Swine inflammation and necrosis syndrome (SINS) is a widespread disease in pigs, causing pain, suffering, and damage. Inflammation is documented at different levels based on clinical signs, histopathology, clinical chemistry, metabolomics and transcriptomics. The influence of sow and boar, as well as a heritability of around 0.3, suggest a genetic component to the disease. The aim of the present study was to identify functional single nucleotide polymorphisms (SNPs) in the vicinity of gene markers previously mapped using GWAS. DNA samples were available from 234 already phenotyped piglets. These animals were re-sequenced with additional prior enrichment. The nine selected chromosomal regions cover a total length of 22 Mbp. The genome-wide association study (GWAS) revealed two series with a total of 15 significant missense polymorphisms on chromosomes 11, 14, and 15. The homozygous genotypes of the most discriminating SNPs in series 1 resulted in SINS scores of 3.5 and 17.9, respectively. Despite the partial linkage of the SNPs, interesting candidate genes were defined. The results allow a significant narrowing of the possible candidate genes for understanding the pathogenesis of SINS and for future use in selection breeding to overcome the syndrome. Further studies should be carried out on larger animal populations.

Animal-based measures, such as detecting inflammation in areas like the tail, ears, teats, coronary band, heels and claws (Swine Inflammation and Necrosis Syndrome, SINS), are used to monitor animal health and welfare. When parameters deviate from the established range, these measures enable prompt action to adjust husbandry practices, feeding regimens and management strategies. In addition to environmental factors, genetics have been shown to play a key role in inflammation and necrosis processes, and selection can reduce the severity of the disease. This study examined whether different breeds of AI boar exhibit different signs of SINS and how these signs are associated with SINS in their offspring when they are suckling piglets and weaners. Initially, 286 AI boars of 7 breeds from a German artificial insemination center were evaluated for SINS. The following parameters were assessed: tail base, tail tip, ears, skin, scrotum, coronary bands, heels and claws. Subsequently, 23 Pietrain and Duroc boars were used in combination with a Topigs DL sow line. The progeny of the AI boars was evaluated as suckling and weaned piglets, with the assessment framework encompassing SINS traits. The results revealed significant differences between the breeds and lines, as well as a strong correlation between the SINS phenotypes of the AI boars and the SINS scores of their offspring. The offspring of the 25% most extreme boars exhibited a 17% variation in SINS scores. This association was particularly evident when comparing the boars’ tail base. However, the development of the boars’ heels and claws was found to be significantly influenced by mechanical environmental factors and not associated with the piglets’ scores. These findings imply that heritable, endogenous processes, as proposed for SINS, also visibly impact the phenotype of the AI boar. This study’s fundamental premise suggests that pre-selecting AI boars could mitigate the occurrence of SINS and enhance piglet health and welfare.

Tail docking is still used in pigs to reduce the prevalence of tail biting, although it is purely symptomatic and contrary to animal welfare. Genetic selection for shorter tails might, however, help to avoid tail docking and has therefore been proposed. A genetic basis for tail length is known for many species. Variability in tail length, including moderate heritability, has also been demonstrated in pigs. The aim of the present study was to identify genetic markers for tail length and to define candidate genes. To this end, 140 piglets were phenotyped and genotyped at 3 days of age and a genome-wide association study was performed. Seven SNPs were mapped on chromosomes 1, 2, 6, 11, and 15. Two linked SNPs on chromosome 2 resulted in a functional amino acid exchange. The genotypes at the SNPs were only associated with small differences in relative tail length of up to 16.5% (short genotype versus long genotype at SSC15), but at the same time with the occurrence of malformations in the form of tail kinks. The small effect size and the association between tail length and tail kinks, together with the generally pure symptomatic effect on tail biting, argue against the applicability of selection for shorter tails in pigs.