Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Simple Summary The discovery of the genome has been one of the greatest advances in the development of tools for the genetic improvement of cattle in the last decades. The use of information derived from genomics has been demonstrated to be an efficient alternative for the validation of kinship, adjusted mating, and conservation strategies to generate dairy cattle with desirable traits. However, the impact of the genetic improvement strategies in breeding programs has closed bloodlines in several milk breeds, consequently generating inbreeding depression. Thus, to mitigate the negative effects of inbreeding, several tools associated with genomic analysis are currently available that may be useful to reverse undesirable genetic trends. The present review will provide an understanding of the importance of genomic analysis and how it can be used to mitigate the negative effects of inbreeding depression on different traits related to production, reproduction, health, animal welfare, linear type traits, and adaptability in dairy cattle. A historical overview of genomics and future perspectives will also be covered. Abstract Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.