Table 1.
Description of traits and base models.
Table 2.
Pearson correlations between adjusted traits.
Fig 1.
Process of epistasis significance testing.
Graphic represents analysis of growth from 46–210 days for loci on chromosomes 1–4 paired with loci on chromosomes 5–7. The level of the residual sum of squares (SSE) below a significance threshold is shown for pairs of loci. Black lines represent QTL spans for loci identified in the independent QTL analysis. (A) Level of SSE below genomewide threshold (SSEgenome). (B) Level of SSE below locus-specific threshold (SSEspecific), where appropriate, and the genomewide threshold, otherwise. Black crosses show pairs taken forward for further testing and red crosses show pairs that were discarded because of edge effects.
Table 3.
Growth QTL.
Table 4.
Percentage residual variance explained by QTL.
Table 5.
Epistatic pairs.
Table 6.
Independent QTL.
Fig 2.
Epistatic network of Q2.1, Q3.1 and Q7.1.
Interactions are shown by lines between loci. Ages where epistasis occurred are shown at the top of the diagram. When a pair was pointwise significant at a second age this is shown in brackets underneath the interaction.
Fig 3.
Standardized genotypic values are shown for the nine genotype combinations at a pair of loci. Values were standardized by dividing them by the square root of the residual variance from the base model. Tick marks on the x-axis give the genotype at the first QTL and different line types represent the genotype at the second QTL. E represents the Erhualian allele and W the White Duroc allele. Genomewide significant epistasis is shown in black and pointwise significant interactions are shown in grey. The two pairs involving Q2.1 are each illustrated for a selected genotype at the third locus. (A) Epistasis between Q7.1 and Q4.2 for birth weight. (B) Epistasis between Q7.1 and Q3.1 for growth from days 21–46. (C) Epistasis between Q7.1 and Q4.2 for growth from days 46–120. (D) Epistasis between Q2.1 and Q7.2 for growth from days 46–120. (E) Epistasis between Q1.2 and Q8 for growth from days 120–210. (F) Epistasis between Q2.2 and Q4.1 for growth from days 120–210. (G) Epistasis between Q13 and Q6.1 for growth from days 120–210. (H) Epistasis between Q13 and Q6 for growth from days 46–210. (I) Epistasis between Q2.1 and Q7.2 when Q3.1 has genotype EW for growth from days 46–210. (J) Epistasis between Q2.1 and Q3.1 when Q7.2 has genotype EE for growth from days 46–210. (K) Epistasis between Q1.2 and Q8 for growth from 46–210 days.
Table 7.
Epistatic effects and values estimated in the independent effects model.
Table 8.
Residual variance explained by independent effects model and additional variance explained by epistatic model.