Since 2009, genomic selection (GS) has been widely applied in Holstein Friesian (HF) breeding programs. In this study, we evaluated how the introduction of GS in the Dutch-Flemish HF breeding program has affected inbreeding and kinship trends, using both pedigree-based and genomic measures. Rates of inbreeding and kinship for artificial insemination (AI) bulls increased with the introduction of GS, from 0.1-0.7% in 2003-2009 to 1.6-2.5% in 2009-2015. Rates of inbreeding and kinship for cows also increased with GS, although they were lower than for AI-bulls (i.e. 0.79-1.14% in 2009-2017). Levels of identical by state (IBS), which include relatedness due to both recent and distant common ancestors, increased faster than levels of identical by descent (IBD), which include only recent inbreeding and kinship. Accumulation of inbreeding varied substantially across the genome over time, with specific regions showing a striking increase in inbreeding since the introduction of GS. These findings emphasize the need for efficient genomic management of inbreeding in GS-schemes.

Harmen P Doekes, Roel F Veerkamp, Sipke J Hiemstra, Piter Bijma, Sijne van der Beek, Jack J Windig

Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume Theory to Application 2, , 90, 2018
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