Abstract
BackgroundIn France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved.MethodsWe compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection.ResultsGenomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds.ConclusionsWith the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future.
Highlights
In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically
Quality control filtering was performed by removing single nucleotide polymorphisms (SNPs) that were genotyped in less than 95% individuals and SNPs with a minor allele frequency (MAF) lower than 1%
After the introduction of genomic selection, the annual genetic gain increased based on estimated breeding values for bulls of three large French dairy cattle breeds: Montbéliarde, Normande and Holstein
Summary
In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. The estimation of pedigree-based breeding values at birth depends mostly on information about related individuals, resulting in a low reliability and a high correlation between estimated breeding values of relatives. These high correlations decrease only later in the life of an animal when information based on its own performance or performances of the progeny becomes available. Methods to balance inbreeding and genetic gain in breeding schemes, such as optimal contribution selection [6], allow for better conservation of genetic diversity when based on genomic information rather than on pedigree data [7, 8]. GS was expected to reduce the rate of inbreeding and to increase genetic gain per generation at the same time [2]
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