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

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.

Keywords: dairy cattle; environment; gene edition; genomic analysis; health; linear types; nutrition; production; reproduction; welfare.

Figure 1

Brief historical evolution of genomics. Origins of classic genetic knowledge are undoubtedly based on Mendel’s discoveries on the inheritance of characters in plants in the XIX century. During the early XX century concepts of genes and chromosome theory became consolidated. Later, during the XX century advances on the chemical basis of inheritance, the breaking of the genetic code and gene regulation discoveries marked the development of genomics and the development of genomic tools in animal science. An impacting development in genomics was the sequencing of the whole human genome in the early XXI century, followed by the ultimate application of this knowledge, the discovery of the gene-editing tools. This led to the awarding of the Nobel Prize to women researchers Charpentier and Doudna in 2020 [14,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37].

Figure 2

Overview of the impact of genomics on several dairy science topics. (1) Method used for the direct selection of heritable measures of gene expression. (2) A statistical framework for genomic estimations. (3) Genomic relationship matrices for highly accurate estimation of genomic estimated breeding values (GEBV). (4) Unique data resolution methods in very large animal populations; GS = iterative Gauss–Seidel; PCG = preconditioned conjugate gradient; one-step GREML = genome-based restricted maximum likelihood used for >50,000 genotyped animal populations. (5) Analysis of the genetic diversity determining population structure, performing high-density genetic maps and providing genotypes for genome-wide association analysis. (6) Determination of the genomic inbreeding footprint for a specific subpopulation by estimating the individual autozygosity. Under each dairy science topic (production, reproduction, health and animal welfare, environment, linear type traits) examples of relevant traits studied through genomic tools to date are listed.