Volume 8, Issue 17 (1-2018)
rap 2018, 8(17): 130-139 |
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Ehsani niya J, Ghavi Hossein-Zadeh N, Shadparvar A A. (2018). Heterogeneity of Variance Components for Milk Protein Yield in Different Levels of Herd-year Production and Its Effects on Genetic Parameters and Estimated Breeding Value of Iranian Holsteins. rap. 8(17), 130-139. doi:10.29252/rap.8.17.130
URL: http://rap.sanru.ac.ir/article-1-863-en.html
URL: http://rap.sanru.ac.ir/article-1-863-en.html
Abstract: (3803 Views)
This study was carried out to investigate different data transformation methods on homogeneity and heterogeneity of variance components. Data included 305-day lactation records for protein yield from the first three lactations of Iranian Holstein cows collected from 1983 to 2014 by the Animal Breeding Center and Promotion of Animal Products of Iran. Data included 141670 records for 1st lactation, 115395 records for 2nd lactation and 82529 records for 3rd lactation. Records were categorized to 3 classes according to the average of herd-year production. For testing the heterogeneity of variance components Bartlet test was used and it was significant among all three lactations. A pre-correction method and two different data transformation methods including Box-Cox and Square root were used to correct for heterogeneity of variance. Genetic parameter and heritability estimates were estimated by VCE program, under an animal model. Spearman correlations and proportion of animals selected before and after data transformation were also estimated. Application of the Visscher adjustment method resulted in slightly higher heritabilities, which may be due to the more accurate estimation of additive genetic effects when heterogeneity is considered. Heterogeneity of variance had a significant effect on re-ranking and selection of 5% top sires and 1% of top dams. Pre-correction, Box-Cox and Square root method caused a proportion of 4%, 19% and 10% of top sires and 10%, 21% and 7% of top dams, respectively, to be excluded from selection when compared to the homogenous variance scenario. The results of this research indicate that the variance between different levels of herd-year production is not homogeneous and may influence the ranking and genetic evaluation of top cows.
Type of Study: Research |
Subject:
Special
Received: 2018/01/10 | Accepted: 2018/01/10 | Published: 2018/01/10
Received: 2018/01/10 | Accepted: 2018/01/10 | Published: 2018/01/10
References
1. Boldman, K.G. and A.E. Freeman. 1990. Adjustment for heterogeneity of variances by herd production in dairy cow and sire evaluation. Journal of Dairy Science, 73: 503-512. [DOI:10.3168/jds.S0022-0302(90)78698-5]
2. Brebes, B., V. Ducrocq, J.L. Foulley, M. Protais, A. Tavernier, M. Tixier-Boichard and C. Beaumont. 1993. Box-Cox transformation of egg-production traits of laying hens to improve genetic parameter estimation and breeding evaluation. Livestock Production Science, 33: 313-326. [DOI:10.1016/0301-6226(93)90010-F]
3. Dahlin, A., U.N. Khan, A.H. Zafar, M. Saleem, M.A. Chaudhry and J. Philipsson. 1998. Genetic and environmental causes of variation in milk production traits of Sahiwal cattle in Pakistan. Journal of Animal Science, 66(2): 307-318. [DOI:10.1017/S1357729800009437]
4. De Veer, J.C. and L.D. Van Veleck. 1987. Genetic parameters for first lactation milk yields at three levels of production. Journal of Dairy Science, 70: 1434-1441. [DOI:10.3168/jds.S0022-0302(87)80166-2]
5. Gengler, N., G.R. Wiggans and A. Gillon. 2004. Estimated heterogeneity of phenotypic variance of test-day yield with a structural variance model. Journal of Dairy Science, 87: 1908-1916. [DOI:10.3168/jds.S0022-0302(04)73349-4]
6. Groeneveld, E., M. Kovac and N. Mielenz. 2008. VCE User's Guide and Reference Manual. Version 6.0. Institute of Farm Animal Genetics, Neustadt, Germany, 1-125.
7. Hill,W. G. 1984. On selection among groups with heterogeneous variance. Animal Production, 39: 473-477. [DOI:10.1017/S0003356100032220]
8. Huquet, B., H.L. Leclerc and V. Ducrocq. 2012. Modelling and estimation of genotype by environment interactions for production traits in French dairy cattle. Genetic Selection Evolution, 44(35): 1-14. [DOI:10.1186/1297-9686-44-35]
9. Ibanez, M.A., M.J. Carabano, J.L. Foulley and R. Alenda. 1996. Heterogeneity of herd-period phenotypic variances in the Spanish Holstein-Friesian cattle: sources of heterogeneity and genetic evaluation. Livestock Production Science, 45: 137-147. [DOI:10.1016/0301-6226(96)00012-7]
10. Ibanez, M.A., M.J. Carabano and R. Alenda. 1999. Identification of sources of heterogeneous residual and genetic variances in milk yield data from the Spanish Holstein-Friesian population and impact on genetic evaluation. Livestock Production Science, 59: 33-49. [DOI:10.1016/S0301-6226(99)00006-8]
11. Kizilkaya, K. and R.J. Tempelman. 2005. A general approach to mixed effects modeling of residual variances in generalized linear mixed models Genetic Selection Evolution, 37(1): 31-56. [DOI:10.1051/gse:2004035]
12. Kominakis, A., E. Rogdakis and K. Koutsotolis. 1998. Genetic parameters for milk yield and litter size in Boutsiko dairy sheep. Canadian Journal of Animal Science, 78: 525-532. [DOI:10.4141/A98-049]
13. Lidauer, M., R. Emmerling and E.A. Mantysaari. 2008. Multiplicative random regression model for heterogeneous variance adjustment in genetic evaluation for milk yield in Simmental. Animal Breeding and Genetics, 125(3): 147-159. [DOI:10.1111/j.1439-0388.2008.00728.x]
14. Lino-Lourenço, D.A., C.A. Lopes de Oliveira, E.N. Martins, M.C. Paula Leite, F.C.M. Maiaand and A.I. Santos. 2012. Heterogeneous genetic (co)variances in simulated closed herds under selection. Maringá, 34(1): 83-90. [DOI:10.4025/actascianimsci.v34i1.10934]
15. Markus, S., E.A. Mantysaari, I. Stranden, J.A. Eriksson and M.H. Lidauer. 2014. Comparison of multiplicative heterogeneous variance adjustment models for genetic evaluations. Journal of Animal Breeding and Genetics, 22: 61‐65.
16. Matzuk, M., M. Lamb and J. Dolores. 2002. Genetic dissection of mammalian fertility pathways.Nature publishing Group, Basingstoke, ROYAUME-UNI. [DOI:10.1038/ncb-nm-fertilityS41]
17. Meuwissen, T.H.E., G. De Jong and B. Engel. 1996. Joint estimation of breeding values and heterogeneous variances of large data files. Journal of Dairy Science, 79: 310-316. [DOI:10.3168/jds.S0022-0302(96)76365-8]
18. Microsoft Visual FoxPro 9.0. Copyright© 1988-2004, Microsoft Corporation.
19. Mulder, H.A., P. Bijma and W.G. Hill. 2007. Prediction of breeding values and selection response with genetic heterogeneity of environmental variance. Genetics, 175: 1895-1910. [DOI:10.1534/genetics.106.063743]
20. Nakaoka, H., A. Narita, T. Ibi, Y. Sasae, T. Miyake, T. Yamada and Y. Sasaki. 2007. Effectiveness of adjusting for heterogeneity of variance in genetic evaluation of Japanese Black cattle. Journal of Animal Science, 85: 2429-2436. [DOI:10.2527/jas.2007-0063]
21. Neves, H.H.R., R. Carvalheiro and S.A. Queiroz. 2012. Genetic variability of residual variance of weight traits in Nellore beef cattle. Livestock Science, 142(1-3): 164-169. [DOI:10.1016/j.livsci.2011.07.010]
22. Nikolaou, M., A.P. Kominakis, E. Rogdakis and S. Zampitis. 2004. Effect of mean and variance heterogeneity on genetic evaluations of Lesbos dairy sheep. Livestock Production Science, 88: 107-115. [DOI:10.1016/j.livprodsci.2003.09.025]
23. Rekaya, R., M.J. Carabaño and M.A. Toro. 2000. Assessment of heterogeneity of residual variances using changepoint techniques. Genetic Selection Evolution, 32(4): 383-394. [DOI:10.1186/1297-9686-32-4-383]
24. Robert-Granie, C., B. Bonaıti, D. Boichard and A. Barbat. 1999. Accounting for variance heterogeneity in French dairy cattle genetic evaluation. Livestock Production Science, 60: 343-357. [DOI:10.1016/S0301-6226(99)00105-0]
25. Sargolzaei, M., H. Iwaisaki and J.J. Colleau. 2006. CFC: A tool for monitoring genetic diversity. Proc. 8th World Congr. Genet. Appl. Livest. Prod., CD-ROM Communication 27-28. Belo Horizonte, Brazil, Aug. 13-18.
26. SAS, 2009. Release 9.1. SAS Institute Inc., Cary, North Carolia, USA.
27. Strabel, T. and T. Szwaczkowski. 1997. Additive genetic and permanent environmental variance components for test day milk traits in Black-White cattle. Livestock Production Science, 48: 91-98. [DOI:10.1016/S0301-6226(97)00005-5]
28. Strabel, T., T. Jankowski and J. Jamrozik. 2006. Adjustments for heterogeneous herd-year variances in a random regression model for genetic evaluations of polish Black-and-White cattle. Journal of Applied Genetics, 47: 125-130. [DOI:10.1007/BF03194611]
29. Szydowski, M. and T. Szwaczkowski. 1993. The effect of grouping herds according to production level on the heritability of milk traits in cattle. Animal Science Pap Rep, 11: 295-300.
30. Urioste, J.I., D. Gianola, R. Rekaya, W.F. Fikse and K.A. Weigel. 2001. Evaluation of extent and amount of heterogeneous variance for milk yield in Uruguayan Holsteins. Journal of Animal Science, 72: 259-268. [DOI:10.1017/S1357729800055752]
31. Van der Werf, J.H.J., T.H.E. Meuwissen and G. De Jong. 1994. Effect of correction for heterogeneity of variances on bias and accuracy of breeding value estimation for Dutch dairy cattle. Journal of Dairy Science, 77: 3174-3184. [DOI:10.3168/jds.S0022-0302(94)77260-X]
32. Varkoohi, S., H. Merabani-Yeganeh, S.R. Miraei-Ashtiyani and N. Ghavi-Hossein-zadeh. 2007. Heterogeneity of variance for milk traits at climatical regions in Holstein dairy cattle in Iran and the best methods for data transformation. Journal of Pakistan biological science, 10(9): 1556-1558. [DOI:10.3923/pjbs.2007.1556.1558]
33. Visscher, P.M., R. Thompson and W.G. Hill. 1991. Estimation of genetic and environmental variances for fat yield in individual herds and an investigation into heterogeneity of variance between herds. Livestock Production Science, 28: 273-290. [DOI:10.1016/0301-6226(91)90010-N]
34. Wiggans, G.R. and P.M. Van Raden. 1991. Method and effect of adjustment for heterogeneous variance. Journal of Dairy Science, 4: 4350- 4357. [DOI:10.3168/jds.S0022-0302(91)78631-1]
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