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Ghaderi Zefreh M, Doeschl-Wilson AB, Riggio V, Matika O, Pong-Wong R. Exploring the value of genomic predictions to simultaneously improve production potential and resilience of farmed animals. Front Genet 2023; 14:1127530. [PMID: 37252663 PMCID: PMC10213464 DOI: 10.3389/fgene.2023.1127530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 05/02/2023] [Indexed: 05/31/2023] Open
Abstract
Sustainable livestock production requires that animals have a high production potential but are also highly resilient to environmental challenges. The first step to simultaneously improve these traits through genetic selection is to accurately predict their genetic merit. In this paper, we used simulations of sheep populations to assess the effect of genomic data, different genetic evaluation models and phenotyping strategies on prediction accuracies and bias for production potential and resilience. In addition, we also assessed the effect of different selection strategies on the improvement of these traits. Results show that estimation of both traits greatly benefits from taking repeated measurements and from using genomic information. However, the prediction accuracy for production potential is compromised, and resilience estimates tends to be upwards biased, when families are clustered in groups even when genomic information is used. The prediction accuracy was also found to be lower for both traits, resilience and production potential, when the environment challenge levels are unknown. Nevertheless, we observe that genetic gain in both traits can be achieved even in the case of unknown environmental challenge, when families are distributed across a large range of environments. Simultaneous genetic improvement in both traits however greatly benefits from the use of genomic evaluation, reaction norm models and phenotyping in a wide range of environments. Using models without the reaction norm in scenarios where there is a trade-off between resilience and production potential, and phenotypes are collected from a narrow range of environments may result in a loss for one trait. The study demonstrates that genomic selection coupled with reaction-norm models offers great opportunities to simultaneously improve productivity and resilience of farmed animals even in the case of a trade-off.
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Affiliation(s)
- Masoud Ghaderi Zefreh
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Valentina Riggio
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Oswald Matika
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
| | - Ricardo Pong-Wong
- The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, United Kingdom
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Salvian M, Silveira RMF, Petrini J, Rovadoscki GA, Iung LHDS, Ramírez-Díaz J, Carrara ER, Pertile SFN, Cassoli LD, Machado PF, Mourão GB. Heat stress on breeding value prediction for milk yield and composition of a Brazilian Holstein cattle population. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023; 67:347-354. [PMID: 36580141 DOI: 10.1007/s00484-022-02413-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 09/27/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Due to the high milk production of Holstein cows, many countries have chosen to import semen to improve local dairy herds. This strategy would be more effective if this semen was used in the same environment conditions in which the bulls were selected. If the effect of genotype by environment (G × E) interaction is not considered, the estimated breeding values (EBVs) may vary, potentially reducing the selection response. We evaluate the impact of heat stress on selection for milk yield and composition of Holstein cows using random regression models. To verify the interference of heat stress in milk yield (MY) and composition traits (fat, protein, total saturated, and total unsaturated fatty acids content in milk), temperature-humidity index (THI) on test-day milk records was used. The threshold value to divide the environments using test-day information from Brazilian Holstein cows was 72 units of THI, i.e., < 72 represented no heat stress and > 72 represented heat stress. Legendre polynomials of second-order (Leg 2) model and two lactation points (33 and 122 DIM) were used to estimate heritabilities and EBVs for five important dairy traits. The heritabilities of milk components and fatty acids were low (0.09-0.29), regardless of lactation period and degree of heat stress, with the exception of protein content (0.30-0.35). Fat content was the only milk component that was reduced according to the degree of heat stress and lactation period. The EBVs tended to decrease in heat stress conditions, thus animals with high genetic potential demonstrated evidence of G × E interaction. However, acclimatization of dairy cows to heat stress in the farm production systems may have been responsible for the low differences among genetic parameters and EBVs with and without heat stress found in this study.
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Affiliation(s)
- Mayara Salvian
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Robson Mateus Freitas Silveira
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Julina Petrini
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Laiza Helena de Souza Iung
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Johanna Ramírez-Díaz
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Eula Regina Carrara
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Simone Fernanda Nedel Pertile
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Laerte Dagher Cassoli
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Paulo Fernando Machado
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil
| | - Gerson Barreto Mourão
- Department of Animal Science, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Av. Pádua Dias, 11. Piracicaba13.418-900, São Paulo, Brazil.
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Heteroscedastic Reaction Norm Models Improve the Assessment of Genotype by Environment Interaction for Growth, Reproductive, and Visual Score Traits in Nellore Cattle. Animals (Basel) 2022; 12:ani12192613. [PMID: 36230355 PMCID: PMC9559514 DOI: 10.3390/ani12192613] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/19/2022] [Accepted: 09/25/2022] [Indexed: 11/17/2022] Open
Abstract
The assessment of the presence of genotype by environment interaction (GxE) in beef cattle is very important in tropical countries with diverse climatic conditions and production systems. The present study aimed to assess the presence of GxE by using different reaction norm models for eleven traits related to growth, reproduction, and visual score in Nellore cattle. We studied five reaction norm models (RNM), fitting a linear model considering homoscedastic residual variance (RNM_homo), and four models considering heteroskedasticity, being linear (RNM_hete), quadratic (RNM_quad), linear spline (RNM_l-l), and quadratic spline (RNM_q-q). There was the presence of GxE for age at first calving (AFC), scrotal circumference (SC), weaning to yearling weight gain (WYG), and yearling weight (YW). The best models were RNM_l-l for YW and RNM_q-q for AFC, SC, and WYG. The heritability estimates for RNM_l-l ranged from 0.07 to 0.20, 0.42 to 0.61, 0.24 to 0.42, and 0.47 to 0.63 for AFC, SC, WYG, and YW, respectively. The heteroskedasticity in reaction norm models improves the assessment of the presence of GxE for YW, WYG, AFC, and SC. Additionally, the trajectories of reaction norms for these traits seem to be affected by a non-linear component, and selecting robust animals for these traits is an alternative to increase production and reduce environmental sensitivity.
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Song H, Wang X, Guo Y, Ding X. G × EBLUP: A novel method for exploring genotype by environment interactions and genomic prediction. Front Genet 2022; 13:972557. [PMID: 36171888 PMCID: PMC9510768 DOI: 10.3389/fgene.2022.972557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022] Open
Abstract
Genotype by environment (G × E) interaction is fundamental in the biology of complex traits and diseases. However, most of the existing methods for genomic prediction tend to ignore G × E interaction (GEI). In this study, we proposed the genomic prediction method G × EBLUP by considering GEI. Meanwhile, G × EBLUP can also detect the genome-wide single nucleotide polymorphisms (SNPs) subject to GEI. Using comprehensive simulations and analysis of real data from pigs and maize, we showed that G × EBLUP achieved higher efficiency in mapping GEI SNPs and higher prediction accuracy than the existing methods, and its superiority was more obvious when the GEI variance was large. For pig and maize real data, compared with GBLUP, G × EBLUP showed improvement by 3% in the prediction accuracy for backfat thickness, while our findings indicated that the trait of days to 100 kg of pig was not affected by GEI and G × EBLUP did not improve the accuracy of genomic prediction for the trait. A significant advantage was observed for G × EBLUP in maize; the prediction accuracy was improved by ∼5.0 and 7.7% for grain weight and water content, respectively. Furthermore, G × EBLUP was not influenced by the number of environment levels. It could determine a favourable environment using SNP Bayes factors for each environment, implying that it is a robust and useful method for market-specific animal and plant breeding. We proposed G × EBLUP, a novel method for the estimation of genomic breeding value by considering GEI. This method identified the genome-wide SNPs that were susceptible to GEI and yielded higher genomic prediction accuracies and lower mean squared error compared with the GBLUP method.
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Affiliation(s)
- Hailiang Song
- Beijing Key Laboratory of Fisheries Biotechnology, Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xue Wang
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yi Guo
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Xiangdong Ding, , orcid.org/0000000226842551
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Le V, Rohmer T, David I. Impact of environmental disturbances on estimated genetic parameters and breeding values for growth traits in pigs. Animal 2022; 16:100496. [DOI: 10.1016/j.animal.2022.100496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 10/18/2022] Open
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Suitability of GWAS as a Tool to Discover SNPs Associated with Tick Resistance in Cattle: A Review. Pathogens 2021; 10:pathogens10121604. [PMID: 34959558 PMCID: PMC8707706 DOI: 10.3390/pathogens10121604] [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: 10/18/2021] [Revised: 11/22/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the biological mechanisms underlying tick resistance in cattle holds the potential to facilitate genetic improvement through selective breeding. Genome wide association studies (GWAS) are popular in research on unraveling genetic determinants underlying complex traits such as tick resistance. To date, various studies have been published on single nucleotide polymorphisms (SNPs) associated with tick resistance in cattle. The discovery of SNPs related to tick resistance has led to the mapping of associated candidate genes. Despite the success of these studies, information on genetic determinants associated with tick resistance in cattle is still limited. This warrants the need for more studies to be conducted. In Africa, the cost of genotyping is still relatively expensive; thus, conducting GWAS is a challenge, as the minimum number of animals recommended cannot be genotyped. These population size and genotype cost challenges may be overcome through the establishment of collaborations. Thus, the current review discusses GWAS as a tool to uncover SNPs associated with tick resistance, by focusing on the study design, association analysis, factors influencing the success of GWAS, and the progress on cattle tick resistance studies.
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Li X, Song H, Zhang Z, Huang Y, Zhang Q, Ding X. The theory on and software simulating large-scale genomic data for genotype-by-environment interactions. BMC Genomics 2021; 22:877. [PMID: 34865618 PMCID: PMC8647494 DOI: 10.1186/s12864-021-08191-z] [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: 04/19/2021] [Accepted: 11/19/2021] [Indexed: 11/10/2022] Open
Abstract
Background With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches. Results We proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account. Conclusions This tool is useful for assessing genotype-by-environment interactions and threshold traits methods.
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Affiliation(s)
- Xiujin Li
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangdong, 510225, Guangzhou, People's Republic of China
| | - Hailiang Song
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Zhe Zhang
- Guangdong Provincial Key Lab of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yunmao Huang
- Guangdong Provincial Key Laboratory of Waterfowl Healthy Breeding, College of Animal Science & Technology, Zhongkai University of Agriculture and Engineering, Guangdong, 510225, Guangzhou, People's Republic of China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, 271001, Taian, China
| | - Xiangdong Ding
- Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.
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Rodrigues FB, Malhado CHM, Carneiro PLS, Ambrosini DP, Rezende MPG, Bozzi R, Song J. Genotype by environment interactions for body weight in Mediterranean buffaloes using reaction norm models. REV COLOMB CIENC PEC 2021. [DOI: 10.17533/udea.rccp.v34n2a05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background: Buffalo breeding has significantly increased in Brazil over recent years. However, few genetic evaluations have been conducted. Objective: To assess Genotype x Environment Interactions in the Mediterranean Water Buffalo in Brazil, for weight at 205 days of age, using reaction norm models via random regression. Methods: Data for buffaloes born between 1990 and 2014 were collected from five farms ascribed to the Brazilian Buffaloe Improvement Program, located in the North (1), Northeast (1), South (2) and Southeast (1) regions of Brazil. The initial database consisted of 5,280 observations at 205 days of age (W205). We assessed fit using two hierarchical reaction norm models: a two-step (HRNM2s) and a one-step (HRNM1s). Model fit was estimated using the Deviance Information Criterion, Deviance Based on Bayes Factors and Deviance based on Conditional Predictive Ordinate. The environmental descriptors were created to group individuals into common production environments based on year, season, herd and sex. Results: The best fit was obtained for the hierarchical reaction norm model with one-step (HRNM1s). Direct heritability estimates for this model ranged from 0.17 to 0.67 and the maternal heritability from 0.02 to 0.11 with increasing environmental gradient. Lower correlations among the sire classifications were obtained in comparison with HRNM1s in environments with low and high management, confirming the presence of genotype x environment interactions. Conclusion: We recommend a wider application of genetic evaluation in buffalo aimed at identifying optimal genotypes within specific environments.
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Tsartsianidou V, Kapsona VV, Sánchez-Molano E, Basdagianni Z, Carabaño MJ, Chatziplis D, Arsenos G, Triantafyllidis A, Banos G. Understanding the seasonality of performance resilience to climate volatility in Mediterranean dairy sheep. Sci Rep 2021; 11:1889. [PMID: 33479419 PMCID: PMC7820498 DOI: 10.1038/s41598-021-81461-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/14/2020] [Indexed: 01/26/2023] Open
Abstract
As future climate challenges become increasingly evident, enhancing performance resilience of farm animals may contribute to mitigation against adverse weather and seasonal variation, and underpin livestock farming sustainability. In the present study, we develop novel seasonal resilience phenotypes reflecting milk production changes to fluctuating weather. We evaluate the impact of calendar season (autumn, winter and spring) on animal performance resilience by analysing 420,534 milk records of 36,908 milking ewes of the Chios breed together with relevant meteorological data from eastern Mediterranean. We reveal substantial seasonal effects on resilience and significant heritable trait variation (h2 = 0.03–0.17). Resilience to cold weather (10 °C) of animals that start producing milk in spring was under different genetic control compared to autumn and winter as exemplified by negative genetic correlations (− 0.09 to − 0.27). Animal resilience to hot weather (25 °C) was partially under the same genetic control with genetic correlations between seasons ranging from 0.43 to 0.86. We report both favourable and antagonistic associations between animal resilience and lifetime milk production, depending on calendar season and the desirable direction of genetic selection. Concluding, we emphasise on seasonal adaptation of animals to climate and the need to incorporate the novel seasonal traits in future selective breeding programmes.
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Affiliation(s)
- Valentina Tsartsianidou
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
| | - Vanessa Varvara Kapsona
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK
| | - Enrique Sánchez-Molano
- Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Zoitsa Basdagianni
- Department of Animal Production, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Jesús Carabaño
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040, Madrid, Spain
| | - Dimitrios Chatziplis
- Laboratory of Agrobiotechnology and Inspection of Agricultural Products, Department of Agriculture, International Hellenic University, Alexander Campus, 57400, Sindos, Greece
| | - Georgios Arsenos
- Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Banos
- Department of Animal and Veterinary Sciences, Scotland's Rural College, Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, UK.,Laboratory of Animal Husbandry, School of Veterinary Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
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Negri R, Aguilar I, Feltes GL, Cobuci JA. Selection for Test-Day Milk Yield and Thermotolerance in Brazilian Holstein Cattle. Animals (Basel) 2021; 11:ani11010128. [PMID: 33430092 PMCID: PMC7827621 DOI: 10.3390/ani11010128] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/25/2020] [Accepted: 12/29/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Interest in selection for milk yield and thermotolerance in cattle has grown, since heat stress has caused great losses in milk yield. However, few studies on how to carry out concurrent selection are available. Milk yield was analyzed by traditional methods, including heat stress indicators, in genetic evaluation. The results showed that the best sires for milk yield are not the best for heat tolerance, and only a small proportion of individuals have the aptitude for joint selection. Despite a small population fraction allowed for joint selection, sufficient genetic variability for selecting more resilient sires was found, which promoted concomitant genetic gains in milk yield and thermotolerance. Abstract Intense selection for milk yield has increased environmental sensitivity in animals, and currently, heat stress is an expensive problem in dairy farming. The objectives were to identify the best model for characterizing environmental sensitivity in Holstein cattle, using the test-day milk yield (TDMY) combined with the temperature–humidity index (THI), and identify sires genetically superior for heat-stress (HS) tolerance and milk yield, through random regression. The data comprised 94,549 TDMYs of 11,294 first-parity Holstein cows in Brazil, collected from 1997 to 2013. The yield data were fitted to Legendre orthogonal polynomials, linear splines and the Wilmink function. The THI (the average of two days before the dairy control) was used as an environmental gradient. An animal model that fitted production using a Legendre polynomials of quartic order for the days in milk and quadratic equations for the THI presented a better quality of fit (Akaike’s information criterion (AIC) and Bayesian information criterion (BIC)). The Spearman correlation coefficient of greatest impact was 0.54, between the top 1% for TDMY and top 1% for HS. Only 9% of the sires showed plasticity and an aptitude for joint selection. Thus, despite the small population fraction allowed for joint selection, sufficient genetic variability for selecting more resilient sires was found, which promoted concomitant genetic gains in milk yield and thermotolerance.
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Affiliation(s)
- Renata Negri
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil;
- Correspondence: (R.N.); (J.A.C.)
| | - Ignacio Aguilar
- Department of Animal Breeding, Instituto Nacional de Investigación Agropecuaria, Montevideo 11100, Uruguay;
| | - Giovani Luis Feltes
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil;
| | - Jaime Araújo Cobuci
- Department of Animal Science, Federal University of Rio Grande do Sul, Porto Alegre 91540-000, Brazil;
- Correspondence: (R.N.); (J.A.C.)
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Silva DA, Lopes PS, Costa CN, Silva AA, Silva HT, Silva FF, Veroneze R, Thompson G, Carvalheira J. Genotype by environment interaction for Holstein cattle populations using autoregressive and within- and across-country multi-trait reaction norms test-day models. Animal 2020; 15:100084. [PMID: 33712214 DOI: 10.1016/j.animal.2020.100084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 10/22/2022] Open
Abstract
The progenies of international bulls in diverse climatic conditions and management levels may lead to different expressions of their genetic potential resulting in a re-ranking of these bulls. Therefore, evaluate the presence of genotype by environment interaction (G×E) within and across countries is important to guide the decision-making on alternative selection strategies. Thus, a two-step reaction norm (RN) approach was used to investigate the presence of G×E in Portuguese and Brazilian Holstein cattle. In step 1, we performed a within-country genetic evaluation using an autoregressive model to obtain precorrected phenotypes and environmental gradients (herd test-day solutions, HTD levels). In step 2, the precorrected phenotypes were considered as two distinct traits in a bi-trait RN model to estimate variance components across HTD levels, genetic correlation between HTD levels in Portugal and Brazil, and RN of the estimated breeding values. Additionally, the genetic correlation between countries using a bi-trait random regression (RR) sire model was obtained. In step 1, genetic additive variance for milk yield (MY) in Portugal was 14.1% higher than in Brazil. For somatic cell score (SCS), the genetic additive variance in Portugal was 12.7% lower than in Brazil. Although similar heritability estimates for SCS were observed in both countries, MY heritabilities were 0.31 for Portugal and 0.23 for Brazil. Genetic correlations (SD) between both countries obtained using RR sire model were 0.78 (0.051) for MY and 0.75 (0.062) for SCS. In step 2, MY genetic correlations among HTD levels within countries were higher than 0.94 for Portugal and 0.98 for Brazil. Somatic cell score genetic correlations among HTD levels ranged from 0.70 to 0.99 for Portugal and from 0.84 to 0.99 for Brazil. The average (SD) of genetic correlation estimates between Portuguese and Brazilian HTD levels were 0.74 (0.009) for MY and 0.57 (0.060) for SCS. These results suggest the presence of G×E for MY and SCS of Holstein cattle between both countries. Although there was no indication of G×E between Brazilian herd environments, the low genetic correlation for SCS indicates potential re-ranking of bulls between extreme environmental gradient in Portugal. Overall, the results of this study evidence the importance of national and international genetic evaluation systems to assist dairy farmers in the selection of the best genotypes to obtain the expected returns from investments in imported semen and to realize genetic progress in dairy populations under local environmental conditions.
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Affiliation(s)
- D A Silva
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - P S Lopes
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - C N Costa
- Embrapa Gado de Leite, 36038-330 Juiz de Fora, Brazil
| | - A A Silva
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - H T Silva
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - F F Silva
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - R Veroneze
- Department of Animal Science, Universidade Federal de Viçosa, 36570-000 Viçosa, Brazil
| | - G Thompson
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBio), University of Porto, 4485-661 Vairão, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - J Carvalheira
- Research Center in Biodiversity and Genetic Resources (CIBIO-InBio), University of Porto, 4485-661 Vairão, Portugal; Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313 Porto, Portugal.
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Song H, Zhang Q, Ding X. The superiority of multi-trait models with genotype-by-environment interactions in a limited number of environments for genomic prediction in pigs. J Anim Sci Biotechnol 2020; 11:88. [PMID: 32974012 PMCID: PMC7507970 DOI: 10.1186/s40104-020-00493-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/07/2020] [Indexed: 11/21/2022] Open
Abstract
Background Different production systems and climates could lead to genotype-by-environment (G × E) interactions between populations, and the inclusion of G × E interactions is becoming essential in breeding decisions. The objective of this study was to investigate the performance of multi-trait models in genomic prediction in a limited number of environments with G × E interactions. Results In total, 2,688 and 1,384 individuals with growth and reproduction phenotypes, respectively, from two Yorkshire pig populations with similar genetic backgrounds were genotyped with the PorcineSNP80 panel. Single- and multi-trait models with genomic best linear unbiased prediction (GBLUP) and BayesC π were implemented to investigate their genomic prediction abilities with 20 replicates of five-fold cross-validation. Our results regarding between-environment genetic correlations of growth and reproductive traits (ranging from 0.618 to 0.723) indicated the existence of G × E interactions between these two Yorkshire pig populations. For single-trait models, genomic prediction with GBLUP was only 1.1% more accurate on average in the combined population than in single populations, and no significant improvements were obtained by BayesC π for most traits. In addition, single-trait models with either GBLUP or BayesC π produced greater bias for the combined population than for single populations. However, multi-trait models with GBLUP and BayesC π better accommodated G × E interactions, yielding 2.2% – 3.8% and 1.0% – 2.5% higher prediction accuracies for growth and reproductive traits, respectively, compared to those for single-trait models of single populations and the combined population. The multi-trait models also yielded lower bias and larger gains in the case of a small reference population. The smaller improvement in prediction accuracy and larger bias obtained by the single-trait models in the combined population was mainly due to the low consistency of linkage disequilibrium between the two populations, which also caused the BayesC π method to always produce the largest standard error in marker effect estimation for the combined population. Conclusions In conclusion, our findings confirmed that directly combining populations to enlarge the reference population is not efficient in improving the accuracy of genomic prediction in the presence of G × E interactions, while multi-trait models perform better in a limited number of environments with G × E interactions.
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Affiliation(s)
- Hailiang Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian, 271001 China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
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Song H, Zhang Q, Misztal I, Ding X. Genomic prediction of growth traits for pigs in the presence of genotype by environment interactions using single-step genomic reaction norm model. J Anim Breed Genet 2020; 137:523-534. [PMID: 32779853 DOI: 10.1111/jbg.12499] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 12/16/2022]
Abstract
Economically important traits are usually complex traits influenced by genes, environment and genotype-by-environment (G × E) interactions. Ignoring G × E interaction could lead to bias in the estimation of breeding values and selection decisions. A total of 1,778 pigs were genotyped using the PorcineSNP80 BeadChip. The existence of G × E interactions was investigated using a single-step reaction norm model for growth traits of days to 100 kg (AGE) and backfat thickness adjusted to 100 kg (BFT), based on a pedigree-based relationship matrix (A) or a genomic-pedigree joint relationship matrix (H). In the reaction norm model, the herd-year-season effect was measured as the environmental variable (EV). Our results showed no G × E interactions for AGE, but for BFT. For both AGE and BFT, the genomic reaction norm model (H) produced more accurate predictions than the conventional reaction norm model (A). For BFT, the accuracies were greater based on the reaction norm model than those based on the reduced model without exploiting G × E interaction, with EV ranging from 0.5 to 1, and accuracy increasing by 3.9% and 4.6% in the reaction norm model based on A and H matrices, respectively, while reaction norm model yielded approximately 8.4% and 7.9% lower accuracy for EVs ranging from 0 to 0.4, based on A and H matrices, respectively. In addition, for BFT, the highest accuracy was obtained in the BJLM6 farm for realizing directional selection. This study will help to apply G × E interactions to practical genomic selection.
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Affiliation(s)
- Hailiang Song
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
| | - Qin Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, P.R. China
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, P.R. China
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Delgadillo Liberona JS, Langdon JM, Herring AD, Blackburn HD, Speidel SE, Sanders S, Riley DG. Random regression of Hereford percentage intramuscular fat on geographical coordinates. J Anim Sci 2020; 98:skz359. [PMID: 31768519 PMCID: PMC6986430 DOI: 10.1093/jas/skz359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 11/23/2019] [Indexed: 11/13/2022] Open
Abstract
Accounting for genotype-environment interactions may improve genetic prediction and parameter estimation. The objective was to use random regression analyses to estimate variances and thereby heritability for intramuscular fat (IMF) across longitude and latitude coordinates within the continental United States. Records from the American Hereford Association (n = 169,440) were used. Analyses were first conducted using the continental United States in its entirety, and then as subdivided into two or four regions. Data were analyzed with an animal model, and linear and quadratic random regressions of additive genetic merit on longitude or latitude as covariate (separately). Subdivided data were analyzed with linear random regressions unique to regions. Regions were North and South separated at 40°N latitude, or West and East separated at 99°W longitude using longitude or latitude as covariate, respectively. Further subdivision to four regions included additional boundaries of 44.46° and 36.46°N latitude and 104.55° and 92.22°W longitude. The estimated heritability of IMF from the traditional model was 0.19 ± 0.004. Without regional subdivision of data, quadratic random regression had the best fit for the data based on likelihood ratio tests using longitude or latitude as covariate (P < 0.01). Estimates of heritability from quadratic random regression on latitude ranged from 0.12 in the South to a high of 0.27 at the extreme Northern latitude. Estimates of heritability from quadratic random regression on longitude ranged from 0.17 in the middle of the parameter space (corresponding to the central United States) to 0.37; higher estimates were noted at the extremes, that is, the far West and East longitudes. Random regression analyses of data divided into regions were conducted with a linear coefficient, as increasing to a quadratic polynomial was never accomplished. Results from random regression on latitude in the East region were similar to results from analyses without regions (h2 ranged from 0.09 to 0.32); however, estimates of heritability in the West region had a lower range from South to North (0.14 to 0.27). Estimates of heritability from random regression on longitude with data divided into two regions were similar to those from analyses that did not include region. Estimates in the South region were somewhat lower and had a lower range (0.15 to 0.31) than those from the North region (0.19 to 0.47). When data were further subdivided, estimation of only a subset of covariances among random regression coefficients was possible, that is, within-region covariances of intercept and linear terms (latitude); those and covariances between all linear random regression coefficients were estimated when longitude was the covariate. Results from random regression analyses of data with four regions modeled produced very high estimates of heritability in low latitudes in the furthest West and high latitudes in the furthest East region, with approximate difference of 0.3 and 0.2 between estimates in the two West regions and the two East regions, respectively. Results from random regression on longitude indicated higher estimates of heritability in North region, especially at the furthest East longitudes of the most Northern region. There appeared to be substantial additive genetic variance differences, as well as estimates of heritability, that correspond to different geographical environments as modeled by random regressions on within-region latitude or longitude coordinates.
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Affiliation(s)
| | - John M Langdon
- Department of Animal Science, Texas A&M University, College Station, TX
| | - Andy D Herring
- Department of Animal Science, Texas A&M University, College Station, TX
| | | | - Scott E Speidel
- Department of Animal Science, Colorado State University, Fort Collins, CO
| | | | - David G Riley
- Department of Animal Science, Texas A&M University, College Station, TX
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Variance heterogeneity and genotype by environment interactions in native Black and White dual-purpose cattle for different herd allocation schemes. Animal 2019; 13:2146-2155. [PMID: 30854999 DOI: 10.1017/s1751731119000144] [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] [Indexed: 11/06/2022] Open
Abstract
Black and White dual-purpose cattle (DSN) are kept in diverse production systems, but the same set of genetic parameters is used for official national genetic evaluations, neglecting the herd or production system characteristics. The aim of the present study was to infer genetic (co)variance components within and across defined herd descriptor groups or clusters, considering only herds keeping the local and endangered DSN breed. The study considered 3659 DSN and 2324 Holstein Friesian (HF) cows from parities one to three. The 46 herds always kept DSN cows, but in most cases, herds were 'mixed' herds (Mixed), including both genetic lines HF and DSN. In order to study environmental sensitivity, we had a focus on the naturally occurring negative energy balance in the early lactation period. In consequence, traits were records from the 1st official test-day after calving for milk yield (Milk-kg), somatic cell score (SCS) and fat-to-protein ratio (FPR). Genetic parameters were estimated in bivariate runs (separate runs for the three genetic lines Mixed, HF and DSN), defining the same trait from different herd groups or clusters as different traits. Additive-genetic variances and heritabilities were larger in herd groups that indicated superior herd management, implying that cow records from these herds allow a better genetic differentiation. Superior herd management included larger herds, low calving age, high herd production levels and low intra-herd somatic cell count. Herd descriptor group differences in additive-genetic variances for Milk-kg were stronger in HF than in DSN, indicating environmental sensitivity for DSN. Similar variance components and heritabilities across groups, clusters and genetic lines were found for data stratification according to geographical descriptors altitude and latitude. Considering 72 bivariate herd group runs, 29 genetic correlations were very close to 1 (mostly for Milk-kg). Somatic cell score was the trait showing the smallest genetic correlations, especially in the DSN analyses, and when stratifying herds according to genetic line compositions (rg=0.11), or according to the percentage of natural service sires (rg=0.08). For estimations based on the results of a cluster analysis considering several herd descriptors simultaneously, indications for genotype × environment interactions could be found for SCS, but genetic correlations were larger than 0.80 for Milk-kg and FPR. In conclusion, we suggest multiple-trait animal model applications in genetic evaluations, in order to select the best sires for specific herd environments or herd clusters.
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Freitas GR, Hurtado-Lugo NA, de Abreu Dos Santos DJ, Aspilcueta Borquis RR, Pegolo NT, Tonhati H, de Araújo Neto FR. Genotype-environment interaction for age at first calving in buffaloes, using the reaction norm model. Reprod Domest Anim 2019; 54:727-732. [PMID: 30740786 DOI: 10.1111/rda.13414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 01/27/2019] [Indexed: 11/28/2022]
Abstract
The objective of this study was to evaluate the genotype-environment interaction effect on age at first calving in buffaloes. The records were analysed using two approaches: (a) standard animal model and (b) reaction norm model. For the reaction norm analysis, two environmental gradients were formed, using age of first calving or milk yield group contemporary average. The results showed differences in the heritability estimates when using the two approaches. The reaction norm model indicated high heritability in more favourable environments and low magnitude genetic correlations between extreme environments. Based on our findings, we verified the significance of the genotype-environment interaction effect on age at first calving in buffaloes.
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Dakhlan A, Moghaddar N, van der Werf JHJ. Genotype × birth type or rearing-type interactions for growth and ultrasound scanning traits in Merino sheep. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an17464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study explores the interaction between genetic potential for growth in Merino lambs and their birth type (BT) or rearing type (RT). Data on birthweight (BWT), weaning weight (WWT), post-weaning weight (PWWT), scan fat (PFAT) and eye muscle depth (PEMD) were used from 3920 single and 4492 twin-born lambs from 285 sires and 5279 dams. Univariate analysis showed a significant sire × BT interaction accounting for 1.59% and 2.49% of the phenotypic variation for BWT and WWT, respectively, and no significant effect for PWWT, PFAT and PEMD. Sire × RT interaction effects were much smaller and only significant for PEMD. Bivariate analysis indicated that the genetic correlation (rg) between trait expression in lambs born and reared as singles versus those born and reared as twins were high for BWT, WWT, PWWT (0.91 ± 0.02 – 0.96 ± 0.01), whereas rg for PFAT and PEMD were lower (0.81 ± 0.03 and 0.86 ± 0.02). The rg between traits expressed in lambs born and reared as singles versus those born as twins but reared as singles were lower: 0.77 ± 0.08, 0.88 ± 0.03, 0.66 ± 0.06 and 0.61 ± 0.08 for WWT, PWWT, PFAT and PEMD, respectively. A different RT only affected the expression of breeding values for PFAT and PEMD (rg 0.62 ± 0.04 and 0.47 ± 0.03, respectively). This study showed genotype × environment interaction for BWT and WWT (sire × BT interaction) and for PEMD (sire by RT interaction). However, sires’ breeding value of a model that accounts for sire × BT interaction provides a very similar ranking of sires compared with a model that ignores it, implying that there is no need to correct for the effect in models for genetic evaluation.
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da Costa Caetano G, Fonseca Silva F, Calderano A, Pinheiro Silva L, Corrêa Ribeiro J, Tavares Oliveira L, Reis Mota R. Genotype and protein level interaction in growth traits of meat-type quail through reaction norm models. JOURNAL OF ANIMAL AND FEED SCIENCES 2017. [DOI: 10.22358/jafs/79806/2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Selection in the presence of a genotype by environment interaction: response in environmental sensitivity. ACTA ACUST UNITED AC 2016. [DOI: 10.1017/s1357729800058604] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
AbstractThe effect of selection for high phenotypic value in the presence of a genotype by environment interaction (G ✕ E, i.e. genetic variation for environmental sensitivity) and an improving environment was studied in a simulation. Environmental sensitivity was evaluated by using reaction norms, which describe the phenotype expressed by a genotype as a function of the environment. Three types of reaction norms (linear, quadratic and sigmoid), and two selection schemes (mass selection and progeny test selection) were studied. Environmental sensitivity was measured as the weighted average of the absolute value of the first derivative of the reaction norm function. Results showed that environmental sensitivity increased in response to selection for high phenotypic value in the presence of G ✕ E and an improving environment when reaction norms were linear or quadratic. For sigmoid reaction norms, approximating threshold characters, environmental sensitivity increased within the environmental range encompassing the threshold. With mass selection and/or non-linear reaction norms, environmental sensitivity increased even without environmental change.
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Ambrosini DP, Malhado CHM, Filho RM, Cardoso FF, Carneiro PLS. Genotype × environment interactions in reproductive traits of Nellore cattle in northeastern Brazil. Trop Anim Health Prod 2016; 48:1401-7. [DOI: 10.1007/s11250-016-1105-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/15/2016] [Indexed: 10/21/2022]
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21
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Li L, Hermesch S. Environmental variation and breed sensitivity for growth rate and backfat depth in pigs. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an14066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This study investigated the magnitude of environmental variation and compared the environmental sensitivity of Large White, Landrace and Duroc pigs based on reaction norms analyses for lifetime average daily gain (ADG) and backfat depth (BF). Data comprised 265 165 records collected between 2000 and 2010 on pigs from nine herds in Australia. Four environmental descriptors [the phenotypic mean and three least-squares means of contemporary groups (CG) of linear mixed models fitting fixed effects only or fitting sire or animal as additional random effects] were compared in order to quantify the environmental variation based on herd-by-birth month (HBM) and herd-by-birth week (HBW) CG for ADG and BF. Similar levels of variation were found for environmental descriptors based on HBM or HBW CG definitions for both traits but the accuracy of estimates for environmental descriptors was higher for HBM than HBW. The standard deviations of environmental descriptors were 31 (35) g/day for ADG and 1.0 (1.1) mm for BF based on the animal model fitting HBM (HBW), which are similar to the genetic standard deviations usually observed for these traits. Most of this variation in environmental conditions was also observed within years and within herds. Landrace had the highest ADG and Large White had the lowest BF across the environmental range. Significant breed-by-environment interaction was found for ADG but not for BF. Duroc was least sensitive and Large White was most sensitive indicating that the leaner breed was less able to perform consistently across the observed range of environmental conditions in this study.
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Multiple-breed reaction norm animal model accounting for robustness and heteroskedastic in a Nelore–Angus crossed population. Animal 2016; 10:1093-100. [DOI: 10.1017/s1751731115002815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Rauw WM, Gomez-Raya L. Genotype by environment interaction and breeding for robustness in livestock. Front Genet 2015; 6:310. [PMID: 26539207 PMCID: PMC4612141 DOI: 10.3389/fgene.2015.00310] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/28/2015] [Indexed: 01/14/2023] Open
Abstract
The increasing size of the human population is projected to result in an increase in meat consumption. However, at the same time, the dominant position of meat as the center of meals is on the decline. Modern objections to the consumption of meat include public concerns with animal welfare in livestock production systems. Animal breeding practices have become part of the debate since it became recognized that animals in a population that have been selected for high production efficiency are more at risk for behavioral, physiological and immunological problems. As a solution, animal breeding practices need to include selection for robustness traits, which can be implemented through the use of reaction norms analysis, or though the direct inclusion of robustness traits in the breeding objective and in the selection index. This review gives an overview of genotype × environment interactions (the influence of the environment, reaction norms, phenotypic plasticity, canalization, and genetic homeostasis), reaction norms analysis in livestock production, options for selection for increased levels of production and against environmental sensitivity, and direct inclusion of robustness traits in the selection index. Ethical considerations of breeding for improved animal welfare are discussed. The discussion on animal breeding practices has been initiated and is very alive today. This positive trend is part of the sustainable food production movement that aims at feeding 9.15 billion people not just in the near future but also beyond.
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Affiliation(s)
- Wendy M. Rauw
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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Jesuyon OMA, Oseni SO. Seasonal sensitivity of genotypes in the humid tropics and its application to chicken breeding. Arch Anim Breed 2015. [DOI: 10.5194/aab-58-261-2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. The study was aimed at elucidating the effect of seasons, namely the early wet (EW), late wet (LW), early dry (ED) and late dry (LD) seasons, on genotype sensitivity, its magnitude and application for selection and management of chickens of Bovan Nera (BN) and ISA Brown (IB) origins. Breeding and hatching records from 1999 to 2008 were collected from CHI (Ajanla) Farms and hatchery records, Ibadan, Nigeria. Cock weight (CW), hen weight (HW), hen-house egg production (HHP), egg weight (EW), fertility of egg set (FES) and pullet day-old chicks (PDC) hatched were examined. ANOVA revealed that there was significant (P < 0.05) genotype × season interaction effect. This interaction was observed between genotypic values when compared between seasons within parameters. Within-season sensitivity parameters indicated that BN was more sensitive than IB in HW and FES for all seasons. In ED and LD seasons, sensitivity values were inconsistent in pattern with output levels of FES, HES and PDC hatched because of interaction between genotypes and seasons. Within the LW season, all sensitivity indices for genotypes were consistent in magnitude with productive and reproductive values. Therefore, a genotype's seasonal sensitivity indices could be utilized for direct antagonistic selection in LW season between genotypes in humid tropics.
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Bignardi AB, El Faro L, Pereira RJ, Ayres DR, Machado PF, Albuquerque LGD, Santana ML. Reaction norm model to describe environmental sensitivity across first lactation in dairy cattle under tropical conditions. Trop Anim Health Prod 2015; 47:1405-10. [DOI: 10.1007/s11250-015-0878-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/15/2015] [Indexed: 10/23/2022]
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Kantanen J, Løvendahl P, Strandberg E, Eythorsdottir E, Li MH, Kettunen-Præbel A, Berg P, Meuwissen T. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries. Front Genet 2015; 6:52. [PMID: 25767477 PMCID: PMC4341116 DOI: 10.3389/fgene.2015.00052] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/05/2015] [Indexed: 12/16/2022] Open
Abstract
Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.
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Affiliation(s)
- Juha Kantanen
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Department of Biology, University of Eastern Finland , Kuopio, Finland
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University , Tjele, Denmark
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala, Sweden
| | - Emma Eythorsdottir
- Faculty of Land and Animal Resources, Agricultural University of Iceland , Reykjavik, Iceland
| | - Meng-Hua Li
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing, China
| | | | - Peer Berg
- NordGen - Nordic Genetic Resource Center , Aas, Norway
| | - Theo Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences , Aas, Norway
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Phenotypic plasticity of composite beef cattle performance using reaction norms model with unknown covariate. Animal 2012; 7:202-10. [PMID: 23032089 DOI: 10.1017/s1751731112001711] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The objective of the present study was to determine the presence of genotype by environment interaction (G × E) and to characterize the phenotypic plasticity of birth weight (BW), weaning weight (WW), postweaning weight gain (PWG) and yearling scrotal circumference (SC) in composite beef cattle using the reaction norms model with unknown covariate. The animals were born between 1995 and 2008 on 33 farms located throughout all Brazilian biomes between latitude -7° and -31°, longitude -40° and -63°. The contemporary group was chosen as the environmental descriptor, that is, the environmental covariate of the reaction norms. In general, higher estimates of direct heritability were observed in extreme favorable environments. The mean of direct heritability across the environmental gradient ranged from 0.05 to 0.51, 0.09 to 0.43, 0.01 to 0.43 and from 0.12 to 0.26 for BW, WW, PWG and SC, respectively. The variation in direct heritability observed indicates a different response to selection according to the environment in which the animals of the population are evaluated. The correlation between the level and slope of the reaction norm for BW and PWG was high, indicating that animals with higher average breeding values responded better to improvement in environmental conditions, a fact characterizing a scale of G × E. Low correlation between the intercept and slope was obtained for WW and SC, implying re-ranking of animals in different environments. Genetic variation exists in the sensitivity of animals to the environment, a fact that permits the selection of more plastic or robust genotypes in the population studied. Thus, the G × E is an important factor that should be considered in the genetic evaluation of the present population of composite beef cattle.
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Genotype by environment interaction for litter size in pigs as quantified by reaction norms analysis. Animal 2008; 2:1742-7. [DOI: 10.1017/s1751731108003145] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Skovsted K, Henryon M, Rydhmer L, Jensen J, Solanes FX. Growth rate of growing pigs is weakly correlated genetically with litter size, while the amount of genetic variation for growth rate changes with litter size. ACTA AGR SCAND A-AN 2005. [DOI: 10.1080/09064700500356216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Petersson KJ, Kolmodin R, Strandberg E. Genotype by environment interaction for length of productive life in Swedish Red and White dairy cattle. ACTA AGR SCAND A-AN 2005. [DOI: 10.1080/09064700510009252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Kristensen TN, Løvendahl P, Berg P, Loeschcke V. Hsp72 is present in plasma from Holstein-Friesian dairy cattle, and the concentration level is repeatable across days and age classes. Cell Stress Chaperones 2005; 9:143-9. [PMID: 15497501 PMCID: PMC1065294 DOI: 10.1379/csc-17.1] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Although heat shock proteins (Hsps) are primarily considered as being intracellular, this study identified the presence of Hsp72 in plasma from female Holstein-Friesian dairy cattle. Plasma samples were collected from the same animals at different ages and on different days after calving and accordingly divided into 5 age classes. The age classes were calves less than 235 days of age, young heifers between 235 and 305 days of age, older heifers between 305 and 560 days of age, cows early in lactation, and cows later in lactation. For a subsample of animals within each age class, replicate plasma samples were collected from 1 to 7 days apart to test whether the Hsp72 concentration levels are repeatable on this shorter timescale. Hsp72 was observed in plasma samples from animals of all 5 age classes. For animals with blood samples taken a few days apart, the repeatability (within age class) of the Hsp72 concentration was 0.52 +/- 0.06. Age and days from calving significantly affected the Hsp72 concentration level. The highest Hsp72 level was observed in older heifers (305-560 days of age). The repeatability of Hsp72 concentrations across age classes within animal was 0.22 +/- 0.06. High environmental sensitivity and negative genetic associations between production and health traits in this high-producing breed have been documented earlier. Hsp72 is believed to be strictly stress inducible, and the finding of Hsp72 in plasma indicates that even apparently healthy individuals may experience extrinsic or intrinsic stress (or both).
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Affiliation(s)
- Torsten Nygaard Kristensen
- Department of Animal Breeding and Genetics, Danish Institute of Agricultural Sciences, PO Box 50, DK-8830 Tjele, Denmark.
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Abstract
Past developments in livestock breeding have led to considerable genetic change in production traits, but the follow-up of nutrition and management is often incomplete. The pig production sector is moving to hotter climates, and to more intensive and limiting conditions. This increases demands for animal robustness. Robustness can be implemented as a breeding objective trait just like production traits. Breeding for robustness is feasible, but requires substantial investment in data and technology. As for all low-heritability traits with complicated data recording, DNA markers provide a useful tool to support selection; this requires good association studies and ongoing multiple marker development. Breeding for increased robustness must be implemented in balance with breeding for increased production. It is therefore useful to define robustness in terms of performance-relevant issues. A convenient approach is through the environmental sensitivity of the expression of genetic production potential. Environmental sensitivity illustrates loss of flexibility to deal with intensive or limiting conditions, due to unbalanced resource allocation. It can be quantified for individual animals in terms of reaction norm parameters, which can be used as estimated breeding values to support selection. The challenges of implementing such a system will be (i) the set-up of proper data collection in a wide range of environmental settings; (ii) the development of proper data processing tools; (iii) the design of suitable breeding objectives and selection criteria, including MAS; and (iv) the successful integration of the first 3 objectives.
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