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Maskal JM, Pedrosa VB, Rojas de Oliveira H, Brito LF. A comprehensive meta-analysis of genetic parameters for resilience and productivity indicator traits in Holstein cattle. J Dairy Sci 2024; 107:3062-3079. [PMID: 38056564 DOI: 10.3168/jds.2023-23668] [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: 04/26/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023]
Abstract
Selection for resilience indicator (RIND) traits in Holstein cattle is becoming an important breeding objective as the worldwide population is expected to be exposed to increased environmental stressors due to both climate change and changing industry standards. However, genetic correlations between RIND and productivity indicator (PIND) traits, which are already being selected for and have the most economic value, are often unfavorable. As a result, it is necessary to fully understand these genetic relationships when incorporating novel traits into selection indices, so that informed decisions can be made to fully optimize selection for both groups of traits. In the past 2 decades, there have been many estimates of RIND traits published in the literature, albeit in small populations. To provide valuable pooled summary estimates, a random-effects meta-analysis was conducted for heritability and genetic correlation estimates for PIND and RIND traits in worldwide Holstein cattle. In total, 926 heritability estimates for 9 PIND and 27 RIND traits, along with 362 estimates of genetic correlation (PIND × RIND traits) were collected. Resilience indicator traits were grouped into the following subgroups: Metabolic Diseases, Hoof Health, Udder Health, Fertility, Heat Tolerance, Longevity, and Other. Pooled estimates of heritability for PIND traits ranged from 0.201 ± 0.05 (energy-corrected milk) to 0.377 ± 0.06 (protein content), while pooled estimates of heritability for RIND traits ranged from 0.032 ± 0.02 (incidence of lameness, incidence of milk fever) to 0.497 ± 0.05 (measures of body weight). Pooled estimates of genetic correlations ranged from -0.360 ± 0.25 (protein content vs. milk acetone concentration) to 0.535 ± 0.72 (measures of fat-to-protein ratio vs. milk acetone concentration). Additionally, out of 243 potential genetic correlations between PIND and RIND traits that could have been reported, only 40 had enough published estimates to implement the meta-analysis model. Our results confirmed that the interactions between PIND and RIND traits are complex, and all relationships should be evaluated when incorporating novel traits into selection indices. This study provides a valuable reference for breeders looking to incorporate RIND traits for Holstein cattle into selection indices.
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Affiliation(s)
- Jacob M Maskal
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
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Sousa LPB, Pinto LFB, Cruz VAR, Oliveira GA, Rojas de Oliveira H, Chud TS, Pedrosa VB, Miglior F, Schenkel FS, Brito LF. Genome-wide association and functional genomic analyses for various hoof health traits in North American Holstein cattle. J Dairy Sci 2024; 107:2207-2230. [PMID: 37939841 DOI: 10.3168/jds.2023-23806] [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: 05/28/2023] [Accepted: 10/19/2023] [Indexed: 11/10/2023]
Abstract
Hoof diseases are a major welfare and economic issue in the global dairy cattle production industry, which can be minimized through improved management and breeding practices. Optimal genetic improvement of hoof health could benefit from a deep understanding of the genetic background and biological underpinning of indicators of hoof health. Therefore, the primary objectives of this study were to perform genome-wide association studies, using imputed high-density genetic markers data from North American Holstein cattle, for 8 hoof-related traits: digital dermatitis, sole ulcer, sole hemorrhage, white line lesion, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, and toe ulcer, and a hoof health index. De-regressed estimated breeding values from 25,580 Holstein animals were used as pseudo-phenotypes for the association analyses. The genomic quality control, genotype phasing, and genotype imputation were performed using the PLINK (version 1.9), Eagle (version 2.4.1), and Minimac4 software, respectively. The functional genomic analyses were performed using the GALLO R package and the DAVID platform. We identified 22, 34, 14, 22, 28, 33, 24, 43, and 15 significant markers for digital dermatitis, heel horn erosion, interdigital dermatitis, interdigital hyperplasia, sole hemorrhage, sole ulcer, toe ulcer, white line lesion disease, and the hoof health index, respectively. The significant markers were located across all autosomes, except BTA10, BTA12, BTA20, BTA26, BTA27, and BTA28. Moreover, the genomic regions identified overlap with various previously reported quantitative trait loci for exterior, health, meat and carcass, milk, production, and reproduction traits. The enrichment analyses identified 44 significant gene ontology terms. These enriched genomic regions harbor various candidate genes previously associated with bone development, metabolism, and infectious and immunological diseases. These findings indicate that hoof health traits are highly polygenic and influenced by a wide range of biological processes.
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Affiliation(s)
- Luis Paulo B Sousa
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Luis Fernando B Pinto
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Valdecy A R Cruz
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, 40170-110, Brazil
| | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Hinayah Rojas de Oliveira
- 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
| | - Tatiane S Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; PEAK, Madison, WI 53718
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Lactanet Canada, Guelph, ON, N1K 1E5, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Luiz 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.
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Lynch C, Leishman EM, Miglior F, Kelton D, Schenkel FS, Baes CF. Review: Opportunities and challenges for the genetic selection of dairy calf disease traits. Animal 2024:101141. [PMID: 38641517 DOI: 10.1016/j.animal.2024.101141] [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: 10/08/2023] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/21/2024] Open
Abstract
Interest in dairy cow health continues to grow as we better understand health's relationship with production potential and animal welfare. Over the past decade, efforts have been made to incorporate health traits into national genetic evaluations. However, they have focused on the mature cow, with calf health largely being neglected. Diarrhoea and respiratory disease comprise the main illnesses with regard to calf health. Conventional methods to control calf disease involve early separation of calves from the dam and housing calves individually. However, public concern regarding these methods, and growing evidence that these methods may negatively impact calf development, mean the dairy industry may move away from these practices. Genetic selection may be a promising tool to address these major disease issues. In this review, we examined current literature for enhancing calf health through genetics and discussed alternative approaches to improve calf health via the use of epidemiological modelling approaches, and the potential of indirectly selecting for improved calf health through improving colostrum quality. Heritability estimates on the observed scale for diarrhoea ranged from 0.03 to 0.20, while for respiratory disease, estimates ranged from 0.02 to 0.24. The breadth in these ranges is due, at least in part, to differences in disease prevalence, population structure, data editing and models, as well as data collection practices, which should be all considered when comparing literature values. Incorporation of epidemiological theory into quantitative genetics provides an opportunity to better determine the level of genetic variation in disease traits, as it accounts for disease transmission among contemporaries. Colostrum intake is a major determinant of whether a calf develops either respiratory disease or diarrhoea. Colostrum traits have the advantage of being measured and reported on a continuous scale, which removes the issues classically associated with binary disease traits. Overall, genetic selection for improved calf health is feasible. However, to ensure the maximum response, first steps by any industry members should focus efforts on standardising recording practices and encouragement of uploading information to genetic evaluation centres through herd management software, as high-quality phenotypes are the backbone of any successful breeding programme.
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Affiliation(s)
- C Lynch
- Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - E M Leishman
- Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada; Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - F Miglior
- Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada; Lactanet Canada, Guelph, ON N1K-1E5, Canada
| | - D Kelton
- Department of Population Medicine, University of Guelph, Ontario N1G-2W1, Canada
| | - F S Schenkel
- Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada
| | - C F Baes
- Centre for the Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, Canada; Institute of Genetics, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern 3001, Switzerland.
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Wang A, Su G, Brito LF, Zhang H, Shi R, Liu D, Guo G, Wang Y. Investigating the relationship between fluctuations in daily milk yield as resilience indicators and health traits in Holstein cattle. J Dairy Sci 2024; 107:1535-1548. [PMID: 37690717 DOI: 10.3168/jds.2023-23495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/05/2023] [Indexed: 09/12/2023]
Abstract
Disease-related milk losses directly affect dairy herds' profitability and the production efficiency of the dairy industry. Therefore, this study aimed to quantify phenotypic variability in milk fluctuation periods related to diseases and to explore milk fluctuation traits as indicators of disease resilience. By combining high-frequency daily milk yield data with disease records of cows that were treated and recovered from the disease, we estimated milk variability trends within a fixed period around the treatment day of each record for 5 diseases: udder health, reproductive disorders, metabolic disorders, digestive disorders, and hoof health. The average milk yield decreased rapidly from 6 to 8 d before the treatment day for all diseases, with the largest milk reduction observed on the treatment day. Additionally, we assessed the significance of milk fluctuation periods highly related to diseases by defining milk fluctuations as a period of at least 10 consecutive days in which milk yield fell below 90% of the expected milk production values at least once. We defined the development and recovery phases of milk fluctuations using 3,847 milk fluctuation periods related to disease incidences, and estimated genetic parameters of milk fluctuation traits, including milk losses, duration of the fluctuation, variation rate in daily milk yield, and standard deviation of milk deviations for each phase and their genetic correlation with several important traits. In general, the disease-related milk fluctuation periods lasted 21.19 ± 10.36 d with a milk loss of 115.54 ± 92.49 kg per lactation. Compared with the development phase, the recovery phase lasted an average of 3.3 d longer, in which cows produced 11.04 kg less milk and exhibited a slower variation rate in daily milk yield of 0.35 kg/d. There were notable differences in milk fluctuation traits depending on the disease, and greater milk losses were observed when multiple diseases occurred simultaneously. All milk fluctuation traits evaluated were heritable with heritability estimates ranging from 0.01 to 0.10, and moderate to high genetic correlations with milk yield (0.34 to 0.64), milk loss throughout the lactation (0.22 to 0.97), and resilience indicator (0.39 to 0.95). These results indicate that cows with lower milk losses and higher resilience tend to have more stable milk fluctuations, which supports the potential for breeding for more disease-resilient cows based on milk fluctuation traits. Overall, this study confirms the high effect of diseases on milk yield variability and provides insightful information about their relationship with relevant traits in Holstein cattle. Furthermore, this study shows the potential of using high-frequency automatic monitoring of milk yield to assist on breeding practices and health management in dairy cows.
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Affiliation(s)
- Ao Wang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction (MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Hailiang Zhang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction (MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Rui Shi
- Key Laboratory of Animal Genetics, Breeding, and Reproduction (MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Dengke Liu
- Hebei Sunlon Modern Agricultural Technology Co. Ltd., 073000, Dingzhou, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding, and Reproduction (MARA), National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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Lynch C, Schenkel FS, van Staaveren N, Miglior F, Kelton D, Baes CF. Investigating the potential for genetic selection of dairy calf disease traits using management data. J Dairy Sci 2024; 107:1022-1034. [PMID: 37730178 DOI: 10.3168/jds.2023-23780] [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: 05/23/2023] [Accepted: 08/30/2023] [Indexed: 09/22/2023]
Abstract
Genetic selection could be a tool to help improve the health and welfare of calves; however, to date, there is limited research on the genetics of calfhood diseases. This study aimed to understand the current impact of calf diseases, by investigating incidence rates, estimating genetic parameters, and providing industry recommendations to improve calf disease recording practices on farms. Available calf disease data composed of 69,695 Holstein calf disease records for respiratory problems (RESP) and diarrhea (DIAR), from 62,361 calves collected on 1,617 Canadian dairy herds from 2006 to 2021. Single- and multiple-trait analysis using both a threshold and linear animal model for each trait were evaluated. Furthermore, each trait was analyzed using 2 scenarios with respect to minimum disease incidence threshold criterion (herd-year incidence of at least 1% and 5%) to highlight the effect of different filtering thresholds on selection potential. Observed scale heritability estimates for RESP and DIAR ranged from 0.02 to 0.07 across analyses, while estimated genetic correlations between the traits ranged from 0.50 to 0.62. Sires were compared based on their estimated breeding value and their diseased daughter incidence rates. On average, calves born to the bottom 10% of sires were 1.8 times more likely to develop RESP and 1.9 times to develop DIAR compared with daughters born to the top 10% of sires. Results from the current study are promising for the inclusion of both DIAR and RESP in Canadian genetic evaluations. However, for effective genetic evaluation, standardized approaches on data collection and industry outreach to highlight the importance of collecting and uploading this information to herd management software is required. In particular, it is important that the herd management software is accessible to the national milk recording system to allow for use in national genetic evaluation.
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Affiliation(s)
- C Lynch
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - N van Staaveren
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Lactanet Canada, Guelph, ON, N1K 1E5, Canada
| | - D Kelton
- Department of Population Medicine, University of Guelph, Ontario, N1G 2W1, Canada
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, 3001, Switzerland.
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van Staaveren N, Hyland E, Houlahan K, Lynch C, Miglior F, Kelton DF, Schenkel FS, Baes CF. Recording of calf diseases for potential use in breeding programs: a case study on calf respiratory illness and diarrhea. CANADIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1139/cjas-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Calf diseases remain a challenge for dairy producers from both an economic and welfare perspective. Genetically selecting for disease resistance in calves is a promising approach that could contribute to sustainable dairy farming. Genetic evaluations, however, require well-defined and consistently recorded phenotypes to be successful. Therefore, this study aimed to understand the current state of calf disease recording on Ontario farms. Calf disease records of respiratory illness and diarrhea were available from the national milk recording organization (Lactanet Canada, Guelph, Ontario, Canada) from 2009 to 2020. A case study was conducted to describe calf disease diagnoses and recording practices by surveying a subset of 13 Ontario dairy producers. The percentage of milk recorded farms that recorded calf respiratory illness and calf diarrhea increased from 2.6% in 2009 to 11.1% in 2020. Potential sources of data loss were identified along the information chain from farm to genetic evaluation database. Clear definitions and thresholds to diagnose calf disease, standard operating procedures for data recording, as well as a data transfer pipeline, which includes exchange formats, are needed to facilitate the inclusion of calf health traits in genetic evaluations.
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Li B, Barden M, Kapsona V, Sánchez-Molano E, Anagnostopoulos A, Griffiths BE, Bedford C, Dai X, Coffey M, Psifidi A, Oikonomou G, Banos G. Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models. Genet Sel Evol 2023; 55:16. [PMID: 36899300 PMCID: PMC9999328 DOI: 10.1186/s12711-023-00784-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/08/2023] [Indexed: 03/12/2023] Open
Abstract
BACKGROUND Lameness in dairy cattle is primarily caused by foot lesions including the claw horn lesions (CHL) of sole haemorrhage (SH), sole ulcers (SU), and white line disease (WL). This study investigated the genetic architecture of the three CHL based on detailed animal phenotypes of CHL susceptibility and severity. Estimation of genetic parameters and breeding values, single-step genome-wide association analyses, and functional enrichment analyses were performed. RESULTS The studied traits were under genetic control with a low to moderate heritability. Heritability estimates of SH and SU susceptibility on the liability scale were 0.29 and 0.35, respectively. Heritability of SH and SU severity were 0.12 and 0.07, respectively. Heritability of WL was relatively lower, indicating stronger environmental influence on the presence and development of WL than the other two CHL. Genetic correlations between SH and SU were high (0.98 for lesion susceptibility and 0.59 for lesion severity), whereas genetic correlations of SH and SU with WL also tended to be positive. Candidate quantitative trait loci (QTL) were identified for all CHL, including some on Bos taurus chromosome (BTA) 3 and 18 with potential pleiotropic effects associated with multiple foot lesion traits. A genomic window of 0.65 Mb on BTA3 explained 0.41, 0.50, 0.38, and 0.49% of the genetic variance for SH susceptibility, SH severity, WL susceptibility, and WL severity, respectively. Another window on BTA18 explained 0.66, 0.41, and 0.70% of the genetic variance for SH susceptibility, SU susceptibility, and SU severity, respectively. The candidate genomic regions associated with CHL harbour annotated genes that are linked to immune system function and inflammation responses, lipid metabolism, calcium ion activities, and neuronal excitability. CONCLUSIONS The studied CHL are complex traits with a polygenic mode of inheritance. Most traits exhibited genetic variation suggesting that animal resistance to CHL can be improved with breeding. The CHL traits were positively correlated, which will facilitate genetic improvement for resistance to CHL as a whole. Candidate genomic regions associated with lesion susceptibility and severity of SH, SU, and WL provide insights into a global profile of the genetic background underlying CHL and inform genetic improvement programmes aiming at enhancing foot health in dairy cattle.
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Affiliation(s)
- Bingjie Li
- Department of Animal and Veterinary Sciences, The Roslin Institute Building, Scotland's Rural College (SRUC), Easter Bush, Midlothian, EH25 9RG, UK.
| | - Matthew Barden
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Vanessa Kapsona
- Department of Animal and Veterinary Sciences, The Roslin Institute Building, Scotland's Rural College (SRUC), Easter Bush, Midlothian, EH25 9RG, UK
| | - Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Alkiviadis Anagnostopoulos
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Bethany Eloise Griffiths
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Cherril Bedford
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Xiaoxia Dai
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Mike Coffey
- Department of Animal and Veterinary Sciences, The Roslin Institute Building, Scotland's Rural College (SRUC), Easter Bush, Midlothian, EH25 9RG, UK
| | - Androniki Psifidi
- Department of Clinical Science and Services, Royal Veterinary College, Hawkshead Lane, Hatfield, Hertfordshire, AL9 7TA, UK
| | - Georgios Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, The Roslin Institute Building, Scotland's Rural College (SRUC), Easter Bush, Midlothian, EH25 9RG, UK.
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Barden M, Anagnostopoulos A, Griffiths BE, Li B, Bedford C, Watson C, Psifidi A, Banos G, Oikonomou G. Genetic parameters of sole lesion recovery in Holstein cows. J Dairy Sci 2023; 106:1874-1888. [PMID: 36710182 PMCID: PMC9947741 DOI: 10.3168/jds.2022-22064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/10/2022] [Indexed: 01/29/2023]
Abstract
Sole hemorrhage and sole ulcers, referred to as sole lesions, are important causes of lameness in dairy cattle. The objective of this study was to estimate the genetic parameters of a novel trait reflecting how well cows recovered from sole lesions and the genetic correlation of this trait with overall susceptibility to sole lesions. A cohort of Holstein dairy cows was prospectively enrolled on 4 farms and assessed at 4 timepoints: before calving, immediately after calving, in early lactation, and in late lactation. At each timepoint, sole lesions were recorded at the claw level by veterinary surgeons and used to define 2 binary traits: (1) susceptibility to sole lesions-whether animals were affected with sole lesions at least once during the study or were unaffected at every assessment, and (2) sole lesion recovery-whether sole lesions healed between early and late lactation. Animals were genotyped and pedigree details extracted from the national database. Analyses were conducted with BLUPF90 software in a single-step framework; genetic parameters were estimated from animal threshold models using Gibbs sampling. The genetic correlation between both traits was approximated as the correlation between genomic estimated breeding values, adjusting for their reliabilities. A total of 2,025 animals were used to estimate the genetic parameters of sole lesion susceptibility; 44% of animals recorded a sole lesion at least once during the study period. The heritability of sole lesion susceptibility, on the liability scale, was 0.25 (95% highest density interval = 0.16-0.34). A total of 498 animals were used to estimate the genetic parameters of sole lesion recovery; 71% of animals had recovered between the early and late lactation assessments. The heritability of sole lesion recovery, on the liability scale, was 0.27 (95% highest density interval = 0.02-0.52). The approximate genetic correlation between each trait was -0.11 (95% confidence interval = -0.20 to -0.02). Our results indicate that recovery from sole lesions is heritable. If this finding is corroborated in further studies, it may be possible to use selective breeding to reduce the frequency of chronically lame cows. As sole lesion recovery appears to be weakly genetically related to sole lesion susceptibility, successful genetic improvement of sole lesion recovery would benefit from selection on this trait directly.
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Affiliation(s)
- Matthew Barden
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom
| | - Alkiviadis Anagnostopoulos
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom
| | - Bethany E. Griffiths
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom
| | - Bingjie Li
- Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Cherry Bedford
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom
| | - Chris Watson
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom
| | - Androniki Psifidi
- Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, AL9 7TA, United Kingdom
| | - Georgios Banos
- Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - Georgios Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, CH64 7TE, United Kingdom.
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Ferrari V, Visentin G, van Kaam J, Penasa M, Marusi M, Finocchiaro R, Cassandro M. Genetic and nongenetic variation of heifer fertility in Italian Holstein cattle. JDS COMMUNICATIONS 2022; 4:35-39. [PMID: 36713130 PMCID: PMC9873663 DOI: 10.3168/jdsc.2022-0270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022]
Abstract
Excellent fertility performance is important to maximize farmers' profit and to reduce the number of culled animals. Although female fertility of adult cows has been included in Italian Holstein breeding objectives since 2009, little has been done to quantify genetic variation of heifer fertility characteristics so far. The aim of the present study was to estimate genetic parameters of 4 fertility traits in nulliparous Italian Holstein heifers and to develop an aggregate selection index to improve heifer fertility. Data were retrieved from the national fertility database and included information on insemination, calving, and pregnancy diagnosis dates. The investigated phenotypes (mean ± standard deviation) were age at first insemination (AFI, mo; 17.25 ± 2.89), nonreturn rate at 56 d from the first insemination (NRR56, binary; 0.78 ± 0.41), conception rate at first insemination (CR, binary; 0.61 ± 0.49), and interval from first to last insemination (IFL, d; 26.09 ± 51.85). Genetic parameters were estimated using a 4-trait animal model that included the following fixed effects: herd-year of birth and month of birth for AFI, and herd-year-season of birth and month-year of insemination for IFL, NRR56, and CR; the animal additive genetic effect (fitted to the pedigree-based relationship matrix) was considered as a random term. An aggregate index was developed from the estimated additive genetic (co)variance matrix by considering CR as the breeding goal and AFI, NRR56, and IFL as selection criteria. Heritability estimates from average covariance matrices ranged from 0.012 (CR) to 0.015 (IFL), with the exception of AFI (0.071). Conception rate at first insemination was strongly correlated with both IFL (-0.730) and NRR56 (0.668), and weakly to AFI (-0.065), and the relative emphasis placed on each selection criteria in the aggregate index was 10%, 47%, and 43% for AFI, IFL, and NRR56, respectively. The results of the present study suggest that heifer fertility should be considered as an additional trait in the breeding objectives of Italian Holstein.
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Affiliation(s)
- V. Ferrari
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, Via Bergamo 292, 26100, Cremona (CR), Italy,Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - G. Visentin
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia (BO), Italy
| | - J.B.C.H.M. van Kaam
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, Via Bergamo 292, 26100, Cremona (CR), Italy
| | - M. Penasa
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
| | - M. Marusi
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, Via Bergamo 292, 26100, Cremona (CR), Italy
| | - R. Finocchiaro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, Via Bergamo 292, 26100, Cremona (CR), Italy,Corresponding author
| | - M. Cassandro
- Associazione Nazionale Allevatori della Razza Frisona, Bruna e Jersey Italiana, Via Bergamo 292, 26100, Cremona (CR), Italy,Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell'Università 16, 35020, Legnaro (PD), Italy
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10
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Sölzer N, May K, Yin T, König S. Genomic analyses of claw disorders in Holstein cows: Genetic parameters, trait associations, and genome-wide associations considering interactions of SNP and heat stress. J Dairy Sci 2022; 105:8218-8236. [PMID: 36028345 DOI: 10.3168/jds.2022-22087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/31/2022] [Indexed: 11/19/2022]
Abstract
The aim of the present study was an in-depth genomic analysis to understand the genomic mechanisms of the 3 claw disorders dermatitis digitalis (DD), interdigital hyperplasia (HYP), and sole ulcer (SU). In this regard, we estimated genetic parameters based on genomic relationship matrices, performed genome-wide association studies, annotated potential candidate genes, and inferred genetic associations with breeding goal traits considering the most important chromosomal segments. As a further novelty of this study, we inferred possible SNP × heat stress interactions for claw disorders. The study consisted of 17,264 first-lactation Holstein Friesian cows kept in 50 large-scale contract herds. The disease prevalence was 15.96, 2.36, and 8.20% for DD, HYP, and SU, respectively. The remaining breeding goal traits consisted of type traits of the feet and leg composite, female fertility, health traits, and 305-d production traits. The final genotype data set included 44,474 SNPs from the 17,264 genotyped cows. Heritabilities for DD, HYP, and SU were estimated in linear and threshold models considering the genomic relationship matrix (G matrix). Genetic correlations with breeding goal traits based on G were estimated in a series of bivariate linear models, which were verified via SNP effect correlations for specific chromosome segments (i.e., segments harboring potential candidate genes for DD, HYP, and SU). Genome-wide association studies were performed for all traits in a case-control design by applying a single SNP linear mixed model. Furthermore, for DD, HYP, and SU, we modeled SNP × heat stress interactions in genome-wide association studies. Single nucleotide polymorphism-based heritabilities were 0.04 and 0.08 for DD, 0.03 and 0.10 for SU, and 0.03 and 0.23 for HYP from linear and threshold models, respectively. The genetic correlations between DD, HYP, and SU with conformation traits from the feet and leg composite were positive throughout, indicating the value of indirect selection on conformation traits to improve claw health. Genetic correlations between DD, SU, and HYP with other breeding goal traits indicated impaired female fertility, impaired udder health status, and productivity decline of diseased cows. Genetic correlations among DD, SU, and HYP were moderate to large, indicating that different claw disorders have similar genetic mechanisms. Nevertheless, we identified disease-specific potential candidate genes, and genetic associations based on the surrounding SNPs partly differed from the genetic correlations. Especially for candidate genes contributing to 2 traits simultaneously, correlations based on SNP effects from the respective chromosome segment were close to 1 or to -1. In this regard, we annotated the candidate genes KRT33A and KRT33B for HYP and DD, KIF27 for HYP and calving to first insemination, and MAN1A1 for SU and the production traits. For SNP × heat stress interactions, we identified significant SNPs on BTA 2, 4, 5, 7, 8, 9, 13, 22, 25, and 28, and we annotated the potential candidate genes FSIP2, CLCN1, ADGRV1, DOP1A, THBD, and RHOBTB1. Results indicate gene-specific mechanisms of the claw disorders only in specific environments.
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Affiliation(s)
- Niklas Sölzer
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Giessen, 35390 Giessen, Germany.
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11
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Zhang H, Wang K, An T, Zhu L, Chang Y, Lou W, Liu L, Guo G, Liu A, Su G, Brito LF, Wang Y. Genetic parameters for dairy calf and replacement heifer wellness traits and their association with cow longevity and health indicators in Holstein cattle. J Dairy Sci 2022; 105:6749-6759. [PMID: 35840408 DOI: 10.3168/jds.2021-21450] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/19/2022] [Indexed: 11/19/2022]
Abstract
High mortality and involuntary culling rates cause great economic losses to the worldwide dairy cattle industry. However, there is low emphasis on wellness traits in replacement animals (dairy calves and replacement heifers) during their development stages in modern dairy cattle breeding programs. Therefore, the main objectives of this study were to estimate genetic parameters of wellness traits in replacement cattle (replacement wellness traits) and obtain their genetic correlations with 12 cow health and longevity traits in the Chinese Holstein population. Seven replacement wellness traits were analyzed, including birth weight, survival from 3 to 60 d (Sur1), survival from 61 to 365 d (Sur2), survival from 366 d to the first calving (Sur3), calf diarrhea, calf pneumonia, and calf serum total protein (STP). Single and bivariate animal models were employed to estimate (co)variance components using the data from 189,980 Holstein cattle. The genetic correlations between replacement wellness traits and cow longevity, health traits were calculated by employing bivariate models, including 6 longevity traits and 6 health traits (clinical mastitis, metritis, ketosis, displaced abomasum, milk fever, and hoof health or hoof disease). The estimated heritabilities (± SE) were 0.335 (± 0.008), 0.088 (± 0.005), 0.166 (± 0.006), 0.102 (±0 .006), 0.048 (± 0.003), 0.063 (± 0.004), and 0.170 (± 0.019) for birth weight, Sur1, Sur2, Sur3, pneumonia, diarrhea, and STP, respectively. The majority of the genetic correlations among the 7 replacement wellness traits were negligible. The genetic correlations among Sur1, Sur2, and Sur3 ranged from 0.112 (Sur1 and Sur3) to 0.445 (Sur1 and Sur2) when fitting a linear model (estimates in the observed scale), and from 0.560 (Sur1 and Sur3) to 0.773 (Sur1 and Sur2) when fitting a threshold model (estimates in the liability scale). The genetic correlations between replacement wellness and cow longevity were low (absolute value lower than 0.30), but some of them were significantly different from zero. Compared with other replacement wellness traits, Sur3 and STP had relatively high genetic correlations with cow longevity. Replacement wellness traits are heritable and can be improved through direct genetic and genomic selection. The results from the current study will contribute for better balancing dairy cattle breeding goals to genetically improve dairy cattle wellness in the period from birth to first calving.
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Affiliation(s)
- Hailiang Zhang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kai Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao An
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Zhu
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yao Chang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Wenqi Lou
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lin Liu
- Beijing Dairy Center, Beijing, 100192, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd., Beijing, 100176, China
| | - Aoxing Liu
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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12
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Barden M, Anagnostopoulos A, Griffiths BE, Bedford C, Winters M, Li B, Coffey M, Psifidi A, Banos G, Oikonomou G. Association between a genetic index for lameness resistance and the incidence of claw horn lesions in Holstein cows. Vet Rec 2022; 191:e1632. [PMID: 35468242 DOI: 10.1002/vetr.1632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/15/2022] [Accepted: 03/23/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND This study aimed to determine the association between the lameness advantage genetic index and four outcomes: sole haemorrhage (SH), sole ulcers (SU), white line lesions (WL), and lameness during mobility scoring. METHODS We enrolled 2352 Holstein cows from four predominantly housed dairy herds in the UK. Cows were mobility scored and foot lesions recorded at four time points from before calving to late lactation. Cows were genotyped and genetic indexes were assigned to each cow following national genetic evaluations. Lameness records and genetic indexes were matched for 2107 cows. Four separate multivariable logistic regression models, which included farm and parity as covariables, were used to quantify the association between the lameness advantage index and whether animals were affected by SH, SU, WL, or lameness. RESULTS The odds ratios (95% confidence intervals) for one-point increases in the lameness advantage index were 0.79 (0.72-0.86), 0.68 (0.59-0.78), 0.94 (0.84-1.04), and 0.82 (0.74-0.91) for SH, SU, WL, and lameness, respectively. The same trends were present when the sire's lameness advantage index was evaluated in place of the animal's own, although the strength of this association was generally weaker. CONCLUSION The lameness advantage index is associated with SH, SU, and lameness, therefore selection on the lameness advantage index could be considered in herds aiming to reduce lameness. Where genomic testing of heifers is not conducted, sire lameness advantage index may still be effective to reduce SH and SU incidence.
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Affiliation(s)
- Matthew Barden
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, UK
| | - Alkiviadis Anagnostopoulos
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, UK
| | - Bethany E Griffiths
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, UK
| | - Cherril Bedford
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, UK
| | - Marco Winters
- Agriculture and Horticulture Development Board, Stoneleigh Park, Kenilworth, UK
| | - Bingjie Li
- Animal & Veterinary Sciences, SRUC, Roslin Institute Building, Easter Bush, Midlothian, UK
| | - Mike Coffey
- Animal & Veterinary Sciences, SRUC, Roslin Institute Building, Easter Bush, Midlothian, UK
| | - Androniki Psifidi
- Department of Clinical Science and Services, Royal Veterinary College, North Mymms, Hertfordshire, UK
| | - Georgios Banos
- Animal & Veterinary Sciences, SRUC, Roslin Institute Building, Easter Bush, Midlothian, UK
| | - Georgios Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Leahurst Campus, Liverpool, UK
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13
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Lai E, Danner AL, Famula TR, Oberbauer AM. Pleiotropic Loci Associated With Foot Disorders and Common Periparturient Diseases in Holstein Cattle. Front Genet 2021; 12:742934. [PMID: 34938311 PMCID: PMC8685441 DOI: 10.3389/fgene.2021.742934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Lameness is an animal welfare issue that incurs substantial financial and environmental costs. This condition is commonly caused by digital dermatitis (DD), sole ulcers (SU), and white line disease (WLD). Susceptibility to these three foot disorders is due in part to genetics, indicating that genomic selection against these foot lesions can be used to reduce lameness prevalence. It is unclear whether selection against foot lesions will lead to increased susceptibility to other common diseases such as mastitis and metritis. Thus, the aim of this study was to determine the genetic correlation between causes of lameness and other common health disorders to identify loci contributing to the correlation. Genetic correlation estimates between SU and DD and between SU and WLD were significantly different from zero (p < 0.05), whereas estimates between DD and mastitis, DD and milk fever, and SU and metritis were suggestive (p < 0.1). All five of these genetic correlation estimates were positive. Two-trait genome-wide association studies (GWAS) for each of these five pairs of traits revealed common regions of association on BTA1 and BTA8 for pairs that included DD or SU as one of the traits, respectively. Other regions of association were unique to the pair of traits and not observed in GWAS for other pairs of traits. The positive genetic correlation estimates between foot disorders and other health disorders imply that selection against foot disorders may also decrease susceptibility to other health disorders. Linkage disequilibrium blocks defined around significant and suggestive SNPs from the two-trait GWAS included genes and QTL that were functionally relevant, supporting that these regions included pleiotropic loci.
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Affiliation(s)
| | | | | | - Anita M. Oberbauer
- Animal Science Department, University of California, Davis, Davis, CA, United States
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14
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Basiel BL, Hardie LC, Heins BJ, Dechow CD. Genetic parameters and genomic regions associated with horn fly resistance in organic Holstein cattle. J Dairy Sci 2021; 104:12724-12740. [PMID: 34482984 DOI: 10.3168/jds.2021-20366] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022]
Abstract
Horn flies (Haematobia irritans [L.]) contribute to major economic losses of pastured cattle operations, particularly in organic herds because of limitations on control methods that can be used. The objectives of this research were to determine if resistance to horn flies is a heritable trait in organic Holstein cattle, determine associations with yield traits, and to detect genomic regions associated with fly infestation. Observations of fly load were recorded from 1,667 pastured Holstein cows, of which 640 were genotyped, on 13 organic dairies across the United States. Fly load score was determined using a 0 to 4 scale based on fly coverage from chine to loin on one side of the body, with 0 indicating few to no flies and 4 indicating high infestation. The scoring system was validated by counting flies from photographs taken at the time of scoring from 252 cows. To mitigate the effect of our data structure on potential selection bias effects on genetic parameter estimates, survival to subsequent lactations of scored animals and herd-mates that had been culled before the trial was accounted for as the trait stayability. Genetic parameters were estimated using single-step genomic analysis with 3-trait mixed models that included fly score, stayability, and a third phenotype. Model effects differed by variable, but fixed effects generally included a contemporary group, scorer, parity, and stage of lactation; random effects included animal, permanent environment, and residual error. A genome-wide association study was performed by decomposing estimated breeding values into marker effects to detect significant genomic regions associated with fly score. The rank correlation between the subjective fly score and the objective count was 0.79. The average heritability of fly score (± standard error) estimated across multiple models was 0.25 ± 0.04 when a known Holstein maternal grandsire was required and 0.19 ± 0.03 when only a known Holstein sire was required. Genetic correlation estimates with yield traits were moderately positive, but a greater fly load was associated with reduced yield after accounting for genetic merit. Lower fly loads were associated with white coat coloration; a significant genomic region on Bos taurus autosome 6 was identified that contains the gene KIT, which was the most plausible candidate gene for fly resistance because of its role in coat pattern and coloration. The magnitude of heritable variation in fly infestation is similar to other traits included in selection programs, suggesting that producers can select for resistance to horn flies.
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Affiliation(s)
- B L Basiel
- Department of Animal Science, Pennsylvania State University, University Park 16802
| | - L C Hardie
- Department of Animal Science, Pennsylvania State University, University Park 16802
| | - B J Heins
- Department of Animal Science, University of Minnesota, St. Paul 55108
| | - C D Dechow
- Department of Animal Science, Pennsylvania State University, University Park 16802.
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15
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Oliveira Junior GA, Schenkel FS, Alcantara L, Houlahan K, Lynch C, Baes CF. Estimated genetic parameters for all genetically evaluated traits in Canadian Holsteins. J Dairy Sci 2021; 104:9002-9015. [PMID: 33934872 DOI: 10.3168/jds.2021-20227] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022]
Abstract
Genetic improvement is a crucial tool to deal with the increasing demand for high quality, sustainably produced dairy. Breeding programs are based on genetic parameters, such as heritability and genetic correlations, for economically important traits in a population. In this study, we estimated population genetic parameters and genetic trends for 67 traits evaluated on heifers and first-lactation Canadian Holstein cows. The data consisted of approximately 500,000 records with pedigree information collected from 1980 to 2019. Genetic parameters were estimated using bivariate linear animal models under a Bayesian approach. Analyses for the 67 traits resulted in 2,211 bivariate combinations, from which the estimated genetic parameters are reported here. The most highly heritable traits were fat percent (0.66) and protein percent (0.69), followed by stature (0.47). Lowest heritabilities (0.01) were observed for disease-related traits, such as lameness and toe ulcer, and calf survival. The genetic correlations between gestation length, calf size, and calving ease measured on both heifer and cows were close to unity. On the other hand, traits such as body condition score and pin width, cystic ovaries and sole ulcer, rear teat placement, and toe ulcer were genetically unrelated. This study reports genetic parameters that have not been previously published for Canadian Holstein cows, and provides updates of those previously estimated. These estimates are useful for building new indexes, updating existing selection indexes, and for predicting correlated responses due to inclusion of novel traits in the breeding programs.
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Affiliation(s)
- G A Oliveira Junior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - L Alcantara
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - K Houlahan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - C Lynch
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - C F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, 3001, Switzerland
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16
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Butty AM, Chud TCS, Cardoso DF, Lopes LSF, Miglior F, Schenkel FS, Cánovas A, Häfliger IM, Drögemüller C, Stothard P, Malchiodi F, Baes CF. Genome-wide association study between copy number variants and hoof health traits in Holstein dairy cattle. J Dairy Sci 2021; 104:8050-8061. [PMID: 33896633 DOI: 10.3168/jds.2020-19879] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/31/2021] [Indexed: 01/06/2023]
Abstract
Genome-wide association studies based on SNP have been completed for multiple traits in dairy cattle; however, copy number variants (CNV) could add genomic information that has yet to be harnessed. The objectives of this study were to identify CNV in genotyped Holstein animals and assess their association with hoof health traits using deregressed estimated breeding values as pseudophenotypes. A total of 23,256 CNV comprising 1,645 genomic regions were identified in 5,845 animals. Fourteen genomic regions harboring structural variations, including 9 deletions and 5 duplications, were associated with at least 1 of the studied hoof health traits. This group of traits included digital dermatitis, interdigital dermatitis, heel horn erosion, sole ulcer, white line lesion, sole hemorrhage, and interdigital hyperplasia; no regions were associated with toe ulcer. Twenty candidate genes overlapped with the regions associated with these traits including SCART1, NRXN2, KIF26A, GPHN, and OR7A17. In this study, an effect on infectious hoof lesions could be attributed to the PRAME (Preferentially Expressed Antigen in Melanoma) gene. Almost all genes detected in association with noninfectious hoof lesions could be linked to known metabolic disorders. The knowledge obtained considering information of associated CNV to the traits of interest in this study could improve the accuracy of estimated breeding values. This may further increase the genetic gain for these traits in the Canadian Holstein population, thus reducing the involuntary animal losses due to lameness.
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Affiliation(s)
- Adrien M Butty
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Tatiane C S Chud
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Diercles F Cardoso
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Lucas S F Lopes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Filippo Miglior
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Flavio S Schenkel
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Angela Cánovas
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Irene M Häfliger
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland
| | - Cord Drögemüller
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2R3, Canada
| | - Francesca Malchiodi
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada; The Semex Alliance, Guelph, Ontario N1H 6J2, Canada
| | - Christine F Baes
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, Ontario N1G 2W1, Canada; Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3012, Switzerland.
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17
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Luo H, Brito LF, Li X, Su G, Dou J, Xu W, Yan X, Zhang H, Guo G, Liu L, Wang Y. Genetic parameters for rectal temperature, respiration rate, and drooling score in Holstein cattle and their relationships with various fertility, production, body conformation, and health traits. J Dairy Sci 2021; 104:4390-4403. [PMID: 33685707 DOI: 10.3168/jds.2020-19192] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/03/2020] [Indexed: 12/12/2022]
Abstract
Genetic selection for improved climatic resilience is paramount to increase the long-term sustainability of high-producing dairy cattle, especially in face of climate change. Various physiological indicators, such as rectal temperature (RT), respiration rate score (RR), and drooling score (DS), can be used to genetically identify animals with more effective coping mechanisms in response to heat stress events. In this study, we investigated genetic parameters for RT, RR (score from 1-3), and DS (score from 1-3). Furthermore, we assessed the genetic relationship among these indicators and other economically important traits for the dairy cattle industry. After data editing, 59,265 (RT), 30,290 (RR), and 30,421 (DS) records from 13,592 lactating Holstein cows were used for the analyses. Variance components were estimated based on a multiple-trait repeatability animal model. The heritability ± standard error estimate for RT, RR, and DS was 0.06 ± 0.01, 0.04 ± 0.01, and 0.02 ± 0.01, respectively, whereas their repeatability was 0.19, 0.14, and 0.14, respectively. Moderate genetic correlations of RR with RT and DS (0.26 ± 0.11 and 0.25 ± 0.16) and nonsignificant correlation between RT and DS (-0.11 ± 0.14) were observed. Furthermore, the approximate genetic correlations between RT, RR, and DS with 12 production, 29 conformation, 5 fertility and reproduction, 5 health, and 9 longevity-indicator traits were assessed. In general, the approximate genetic correlations calculated were low to moderate. In summary, 3 physiological indicators of heat stress response were measured in a large number of animals and shown to be lowly heritable. There is a value in developing a selection index including all the 3 indicators to improve heat tolerance in dairy cattle. All the unfavorable genetic relationships observed between heat tolerance and other economically important traits can be accounted for in a selection index to enable improved climatic resilience while also maintaining or increasing productivity in Holstein cattle.
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Affiliation(s)
- H Luo
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - X Li
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - G Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Tjele 8830, Denmark
| | - J Dou
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - W Xu
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - X Yan
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - H Zhang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - G Guo
- Beijing Sunlon Livestock Development Co. Ltd., 100029, Beijing, China
| | - L Liu
- Beijing Dairy Cattle Center, 100192, Beijing, China
| | - Y Wang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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18
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Parker Gaddis KL, VanRaden PM, Cole JB, Norman HD, Nicolazzi E, Dürr JW. Symposium review: Development, implementation, and perspectives of health evaluations in the United States. J Dairy Sci 2020; 103:5354-5365. [PMID: 32331897 DOI: 10.3168/jds.2019-17687] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 02/29/2020] [Indexed: 12/28/2022]
Abstract
The rate at which new traits are being developed is increasing, leading to an expanding number of evaluations provided to dairy producers, especially for functional traits. This review will discuss the development and implementation of genetic evaluations for direct health traits in the United States, as well as potential future developments. Beginning in April 2018, routine official genomic evaluations for 6 direct health traits in Holsteins were made available to US producers from the Council on Dairy Cattle Breeding (Bowie, MD). Traits include resistance to milk fever, displaced abomasum, ketosis, clinical mastitis, metritis, and retained placenta. These health traits were included in net merit indices beginning in August 2018, with a total weight of approximately 2%. Previously, improvement of cow health was primarily made through changes to management practices or genetic selection on indicator traits, such as somatic cell score, productive life, or livability. Widespread genomic testing now allows for accelerated improvement of traits with low heritabilities such as health; however, phenotypes remain essential to the success of genomic evaluations. Establishment and maintenance of data pipelines is a critical component of health trait evaluations, as well as appropriate data quality control standards. Data standardization is a necessary process when multiple data sources are involved. Model refinement continues, including implementation of variance adjustments beginning with the April 2019 evaluation. Mastitis evaluations are submitted to Interbull along with somatic cell score for international validation and evaluation of udder health. Additional areas of research include evaluation of other breeds for direct health traits, use of multiple-trait models, and evaluations for additional functional traits such as calf health and feed efficiency. Future developments will require new and continued cooperation among numerous industry stakeholders. There is more information available than ever before with which to make better selection decisions; however, this also makes it increasingly important to provide accurate and unbiased information.
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Affiliation(s)
| | - P M VanRaden
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - J B Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - H D Norman
- Council on Dairy Cattle Breeding, Bowie, MD 20716
| | - E Nicolazzi
- Council on Dairy Cattle Breeding, Bowie, MD 20716
| | - J W Dürr
- Council on Dairy Cattle Breeding, Bowie, MD 20716
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19
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Malchiodi F, Jamrozik J, Christen AM, Fleming A, Kistemaker GJ, Richardson C, Daniel V, Kelton DF, Schenkel FS, Miglior F. Symposium review: Multiple-trait single-step genomic evaluation for hoof health. J Dairy Sci 2020; 103:5346-5353. [PMID: 32331881 DOI: 10.3168/jds.2019-17755] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/17/2020] [Indexed: 11/19/2022]
Abstract
Hoof lesions represent an important issue in modern dairy herds, with reported prevalence in different countries ranging from 40 to 70%. This high prevalence of hoof lesions has both economic and social consequences, resulting in increased labor expenses and decreasing animal production, longevity, reproduction, health, and welfare. Therefore, a key goal of dairy herds is to reduce the incidence of hoof lesions, which can be achieved both by improving management practices and through genetic selection. The Canadian dairy industry has recently released a hoof health sub-index. This national genetic evaluation program for hoof health was achieved by creating a centralized data collection system that routinely transfers data recorded by hoof trimmers into a coherent and sustainable national database. The 8 most prevalent lesions (digital dermatitis, interdigital dermatitis, interdigital hyperplasia, heel horn erosion, sole hemorrhage, sole ulcer, toe ulcer, and white line lesion) in Canada are analyzed with a multiple-trait model using a single-step genomic BLUP method. Estimated genomic breeding values for each lesion are combined into a sub-index according to their economic value and prevalence. In addition, data recorded within this system were used to create an interactive management report for dairy producers by Canadian DHI, including the prevalence of lesions on farm, their trends over time, and benchmarks with provincial and national averages.
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Affiliation(s)
- F Malchiodi
- Semex Alliance, Guelph, ON, N1H 6J2, Canada; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 1Y2, Canada.
| | - J Jamrozik
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 1Y2, Canada; Lactanet Canada, Guelph, ON N1K 1E5, Canada
| | - A-M Christen
- Lactanet Canada, Sainte-Anne-de-Bellevue, QC H9X 3R4, Canada
| | - A Fleming
- Lactanet Canada, Guelph, ON N1K 1E5, Canada
| | | | - C Richardson
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria 3086, Australia
| | - V Daniel
- Vic's Custom Clips, Arva, ON N0M 1C0, Canada
| | - D F Kelton
- Department of Population Medicine, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 1Y2, Canada
| | - F S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 1Y2, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 1Y2, Canada
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20
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Suchocki T, Egger-Danner C, Schwarzenbacher H, Szyda J. Two-stage genome-wide association study for the identification of causal variants underlying hoof disorders in cattle. J Dairy Sci 2020; 103:4483-4494. [PMID: 32229114 DOI: 10.3168/jds.2019-17542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/11/2019] [Indexed: 11/19/2022]
Abstract
Feet and legs disorders influence dairy cattle breeding by their effect on animal welfare, economic losses due to lower production and fertility, costs of treatment, and problems with herd management. In our study, we estimated heritabilities and performed a 2-step GWAS for 3 traits describing hoof health: hoof health status defined by a veterinarian (HSV), hoof health status defined by a claw trimmer (HSC), and the total number of hoof disorders (NHD), scored in 1,998 Fleckvieh and 979 Braunvieh cows. The individuals were genotyped with a high-density (HD) panel consisting of 76,934 SNP. For significant genomic regions, the SNP information was enhanced by SNP imputed from the whole-genome sequence of Fleckvieh and Braunvieh bulls from the 1000 Bulls Genome project. The heritabilities were estimated to be 0.035 for HSV, 0.249 for HSC, and 0.279 for NHD. Based on the first-stage GWAS with SNP from the HD panel, 7 significant genomic regions on 6 chromosomes were defined: (1) 120 SNP spanning 15,522 bp on BTA1, including the TOPBP1 gene; (2) 4,139 SNP spanning 1,426,046 bp on BTA7, including the RIOK2 and RGMB genes; (3) 167 SNP spanning 167,352 bp on BTA13, including the C13H20orf194 gene; (4) 2 regions on BTA14, one harboring 1,071 SNP spanning 380,024 bp, including RRM2B and NCALD, and the other comprising 632 SNP spanning 385,111 bp, including STK3; (5) 328 SNP on BTA15, spanning 235,567 bp between FAM168A and PLEKHB1; and (6) 1,549 SNP on BTA22, spanning 596,101 bp in the neighborhood of PTPRG. Then, we conducted a second-stage GWAS based on SNP from whole-genome sequences within the significant regions obtained in the first stage of the analysis. For HSV, the highest additive effect was estimated for 23 SNP located within a region on BTA15, close to FAM168A, corresponding to a predicted gene sequence. For HSC, the highest additive effect was attributed to 44 SNP located within a region of BTA22 corresponding to 4 predicted gene sequences, with rs135082893 within a sequence encoding a microRNA. Another potential causal mutation for HSC was rs134142607 on BTA13, within the exon of C13H20orf194. For NHD, 33 SNP with the highest estimated effect were located on BTA7 within a region of a predicted gene positioned between RIOK2 and RGMB. On BTA14, all significant SNP were located in introns of STK3, which is responsible for the "abnormal gait" phenotype in mice.
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Affiliation(s)
- T Suchocki
- Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631 Wroclaw, Poland; National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
| | - Ch Egger-Danner
- ZuchtData EDV-Dienstleistungen GmbH, Dresdner Straße 89/19, 1200 Vienna, Austria
| | - H Schwarzenbacher
- ZuchtData EDV-Dienstleistungen GmbH, Dresdner Straße 89/19, 1200 Vienna, Austria
| | - J Szyda
- Biostatistics group, Department of Genetics, Wroclaw University of Environmental and Life Sciences, Kozuchowska 7, 51-631 Wroclaw, Poland; National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland
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21
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Wendler P, Ertl N, Flügger M, Sós E, Torgerson P, Paul Heym P, Schiffmann C, Clauss M, Hatt JM. Influencing factors on the foot health of captive Asian elephants (Elephas maximus) in European zoos. Zoo Biol 2019; 39:109-120. [PMID: 31750965 DOI: 10.1002/zoo.21528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 10/04/2019] [Accepted: 11/07/2019] [Indexed: 11/09/2022]
Abstract
Pathological lesions of feet occur frequently in captive elephant populations. To improve foot health, it is important to identify risk factors associated with such pathologies. Several previous studies have analyzed potentially influencing factors but were limited, for example, by small sample sizes. This study analyzed the relationship between 87 independent variables and the foot health score of 204 Asian elephants (Elephas maximus) in European zoos using bivariate correlation, multivariable regression models, and principal component analysis (PCA). Correlation and regression tests revealed significant results for 30 different variables, mainly with small effect sizes. Only three variables were significant in more than one test: sex, time spent indoors, and time spent on hard ground, with lower scores (i.e. less or less severe pathological lesions) in females, and when less time is spent indoors or on hard ground. Due to small effect sizes and differing results of the statistical tests, it is difficult to determine which risk factors are most important. Instead, a holistic consideration appears more appropriate. A biplot of the PCA shows that factors representing more advanced husbandry conditions (e.g. large areas, high proportions of sand flooring) were associated with each other and with decreased foot scores, whereas indicators of more limited conditions (e.g. high proportions of hard ground, much time spent indoors) were also associated with each other but increased the foot score. In conclusion, instead of resulting from just one or two factors, reduced foot health might be an indicator of a generally poorer husbandry system.
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Affiliation(s)
- Paulin Wendler
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nicolas Ertl
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Endre Sós
- Budapest Zoo & Botanical Garden, Budapest, Hungary
| | - Paul Torgerson
- Section of Epidemiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | | | - Christian Schiffmann
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Marcus Clauss
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jean-Michel Hatt
- Clinic for Zoo Animals, Exotic Pets and Wildlife, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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22
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Sánchez-Molano E, Bay V, Smith RF, Oikonomou G, Banos G. Quantitative Trait Loci Mapping for Lameness Associated Phenotypes in Holstein-Friesian Dairy Cattle. Front Genet 2019; 10:926. [PMID: 31636655 PMCID: PMC6787292 DOI: 10.3389/fgene.2019.00926] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 09/05/2019] [Indexed: 01/08/2023] Open
Abstract
Lameness represents a significant challenge for the dairy cattle industry, resulting in economic losses and reduced animal health and welfare. The existence of underlying genomic variation for lameness associated traits has the potential to improve selection strategies by using genomic markers. Therefore, the aim of this study was to identify genomic regions and potential candidate genes associated with lameness traits. Lameness related lesions and digital cushion thickness were studied using records collected by our research team, farm records, and a combination of both. Genome-wide analyses were performed to identify significant genomic effects, and a combination of single SNP association analysis and regional heritability mapping was used to identify associated genomic regions. Significant genomic effects were identified for several lameness related traits: Two genomic regions were identified on chromosome 3 associated with digital dermatitis and interdigital hyperplasia, one genomic region on chromosome 23 associated with interdigital hyperplasia, and one genomic region on chromosome 2 associated with sole haemorrhage. Candidate genes in those regions are mainly related to immune response and fibroblast proliferation. Quantitative trait loci (QTL) identified in this study could enlighten the understanding of lameness pathogenesis, providing an opportunity to improve health and welfare in dairy cattle with the addition of these regions into selection programs.
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Affiliation(s)
- Enrique Sánchez-Molano
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom
| | - Veysel Bay
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Bandirma Sheep Research Institute, The Ministry of Agriculture and Forestry, Balikesir, Turkey
| | - Robert F Smith
- Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Liverpool, United Kingdom
| | - Georgios Oikonomou
- Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom.,Institute of Veterinary Science, University of Liverpool, Leahurst Campus, Liverpool, United Kingdom
| | - Georgios Banos
- The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Edinburgh, United Kingdom.,The Roslin Institute Building, Scotland's Rural College, Easter Bush, Edinburgh, United Kingdom
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23
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Narayana SG, Miglior F, Naqvi SA, Malchiodi F, Martin P, Barkema HW. Genetic analysis of subclinical mastitis in early lactation of heifers using both linear and threshold models. J Dairy Sci 2018; 101:11120-11131. [DOI: 10.3168/jds.2018-15126] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
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24
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Miglior F, Fleming A, Malchiodi F, Brito LF, Martin P, Baes CF. A 100-Year Review: Identification and genetic selection of economically important traits in dairy cattle. J Dairy Sci 2018; 100:10251-10271. [PMID: 29153164 DOI: 10.3168/jds.2017-12968] [Citation(s) in RCA: 208] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/09/2017] [Indexed: 01/14/2023]
Abstract
Over the past 100 yr, the range of traits considered for genetic selection in dairy cattle populations has progressed to meet the demands of both industry and society. At the turn of the 20th century, dairy farmers were interested in increasing milk production; however, a systematic strategy for selection was not available. Organized milk performance recording took shape, followed quickly by conformation scoring. Methodological advances in both genetic theory and statistics around the middle of the century, together with technological innovations in computing, paved the way for powerful multitrait analyses. As more sophisticated analytical techniques for traits were developed and incorporated into selection programs, production began to increase rapidly, and the wheels of genetic progress began to turn. By the end of the century, the focus of selection had moved away from being purely production oriented toward a more balanced breeding goal. This shift occurred partly due to increasing health and fertility issues and partly due to societal pressure and welfare concerns. Traits encompassing longevity, fertility, calving, health, and workability have now been integrated into selection indices. Current research focuses on fitness, health, welfare, milk quality, and environmental sustainability, underlying the concentrated emphasis on a more comprehensive breeding goal. In the future, on-farm sensors, data loggers, precision measurement techniques, and other technological aids will provide even more data for use in selection, and the difficulty will lie not in measuring phenotypes but rather in choosing which traits to select for.
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Affiliation(s)
- Filippo 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.
| | - Allison Fleming
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Francesca Malchiodi
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Pauline Martin
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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25
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Heringstad B, Egger-Danner C, Charfeddine N, Pryce J, Stock K, Kofler J, Sogstad A, Holzhauer M, Fiedler A, Müller K, Nielsen P, Thomas G, Gengler N, de Jong G, Ødegård C, Malchiodi F, Miglior F, Alsaaod M, Cole J. Invited review: Genetics and claw health: Opportunities to enhance claw health by genetic selection. J Dairy Sci 2018. [DOI: 10.3168/jds.2017-13531] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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26
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Croué I, Fikse F, Johansson K, Carlén E, Thomas G, Leclerc H, Ducrocq V. Genetic evaluation of claw health traits accounting for potential preselection of cows to be trimmed. J Dairy Sci 2017; 100:8197-8204. [DOI: 10.3168/jds.2017-13002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/12/2017] [Indexed: 11/19/2022]
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