The Sol 33 locus had one fixed allele in the four populations (Table 2).
All loci showed monomorphic states (fixed alleles) in at least one population: Aguachil has one fixed allele in two loci (Sat 5 and Sol 33), San Francisco del Mar Viejo in three loci (Sat 5, Sat 12 and Sol 33), Montecillo Santa Cruz in three loci (Sat 2, Sat 3 and Sol 33), and Santa Maria del Mar in two loci (Sat 2 and Sol 33) (Table 2).
Figure 3 shows that the predicted variance-covariance components, equations (15) and (16), fit very well to those observed in the simulation with fixed allele effects.
The analyses so far have focused on variance-covariance components for fixed allele effects at each locus.
There were no fixed allele
differences between populations, and exact tests for population differentiation revealed significant allele differences only in six of the 22 polymorphic loci (6GPDH, PEP-A, PEP-B, PGI, EST-2, G6PDH; P [less than] 0.05).
When the series of POD tests (Tests 2 and 3) were applied, most of the non-POD QTL with large or medium effects (close to 100%) were not classified as POD under the assumption of fixed alleles
in the grand parents.
However, the high number of fixed (-) alleles has a smaller effect than might be expected on the genetic mean attained at Cycle 15 because the fixed alleles
have allelic effects lower than one.
The proportion of SNPs with zero MAF was highest in Hanwoo, reflecting the presence of single fixed alleles
. On the other hand, all the breeds had almost similar values for intermediate and common MAF classes.
In most cases, these were common alleles shared with other species, although two fixed alleles
, one in slow LAP and one in slow GOT were absent or rare outside the clade.