Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs

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.

Reproduction traits of heterozygousmyostatinknockout sows crossbred with homozygousmyostatinknockout boars

“…One possible reason for the higher rate of umbilical hernias is that the pigs used in our study are ternary hybrid pigs (Duroc boars × Landrace × Large White). The other reason may is related to genomics as genomic analysis showed that collagen‐related genes in pigs with umbilical hernia were down‐regulated (Souza et al., 2020), while the collagen content in our homozygous MSTN −/− pigs muscle was significantly decreased (Data not shown). This may explain the higher rate of umbilical hernias in homozygous MSTN −/− piglets.…”

Genes and SNPs Involved with Scrotal and Umbilical Hernia in Pigs

“…Eighteen pigs were selected from a Landrace female line from the same nucleus farm, located in Santa Catarina State, SC, Brazil. From those, five were females affected (case) with UH, five healthy (control) females for UH, four males with SH and four control males for SH, as described by Souza et al [ 7 ] and Romano et al [ 6 ]. Control animals were healthy pigs, without any type of hernia, came from hernia-free litter and were from the same management group of their respective cases.…”

“…The samples previously collected were routinely processed for histopathology as described by Souza et al [ 7 ]. Briefly, sample tissues were dehydrated in increasing concentrations of ethanol, diaphanized with xylol and embedded in paraffin.…”

“…Meat quality and feed efficiency are traits that have been prioritized by genetic breeding programs [ 2 , 3 , 4 ]. However, in recent years, studies have also been carried out to improve our knowledge on diseases that persist in production, which bring losses to the entire chain [ 5 , 6 , 7 , 8 , 9 ]. Among these, scrotal (SH)/inguinal (IH) and umbilical hernias (UH) are birth defects often found in pigs [ 10 ], causing pain and discomfort to the animals and, consequently, economic losses related to reduced performance [ 11 , 12 ] and increased risk of death [ 13 ].…”

“…Another approach that has recently been used to investigate the genetic mechanisms involved with these defects is the whole transcriptome study. Functional candidate genes were prospected for scrotal [ 6 ] and umbilical [ 7 ] hernias based on differentially expressed (DE) genes between affected and unaffected pigs in the inguinal and umbilical ring tissues, respectively, using RNA sequencing (RNA-Seq). Information about gene expression in those tissues is scarce and there are still many gaps to be elucidated.…”