The procedure of estimating these variance components followed C ockerham (1954), assuming independence between two loci of each QTL pair and between QTL pairs.
In vitro studies of the haloarchaeal genus Haloferax have demonstrated their ability to frequently exchange DNA between species, whereas rates of homologous recombination estimated from natural populations in the genus Halorubrum are high enough to maintain random association of alleles between five loci.
The distribution of WC1 genes between two loci is reminiscent of the two TCR gamma loci for cattle and sheep (TRG1 and TRG2) where it is predicted that a number of duplication events and a subsequent translocation event resulted in the formation of the TRG2 locus [ 51].
Only markers with a MAF greater than 0.1 were considered in this analysis, because the power of detection of LD between two loci is minimal when at least one of the loci has an extreme allele frequency [ 20].
We created dummy variables coding the three genotypes per locus −1,0 and 1 and compared the likelihood of the model including the interaction term between two loci with the likelihood of the model with only the two main effects present.
Many animal breeding populations have also been created by the artificial admixing of two other populations (see [ 31] for a review), but the amount of LD created between two loci depends on the difference of allele frequencies at these loci between the initial populations.
Another E-QTL detected in the same environment was observed between two loci (Seq19B01 and TC3E02) of LG_AhXIII with 5.12 % PVE.
Third, we performed two tests that, according to recent comparative studies, are the most powerful for detecting multiplicative interaction between two loci in a series of scenarios, provided that the two loci are in linkage equilibrium [ 15, 16].
Exact Fisher tests were carried out for all the possible combinations to test whether the haplotype frequencies between two loci were the product of the allele frequency corresponding to the two loci.
The intensity of LD between two loci is measured based on the frequency of alleles, using indexes such as D, D' and r, and it ranges from completely random (| D| = | D'| = r = 0) to complete LD (| D| = 0·25, | D'| = r = 1) (Gaut and Long, 2003).
