator of transcription 5B and 3 (STAT5B and STAT3, respectively) and cytokine‐inducible SH2‐containing protein (CISH). WGS data resulted in a slight increase in prediction accuracy compared with pedigree‐based method, whereas preselected SNPs based on the top GWAS hits improved prediction accuracies, with values ranging from 1.2 to 13.3%. Our results support the evidence of the polygenic nature of growth traits when measured under heat stress. The accuracies of GP can be improved using preselected variants from GWAS, and the use of WGS marginally increases prediction accuracy.
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Affiliation(s)
- Grazyella M. Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile Santiago Chile
| | - José M. Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile Santiago Chile
- Núcleo Milenio INVASAL Concepción Chile
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Ariel O, Brouard JS, Marete A, Miglior F, Ibeagha-Awemu E, Bissonnette N. Genome-wide association analysis identified both RNA-seq and DNA variants associated to paratuberculosis in Canadian Holstein cattle 'in vitro' experimentally infected macrophages. BMC Genomics 2021; 22:162. [PMID: 33678157 PMCID: PMC7938594 DOI: 10.1186/s12864-021-07487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 02/26/2021] [Indexed: 12/22/2022] Open
Abstract
Background Mycobacterium avium ssp. paratuberculosis (MAP) is the causative agent of paratuberculosis, or Johne’s disease (JD), an incurable bovine disease. The evidence for susceptibility to MAP disease points to multiple interacting factors, including the genetic predisposition to a dysregulation of the immune system. The endemic situation in cattle populations can be in part explained by a genetic susceptibility to MAP infection. In order to identify the best genetic improvement strategy that will lead to a significant reduction of JD in the population, we need to understand the link between genetic variability and the biological systems that MAP targets in its assault to dominate macrophages. MAP survives in macrophages where it disseminates. We used next-generation RNA (RNA-Seq) sequencing to study of the transcriptome in response to MAP infection of the macrophages from cows that have been naturally infected and identified as positive for JD (JD (+); n = 22) or negative for JD (healthy/resistant, JD (−); n = 28). In addition to identifying genetic variants from RNA-seq data, SNP variants were also identified using the Bovine SNP50 DNA chip. Results The complementary strategy allowed the identification of 1,356,248 genetic variants, including 814,168 RNA-seq and 591,220 DNA chip variants. Annotation using SnpEff predicted that the 2435 RNA-seq genetic variants would produce high functional effect on known genes in comparison to the 33 DNA chip variants. Significant variants from JD(+/−) macrophages were identified by genome-wide association study and revealed two quantitative traits loci: BTA4 and 11 at (P < 5 × 10− 7). Using BovineMine, gene expression levels together with significant genomic variants revealed pathways that potentially influence JD susceptibility, notably the energy-dependent regulation of mTOR by LKB1-AMPK and the metabolism of lipids. Conclusion In the present study, we succeeded in identifying genetic variants in regulatory pathways of the macrophages that may affect the susceptibility of cows that are healthy/resistant to MAP infection. RNA-seq provides an unprecedented opportunity to investigate gene expression and to link the genetic variations to biological pathways that MAP normally manipulate during the process of killing macrophages. A strategy incorporating functional markers into genetic selection may have a considerable impact in improving resistance to an incurable disease. Integrating the findings of this research into the conventional genetic selection program may allow faster and more lasting improvement in resistance to bovine paratuberculosis in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07487-4.
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Affiliation(s)
- Olivier Ariel
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Jean-Simon Brouard
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Andrew Marete
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Filippo Miglior
- Center of Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G 2W1, Canada.,Canadian Dairy Network, Guelph, ON, N1K 1E5, Canada
| | - Eveline Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, J1M 0C8, Canada.
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Chen SY, Oliveira HR, Schenkel FS, Pedrosa VB, Melka MG, Brito LF. Using imputed whole-genome sequence variants to uncover candidate mutations and genes affecting milking speed and temperament in Holstein cattle. J Dairy Sci 2020; 103:10383-10398. [PMID: 32952011 DOI: 10.3168/jds.2020-18897] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 12/12/2022]
Abstract
Milking speed (MS) and temperament (MT) are 2 workability traits of great importance in dairy cattle production and breeding. This is mainly due to an increased intensification of the worldwide production systems and greater adoption of precision technologies with less human-cattle interaction. Both MS and MT are heritable traits and thus, genomic selection is a promising tool to expedite their genetic progress. However, the genetic architecture and biological mechanisms underlying the phenotypic expression of these traits remain underexplored. In this study, we investigated the association of >5.7 million imputed whole-genome sequence variants with MT and MS in 4,381 and 4,219 North American Holstein cattle, respectively. The statistical analyses were performed using a mixed linear model fitting a polygenic effect. We detected 40 and 35 significant SNPs independently associated with MT and MS, respectively, which were distributed across 26 chromosomes. Eight candidate genes (GRIN3A, KCNJ3, BOSTAUV1R417, BOSTAUV1R419, MAP2K5, KCTD3, GAP43, and LSAMP) were suggested to play an important role in MT as they are involved in biologically relevant pathways, such as glutamatergic synapse, vomeronasal receptor and oxytocin signaling. Within their coding and upstream sequences, we used an independent data set to further detect or validate significantly differentiated SNP between cattle breeds with known differences in MT. There were fewer candidate genes potentially implicated in MS, but immunity-related genes (e.g., BOLA-NC1 and LOC512672), also identified in other populations, were validated in this study. The significant SNP and novel candidate genes identified contribute to a better understanding of the biological mechanisms underlying both traits in dairy cattle. This information will also be useful for the optimization of prediction of genomic breeding values by giving greater weights to SNP located in the genomic regions identified.
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Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, 54022
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907.
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Ramzan F, Gültas M, Bertram H, Cavero D, Schmitt AO. Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations. Genes (Basel) 2020; 11:E892. [PMID: 32764260 PMCID: PMC7465705 DOI: 10.3390/genes11080892] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/28/2020] [Accepted: 08/03/2020] [Indexed: 12/21/2022] Open
Abstract
Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype-phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic loci with weak individual effects on the trait under investigation. Thus, it can be hypothesized that many genomic variants that have a small, however real, effect remain unnoticed in many GWAS approaches. Here, we propose a two-step procedure to address this problem. In a first step, cubic splines are fitted to the test statistic values and genomic regions with spline-peaks that are higher than expected by chance are considered as quantitative trait loci (QTL). Then the SNPs in these QTLs are prioritized with respect to the strength of their association with the phenotype using a Random Forests approach. As a case study, we apply our procedure to real data sets and find trustworthy numbers of, partially novel, genomic variants and genes involved in various egg quality traits.
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Affiliation(s)
- Faisal Ramzan
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Department of Animal Breeding and Genetics, University of Agriculture Faisalabad, 38000 Faisalabad, Pakistan
| | - Mehmet Gültas
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
| | - Hendrik Bertram
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
| | | | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.R.); (M.G.); (H.B.)
- Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, Georg-August University, 37075 Göttingen, Germany
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