Impact of genomic selection on genetic diversity in 5 local European cattle breeds

Genomic selection (GS) has revolutionized animal breeding and accelerated genetic gains in breeding programs. Although GS has become common in cosmopolitan dairy cattle breeds, its implementation in local breeds has begun only more recently, or is still in progress. However, the introduction of GS in some cosmopolitan breeds has also been associated with increased inbreeding rates, raising concerns about the potential effects of GS on genetic diversity in smaller or local breeds. Our aim was to investigate the impact of GS on genetic diversity in 5 (small) local cattle breeds from 3 European countries: Meuse Rhine Yssel (MRY; from the Netherlands); Norwegian Red (Norsk Rødt Fe, NRF; from Norway); and Abondance (ABO; from France), Tarentaise (TAR; from France), and Vosgienne (VOS; from France). We investigated changes in population demographic structure, as well as trends and rates of kinship and inbreeding, using both pedigree- and genomic-based measures. The population size varied depending on the breed, with Vosgienne being the smallest and NRF being the largest. Single nucleotide polymorphism genotypes were available for 4,645 MRY, 193,489 NRF, 16,387 ABO, 8,578 TAR, and 4,472 VOS animals. Animals were genotyped with more than 40,000 SNPs. Overall, following the implementation of GS in these breeds, we observed a reduction of up to 4 years in generation intervals for sires, fewer calves that later became sires, and, for the French breeds, a broader sire usage. Such changes were likely due to GS enabling the preselection and screening of more young bulls. Additionally, the contributions of the top 10 sires were more evenly distributed after the introduction of GS. Although changes in inbreeding and kinship rates occurred after the introduction of GS, we found no consistent pattern across breeds: pedigree (and genomic runs of homozygosity [ROH]-based) inbreeding rates per generation increased in MRY from -0.67 before GS to 0.51 after GS (from -1.12 to 0.93) and TAR from 0.35 to 0.93 (from 0.68 to 0.86), but decreased in NRF from 0.26 to 0.05 (from 0.10 to 0.06), Abondance from 1.19 to 0.99 (from 2.39 to 0.58), and Vosgienne from 0.53 to 0.23 (from 0.88 to 0.19). Moreover, analysis of genomic ROH-based inbreeding by length class showed that after the implementation of GS, the largest changes in inbreeding level and inbreeding rates per generation occurred for shorter ROH segments. Our study suggests that changes and increases in inbreeding rates may occur after the introduction of GS, although they may not be directly due to the introduction of GS per se, but rather due to population management strategies, such as optimal contribution selection. Our findings emphasize the importance of monitoring changes in both genetic diversity and population demographic structure after implementing GS in local breeds, as well as adjusting breeding strategies when needed to ensure long-term sustainability.