Table 4.

Lead SNP (SNP with highest p-value) within genomic regions significantly, or suggestively associated with KLH-binding natural antibody (NAb) titers, and total antibody concentrations (μg/ml) in an adolescent White Leghorn chicken population.

Trait	Chromosome	Position	SNP name	−log10(p)	nAA	nAB	nBB	AA (SE)a	ABa	BB (SE)a	${\mathrm{\sigma }}_{\text{SNP}}^{\text{2}}∕{\mathrm{\sigma }}_{\text{a}}^{\text{2}}$ (%)
IgM	4	69,702,481	rs15614874	13.84b	477	824	326	−0.58y (0.06)	0z	0.01z (0.06)	57.6
IgT		69,587,709	rs313004783	5.21	480	807	338	−0.34y (0.08)	0z	0.09yz (0.08)	16.0
tIgM		69,814,286	rs313437715	6.90b	465	821	333	−40.7y,c	0z	6.2z,c	14.1
IgA	9	12,261,658	rs15969591	4.58	814	708	86	0.18 (0.06)	0	0.53 (0.13)	13.5
IgAd	18	10,131,465	rs10731438	4.55	1,133	430	45	−0.05y (0.07)	0y	0.78z (0.18)	0.2

Analyzed traits were KLH-binding IgM NAb (IgM) titer, KLH-binding IgA NAb (IgA) titer, KLH-binding IgG NAb (IgG) titer, total KLH-binding NAb (IgT) titer, total IgM (tIgM) concentration, total IgA (tIgA) concentration, total IgG (tIgG) concentration, and total antibody (tIgT) concentration. tIgM, tIgA, tIgG, and tIgT were log₁₀-tranformed for the analyses. The table shows: trait, chromosome of associated genomic region, position of lead SNP, name of lead SNP, −log₁₀(p-value_{lead SNP}) (italic for suggestive association), number of chickens per genotype class, effect of genotype classes (and SE) in titer points for NAb, or μg/ml for total antibody concentrations, and percentage of additive genetic variance explained by the lead SNP (${\mathrm{\sigma }}_{\text{SNP}}^{\text{2}}∕{\mathrm{\sigma }}_{\text{a}}^{\text{2}}\times \mathrm{100\%}$). Genotype classes with significantly (p-value ≤ 0.05) different effects are indicated by different superscripts (y or z). Positions are based on Gallus_gallus-5.0.

^aGenotype effects are compared to the AB genotype class, which was set to 0 (zero).

^bGenomic control was applied to the test statistic.

^cThe estimated effects are reported in μg/ml but were calculated from the predicted values on a log₁₀-scale. Predicted values were 2.43 for AA, 2.49 for AB, and 2.50 for BB. Estimated effects based on log₁₀-analysis were −0.06 (0.01) for AA and 0.01 (0.01) for BB.

^dRegion contains three SNP with similar −log₁₀(p-value_SNP). The genotyped SNP is reported.