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Oloo RD, Mrode R, Bennewitz J, Ekine-Dzivenu CC, Ojango JMK, Gebreyohanes G, Mwai OA, Chagunda MGG. Potential for quantifying general environmental resilience of dairy cattle in sub-Saharan Africa using deviations in milk yield. Front Genet 2023; 14:1208158. [PMID: 38162680 PMCID: PMC10757848 DOI: 10.3389/fgene.2023.1208158] [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: 04/18/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Genetic improvement of general resilience of dairy cattle is deemed as a part of the solution to low dairy productivity and poor cattle adaptability in sub-Saharan Africa (SSA). While indicators of general resilience have been proposed and evaluated in other regions, their applicability in SSA remains unexplored. This study sought to test the viability of utilizing log-transformed variance (LnVar), autocorrelation (rauto), and skewness (Skew) of deviations in milk yield as indicators of general resilience of dairy cows performing in the tropical environment of Kenya. Methods: Test-day milk yield records of 2,670 first-parity cows performing in three distinct agroecological zones of Kenya were used. To predict expected milk yield, quantile regression was used to model lactation curve for each cow. Subsequently, resilience indicators were defined based on actual and standardized deviations of observed milk yield from the expected milk yield. The genetic parameters of these indicators were estimated, and their associations with longevity and average test-day milk yield were examined. Results: All indicators were heritable except skewness of actual and standardized deviation. The log-transformed variance of actual (LnVar1) and standardized (LnVar2) deviations had the highest heritabilities of 0.19 ± 0.04 and 0.17 ± 0.04, respectively. Auto-correlation of actual (rauto1) and standardized (rauto2) deviations had heritabilities of 0.05 ± 0.03 and 0.07 ± 0.03, respectively. Weak to moderate genetic correlations were observed among resilience indicators. Both rauto and Skew indicators had negligible genetic correlations with both longevity and average test-day milk yield. LnVar1 and LnVar2 were genetically associated with better longevity (rg = -0.47 ± 0.26 and -0.49 ± 0.26, respectively). Whereas LnVar1 suggested that resilient animals produce lower average test-day milk yield, LnVar2 revealed a genetic association between resilience and higher average test-day milk yield. Discussion: Log transformed variance of deviations in milk yield holds a significant potential as a robust resilience indicator for dairy animals performing in SSA. Moreover, standardized as opposed to actual deviations should be employed in defining resilience indicators because the resultant indicator does not inaccurately infer that low-producing animals are inherently resilient. This study offers an opportunity for enhancing the productivity of dairy cattle performing in SSA through selective breeding for resilience to environmental stressors.
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Affiliation(s)
- Richard D Oloo
- Animal Breeding and Husbandry in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
- Livestock Genetics, International Livestock Research Institute, Nairobi, Kenya
| | - Raphael Mrode
- Livestock Genetics, International Livestock Research Institute, Nairobi, Kenya
- Animal and Veterinary Science, Scotland Rural College, Edinburgh, United Kingdom
| | - Jörn Bennewitz
- Animal Genetics and Breeding, University of Hohenheim, Stuttgart, Germany
| | | | - Julie M K Ojango
- Livestock Genetics, International Livestock Research Institute, Nairobi, Kenya
| | | | - Okeyo A Mwai
- Livestock Genetics, International Livestock Research Institute, Nairobi, Kenya
| | - Mizeck G G Chagunda
- Animal Breeding and Husbandry in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
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Alvarenga AB, Retallick KJ, Garcia A, Miller SP, Byrne A, Oliveira HR, Brito LF. Across-country genetic and genomic analyses of foot score traits in American and Australian Angus cattle. Genet Sel Evol 2023; 55:76. [PMID: 37919645 PMCID: PMC10621155 DOI: 10.1186/s12711-023-00850-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND Hoof structure and health are essential for the welfare and productivity of beef cattle. Therefore, we assessed the genetic and genomic background of foot score traits in American (US) and Australian (AU) Angus cattle and investigated the feasibility of performing genomic evaluations combining data for foot score traits recorded in US and AU Angus cattle. The traits evaluated were foot angle (FA) and claw set (CS). In total, 109,294 and ~ 1.12 million animals had phenotypic and genomic information, respectively. Four sets of analyses were performed: (1) genomic connectedness between US and AU Angus cattle populations and population structure, (2) estimation of genetic parameters, (3) single-step genomic prediction of breeding values, and (4) single-step genome-wide association studies for FA and CS. RESULTS There was no clear genetic differentiation between US and AU Angus populations. Similar heritability estimates (FA: 0.22-0.24 and CS: 0.22-0.27) and moderate-to-high genetic correlations between US and AU foot scores (FA: 0.61 and CS: 0.76) were obtained. A joint-genomic prediction using data from both populations outperformed within-country genomic evaluations. A genomic prediction model considering US and AU datasets as a single population performed similarly to the scenario accounting for genotype-by-environment interactions (i.e., multiple-trait model considering US and AU records as different traits), even though the genetic correlations between countries were lower than 0.80. Common significant genomic regions were observed between US and AU for FA and CS. Significant single nucleotide polymorphisms were identified on the Bos taurus (BTA) chromosomes BTA1, BTA5, BTA11, BTA13, BTA19, BTA20, and BTA23. The candidate genes identified were primarily from growth factor gene families, including FGF12 and GDF5, which were previously associated with bone structure and repair. CONCLUSIONS This study presents comprehensive population structure and genetic and genomic analyses of foot scores in US and AU Angus cattle populations, which are essential for optimizing the implementation of genomic selection for improved foot scores in Angus cattle breeding programs. We have also identified candidate genes associated with foot scores in the largest Angus cattle populations in the world and made recommendations for genomic evaluations for improved foot score traits in the US and AU.
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Affiliation(s)
- Amanda B Alvarenga
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA
| | - Kelli J Retallick
- American Angus Association, Angus Genetics Inc., 3201 Frederick Avenue, Saint Joseph, MO, 64506, USA
| | - Andre Garcia
- American Angus Association, Angus Genetics Inc., 3201 Frederick Avenue, Saint Joseph, MO, 64506, USA
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., 3201 Frederick Avenue, Saint Joseph, MO, 64506, USA
- AGBU, a Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW, 2351, Australia
| | - Andrew Byrne
- Angus Australia, 86 Glen Innes Road, Armidale, NSW, 2350, Australia
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 South Russell Street, West Lafayette, IN, 47907, USA.
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de Souza TC, Pinto LFB, da Cruz VAR, de Oliveira HR, Pedrosa VB, Oliveira GA, Miglior F, Schenkel FS, Brito LF. A comprehensive characterization of longevity and culling reasons in Canadian Holstein cattle based on various systematic factors. Transl Anim Sci 2023; 7:txad102. [PMID: 37841322 PMCID: PMC10576516 DOI: 10.1093/tas/txad102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/25/2023] [Indexed: 10/17/2023] Open
Abstract
The decision of premature culling cows directly impacts the profitability of dairy farms. A comprehensive characterization of the primary causes of culling reasons would greatly improve both management and selection objectives in dairy cattle breeding programs. Therefore, this study aimed to analyze the temporal frequencies of 34 culling reasons in Canadian Holstein cows. After data editing and quality control, records from 3,096,872 cows culled from 9,683 herds spread across Canada were used for the analyses covering the periods from 1996 to 2020. Reproductive issues were the main culling reason accounting for 23.02%, followed by milk production (20.82%), health (20.39%), conformation problems (13.69%), economic factors (13.10%), accidents (5.67%), age-related causes (1.67%), and workability (1.63%). Nearly fifty-eight percent of cows were culled after 47 months of age. The observed frequencies of culling due to economic factors were lower than expected from 1996 to 2014 and higher than expected between 2015 and 2020. Reproduction issues had the highest culling frequencies during fall (24.54%), winter (24.02%), and spring (22.51%), while health issues were the most frequent (22.51%) culling reason in the summer season. Health issues (25.50%) and milk production (27.71%) were the most frequent culling reasons in the provinces of Quebec and Ontario, respectively. Reproductive issues showed the highest frequency across climates based on the Köppen climate classification, except for Csb (Dry-summer subtropical or Mediterranean climate) and Bsk (Middle latitude steppe climate), which correspond to small regions in Canada, where production was the most frequent culling reason (29.42% and 21.56%, respectively). Reproductive and milk performance issues were the two main culling reasons in most ecozones, except in Boreal Shield and Atlantic Marine, where health issues had the highest frequencies (25.12 and 23.75%, respectively). These results will contribute to improving management practices and selective decisions to reduce involuntary culling of Holstein cows.
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Affiliation(s)
- Taiana Cortez de Souza
- Department of Animal Sciences, Federal University of Bahia, Salvador, BA, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Hinayah Rojas de Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Gerson A Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
- Lactanet Canada, Guelph, ON, Canada
| | - Flávio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
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Alvarenga AB, Oliveira HR, Turner SP, Garcia A, Retallick KJ, Miller SP, Brito LF. Unraveling the phenotypic and genomic background of behavioral plasticity and temperament in North American Angus cattle. Genet Sel Evol 2023; 55:3. [PMID: 36658485 PMCID: PMC9850537 DOI: 10.1186/s12711-023-00777-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 01/04/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Longitudinal records of temperament can be used for assessing behavioral plasticity, such as aptness to learn, memorize, or change behavioral responses based on affective state. In this study, we evaluated the phenotypic and genomic background of North American Angus cow temperament measured throughout their lifetime around the weaning season, including the development of a new indicator trait termed docility-based learning and behavioral plasticity. The analyses included 273,695 and 153,898 records for yearling (YT) and cow at weaning (CT) temperament, respectively, 723,248 animals in the pedigree, and 8784 genotyped animals. Both YT and CT were measured when the animal was loading into/exiting the chute. Moreover, CT was measured around the time in which the cow was separated from her calf. A random regression model fitting a first-order Legendre orthogonal polynomial was used to model the covariance structure of temperament and to assess the learning and behavioral plasticity (i.e., slope of the regression) of individual cows. This study provides, for the first time, a longitudinal perspective of the genetic and genomic mechanisms underlying temperament, learning, and behavioral plasticity in beef cattle. RESULTS CT measured across years is heritable (0.38-0.53). Positive and strong genetic correlations (0.91-1.00) were observed among all CT age-group pairs and between CT and YT (0.84). Over 90% of the candidate genes identified overlapped among CT age-groups and the estimated effect of genomic markers located within important candidate genes changed over time. A small but significant genetic component was observed for learning and behavioral plasticity (heritability = 0.02 ± 0.002). Various candidate genes were identified, revealing the polygenic nature of the traits evaluated. The pathways and candidate genes identified are associated with steroid and glucocorticoid hormones, development delay, cognitive development, and behavioral changes in cattle and other species. CONCLUSIONS Cow temperament is highly heritable and repeatable. The changes in temperament can be genetically improved by selecting animals with favorable learning and behavioral plasticity (i.e., habituation). Furthermore, the environment explains a large part of the variation in learning and behavioral plasticity, leading to opportunities to also improve the overall temperament by refining management practices. Moreover, behavioral plasticity offers opportunities to improve the long-term animal and handler welfare through habituation.
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Affiliation(s)
- Amanda B. Alvarenga
- grid.169077.e0000 0004 1937 2197Department of Animal Sciences, Purdue University, West Lafayette, IN USA
| | - Hinayah R. Oliveira
- grid.169077.e0000 0004 1937 2197Department of Animal Sciences, Purdue University, West Lafayette, IN USA ,Lactanet, Guelph, ON Canada
| | - Simon P. Turner
- grid.426884.40000 0001 0170 6644Animal and Veterinary Sciences Department, Scotland’s Rural College, Edinburgh, UK
| | - Andre Garcia
- American Angus Association, Angus Genetics Inc., Saint Joseph, MO USA
| | | | - Stephen P. Miller
- American Angus Association, Angus Genetics Inc., Saint Joseph, MO USA ,grid.1020.30000 0004 1936 7371AGBU, a joint venture of NSW Department of Primary Industries and University of New England, Armidale, 2351 Australia
| | - Luiz F. Brito
- grid.169077.e0000 0004 1937 2197Department of Animal Sciences, Purdue University, West Lafayette, IN USA
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Miller S. Genomic selection in beef cattle creates additional opportunities for embryo technologies to meet industry needs. Reprod Fertil Dev 2022; 35:98-105. [PMID: 36592979 DOI: 10.1071/rd22233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The use of genotype information to improve the predictability of Expected Progeny Difference was first implemented in American Angus cattle in 2009 and has now grown to where over 50% of all registered calves are genotyped. Animals with only a genotype now have genetic prediction accuracy equivalent to eight or more progeny records across all traits. Reproductive technologies have also been widely adopted with approximately 50% of all calves born being the result of artificial insemination. Non-surgical embryo transfer started increasing in the mid 1990s with just over 10% of calves born being the result of embryo transfer since 2005. The number of embryos created with in vitro technologies has risen sharply since 2015 and now accounts for close to 30% of all ET calves. Genomics has enabled embryo technologies to be more impactful, as females can be selected with greater accuracy and sires can be used at earlier ages with moderate accuracy. Large numbers of females genotyped each year also increases the number of selection candidates, increasing the selection intensity. Genomics, combined with increased recording, also provides more information on females. This increases the spread in the estimated index values of current dams, identifying more elite dams for selection as embryo donors. The greater scope of female selection also contributes to better inbreeding management. Commercial animals genotyped could be targeted for oocyte harvesting at slaughter, creating opportunities for low cost high value beef embryos to be used in the beef on dairy segment of the industry.
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Affiliation(s)
- Stephen Miller
- Animal Genetics and Breeding Unit, a joint venture of NSW Department of Primary Industries and the University of New England, University of New England, Armidale, NSW 2351, Australia
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Alvarenga AB, Oliveira HR, Miller SP, Silva FF, Brito LF. Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. Front Genet 2022; 13:794625. [PMID: 35444687 PMCID: PMC9014094 DOI: 10.3389/fgene.2022.794625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.
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Affiliation(s)
- Amanda B Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., St Joseph, MO, United States
| | - Fabyano F Silva
- Department of Animal Sciences, Federal University of Vicosa, Viçosa, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Araujo AC, Carneiro PLS, Alvarenga AB, Oliveira HR, Miller SP, Retallick K, Brito LF. Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle. Genes (Basel) 2021; 13:17. [PMID: 35052358 PMCID: PMC8775055 DOI: 10.3390/genes13010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 01/23/2023] Open
Abstract
Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.
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Affiliation(s)
- Andre C. Araujo
- Graduate Program in Animal Sciences, State University of Southwestern Bahia, Itapetinga 45700-000, Brazil;
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Paulo L. S. Carneiro
- Department of Biology, State University of Southwest Bahia, Jequié 45205-490, Brazil;
| | - Amanda B. Alvarenga
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Hinayah R. Oliveira
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Stephen P. Miller
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Kelli Retallick
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Luiz F. Brito
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
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Yazar Gunes H, González-Murray RA, Sánchez-Castro MA, L. Passafaro T, L. Bernal-Rubio Y, J. Andersen K, Speidel SE, Thomas MG, Enns RM. New approach to sustained cow fertility trait. Transl Anim Sci 2021. [DOI: 10.1093/tas/txab155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Hilal Yazar Gunes
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523-1171, USA
| | | | - Miguel A Sánchez-Castro
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523-1171, USA
- Zoetis, Veterinary Medicine Research and Development, Animal Genetics, Kalamazoo, MI 49007, USA
| | - Tiago L. Passafaro
- Zoetis, Veterinary Medicine Research and Development, Animal Genetics, Kalamazoo, MI 49007, USA
| | - Yeni L. Bernal-Rubio
- Zoetis, Veterinary Medicine Research and Development, Animal Genetics, Kalamazoo, MI 49007, USA
| | - Kent J. Andersen
- Zoetis, Veterinary Medicine Research and Development, Animal Genetics, Kalamazoo, MI 49007, USA
| | - Scott E Speidel
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523-1171, USA
| | - Milton G Thomas
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523-1171, USA
| | - R Mark Enns
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523-1171, USA
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Ogawa S, Kimata M, Ishii K, Uemoto Y, Satoh M. Genetic analysis for sow stayability at different parities in purebred Landrace and Large White pigs. Anim Sci J 2021; 92:e13599. [PMID: 34309970 PMCID: PMC9285752 DOI: 10.1111/asj.13599] [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: 04/16/2021] [Revised: 06/06/2021] [Accepted: 06/24/2021] [Indexed: 01/19/2023]
Abstract
Genetic parameters for sow stayability were estimated from farrowing records of 10,295 Landrace sows and 8192 Large White sows. The record for sow stayability from parity k to parity k + 1 (k = 1, …, 6) was 0 when a sow had a farrowing record at parity k but not at parity k + 1, and 1 when a sow had both records. Heritability was estimated by using single‐trait linear and threshold animal models. Genetic correlations among parities were estimated by using two‐trait linear–linear and single‐trait random regression linear animal models. Genetic correlations with litter traits at birth were estimated by using a two‐trait linear–linear animal model. Heritability estimates by linear model analysis were low (0.065–0.119 in Landrace & 0.061–0.157 in Large White); those by threshold model analysis were higher (0.136–0.200 & 0.110–0.283). Genetic correlations among parities differed between breeds and models. Genetic correlation between sow stayability and number born alive was positive in many cases, implying that selection for number born alive does not reduce sow stayability. The results seem to be affected by decisions on culling made by farmers.
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Affiliation(s)
- Shinichiro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | | | - Kazuo Ishii
- Division of Animal Breeding and Reproduction, Institute of Livestock and Grassland Science, NARO, Tsukuba, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Impact of Censored or Penalized Data in the Genetic Evaluation of Two Longevity Indicator Traits Using Random Regression Models in North American Angus Cattle. Animals (Basel) 2021; 11:ani11030800. [PMID: 33809341 PMCID: PMC8001693 DOI: 10.3390/ani11030800] [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: 01/06/2021] [Revised: 02/06/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023] Open
Abstract
Simple Summary Cow longevity is a key driver of the beef cattle industry profitability that can be improved through genetic and genomic selection. Censored data are commonly dealt with in genetic evaluations of longevity, which can unfavorably impact the accuracy of breeding values and the rates of genetic progress. In this study, we evaluated alternative scenarios to define the best approaches for genetically evaluating longevity in North American Angus cattle in the presence of censored data. Abstract This study aimed to evaluate the impact of different proportions (i.e., 20%, 40%, 60% and 80%) of censored (CEN) or penalized (PEN) data in the prediction of breeding values (EBVs), genetic parameters, and computational efficiency for two longevity indicators (i.e., traditional and functional longevity; TL and FL, respectively). In addition, three different criteria were proposed for PEN: (1) assuming that all cows with censored records were culled one year after their last reported calving; (2) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while censored (missing) records were kept for cows younger than nine years; and (3) assuming that cows with censored records older than nine years were culled one year after their last reported calving, while cows younger than nine years were culled two years after their last reported calving. All analyses were performed using random regression models based on fourth order Legendre orthogonal polynomials. The proportion of commonly selected animals and EBV correlations were calculated between the complete dataset (i.e., without censored or penalized data; COM) and all simulated proportions of CEN or PEN. The computational efficiency was evaluated based on the total computing time taken by each scenario to complete 150,000 Bayesian iterations. In summary, increasing the CEN proportion significantly (p-value < 0.05 by paired t-tests) decreased the heritability estimates for both TL and FL. When compared to CEN, PEN tended to yield heritabilities closer to COM, especially for FL. Moreover, similar heritability patterns were observed for all three penalization criteria. High proportions of commonly selected animals and EBV correlations were found between COM and CEN with 20% censored data (for both TL and FL), and COM and all levels of PEN (for FL). The proportions of commonly selected animals and EBV correlations were lower for PEN than CEN for TL, which suggests that the criteria used for PEN are not adequate for TL. Analyses using COM and CEN took longer to finish than PEN analyses. In addition, increasing the amount of censored records also tended to increase the computational time. A high proportion (>20%) of censored data has a negative impact in the genetic evaluation of longevity. The penalization criteria proposed in this study are useful for genetic evaluations of FL, but they are not recommended when analyzing TL.
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