A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs

BMC Genomics

Jader Silva Lopes¹  Maurício Egídio Cantão²  Marcos Antônio Zanella Mores²  Adriana Mércia Guaratini Ibelli³  Jane de Oliveira Peixoto³  Michele Porto Pires⁴  Essamai Brizola Lagos⁵  Igor Ricardo Savoldi⁶  Mônica Corrêa Ledur⁷  Ricardo Zanella⁸ 

[1] BRF S.A, 82305-100, Curitiba, PR, Brazil;Embrapa Suínos e Aves, 321, 89715-899, Concórdia, SC, Brazil;Embrapa Suínos e Aves, 321, 89715-899, Concórdia, SC, Brazil;Programa de Pós-Graduação em Ciências Veterinárias, Universidade Estadual do Centro-Oeste, 85040-167, Guarapuava, PR, Brazil;Instituto Catarinense de Sanidade Agropecuária, 88034001, Florianópolis, SC, Brazil;Programa de Pós-Graduação em Zootecnia, Universidade Estadual de Ponta Grossa, 84030-900, Ponta Grossa, PR, Brazil;Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, 89815-630, Chapecó, SC, Brazil;Programa de Pós-Graduação em Zootecnia, Universidade do Estado de Santa Catarina, UDESC-Oeste, 89815-630, Chapecó, SC, Brazil;Embrapa Suínos e Aves, 321, 89715-899, Concórdia, SC, Brazil;Universidade de Passo Fundo, 99052-900, Passo Fundo, RS, Brazil;Programa de Mestrado em BioExperimentação, Universidade de Passo Fundo, 99052-900, Passo Fundo, RS, Brazil;

关键词: Candidate genes;    Congenital defects;    RNA-Seq;    SNP;    Swine;   

DOI  :  10.1186/s12864-021-08138-4

来源: Springer

【 摘 要 】

BackgroundUmbilical Hernia (UH) is characterized by the passage of part of the intestine through the umbilical canal forming the herniary sac. There are several potential causes that can lead to the umbilical hernia such as bacterial infections, management conditions and genetic factors. Since the genetic components involved with UH are poorly understood, this study aimed to identify polymorphisms and genes associated with the manifestation of umbilical hernia in pigs using exome and transcriptome sequencing in a case and control design.ResultsIn the exome sequencing, 119 variants located in 58 genes were identified differing between normal and UH-affected pigs, and in the umbilical ring transcriptome, 46 variants were identified, located in 27 genes. Comparing the two methodologies, we obtained 34 concordant variants between the exome and transcriptome analyses, which were located in 17 genes, distributed in 64 biological processes (BP). Among the BP involved with UH it is possible to highlight cell adhesion, cell junction regulation, embryonic morphogenesis, ion transport, muscle contraction, within others.ConclusionsWe have generated the first exome sequencing related to normal and umbilical hernia-affected pigs, which allowed us to identify several variants possibly involved with this disorder. Many of those variants present in the DNA were confirmed with the RNA-Seq results. The combination of both exome and transcriptome sequencing approaches allowed us to better understand the complex molecular mechanisms underlying UH in pigs and possibly in other mammals, including humans. Some variants found in genes and other regulatory regions are highlighted as strong candidates to the development of UH in pigs and should be further investigated.

【 授权许可】

CC BY