Abstract
Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR <0.05), being 145 downregulated and 85 upregulated in the affected compared to the normal pigs. A total of 68 significant biological processes were identified and the most relevant were extracellular matrix, immune system, anatomical development, cell adhesion, membrane components, receptor activation, calcium binding and immune synapse. The results pointed out ACAN, MMPs, COLs, EPYC, VIT, CCBE1 and LGALS3 as strong candidates to trigger umbilical hernias in pigs since they act in the extracellular matrix remodeling and in the production, integrity and resistance of the collagen. We have generated the first transcriptome of the pig umbilical ring tissue, which allowed the identification of genes that had not yet been related to umbilical hernias in pigs. Nevertheless, further studies are needed to identify the causal mutations, SNPs and CNVs in these genes to improve our understanding of the mechanisms of gene regulation.
Highlights
Pig husbandry has become one of the most important activities in livestock production and increment in pig production in the last years has been observed [1,2]
The histopathological evaluation has shown that, in general, the umbilical ring tissue of animals affected with umbilical hernia was thickened by an abundant proliferation of dense connective tissue
Some studies have been performed to identify the genetic factors involved in the development of umbilical hernias, and quantitative trait loci (QTL) regions, SNPs and candidate genes associated with the appearance of this defect have been detected [5,11,12,13]
Summary
Animals and samplingIn this study, 10 unrelated Landrace purebred females from the same nucleus farm, with high sanitary status, located in Santa Catarina State, south of Brazil, with approximately 90 days of age were used in a case and control design. The UH occurrence in this line is around 1.7% From those 10 animals, 5 were affected with umbilical hernia (with intestinal loops forming a herniary sac) and 5 were normal (with no malformations and coming from families with no Transcriptome analysis of umbilical hernias in pigs history of hernias). The animals were transported to the Embrapa Swine and Poultry National Research Center, located in Concordia-SC, to be evaluated and necropsied. Euthanasia was performed by electrocution desensitization for 10 seconds, followed by bleeding, according to the practices recommended by the Embrapa Swine and Poultry National Research Center Ethics Committee on Animal Utilization, approved under protocol #011/2014. Tissue samples were collected from the umbilical ring of normal and umbilical hernia-affected animals. Samples were placed in 4% paraformaldehyde buffer for histopathological analysis and those for gene expression analysis were immediately frozen in liquid nitrogen and, subsequently, stored at -80 ̊C for further RNA extraction
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