Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits
Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-t...
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MDPI AG
2023-10-01
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| Online Access: | https://www.mdpi.com/2076-2615/13/21/3306 |
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| author | Bolívar Samuel Sosa-Madrid Gerasimos Maniatis Noelia Ibáñez-Escriche Santiago Avendaño Andreas Kranis |
| author_facet | Bolívar Samuel Sosa-Madrid Gerasimos Maniatis Noelia Ibáñez-Escriche Santiago Avendaño Andreas Kranis |
| author_sort | Bolívar Samuel Sosa-Madrid |
| collection | DOAJ |
| description | Monitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from small experimental populations selected for a handful of traits. Here, we used a large dataset from a commercial breeding line spread over a period of twenty-three years. A total of 2,059,869 records and 2,062,112 animals in the pedigree were used for the estimations of variance components for the traits: body weight (BWT; 2,059,869 records) and hen-housed egg production (HHP; 45,939 records). Data were analysed with three estimation approaches: sliding overlapping windows, under frequentist (restricted maximum likelihood (REML)) and Bayesian (Gibbs sampling) methods; expected variances using coefficients of the full relationship matrix; and a “double trait covariances” analysis by computing correlations and covariances between the same trait in two distinct consecutive windows. The genetic variance showed marginal fluctuations in its estimation over time. Whereas genetic, maternal permanent environmental, and residual variances were similar for BWT in both the REML and Gibbs methods, variance components when using the Gibbs method for HHP were smaller than the variances estimated when using REML. Large data amounts were needed to estimate variance components and detect their changes. For Gibbs (REML), the changes in genetic variance from 1999–2001 to 2020–2022 were 82.29 to 93.75 (82.84 to 93.68) for BWT and 76.68 to 95.67 (98.42 to 109.04) for HHP. Heritability presented a similar pattern as the genetic variance estimation, changing from 0.32 to 0.36 (0.32 to 0.36) for BWT and 0.16 to 0.15 (0.21 to 0.18) for HHP. On the whole, genetic parameters tended slightly to increase over time. The expected variance estimates were lower than the estimates when using overlapping windows. That indicates the low effect of the drift-selection process on the genetic variance, or likely, the presence of genetic variation sources compensating for the loss. Double trait covariance analysis confirmed the maintenance of variances over time, presenting genetic correlations >0.86 for BWT and >0.82 for HHP. Monitoring genetic variance in broiler breeding programmes is important to sustain genetic progress. Although the genetic variances of both traits fluctuated over time, in some windows, particularly between 2003 and 2020, increasing trends were observed, which warrants further research on the impact of other factors, such as novel mutations, operating on the dynamics of genetic variance. |
| first_indexed | 2024-03-11T11:34:41Z |
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| spelling | doaj.art-72880ce1fe0844d69ea1e6d886e2eebc2023-11-10T14:57:39ZengMDPI AGAnimals2076-26152023-10-011321330610.3390/ani13213306Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive TraitsBolívar Samuel Sosa-Madrid0Gerasimos Maniatis1Noelia Ibáñez-Escriche2Santiago Avendaño3Andreas Kranis4The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UKAviagen Ltd., Newbridge, Edinburgh EH28 8SZ, UKInstitute for Animal Science and Technology, Universitat Politècnica de València, P.O. Box 2201, 46071 Valencia, SpainAviagen Ltd., Newbridge, Edinburgh EH28 8SZ, UKThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UKMonitoring the genetic variance of traits is a key priority to ensure the sustainability of breeding programmes in populations under directional selection, since directional selection can decrease genetic variation over time. Studies monitoring changes in genetic variation have typically used long-term data from small experimental populations selected for a handful of traits. Here, we used a large dataset from a commercial breeding line spread over a period of twenty-three years. A total of 2,059,869 records and 2,062,112 animals in the pedigree were used for the estimations of variance components for the traits: body weight (BWT; 2,059,869 records) and hen-housed egg production (HHP; 45,939 records). Data were analysed with three estimation approaches: sliding overlapping windows, under frequentist (restricted maximum likelihood (REML)) and Bayesian (Gibbs sampling) methods; expected variances using coefficients of the full relationship matrix; and a “double trait covariances” analysis by computing correlations and covariances between the same trait in two distinct consecutive windows. The genetic variance showed marginal fluctuations in its estimation over time. Whereas genetic, maternal permanent environmental, and residual variances were similar for BWT in both the REML and Gibbs methods, variance components when using the Gibbs method for HHP were smaller than the variances estimated when using REML. Large data amounts were needed to estimate variance components and detect their changes. For Gibbs (REML), the changes in genetic variance from 1999–2001 to 2020–2022 were 82.29 to 93.75 (82.84 to 93.68) for BWT and 76.68 to 95.67 (98.42 to 109.04) for HHP. Heritability presented a similar pattern as the genetic variance estimation, changing from 0.32 to 0.36 (0.32 to 0.36) for BWT and 0.16 to 0.15 (0.21 to 0.18) for HHP. On the whole, genetic parameters tended slightly to increase over time. The expected variance estimates were lower than the estimates when using overlapping windows. That indicates the low effect of the drift-selection process on the genetic variance, or likely, the presence of genetic variation sources compensating for the loss. Double trait covariance analysis confirmed the maintenance of variances over time, presenting genetic correlations >0.86 for BWT and >0.82 for HHP. Monitoring genetic variance in broiler breeding programmes is important to sustain genetic progress. Although the genetic variances of both traits fluctuated over time, in some windows, particularly between 2003 and 2020, increasing trends were observed, which warrants further research on the impact of other factors, such as novel mutations, operating on the dynamics of genetic variance.https://www.mdpi.com/2076-2615/13/21/3306additive genetic variancebody weightbroilerchickenshen-housed egg productiontemporal analysis |
| spellingShingle | Bolívar Samuel Sosa-Madrid Gerasimos Maniatis Noelia Ibáñez-Escriche Santiago Avendaño Andreas Kranis Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits Animals additive genetic variance body weight broiler chickens hen-housed egg production temporal analysis |
| title | Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits |
| title_full | Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits |
| title_fullStr | Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits |
| title_full_unstemmed | Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits |
| title_short | Genetic Variance Estimation over Time in Broiler Breeding Programmes for Growth and Reproductive Traits |
| title_sort | genetic variance estimation over time in broiler breeding programmes for growth and reproductive traits |
| topic | additive genetic variance body weight broiler chickens hen-housed egg production temporal analysis |
| url | https://www.mdpi.com/2076-2615/13/21/3306 |
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