Umbilical hernia (UH) is one of the most prevalent defects of swine, affecting their welfare and causing considerable economic loss. The molecular mechanisms behind UH in pigs remain poorly understood. The aim of this study was to verify the association between UH and previously reported DNA variants in the CAPN9, OSM, ITGAM, and NUGGC genes. A case/control study design was applied in two different crossbred cohorts of commercial fatteners containing 412 and 171 pigs, respectively. SNPs within CAPN9, OSM, and ITGAM were analyzed using Sanger sequencing, and 10 SNPs in CAPN9, five in OSM, and two in ITGAM were identified. A structural variant in the NUGGC gene was studied by droplet-digital PCR, and an elevated copy number was detected in only a single individual. Significant differences in allele frequencies for four SNPs in CAPN9 were detected. The haplotype analysis showed the effect on the risk of UH for two genes. The CAGGA haplotype within OSM and AT haplotype in ITGAM reduced the relative risk of UH by 52% and 45%, respectively, confirming that variants in those genes are associated with the risk of UH in pigs. Moreover, the interaction between the CAPN9 haplotype and the sex of animals had also significant impact on UH risk.

Freemartinism is a disorder of sex development (DSD) caused by the formation of placental anastomoses between fetuses of different sex. It leads to development of an abnormal reproductive tract in the female fetus, including the presence of testes or ovotestes. In pig production, such conditions can affect both reproductive performance and meat quality, through undesired boar taint. A common approach to diagnosing freemartinism is to detect leukocyte chimerism (XX/XY). In the study described here, we performed a complex evaluation of 28 DSD pigs with ambiguous external genitalia (enlarged clitoris, presence of scrotum, etc.). Sex chromosomes were cytogenetically identified by Giemsa staining, as well as with fluorescence in situ hybridization (FISH), while Y-linked (ZFY) and X-linked (ZFX) genes were detected by PCR-RFLP. Histological analysis of the gonads was performed on eosin–hematoxylin-stained microscope slides. Chromosome studies revealed that, of 28 DSD animals, 20 were freemartins (38,XX/38,XY), 2 had a female karyotype (38,XX), and 6 had a male karyotype (38,XY). Analysis of breeding data showed that the mean litter size in which DSD animals occurred was about 17. Histology of the gonads could be performed for 8 DSD pigs, including 6 freemartins and 2 XX DSD. In all these cases, testicular tissue without signs of spermatogenesis was seen. In XX DSD pigs, a copy number variation (CNV) polymorphism downstream from SOX9, tentatively associated with this type of DSD, was detected by FISH. On the other hand, the background of the XY DSD remains unknown. Since cytogenetic analysis is labor-intensive and time-consuming, we evaluated the usefulness of the droplet digital PCR (ddPCR) approach to diagnosing XX/XY leukocyte chimerism. Estimation of X and Y chromosome copy numbers was based on the quantitative detection of AMELX and AMELY genes. Different sex chromosome sets (XX, XY and XX/XY) were unequivocally identified by ddPCR. In conclusion, we suggest that freemartinism, beside testicular or ovotesticular XX DSD, is an emerging problem in highly prolific pigs and that detection of XX/XY leukocyte chimerism can be performed using a fast and reliable ddPCR approach.

Testicular XX disorder of sex development (XX DSD, SRY-negative), causing sterility, is quite frequently diagnosed in pig populations, however, its molecular background is still unknown. This disorder may affect carcass quality (boar taint) due to the presence of testicular tissue in animals with ambiguous female external genitalia. A chromosome fragment encompassing the SOX9 gene was previously considered as a candidate region in functional and association studies. We analyzed distribution of polymorphic variants in 5'UTR and in 3'-flanking regions of the SOX9 gene in a cohort of 12 XX DSD pigs and a panel of 116 normal females. Altogether, 8 previously known polymorphic sites were analyzed and no significant association under Bonferroni correction (P > 0.0063) between DSD phenotype and identified SNPs was found. The region harboring the SOX9 gene was also searched for the presence of copy number variation (CNV) by fluorescence in situ hybridization technique (FISH), using a set of 7 BAC probes. A potential CNV region, manifested by size variation (large and small) of fluorescence signals, produced by a single BAC probe hybridizing downstream (approx. 500 kb) of the SOX9 gene, was observed in 4 DSD cases. We conclude, that a new CNV polymorphism in the region harboring SOX9 gene can be considered as a promising marker for the DSD phenotype.