Values greater than 1 indicate a hitch-hiking effect.
For all scenarios, GBLUP showed the largest hitch-hiking effect, followed by BL, BLUP and PS.
In presenting the hitch-hiking effect, only the generations in which QTL were not yet fixed were considered because linked loci would no longer have a hitch-hiking effect if the QTL was fixed [ 10].
If a harmful variation is generated around the Mhc gene via the hitch-hiking effect, then it is likely to be selected against by genetic recombination.
In general, a higher heritability and a lower number of QTL (i.e. a higher allele substitution effect) could result in a stronger hitch-hiking effect surrounding the QTL.
Therefore, it would be interesting to investigate the hitch-hiking effect with much more QTL in further studies, since the suggestion that pedigree inbreeding serves as a good estimator of true inbreeding is difficult to verity from the current results.
Rannala and Reeve (2004) made an assumption that the historical allele frequencies of neutral markers are constant during the whole process, which may not hold for real populations, especially for markers under the hitch-hiking effect.
When implementing long-term genomic selection, strategies for genomic control of inbreeding are essential, due to a considerable hitch-hiking effect, regardless of the method that is used for prediction of EBV.
Signatures of selection can be recognized when adjacent SNPs all show high FST, due to the hitch-hiking effect, implying divergent selection between breeds, or where adjacent SNPs all show low FST, implying balancing selection between breeds.
Figure 5 illustrates the relationship between the hitch-hiking effect and the distance between LN and its nearest QTL and shows a distinct peak in the level of hitch-hiking in the vicinity of the QTL for all scenarios and for all selection criteria.
Signatures of selection can be recognized when adjacent SNPs all show high FST [ 2], due to the hitch-hiking effect [ 33], implying divergent selection between breeds, or where adjacent SNPs all show low FST, implying balancing selection between breeds [ 15, 21].
