1. Coccidiosis data Phenotypes: Body weight gain (WG) Plasma coloration (PC) Cecal lesion score (LES) Hematocrit level (HEMA ) Rectal body temperature (T°) Genotypes: 1536 SNPs X Fayoumi Resistent White Leghorn Sensitive 6 F1 families 860 F2 animals

2. Preliminar epistasis analysis Phenotype: HEMATOCRIT level (%). Genotypes corrected for mendelian errors Data adjusted for sex and hatch effect VCE estimation using GS3 –Including SNP as random, normal effects

3. Choice of SNP of reference Training data: 2 genotype groups (11 and 22) with 150 animals by group at least for each SNP Additive values estimation for all SNPs in each group ( 2 values for each SNP) Estimate GEBVs for “12” animals (test set) through BLUP method by using SNP additive values estimated earlier Minimal GEBVs correlation used as criteria to pick out the SNP of reference

4. Checking on minimal BLUP correlation 1000 simulations under the H0 600 random animals splitted into 2 random groups The actual R for topList SNP of reference was - 0.31

5. Picking interacting SNPs 2 genotype groups (11 and 22) for the SNP of reference SNP additive values estimation (BAYESCPi method) for both groups Plot of estimated values

6. How to select interacting SNPs? Using pi value to get rid of SNP with no effect Different correlation values as threshold Others?