The recent availability of dense panels of single nucleotide polymorphism (SNP) markers has permitted a finer investigation of genome architecture and a deeper understanding of the biology and evolution of livestock species. The utility of these marker panels is based on the concept that information on unobserved causal variants is captured by correlation (linkage disequilibrium) with nearby (observed) markers. 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 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 to improve the modeling of unobserved (causal) variants effect.
The potential utilization of haplotypes in genetic analysis is wide-ranging. The accuracy of genomic prediction and the precision of selection could be improved including the desired functional allele compared to the use of single markers only. In extensive conditions, e.g. in tropically adapted livestock and their crossbreds the haplotypes could be used to pinpoint exact combinations of desired variants. Also the characterization of livestock genetic diversity could be re-imagined in frequently analysed topics such as inbreeding and relatedness patters, but also strengthen newly emerging fields such as landscape genomics, or extended to the investigation of genotype by environment interactions, to include production aspects. These are merely examples of potential research questions.
The Research Topic welcomes empirical studies and theoretical papers exploring, evaluating and improving the use of haplotype analysis in livestock. Future developments in animal breeding and genetics point toward the ever increasing amount of data. Despite the abundance of data our understanding of the genome is imperfect, there is still a lot to be learnt and discovered. By taking the additional step towards haplotypes, a more complex and biologically more correct inheritance patterns the boundaries of science could be further advanced.
The recent availability of dense panels of single nucleotide polymorphism (SNP) markers has permitted a finer investigation of genome architecture and a deeper understanding of the biology and evolution of livestock species. The utility of these marker panels is based on the concept that information on unobserved causal variants is captured by correlation (linkage disequilibrium) with nearby (observed) markers. 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 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 to improve the modeling of unobserved (causal) variants effect.
The potential utilization of haplotypes in genetic analysis is wide-ranging. The accuracy of genomic prediction and the precision of selection could be improved including the desired functional allele compared to the use of single markers only. In extensive conditions, e.g. in tropically adapted livestock and their crossbreds the haplotypes could be used to pinpoint exact combinations of desired variants. Also the characterization of livestock genetic diversity could be re-imagined in frequently analysed topics such as inbreeding and relatedness patters, but also strengthen newly emerging fields such as landscape genomics, or extended to the investigation of genotype by environment interactions, to include production aspects. These are merely examples of potential research questions.
The Research Topic welcomes empirical studies and theoretical papers exploring, evaluating and improving the use of haplotype analysis in livestock. Future developments in animal breeding and genetics point toward the ever increasing amount of data. Despite the abundance of data our understanding of the genome is imperfect, there is still a lot to be learnt and discovered. By taking the additional step towards haplotypes, a more complex and biologically more correct inheritance patterns the boundaries of science could be further advanced.
