Fig 1.
A combined GWAS in four breeds identifies 35 loci associated with IgA levels.
(A-D) The distribution of IgA levels (0–1.40 g/l) clearly varied between the four breeds, here presented as relative frequency (%) and as box plots with the black box marking percentile 25 to 75 and red bar the median. The combined GWAS analyses from four runs (IgA levels divided into 2, 3, 4 and 5 groups) are presented in panel E-H, with the nominal significance defined at-log10p of 3.2 (grey line). In GSD (E), one region (14 SNPs) on CFA5 and single SNPs on CFA8 and CFA23 showed genome wide significance (red line at-log10p of 3.7) based on 1,000 permutations in five groups. In total, 35 suggestively associated loci (8 in GSD, 8 in GR, 3 in LR and 16 in SP) were defined based on LD of r2 >0.8 within 0.5 Mb of the top SNP. The fraction of phenotypic variance explained by (I) phenotypic variance explained by age was the lowest in GSD (4%) and remarkably high in LR (25%) and (J) the top SNP in each of the suggestively associated loci varied from 18% in GSD to 55% in SP.
Table 1.
Genomic loci nominally associated with IgA levels.
Fig 2.
Two risk haplotypes at the German shepherd CFA5 locus results in lower IgA levels.
(A) The genome wide significant locus on CFA5 consisted of 17 SNPs (grey circles) in LD (r2 >0.8) with the top SNP (white), with only the KIRREL3 gene within the associated region and six genes adjacent. (B) The 18 SNPs were phased into 12 different haplotypes, of which nine were rare (N <3). Haplotype 1 was the most common (N = 855) and the remaining two haplotypes; 12 and 3 were more similar to each other than to haplotype 1. (C) Dogs homozygous for haplotype 1 (1/1) represented all groups of IgA evenly, whereas dogs heterozygous 1/12 and 1/3 had significantly lower IgA levels compared to 1/1 (p = 0.04 and 0.0008, respectively).
Fig 3.
The SLIT1 gene harbours an associated haplotype in Shar-Pei and fixed blocks in German shepherd.
(A) In SP, four SNPs (grey circles) suggestively associated to IgA levels, were located within the first intron of SLIT1. (B) A distinct increase in the degree of genetic differentiation (FST) between dogs and wolves span a 75 kb region (windows with FST >0.67 are coloured in black) within the SLIT1 locus, with FST values of two consecutive 50 kb windows reaching 0.68 and 0.67, respectively (windows with FST >0.43 are coloured in grey). More extreme genetic differentiation was only seen in 7% of the whole dog genome, potentially indicating that IgA levels may have been affected in a pleiotropic manner by primary selection affecting another primary target (such as brain function) during dog domestication. Blocks of fixation were identified in GSD, spanning several regulatory sites including binding sites for the transcription factor CTCF. (C) The top SNPs in SP were in high LD (r2 >0.8) and phased into four haplotypes where two were common (1 and 4) and two were rare (2 and 3). Dogs homozygous for 1/1 had significantly higher IgA levels compared to dogs homozygous for 4 (4/4) and heterozygous 4/1 (p = 0.0005 and p = 0.03, respectively). Additionally, homozygous 4/4 had significantly lower IgA levels than heterozygous 4/1 (p = 0.006) indicating an additive effect of the risk and/or protective haplotype.
Table 2.
GRAIL pathways of the IgA associated regions.