2009-Nakaoka_et_al - The use of link provider data to...

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and Y. Sasaki H. Nakaoka, C. Gaillard, K. Fujinaka, N. Watanabe, M. Ito, K. Kawada, T. Ibi, Y. Sasae connected subpopulations The use of link provider data to improve national genetic evaluation across weakly doi: 10.2527/jas.2008-0948 originally published online Sep 2, 2008; 2009.87:62-71. J Anim Sci http://jas.fass.org/cgi/content/full/87/1/62 the World Wide Web at: The online version of this article, along with updated information and services, is located on www.asas.org by on October 22, 2010. jas.fass.org Downloaded from
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ABSTRACT: Data from 3 prefectures and a nation- wide farming corporation were used to assess the use- fulness of the “link provider data” in providing indirect genetic links for the national genetic evaluation for car- cass weight across weakly connected subpopulations of the Japanese Black cattle. The data from the farming corporation provided genetic links to those of all prefec- tures and was therefore used as the link provider data. Two national genetic evaluation strategies under an animal model were compared, based on the generalized coefficient of determination (CD) of contrasts between mean EBV of sires or maternal grandsires (MGS) from different prefectures: strategy PA-1 was a pooled analy- sis of the data sets of the 3 prefectures, and strategy PA-2 was a pooled analysis of the data sets of the 3 prefectures and the farming corporation. The CD of the contrasts were greater for PA-2 than for PA-1. Under PA-2, the CD of the contrasts between mean EBV of sires or MGS ranged from 0.67 to 0.78 or from 0.61 to 0.70, respectively. Pooling the data from the 3 prefec- tures and the farming corporation increased the degree of connectedness through the link provider data rather than the amount of information by adding more data, thus improving the accuracy of prediction. The differ- ences between mean EBV of sires or MGS from differ- ent prefectures were smaller for PA-1 than for PA-2. This finding suggests that genetic differences in carcass weight among prefectures are present, but that they would be confused with the environmental differences under PA-1 because of the lack of genetic connectedness among the prefectures. On the other hand, the genetic differences among the prefectures would be predicted precisely under PA-2 because the genetic connectedness among the prefectures was improved by using the link provider data. The results demonstrate that the link provider data could be used to unify within-prefecture evaluation to form a Japanese national genetic evalua- tion across weakly connected subpopulations. Key words: beef cattle, connectedness, genetic evaluation, link provider data, mixed linear model, precision ©2009 American Society of Animal Science. All rights reserved. J. Anim. Sci. 2009. 87:62–71 doi:10.2527/jas.2008-0948 INTRODUCTION The BLUP procedure (Henderson, 1973) has been a standard method for predicting breeding values of livestock. The BLUP method allows meaningful com- parison of the breeding values across levels of fixed ef- fects (i.e., across management units) if there are genetic links among the units.
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2009-Nakaoka_et_al - The use of link provider data to...

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