Linkage disequilibrium, genomic inbreeding and effective populations size to unravel population history

The use of single nucleotide polymorphism (SNP) data had become commonplace in animal breeding activities and management of livestock populations. The cost-effective genotyping allowed us to assess entire populations and learn about their history on the genomic level. This paper reviews several approaches that are commonly used in the context of genomic diversity in livestock, such as the linkage disequilibrium (LD) and assessment of autozygosity via runs of homozygosity (ROH). Both methods, however, are being used to assess the impact of natural or artificial selection on the livestock genome. Apart from these selection signatures, both the LD and ROH are used to assess the effective population size (Ne), which likewise, serves as a diversity management tool and describes the historical events in populations.