Sironen et al. BMC Genomics 2010, 11:699 http://www.biomedcentral.com/1471-2164/11/699 Page 3 of 8 KAD associated region Figure 2 Manhattan plot of the log10 based P-values across all chromosomes for the KAD in Finnish Yorkshire pig population. The KA- affected haplotypes of marked KAD associated region supported the expected recessive mode of inheritance and had the lowest P-values. After permutation, five SNPs were statistically significant (P-value = 0.0002, Table 1). Four of these SNPs (ALGA0086494, DRGA0015302, MARC0011300, and CASI0005693) are located within a 1.4 Mbp region and were in complete linkage disequilibrium (D’ = 1.0, r2 = 1.0). 12 out of 14 KAD cases had inherited two identical copies of the haplotype covering these and other SNPs between them, indicating an extended homozygos- ity in this region, and thus a common ancestral origin (Figure 3). All KA-affected boars shared a 0.7 Mbp homozygous region between SNPs DIAS0000367 and ALGA0086503 (Figure 3, additional file 1). The CASI0005693 SNP was in stronger linkage disequilibrium with ALGA0086494 and other significant SNPs com- pared with neighbouring SNPs, highlighting that the position of CASI0005693 may change following a more refined genome build in this region (see additional file 1). The fifth significant SNP (MARC0020403) was located 4 Mbp from the other four SNPs, and was shown to be in linkage disequilibrium (D’ = 1.0, r2 = 0.13). Candidate genes HECW2 and STK17b The most promising candidate gene Ubiquitin-protein ligase E3 (HECW2) was located within the haplotype of two SNPs with the highest P-values; ALGA0086494 and DRGA001532 (Table 1, additional file 1). All KA- affected animals were homozygous for these SNPs and only two control animals had the same homozygote alleles as KA-affected boars (Figure 3). Furthermore, one of these two animals appeared to have a SME- defect and another was removed from breeding at young age due to weak leg conformation and therefore no fresh sperm samples were available for analysis. The SME-defect is a cyst malformation in the sperm head, with indications that this is of acrosomal origin [17,18]. HECW2 is expressed in the testis [19] and functions in ubiquitin mediated proteolysis [20]. Ubiquitin signals have been detected during acrosome development [21] and deubiquitinating enzyme mUBPy is upregulated in the testis of wobbler mouse, which is infertile due to the lack of a functional acrosome [22]. Another gene within the KAD homozygous region was serine/threonine kinase 17b (STK17b, DRAK2, additional file 1). STK17b is a serine/threonine kinase, which has a role in the regulation of apoptosis [23-25]. STK17b is highly expressed in the testes where the apoptosis plays an important role during spermatogenesis. Even though Table 1 Genotype counts of cases and controls, nominal, and permutated P-values from the recessive model for the best KAD associated SNPs. Position, bp Genotypes cases Genotypes controls Recessive, P-value Permutated P-value SNP ALGA0086494 DRGA0015302 MARC0011300 CASI0005693 MARC0020403 Chr 15 15 15 15 15 93805621 93835894 94070930 95156189 90155667 14/0/0 14/0/0 14/0/0 14/0/0 12/2/0 2/8/11 2/8/11 2/8/11 2/8/11 0/7/14 1.41E-07 1.41E-07 1.41E-07 1.41E-07 1.66E-07 0.0002 0.0002 0.0002 0.0002 0.0002