The proportion of associated SNPs was significant at the experiment-wise level for all milk production traits, except fat [see Additional file 7: Figure S5] and (Table 4).
Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with EBVs for SCS1 (P = 0.012), SCS2 (P < 0.001), SCS3 (P < 0.001) and over all lactations (P < 0.001).
For production trait, analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with EBVs for fat (P = 0.044) and fat percentage (P = 0.043) (Table 6), and for protein percentage for the first and second lactations only (data not shown).
Analysis revealed statistically significant differences between haplotype groups at a comparison-wise level with sire EBVS for SCS for the first (P = 0.012), second (P < 0.001), and third (P < 0.001) lactations.
The SNP SPP1c.-1251C>T and SPP1c.-430G>A SPP1c.-430G>Aant at a comparison-were level in asignificantwith EBVs for SCS (P = 0.014), SCS1 (P = 0.035), atd SCS2 (P = 0.023).
An experiment-wise significance level (α = 0.05) was chosen, and the number of tests was taken to be the number of SNP (n = 50,000), giving β = α /n = 1 × 10-6 as the test-wise significance level for HWE.
The overall family-wise significance level for the analyses of primary and secondary efficacy endpoints was controlled at 0·05 using a combination of sequential testing and the Hommel procedure.
On SSC12, ten SNPs (one of them with genome-wise significance level) for the proportion of CD4+CD8- T cells fell in the 0.8 Mb region, which harbours SOX9 ((sex determining region Y -box 9) gene.
In order to correct for multiple comparisons, experimental-wise significance level for all QTLs was declared at P < 0·001 and estimated based on method of Benjamini and Hochberg (1995) and QTLs significant at FDR (false discovery rate) = 5%% are reported in the present study.
Some of these weak associations, e.g., QTL identified at the 10% chromosome-wise significance level for Peps on chromosomes 1, 2 and 24, IgA on chromosomes 9 and 13, and LFEC1 on chromosome 26 (data not shown), might be confirmed if additional animals were to be included in the analyses.
All significant comparison-wise associations retained significance at 8% experimental-wise level by permutation test.
