Editorial: Haplotype Analysis Applied to Livestock Genomics

The recent availability of dense panels of single nucleotide polymorphism (SNP) markers has permitted a finer investigation of genome architecture, a deeper understanding of biology and evolution, and the implementation of marker-assisted and genomic selection in livestock species. Paradigmatic examples of the use of SNP panels include understanding domestication, population diversity, inbreeding, admixture, demographic trajectories, identification of loci associated with economically important traits, and accurate prediction of breeding values. The common denominator of the vast majority of the research conducted in livestock to date has relied on analytical tools that treat genetic markers as individual and independent variables. We know, however, that genetic inheritance is driven by segments of closely interlinked nucleotides. Thus, utilizing phased multi-marker segments (i.e., haplotypes) holds the potential of improving existing models. This is particularly true in genome-wide association studies (GWAS) and genomic predictions, which are analyses that rely on the concept that information of unobserved causal variants is captured by correlation (linkage disequilibrium—LD) with nearby (observed) markers. The potential utilization of haplotypes in genetic analysis is highly varied. Haplotypes are used in the imputation process. Imputation is the in silico procedure that allows us to expand upon our information on sparse SNP markers produced by existing microarray data up to the whole-genome sequence level without additional genotyping and sequencing. Since haplotypes may serve as better proxies for causal variants than single SNP markers, the incorporation of haplotype data in genomic predictions seems promising in the absence of information on functional alleles. In extensive conditions, e.g., in the tropics, haplotypes could be used to select favorable combinations of variants in crossbreds and advanced backcross programs to retain those important for adaptation to local environmental conditions as well as those for improved production. Also, the models applied to the characterization of livestock genetic diversity could be re-designed to better estimate relationship and inbreeding, facilitate the investigation of difficult traits, as those involved in adaptation to different production systems and ecosystems, and extend the investigation of genotype-by-environment interaction. Future developments in animal breeding and genetics will be strongly based on the increasing availability of data, both molecular and phenotypic. However, our ability to dissect and understand livestock complex traits is still limited. The use of haplotypes instead of single markers and of more correct inheritance models may contribute to a better understanding of the genetics underlying livestock trait complexity and biology. The “Haplotype Analysis Applied to Livestock” Research Topic is intended to collect empirical studies and theoretical papers exploring, evaluating, and improving the use of haplotype analysis in livestock. After its conclusion, it managed to collect 12 articles from 89 authors, with subjects ranging from relatively straightforward diversity analyses to complex applications to unravel the genetic architecture of quantitative traits. Data used in the research studies were SNP microarray data, whole-genome sequences, or a combination of both. Haplotype size is influenced by recombination, and consequently by the level of linkage disequilibrium (LD) existing in a population. In livestock, LD has been largely influenced by human decisions since domestication, as humans have ruled livestock demography and recent selection intensity and direction. The extent of LD in livestock is reviewed by Qanbari, with a focus on cattle and chicken populations. The study provides insights into pair-wise allelic correlations and haplotype structure in the genomes of livestock. The concept of L