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MOTS-CLES : bovine ; genomic selection ; genetic diversity

Maintaining genetic diversity within populations is important to maintain genetic progress, keep being able to select for new selection objectives and avoid inbreeding pressure. The arrival of genomic selection in large dairy cattle breeds has considerably modified selection programs but its impact on genetic diversity was unknown. In fact, the increase in the number of commercial bulls and the lower dependence on predictions of genetic value of family information had a postiive effect, but the reduction of the generation interval had a very negative effect. This study, performed as part of a PhD study financed by Apis-Gene, was aimed at evaluating this impact, on genetic progress and on genetic diversity, in the three largest French dairy cattle breeds (Montbeliard, Normandy and Holstein) ten years after genomic selection begain.

This study showed that genomic selection led to a big decrease in generation interval by a factor of 1.7, 1.9 and 2 respectively for Montbeliard, Normandy and Holstein cattle breeds. As expected, this decrease in generation interval was accompanied by a very significant increase in annual genetic progress for the three breeds. However, the assessment is more contrasted for genetic diversity. Indeed, the increase in inbreeding remained stable for the Normandy and Montbeliard breeds whereas it accelerated for the Holstein breed. This decrease in genetic diversity was observed with both estimations from geneological data as well as those measured from molecular measurements based on the identification of autozygous regions of the genome (ROH for "run of homozygosity"). The long ROH  represent recent inbreeding whereas short ROH represent older inbreeding. The development of genomic selection also coincided  with a significant increase in ROH size for the holstein breed which was not the case for Normandy and Montbeliard breeds. These results associated with an apparently recent increase (estimated on five generations) of the holstein breed population, shows a significant and rapid decrease of genetic diversity, concomitant with the development of genomic selection. This result may be explained by the fact that the French selection program for the Holstein breed is under important international competition. Thus, to cope with this competition, it is necessary to maintain a maximum genetic proress via the massive use of a small number of elite sires and their progeny, at the expense of genetic variability.

In order to reconcile the maintenance of genetic diversity and the creation of genetic progress, it is necessary to propose and evaluate, in particular through simulations, alternative selection programs. In this context, different strategies for the use of reproductive technologies such as embryo transfer could be studied.

In addition, inbreeding depression is costly in terms of performance and fitness. The detection of regions of the genome responsible for inbreeding pressure and their consideration when choosing individuals to select for will provide an improved management of inbreeding effects.