Table 3 Threshold criteria used in the studies and description of epistatic analyses.

LABayes

2× ln(Bayes factor) ≥ 3

0.08

We equated 2× ln(Bayes factor) with a likelihood

ratio test statistic with one degree of freedom [17]

and calculated the p-value with a χ² approximation.

This method compared models with an increasing number of QTL,

for each chromosome, therefore far fewer tests were

necessary than for the other studies.

LDBayes

-

-

No significance tests were performed.

LDLA1

LD: F > 4^a

0.007

Tests were only performed on markers that had

a significant difference in allele frequency

between high/low offspring from each sire at p < 0.0016.

LDLA: LRT^b > 12.8

0.0003^c

Tests were only performed on markers that had

a significant difference in allele frequency

between high/low offspring from each sire

at p < 0.0016.

LDmulti

8×10^-6

An epistatic analysis was performed.

An epistatic model was tested against two-locus

marginal model (p < 8 × 10^-6)

for pairs of markers significant alone,

against one locus model (p < 1 × 10^-7)

for one significant and one non-significant marker,

and null model for pairs of non-significant markers

(p < 3 × 10^-9).

In last two cases, epistatic model was then tested

against two-locus marginal model at

p < 2 × 10^-5 and p < 5 × 10^-7, respectively.

LDHap

haplotype: HQ^d ≥ 15

2×10^-9e

single marker: LRT >32.8

10^-8

An epistatic analysis was performed

using single marker association on pre-corrected data.

For each 1 cM interval the marker in highest

average LD with the others in the same interval was found.

Each type of epistatic interaction

(e.g. additive by dominance) was then tested

for pairs of these markers at p < 10^-3.

When these were significant epistasis was tested

for all pairs of markers in the two intervals at

p < 10^-6 and pairs within 10 cM of each other were excluded.

LDLA2

LRT > 6

0.014^c

-