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Background <p>Hernias, particularly umbilical hernias (UH), are prevalent anatomical anomalies in swine, leading to significant welfare issues and economic losses. Besides environmental factors also genetic components contribute to the development of UHs, though the exact mechanisms remain unclear. This study employed a multiple approaches integrating RNA-seq, DNA methylation analysis, Sanger sequencing, droplet digital PCR and western blot analysis to investigate the genetic and epigenetic underpinnings of UH in pigs. Muscle tissue from affected and control pigs was examined to identify differentially expressed genes (DEGs) and associated pathways.</p> Results <p>We found 59 significant DEGs, including <i>SIM1</i>, <i>PITX1</i>, <i>HOXA7</i>, <i>METTL21C</i>, <i>PVALB</i>, <i>ALX1</i>, <i>EYA2</i>, and <i>TBX1</i>. Interestingly, RNA-seq analysis of <i>METTL21C</i> revealed its significant upregulation in UH-affected pigs. This was corroborated by epigenetic analysis, which identified hypomethylation at four CpG sites in the <i>METTL21C</i> within potential regulatory region, aligning with increased mRNA levels. Furthermore, Sanger sequencing uncovered an SNP (rs330073569) in the <i>METTL21C</i> regulatory region, which was significantly associated with UH condition. This SNP can potentially alter transcription factor binding leading to enhanced <i>METTL21C</i> transcription, and putatively contributing to the gene’s increased expression in UH pigs.</p> Conclusions <p>This study highlights potential genetic and epigenetic factors in UH etiology. The most significant result suggests that <i>METTL21C</i> plays an important role in the development of UH. This finding makes this gene a promising candidate for further research aimed at better characterizing umbilical hernia in pigs and at potentially eliminating undesirable variants from the gene pool.</p>

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Genetic and epigenetic markers in the METTL21C gene associated with umbilical hernia in pigs

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月18日

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  • Jakub Wozniak,
  • Alicja Szabelska-Beresewicz,
  • Joanna Zyprych-Walczak,
  • Rafal Niemyjski,
  • Klaudia Dudek,
  • Monika Stachowiak,
  • Joanna Nowacka-Woszuk

摘要

Background

Hernias, particularly umbilical hernias (UH), are prevalent anatomical anomalies in swine, leading to significant welfare issues and economic losses. Besides environmental factors also genetic components contribute to the development of UHs, though the exact mechanisms remain unclear. This study employed a multiple approaches integrating RNA-seq, DNA methylation analysis, Sanger sequencing, droplet digital PCR and western blot analysis to investigate the genetic and epigenetic underpinnings of UH in pigs. Muscle tissue from affected and control pigs was examined to identify differentially expressed genes (DEGs) and associated pathways.

Results

We found 59 significant DEGs, including SIM1, PITX1, HOXA7, METTL21C, PVALB, ALX1, EYA2, and TBX1. Interestingly, RNA-seq analysis of METTL21C revealed its significant upregulation in UH-affected pigs. This was corroborated by epigenetic analysis, which identified hypomethylation at four CpG sites in the METTL21C within potential regulatory region, aligning with increased mRNA levels. Furthermore, Sanger sequencing uncovered an SNP (rs330073569) in the METTL21C regulatory region, which was significantly associated with UH condition. This SNP can potentially alter transcription factor binding leading to enhanced METTL21C transcription, and putatively contributing to the gene’s increased expression in UH pigs.

Conclusions

This study highlights potential genetic and epigenetic factors in UH etiology. The most significant result suggests that METTL21C plays an important role in the development of UH. This finding makes this gene a promising candidate for further research aimed at better characterizing umbilical hernia in pigs and at potentially eliminating undesirable variants from the gene pool.