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

Abstract Background Umbilical 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. S...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Igor Ricardo Savoldi, Adriana Mércia Guaratini Ibelli, Maurício Egídio Cantão, Jane de Oliveira Peixoto, Michele Porto Pires, Marcos Antônio Zanella Mores, Essamai Brizola Lagos, Jader Silva Lopes, Ricardo Zanella, Mônica Corrêa Ledur
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Candidate genes Congenital defects RNA-Seq SNP Swine Biotechnology TP248.13-248.65 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/833be1fb71784d6da42ec1109fabcc0b
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:833be1fb71784d6da42ec1109fabcc0b
record_format	dspace
spelling	oai:doaj.org-article:833be1fb71784d6da42ec1109fabcc0b2021-11-14T12:26:59ZA joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs10.1186/s12864-021-08138-41471-2164https://doaj.org/article/833be1fb71784d6da42ec1109fabcc0b2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12864-021-08138-4https://doaj.org/toc/1471-2164Abstract Background Umbilical 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. Results In 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. Conclusions We 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.Igor Ricardo SavoldiAdriana Mércia Guaratini IbelliMaurício Egídio CantãoJane de Oliveira PeixotoMichele Porto PiresMarcos Antônio Zanella MoresEssamai Brizola LagosJader Silva LopesRicardo ZanellaMônica Corrêa LedurBMCarticleCandidate genesCongenital defectsRNA-SeqSNPSwineBiotechnologyTP248.13-248.65GeneticsQH426-470ENBMC Genomics, Vol 22, Iss 1, Pp 1-17 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Candidate genes Congenital defects RNA-Seq SNP Swine Biotechnology TP248.13-248.65 Genetics QH426-470
spellingShingle	Candidate genes Congenital defects RNA-Seq SNP Swine Biotechnology TP248.13-248.65 Genetics QH426-470 Igor Ricardo Savoldi Adriana Mércia Guaratini Ibelli Maurício Egídio Cantão Jane de Oliveira Peixoto Michele Porto Pires Marcos Antônio Zanella Mores Essamai Brizola Lagos Jader Silva Lopes Ricardo Zanella Mônica Corrêa Ledur A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
description	Abstract Background Umbilical 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. Results In 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. Conclusions We 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.
format	article
author	Igor Ricardo Savoldi Adriana Mércia Guaratini Ibelli Maurício Egídio Cantão Jane de Oliveira Peixoto Michele Porto Pires Marcos Antônio Zanella Mores Essamai Brizola Lagos Jader Silva Lopes Ricardo Zanella Mônica Corrêa Ledur
author_facet	Igor Ricardo Savoldi Adriana Mércia Guaratini Ibelli Maurício Egídio Cantão Jane de Oliveira Peixoto Michele Porto Pires Marcos Antônio Zanella Mores Essamai Brizola Lagos Jader Silva Lopes Ricardo Zanella Mônica Corrêa Ledur
author_sort	Igor Ricardo Savoldi
title	A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
title_short	A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
title_full	A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
title_fullStr	A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
title_full_unstemmed	A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
title_sort	joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs
publisher	BMC
publishDate	2021
url	https://doaj.org/article/833be1fb71784d6da42ec1109fabcc0b
work_keys_str_mv	AT igorricardosavoldi ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT adrianamerciaguaratiniibelli ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT mauricioegidiocantao ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT janedeoliveirapeixoto ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT micheleportopires ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT marcosantoniozanellamores ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT essamaibrizolalagos ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT jadersilvalopes ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT ricardozanella ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT monicacorrealedur ajointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT igorricardosavoldi jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT adrianamerciaguaratiniibelli jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT mauricioegidiocantao jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT janedeoliveirapeixoto jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT micheleportopires jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT marcosantoniozanellamores jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT essamaibrizolalagos jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT jadersilvalopes jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT ricardozanella jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs AT monicacorrealedur jointanalysisusingexomeandtranscriptomedataidentifiescandidatepolymorphismsandgenesinvolvedwithumbilicalherniainpigs
_version_	1718429239809671168

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

Ejemplares similares