A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS

Autores
Marcuzzi, Olivia; Calcaterra, Francisco; Olivera, Leónidas H.; Arizmendi, Analía; Henry, M.; Cunha Cardoso, Danielle; Echeverri, Amparo; Lirón, Juan Pedro; Fernández, María Elena; Andrade de Oliveira, Denise A.; Giovambattista, Guillermo
Año de publicación
2025
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The combined use of NGS technologies with bioinformatics tools has significantly advanced research by enabling comprehensive analyses of entire genomes, specific genomic regions of interest, and transcriptomes. Targeted NGS methods, which focus on smaller genome fractions, are widely used to study genetic diseases, epigenetic modifications, microbiomes, and environmental DNA, among other applications. This study aimed to develop a roadmap for detecting and selecting polymorphisms in candidate genes by integrating amplicon NGS-Target techniques with bioinformatics analyses. Sixty-eight genes associated with the hypothalamic-pituitary-gonadal (HPG) axis were selected to develop the amplicon NGS assay, comprising 730 regions that cover a total of 136,274 bp. This method was used to sequence 75 Guzerat cattle, a dual-purpose breed from Brazil, renowned for their high rusticity and adaptability. This Zebu cattle exhibit certain limitations, such as delayed puberty onset, which can reduce reproductive efficiency. Using the GATK protocol a total of 2,600 SNPs and 1,615 indels were detected. A series of consecutive filtering steps (maf, the detection of non-synonymous substitution, phylogenetic amino acid conservation, and biochemical properties) were used, resulting in a subset of 30 candidate SNPs. Then, these polymorphisms were analysed using bioinformatic tools (SIFT, PANTHER, PolyPhen2, and MutPred), identifying 5 SNPs with high effect on the protein. Their structure and stability were estimated using AlphaFold and DDMut. Finally, 3 candidate polymorphisms (IGF1R, LHCGR, TAC3R) with potentially significant effects on the protein remained to be validated through dynamic simulations or in vitro and in vivo experimental assays.
Instituto de Genética Veterinaria
Materia
Ciencias Veterinarias
Bovine
Genotyping by sequencing
Reproductive traits
Polymorphism
Protein modeling
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
SEDICI (UNLP)
Institución
Universidad Nacional de La Plata
OAI Identificador
oai:sedici.unlp.edu.ar:10915/193782
Acceder
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oai_identifier_str oai:sedici.unlp.edu.ar:10915/193782
network_acronym_str SEDICI
repository_id_str 1329
network_name_str SEDICI (UNLP)
spelling A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGSMarcuzzi, OliviaCalcaterra, FranciscoOlivera, Leónidas H.Arizmendi, AnalíaHenry, M.Cunha Cardoso, DanielleEcheverri, AmparoLirón, Juan PedroFernández, María ElenaAndrade de Oliveira, Denise A.Giovambattista, GuillermoCiencias VeterinariasBovineGenotyping by sequencingReproductive traitsPolymorphismProtein modelingThe combined use of NGS technologies with bioinformatics tools has significantly advanced research by enabling comprehensive analyses of entire genomes, specific genomic regions of interest, and transcriptomes. Targeted NGS methods, which focus on smaller genome fractions, are widely used to study genetic diseases, epigenetic modifications, microbiomes, and environmental DNA, among other applications. This study aimed to develop a roadmap for detecting and selecting polymorphisms in candidate genes by integrating amplicon NGS-Target techniques with bioinformatics analyses. Sixty-eight genes associated with the hypothalamic-pituitary-gonadal (HPG) axis were selected to develop the amplicon NGS assay, comprising 730 regions that cover a total of 136,274 bp. This method was used to sequence 75 Guzerat cattle, a dual-purpose breed from Brazil, renowned for their high rusticity and adaptability. This Zebu cattle exhibit certain limitations, such as delayed puberty onset, which can reduce reproductive efficiency. Using the GATK protocol a total of 2,600 SNPs and 1,615 indels were detected. A series of consecutive filtering steps (maf, the detection of non-synonymous substitution, phylogenetic amino acid conservation, and biochemical properties) were used, resulting in a subset of 30 candidate SNPs. Then, these polymorphisms were analysed using bioinformatic tools (SIFT, PANTHER, PolyPhen2, and MutPred), identifying 5 SNPs with high effect on the protein. Their structure and stability were estimated using AlphaFold and DDMut. Finally, 3 candidate polymorphisms (IGF1R, LHCGR, TAC3R) with potentially significant effects on the protein remained to be validated through dynamic simulations or in vitro and in vivo experimental assays.Instituto de Genética Veterinaria2025-10-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArticulohttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://doi.org/10.1186/s12863-025-01365-8http://sedici.unlp.edu.ar/handle/10915/193782enginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-025-01365-8info:eu-repo/semantics/altIdentifier/issn/2730-6844info:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by-nc-sa/4.0/Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)reponame:SEDICI (UNLP)instname:Universidad Nacional de La Platainstacron:UNLP2026-06-23T11:16:25Zoai:sedici.unlp.edu.ar:10915/193782Institucionalhttp://sedici.unlp.edu.ar/Universidad públicaNo correspondehttp://sedici.unlp.edu.ar/oai/snrdalira@sedici.unlp.edu.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:13292026-06-23 11:16:25.769SEDICI (UNLP) - Universidad Nacional de La Platafalse
dc.title.none.fl_str_mv A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
title A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
spellingShingle A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
Marcuzzi, Olivia
Ciencias Veterinarias
Bovine
Genotyping by sequencing
Reproductive traits
Polymorphism
Protein modeling
title_short A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
title_full A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
title_fullStr A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
title_full_unstemmed A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
title_sort A framework for identifying and prioritizing SNPs in genes of the hypothalamic- pituitary-gonadal axis in Guzerat cattle using amplicon-based NGS
dc.creator.none.fl_str_mv Marcuzzi, Olivia
Calcaterra, Francisco
Olivera, Leónidas H.
Arizmendi, Analía
Henry, M.
Cunha Cardoso, Danielle
Echeverri, Amparo
Lirón, Juan Pedro
Fernández, María Elena
Andrade de Oliveira, Denise A.
Giovambattista, Guillermo
author Marcuzzi, Olivia
author_facet Marcuzzi, Olivia
Calcaterra, Francisco
Olivera, Leónidas H.
Arizmendi, Analía
Henry, M.
Cunha Cardoso, Danielle
Echeverri, Amparo
Lirón, Juan Pedro
Fernández, María Elena
Andrade de Oliveira, Denise A.
Giovambattista, Guillermo
author_role author
author2 Calcaterra, Francisco
Olivera, Leónidas H.
Arizmendi, Analía
Henry, M.
Cunha Cardoso, Danielle
Echeverri, Amparo
Lirón, Juan Pedro
Fernández, María Elena
Andrade de Oliveira, Denise A.
Giovambattista, Guillermo
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Ciencias Veterinarias
Bovine
Genotyping by sequencing
Reproductive traits
Polymorphism
Protein modeling
topic Ciencias Veterinarias
Bovine
Genotyping by sequencing
Reproductive traits
Polymorphism
Protein modeling
dc.description.none.fl_txt_mv The combined use of NGS technologies with bioinformatics tools has significantly advanced research by enabling comprehensive analyses of entire genomes, specific genomic regions of interest, and transcriptomes. Targeted NGS methods, which focus on smaller genome fractions, are widely used to study genetic diseases, epigenetic modifications, microbiomes, and environmental DNA, among other applications. This study aimed to develop a roadmap for detecting and selecting polymorphisms in candidate genes by integrating amplicon NGS-Target techniques with bioinformatics analyses. Sixty-eight genes associated with the hypothalamic-pituitary-gonadal (HPG) axis were selected to develop the amplicon NGS assay, comprising 730 regions that cover a total of 136,274 bp. This method was used to sequence 75 Guzerat cattle, a dual-purpose breed from Brazil, renowned for their high rusticity and adaptability. This Zebu cattle exhibit certain limitations, such as delayed puberty onset, which can reduce reproductive efficiency. Using the GATK protocol a total of 2,600 SNPs and 1,615 indels were detected. A series of consecutive filtering steps (maf, the detection of non-synonymous substitution, phylogenetic amino acid conservation, and biochemical properties) were used, resulting in a subset of 30 candidate SNPs. Then, these polymorphisms were analysed using bioinformatic tools (SIFT, PANTHER, PolyPhen2, and MutPred), identifying 5 SNPs with high effect on the protein. Their structure and stability were estimated using AlphaFold and DDMut. Finally, 3 candidate polymorphisms (IGF1R, LHCGR, TAC3R) with potentially significant effects on the protein remained to be validated through dynamic simulations or in vitro and in vivo experimental assays.
Instituto de Genética Veterinaria
description The combined use of NGS technologies with bioinformatics tools has significantly advanced research by enabling comprehensive analyses of entire genomes, specific genomic regions of interest, and transcriptomes. Targeted NGS methods, which focus on smaller genome fractions, are widely used to study genetic diseases, epigenetic modifications, microbiomes, and environmental DNA, among other applications. This study aimed to develop a roadmap for detecting and selecting polymorphisms in candidate genes by integrating amplicon NGS-Target techniques with bioinformatics analyses. Sixty-eight genes associated with the hypothalamic-pituitary-gonadal (HPG) axis were selected to develop the amplicon NGS assay, comprising 730 regions that cover a total of 136,274 bp. This method was used to sequence 75 Guzerat cattle, a dual-purpose breed from Brazil, renowned for their high rusticity and adaptability. This Zebu cattle exhibit certain limitations, such as delayed puberty onset, which can reduce reproductive efficiency. Using the GATK protocol a total of 2,600 SNPs and 1,615 indels were detected. A series of consecutive filtering steps (maf, the detection of non-synonymous substitution, phylogenetic amino acid conservation, and biochemical properties) were used, resulting in a subset of 30 candidate SNPs. Then, these polymorphisms were analysed using bioinformatic tools (SIFT, PANTHER, PolyPhen2, and MutPred), identifying 5 SNPs with high effect on the protein. Their structure and stability were estimated using AlphaFold and DDMut. Finally, 3 candidate polymorphisms (IGF1R, LHCGR, TAC3R) with potentially significant effects on the protein remained to be validated through dynamic simulations or in vitro and in vivo experimental assays.
publishDate 2025
dc.date.none.fl_str_mv 2025-10-28
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Articulo
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.1186/s12863-025-01365-8
http://sedici.unlp.edu.ar/handle/10915/193782
url https://doi.org/10.1186/s12863-025-01365-8
http://sedici.unlp.edu.ar/handle/10915/193782
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/s12863-025-01365-8
info:eu-repo/semantics/altIdentifier/issn/2730-6844
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
eu_rights_str_mv openAccess
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-sa/4.0/
Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:SEDICI (UNLP)
instname:Universidad Nacional de La Plata
instacron:UNLP
reponame_str SEDICI (UNLP)
collection SEDICI (UNLP)
instname_str Universidad Nacional de La Plata
instacron_str UNLP
institution UNLP
repository.name.fl_str_mv SEDICI (UNLP) - Universidad Nacional de La Plata
repository.mail.fl_str_mv alira@sedici.unlp.edu.ar
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