Haplotypes were reconstructed in the three breeds with
PHASE. We found 18 haplotypes present in the DNAJA1
locus: 8 haplotypes in BLA, 12 in CHA, and 6 in LIM,
with only 3 haplotypes shared by all three populations
(Table 3). Three haplotypes were unique to BLA, 8 were
unique to CHA and two haplotype specific to LIM were
detected. Two different haplotypes were found only in
two breeds (one haplotype common to BLA and CHA,
and one haplotype is shared by BLA and LIM). The most
frequent haplotypes are present in all the breeds studied,
whereas the rare haplotypes are exclusive to specific
breeds. The three haplotypes shared by all three populations
(Haplotypes 3, 14 and 17) comprised 93.3, 78.7 and
96.9% of all haplotypes observed in BLA, CHA and LIM,
respectively.