Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system

Autores
Arizmendi, Analía; Barrientos, Laura Soledad; Crespi, Julian Alejandro; Rudd Garces, Gabriela; Giovambattista, Guillermo; Peral Garcia, Pilar
Año de publicación
2019
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Next-generation sequencing (NGS) is a powerful tool to study DNA or RNA samples. New methods and protocols based on NGS have been developed to carry out the analysis of genetic variation for animal parentage testing, disease screening and trait detection. Targeted NGS is aimed at achieving targeted enrichment of genome subregions to reduced significantly the sequencing of genomic loci of interest, as well as costs and efforts, compared with whole-genome sequencing (WGS). We generated genotyping information of 387 targets from 95 clinical canine samples (76 Doberman and 19 Toy Poodle dogs) and 3 control samples using AgriSeq Targeted GBS. Based on these data, we calculated the exclusion power of 228 parentage markers with Cervus 3.0 software. Furthermore, we detected disease/trait markers presenting polymorphism and calculated their allele frequencies within each breed. In the case of parentage markers, the assigned parents showed a higher LOD score (>1.22 x1016), and the available pedigree data of offspring agreed with the assigned parent information. Interestingly, full siblings were also assigned like parents. On the other hand, we found 19 polymorphic disease/trait markers in the total sample, 3 of which (progressive rod-cone degeneration, von Willebrand disease 1 and dilated cardiomyopathy) were validated by pyrosequencing with 100% concordance. The mutant allele for cone-rod dystrophy3 (CRD3) was found in both groups, a variant which had not been reported in either breed to date. Sequencing of genomic loci of interest, costs and efforts can be reduced significantly with targeted NGS as compared with WGS. The AgriSeq Targeted GBS is a very good alternative for the massive genetic evaluation of animal populations.
Fil: Arizmendi, Analía. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Hospital Escuela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Barrientos, Laura Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Crespi, Julian Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Rudd Garces, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
37th International Society of Animal Genetics (ISAG) Conference
Lleida
España
International Society of Animal Genetics (ISAG)
Materia
dogs and related species
animal breeding
high-throughput sequencing
polymorphism
genomic selection
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/195360
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/195360
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping systemArizmendi, AnalíaBarrientos, Laura SoledadCrespi, Julian AlejandroRudd Garces, GabrielaGiovambattista, GuillermoPeral Garcia, Pilardogs and related speciesanimal breedinghigh-throughput sequencingpolymorphismgenomic selectionhttps://purl.org/becyt/ford/4.3https://purl.org/becyt/ford/4Next-generation sequencing (NGS) is a powerful tool to study DNA or RNA samples. New methods and protocols based on NGS have been developed to carry out the analysis of genetic variation for animal parentage testing, disease screening and trait detection. Targeted NGS is aimed at achieving targeted enrichment of genome subregions to reduced significantly the sequencing of genomic loci of interest, as well as costs and efforts, compared with whole-genome sequencing (WGS). We generated genotyping information of 387 targets from 95 clinical canine samples (76 Doberman and 19 Toy Poodle dogs) and 3 control samples using AgriSeq Targeted GBS. Based on these data, we calculated the exclusion power of 228 parentage markers with Cervus 3.0 software. Furthermore, we detected disease/trait markers presenting polymorphism and calculated their allele frequencies within each breed. In the case of parentage markers, the assigned parents showed a higher LOD score (>1.22 x1016), and the available pedigree data of offspring agreed with the assigned parent information. Interestingly, full siblings were also assigned like parents. On the other hand, we found 19 polymorphic disease/trait markers in the total sample, 3 of which (progressive rod-cone degeneration, von Willebrand disease 1 and dilated cardiomyopathy) were validated by pyrosequencing with 100% concordance. The mutant allele for cone-rod dystrophy3 (CRD3) was found in both groups, a variant which had not been reported in either breed to date. Sequencing of genomic loci of interest, costs and efforts can be reduced significantly with targeted NGS as compared with WGS. The AgriSeq Targeted GBS is a very good alternative for the massive genetic evaluation of animal populations.Fil: Arizmendi, Analía. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Hospital Escuela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Barrientos, Laura Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Crespi, Julian Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Rudd Garces, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; ArgentinaFil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina37th International Society of Animal Genetics (ISAG) ConferenceLleidaEspañaInternational Society of Animal Genetics (ISAG)International Society of Animal Genetics2019info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectConferenciaBookhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/195360Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system; 37th International Society of Animal Genetics (ISAG) Conference; Lleida; España; 2019; 16-16CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.isag.us/proceedings.aspinfo:eu-repo/semantics/altIdentifier/doi/https://www.isag.us/Docs/Proceedings/ISAG2019_Proceedings.pdfInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:54:42Zoai:ri.conicet.gov.ar:11336/195360instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:54:42.333CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
title Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
spellingShingle Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
Arizmendi, Analía
dogs and related species
animal breeding
high-throughput sequencing
polymorphism
genomic selection
title_short Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
title_full Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
title_fullStr Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
title_full_unstemmed Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
title_sort Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system
dc.creator.none.fl_str_mv Arizmendi, Analía
Barrientos, Laura Soledad
Crespi, Julian Alejandro
Rudd Garces, Gabriela
Giovambattista, Guillermo
Peral Garcia, Pilar
author Arizmendi, Analía
author_facet Arizmendi, Analía
Barrientos, Laura Soledad
Crespi, Julian Alejandro
Rudd Garces, Gabriela
Giovambattista, Guillermo
Peral Garcia, Pilar
author_role author
author2 Barrientos, Laura Soledad
Crespi, Julian Alejandro
Rudd Garces, Gabriela
Giovambattista, Guillermo
Peral Garcia, Pilar
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv dogs and related species
animal breeding
high-throughput sequencing
polymorphism
genomic selection
topic dogs and related species
animal breeding
high-throughput sequencing
polymorphism
genomic selection
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.3
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Next-generation sequencing (NGS) is a powerful tool to study DNA or RNA samples. New methods and protocols based on NGS have been developed to carry out the analysis of genetic variation for animal parentage testing, disease screening and trait detection. Targeted NGS is aimed at achieving targeted enrichment of genome subregions to reduced significantly the sequencing of genomic loci of interest, as well as costs and efforts, compared with whole-genome sequencing (WGS). We generated genotyping information of 387 targets from 95 clinical canine samples (76 Doberman and 19 Toy Poodle dogs) and 3 control samples using AgriSeq Targeted GBS. Based on these data, we calculated the exclusion power of 228 parentage markers with Cervus 3.0 software. Furthermore, we detected disease/trait markers presenting polymorphism and calculated their allele frequencies within each breed. In the case of parentage markers, the assigned parents showed a higher LOD score (>1.22 x1016), and the available pedigree data of offspring agreed with the assigned parent information. Interestingly, full siblings were also assigned like parents. On the other hand, we found 19 polymorphic disease/trait markers in the total sample, 3 of which (progressive rod-cone degeneration, von Willebrand disease 1 and dilated cardiomyopathy) were validated by pyrosequencing with 100% concordance. The mutant allele for cone-rod dystrophy3 (CRD3) was found in both groups, a variant which had not been reported in either breed to date. Sequencing of genomic loci of interest, costs and efforts can be reduced significantly with targeted NGS as compared with WGS. The AgriSeq Targeted GBS is a very good alternative for the massive genetic evaluation of animal populations.
Fil: Arizmendi, Analía. Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Hospital Escuela; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Barrientos, Laura Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Crespi, Julian Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Rudd Garces, Gabriela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Giovambattista, Guillermo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
Fil: Peral Garcia, Pilar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico CONICET- La Plata. Instituto de Genética Veterinaria "Ing. Fernando Noel Dulout". Universidad Nacional de La Plata. Facultad de Ciencias Veterinarias. Instituto de Genética Veterinaria; Argentina
37th International Society of Animal Genetics (ISAG) Conference
Lleida
España
International Society of Animal Genetics (ISAG)
description Next-generation sequencing (NGS) is a powerful tool to study DNA or RNA samples. New methods and protocols based on NGS have been developed to carry out the analysis of genetic variation for animal parentage testing, disease screening and trait detection. Targeted NGS is aimed at achieving targeted enrichment of genome subregions to reduced significantly the sequencing of genomic loci of interest, as well as costs and efforts, compared with whole-genome sequencing (WGS). We generated genotyping information of 387 targets from 95 clinical canine samples (76 Doberman and 19 Toy Poodle dogs) and 3 control samples using AgriSeq Targeted GBS. Based on these data, we calculated the exclusion power of 228 parentage markers with Cervus 3.0 software. Furthermore, we detected disease/trait markers presenting polymorphism and calculated their allele frequencies within each breed. In the case of parentage markers, the assigned parents showed a higher LOD score (>1.22 x1016), and the available pedigree data of offspring agreed with the assigned parent information. Interestingly, full siblings were also assigned like parents. On the other hand, we found 19 polymorphic disease/trait markers in the total sample, 3 of which (progressive rod-cone degeneration, von Willebrand disease 1 and dilated cardiomyopathy) were validated by pyrosequencing with 100% concordance. The mutant allele for cone-rod dystrophy3 (CRD3) was found in both groups, a variant which had not been reported in either breed to date. Sequencing of genomic loci of interest, costs and efforts can be reduced significantly with targeted NGS as compared with WGS. The AgriSeq Targeted GBS is a very good alternative for the massive genetic evaluation of animal populations.
publishDate 2019
dc.date.none.fl_str_mv 2019
dc.type.none.fl_str_mv info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/conferenceObject
Conferencia
Book
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
status_str publishedVersion
format conferenceObject
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/195360
Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system; 37th International Society of Animal Genetics (ISAG) Conference; Lleida; España; 2019; 16-16
CONICET Digital
CONICET
url http://hdl.handle.net/11336/195360
identifier_str_mv Analysis of clinical samples from Doberman and Toy Poodle dogs with a targeted next-generation genotyping system; 37th International Society of Animal Genetics (ISAG) Conference; Lleida; España; 2019; 16-16
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.isag.us/proceedings.asp
info:eu-repo/semantics/altIdentifier/doi/https://www.isag.us/Docs/Proceedings/ISAG2019_Proceedings.pdf
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv International Society of Animal Genetics
publisher.none.fl_str_mv International Society of Animal Genetics
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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