  Beyond GWAS: alternatives to localize QTLs in farm animals. Two methods that
could be used for QTL mapping as alternatives to standard GWAS are presented.
The first relies on the differential frequency of runs of homozygosity (ROH) in
groups of animals (e.g. cases and controls), while the second stems from
resampling techniques used for the prediction of carriers of a mutation, and is
based on the frequency of inclusion of polymorphisms (SNP) in the predictive
model. ROH were applied to the detection of reproductive diseases in
Holstein-Friesian cattle, while resampling was applied to the detection of
carriers of the BH2 haplotype in Brown Swiss cattle. These alternative
approaches may complement GWAS analyses in localizing more accurately QTLs for
traits of interest in livestock.
