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Emamgholi Begli H, Schaeffer LR, Abdalla E, Lozada-Soto EA, Harlander-Matauschek A, Wood BJ, Baes CF. Genetic analysis of egg production traits in turkeys (Meleagris gallopavo) using a single-step genomic random regression model. Genet Sel Evol 2021; 53:61. [PMID: 34284722 PMCID: PMC8290560 DOI: 10.1186/s12711-021-00655-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 07/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Egg production traits are economically important in poultry breeding programs. Previous studies have shown that incorporating genomic data can increase the accuracy of genetic prediction of egg production. Our objective was to estimate the genetic and phenotypic parameters of such traits and compare the prediction accuracy of pedigree-based random regression best linear unbiased prediction (RR-PBLUP) and genomic single-step random regression BLUP (RR-ssGBLUP). Egg production was recorded on 7422 birds during 24 consecutive weeks from first egg laid. Hatch-week of birth by week of lay and week of lay by age at first egg were fitted as fixed effects and body weight as a covariate, while additive genetic and permanent environment effects were fitted as random effects, along with heterogeneous residual variances over 24 weeks of egg production. Predictions accuracies were compared based on two statistics: (1) the correlation between estimated breeding values and phenotypes divided by the square root of the trait heritability, and (2) the ratio of the variance of BLUP predictions of individual Mendelian sampling effects divided by one half of the estimate of the additive genetic variance. RESULTS Heritability estimates along the production trajectory obtained with RR-PBLUP ranged from 0.09 to 0.22, with higher estimates for intermediate weeks. Estimates of phenotypic correlations between weekly egg production were lower than the corresponding genetic correlation estimates. Our results indicate that genetic correlations decreased over the laying period, with the highest estimate being between traits in later weeks and the lowest between early weeks and later ages. Prediction accuracies based on the correlation-based statistic ranged from 0.11 to 0.44 for RR-PBLUP and from 0.22 to 0.57 for RR-ssGBLUP using the correlation-based statistic. The ratios of the variances of BLUP predictions of Mendelian sampling effects and one half of the additive genetic variance ranged from 0.17 to 0.26 for RR-PBLUP and from 0.17 to 0.34 for RR-ssGBLUP. Although the improvement in accuracies from RR-ssGBLUP over those from RR-PBLUP was not uniform over time for either statistic, accuracies obtained with RR-ssGBLUP were generally equal to or higher than those with RR-PBLUP. CONCLUSIONS Our findings show the potential advantage of incorporating genomic data in genetic evaluation of egg production traits using random regression models, which can contribute to the genetic improvement of egg production in turkey populations.
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Affiliation(s)
- Hakimeh Emamgholi Begli
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada.
| | - Lawrence R Schaeffer
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada
| | - Emhimad Abdalla
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada
| | - Emmanuel A Lozada-Soto
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada
| | - Alexandra Harlander-Matauschek
- Campbell Centre for the Study of Animal Welfare, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada
| | - Benjamin J Wood
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada.,Hybrid Turkeys, A Hendrix Genetics Company, Kitchener, N2K 3S2, Canada.,School of Veterinary Science, University of Queensland, Gatton Campus, Brisbane, QLD, Australia
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, Canada.,Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
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Kijas JW, Gutierrez AP, Houston RD, McWilliam S, Bean TP, Soyano K, Symonds JE, King N, Lind C, Kube P. Assessment of genetic diversity and population structure in cultured Australian Pacific oysters. Anim Genet 2019; 50:686-694. [PMID: 31518019 DOI: 10.1111/age.12845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 01/14/2023]
Abstract
The recent development of Pacific oyster (Crassostrea gigas) SNP genotyping arrays has allowed detailed characterisation of genetic diversity and population structure within and between oyster populations. It also raises the potential of harnessing genomic selection for genetic improvement in oyster breeding programmes. The aim of this study was to characterise a breeding population of Australian oysters through genotyping and analysis of 18 027 SNPs, followed by comparison with genotypes of oyster sampled from Europe and Asia. This revealed that the Australian populations had similar population diversity (HE ) to oysters from New Zealand, the British Isles, France and Japan. Population divergence was assessed using PCA of genetic distance and revealed that Australian oysters were distinct from all other populations tested. Australian Pacific oysters originate from planned introductions sourced from three Japanese populations. Approximately 95% of these introductions were from geographically, and potentially genetically, distinct populations from the Nagasaki oysters assessed in this study. Finally, in preparation for the application of genomic selection in oyster breeding programmes, the strength of LD was evaluated and subsets of loci were tested for their ability to accurately infer relationships. Weak LD was observed on average; however, SNP subsets were shown to accurately reconstitute a genomic relationship matrix constructed using all loci. This suggests that low-density SNP panels may have utility in the Australian population tested, and the findings represent an important first step towards the design and implementation of genomic approaches for applied breeding in Pacific oysters.
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Affiliation(s)
- J W Kijas
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Qld, 4067, Australia
| | - A P Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - R D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - S McWilliam
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, Qld, 4067, Australia
| | - T P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - K Soyano
- Institute for East China Sea Research, Nagasaki University, Nagasaki, 852-8521, Japan
| | | | - N King
- Cawthron Institute, Nelson, New Zealand
| | - C Lind
- CSIRO Agriculture and Food, Hobart, Tasmania, 7004, Australia
| | - P Kube
- CSIRO Agriculture and Food, Hobart, Tasmania, 7004, Australia
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