The highest differentiation peak was found in BTA7:
~50 Mb. This region had previously been identified as
a site containing a signature of selection [12,24]. A
number of features were also identified in this region, including
different LD structure between zebu and taurine
cattle, the presence of imprinted genes, and potential association
to fertility traits. This region is among the very
few regions for positive selection that also contain
CNVs; which may seem antagonistic to purifying selection.
It is not clear at this point how CNV are being kept
in the population at this site and at the same time there
is a differential signal for zebu and taurine cattle. It
could be in consequence that these CNV being less
likely in LD with neighbouring SNPs, because similar
CNVs can occur on different haplotype backgrounds.
Another possibility is that duplications can initiate gene
conversion events, which can then decrease the LD surrounding
such variants. Interestingly, CNVs were often
observed at most candidate sites for balancing selection,
where variation is expected.