Use of supervised machine learning for prediction of genetic values based on two generations of ancestors
DOI:
https://doi.org/10.33448/rsd-v12i6.41904Keywords:
Artificial intelligence; Machine learning; Linear regression.Abstract
Efficient use of tools aimed at accelerating genetic improvement such as targeted mating requires genetic value information from both breeders and mothers, however, low accuracy or lack thereof can compromise genetic improvement programs, thus estimating genetic values of females is challenging. Methodologies that use only information from male ancestors to calculate genetic values of females have already been proposed, however, the emergence of supervised machine learning technologies have made relevant contributions to genetic improvement. Therefore, this study aims to evaluate a methodology based on a supervised linear regression algorithm in function of the consolidated method in literature, which can be employed in genetic improvement programs. The results of Pearson's correlation analysis were all significant (p<0.0001) between predicted values from both models and actual values, showing that both models can be used to estimate genetic values. However, by using the model based on machine learning it was possible to observe errors with smaller standard deviations for the characteristics of milk, fat, protein and productive life, and equal for the other characteristics analyzed, indicating that models using technologies derived from machine learning have promising applications in genetic improvement.
References
Bourdon, R. (2014). Understanding Animal Breeding. (2a ed.), Pearson. p. 560.
Faceli, K., Lorena, A. C., Gama, J. & Carvalho, A. C. P. L. F. (2011). Artificial intelligence: a machine learning approach. Ed. LTC.
Forabosco, F., Jakobsen, J., & Fikse, W. (2009). International genetic evaluation for direct longevity in dairy bulls. Journal of Dairy Science, 92(5), 2338–2347. https://doi.org/10.3168/jds.2008-1214.
Ghotbaldini, H., Mohammadabadi, M., Nezamabadi-pour, H., Babenko, O. I., Bushtruk, M. V., & Tkachenko, S. V. (2019). Predicting breeding value of body weight at 6-month age using Artificial Neural Networks in Kermani sheep breed. Acta Scientiarum. Animal Sciences, 41(1), 45282. https://doi.org/10.4025/actascianimsci.v41i1.45282.
Groen, A. F., & der Waaij, L. V. (1999). Some basics about mating schemes | Interbull Bulletin. https://journal.interbull.org/index.php/ib/article/view/562.
Hedrick, P. W. (1987). Gametic Disequilibrium Measures: Proceed With Caution. Genetics, 117(2), 331–341. https://doi.org/10.1093/genetics/117.2.331.
Jenko, J., Gorjanc, G., Kovač, M., & Ducrocq, V. (2013). Comparison between sire-maternal grandsire and animal models for genetic evaluation of longevity in a dairy cattle population with small herds. Journal of Dairy Science, 96(12), 8002–8013. https://doi.org/10.3168/jds.2013-6830.
Lewontin, R. C. (1988). On measures of gametic disequilibrium. Genetics, 120(3), 849–852. https://doi.org/10.1093/genetics/120.3.849.
Ma, L., Sonstegard, T. S., Cole, J. B., VanTassell, C. P., Wiggans, G. R., Crooker, B. A., Tan, C., Prakapenka, D., Liu, G., Da, Y. (2019). Genome changes due to artificial selection in U.S. Holstein cattle. BMC Genomics, 20(1). https://doi.org/10.1186/s12864-019-5459-x.
Molas, A. (2022). Why do we minimize the mean squared error? Acesso em dez 2022. Towards Data Science. https://towardsdatascience.com/why-do-we-minimize-the-mean-squared-error-3b97391f54c.
Monard, & Baranauskas. (2003). Conceitos sobre aprendizado de máquina. Sistemas Inteligentes Fundamentos e Aplicações. Manole Ltda.
Mrode. (2005). Linear models for the prediction of animal breeding values (3rd ed.). CABU.
Nayeri, S., Sargolzaei, M., & Tulpan, D. (2019). A review of traditional and machine learning methods applied to animal breeding. Animal Health Research Reviews, 20(1), 31–46. https://doi.org/10.1017/s1466252319000148.
Neves, H. H., Carvalheiro, R., Cardoso, V., Fries, L. A., & de Queiroz, S. A. (2009). Acasalamento dirigido para aumentar a produção de animais geneticamente superiores e reduzir a variabilidade da progênie em bovinos. Revista Brasileira de zootecnia, 38(7). https://doi.org/10.1590/S1516-35982009000700006.
Pour Hamidi, S., Mohammadabadi, M. R., Asadi Foozi, M., & Nezamabadi-pour, H. (2017). Prediction of breeding values for the milk production trait in Iranian Holstein cows applying artificial neural networks. Journal of Livestock Science and Technologies, 5(2), 53-61. 10.22103/jlst.2017.10043.1188.
Schenkel, F., & Schaeffer, L. (2008). Effects of nonrandom parental selection on estimation of variance components. Journal of Animal Breeding and Genetics, 117(4), 225–239. https://doi.org/10.1111/j.1439-0388.2000.00262.x
Silva, G. N., Tomaz, R. S., Sant’Anna, I. D. C., Nascimento, M., Bhering, L. L., & Cruz, C. D. (2014). Neural networks for predicting breeding values and genetic gains. Scientia Agricola, 71(6), 494–498. https://doi.org/10.1590/0103-9016-2014-0057.
sklearn.linear_model.LinearRegression. (2022). Acesso em dez 2022. https://scikit-learn/stable/modules/generated/sklearn.linear_model.LinearRegression.html.
Wellmann, R. (2019). Optimum contribution selection for animal breeding and conservation: the R package optiSel. BMC Bioinformatics, 20(1). https://doi.org/10.1186/s12859-018-2450-5.
White, D. J., Wolff, J. N., Pierson, M., & Gemmel, N. J. (2008). Revealing the hidden complexities of mtDNA inheritance. Molecular Ecology, 17(23), 4925–4942. https://doi.org/10.1111/j.1365-294x.2008.03982.x.
Wright, S. (1922). Coefficients of Inbreeding and Relationship. The American Naturalist, 56(645), 330–338. https://doi.org/10.1086/279872.
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