ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero

Autores
Ksouri, Najla; Sanchez, Gerardo; Contreras-Moreira, Bruno; Gogorcena Aoiz, Yolanda
Año de publicación
2022
Idioma
inglés
Tipo de recurso
documento de conferencia
Estado
versión publicada
Descripción
Póster
Double-digest RAD sequencing (ddRAD-Seq) is a powerful method for SNP discovery at a genome-wide scale. It relies on breaking the genome into a certain size of DNA fragments using two restriction enzymes: i) one common cutter with a short recognition site and ii) a low frequency cutter having a large recognition motif . Amplification step in library preparation can introduce PCR artefacts. Those are expected to skew allele frequency by increasing homozygosity leading to false genotype calls. In this context, we carried out a comparison study between DNA-variants generated with duplicates and those generated after removing with either "'SAMtools:rmdup" or "Stacks clone filter". On the other hand, the accuracy of genetic variants identification is a crucial step towards understanding phenotypical traits and monitoring breeding programs. Thereby, a good combination of computational tools for alignment and variant calling is crucial to tackle the possible artifacts. In response to this challenge, three variant callers (BCFtools, Freebayes and GATK-HaplotypeCaller) were combined on top of the BWA-mem read mapper. SNPs derived from the intersection of these callers were used for a genome wide association study to genetic variants associated with agronomic and organoleptic traits (In this poster, we illustrate only one study case trait). A diverse set of 90 peach accessions were sampled from the Experimental Station of Aula Dei (CSIC) located at Zaragoza (northern of Spain). This germplasm collection includes landraces and modem breeding lines from different origins.
EEA San Pedro
Fil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Contreras-Moreira, Bruno. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fuente
X Congreso de Mejora Genética de plantas. Sociedad Española de Ciencias Hortícolas (SECH) y Sociedad Española de Genética (SEG). Pontevedra, España. 19-22 de Septiembre de 2022.
Materia
Prunus persica
Genotipado
Replicación
Biotecnología
Durazno
Genotyping
Replication
Genetic Techniques
Biotechnology
Peaches
ddRAD-seq
GWAS
Estudio de Asociación de Genoma Completo
Nivel de accesibilidad
acceso abierto
Condiciones de uso
http://creativecommons.org/licenses/by-nc-sa/4.0/
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
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network_name_str INTA Digital (INTA)
spelling ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotoneroKsouri, NajlaSanchez, GerardoContreras-Moreira, BrunoGogorcena Aoiz, YolandaPrunus persicaGenotipadoReplicaciónBiotecnologíaDuraznoGenotypingReplicationGenetic TechniquesBiotechnologyPeachesddRAD-seqGWASEstudio de Asociación de Genoma CompletoPósterDouble-digest RAD sequencing (ddRAD-Seq) is a powerful method for SNP discovery at a genome-wide scale. It relies on breaking the genome into a certain size of DNA fragments using two restriction enzymes: i) one common cutter with a short recognition site and ii) a low frequency cutter having a large recognition motif . Amplification step in library preparation can introduce PCR artefacts. Those are expected to skew allele frequency by increasing homozygosity leading to false genotype calls. In this context, we carried out a comparison study between DNA-variants generated with duplicates and those generated after removing with either "'SAMtools:rmdup" or "Stacks clone filter". On the other hand, the accuracy of genetic variants identification is a crucial step towards understanding phenotypical traits and monitoring breeding programs. Thereby, a good combination of computational tools for alignment and variant calling is crucial to tackle the possible artifacts. In response to this challenge, three variant callers (BCFtools, Freebayes and GATK-HaplotypeCaller) were combined on top of the BWA-mem read mapper. SNPs derived from the intersection of these callers were used for a genome wide association study to genetic variants associated with agronomic and organoleptic traits (In this poster, we illustrate only one study case trait). A diverse set of 90 peach accessions were sampled from the Experimental Station of Aula Dei (CSIC) located at Zaragoza (northern of Spain). This germplasm collection includes landraces and modem breeding lines from different origins.EEA San PedroFil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; EspañaFil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; ArgentinaFil: Contreras-Moreira, Bruno. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; EspañaFil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; EspañaSECH-SEG2022-12-29T12:05:58Z2022-12-29T12:05:58Z2022-09info:eu-repo/semantics/conferenceObjectinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfhttp://hdl.handle.net/20.500.12123/13758X Congreso de Mejora Genética de plantas. Sociedad Española de Ciencias Hortícolas (SECH) y Sociedad Española de Genética (SEG). Pontevedra, España. 19-22 de Septiembre de 2022.reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo: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)2025-09-04T09:49:40Zoai:localhost:20.500.12123/13758instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-04 09:49:40.89INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
title ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
spellingShingle ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
Ksouri, Najla
Prunus persica
Genotipado
Replicación
Biotecnología
Durazno
Genotyping
Replication
Genetic Techniques
Biotechnology
Peaches
ddRAD-seq
GWAS
Estudio de Asociación de Genoma Completo
title_short ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
title_full ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
title_fullStr ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
title_full_unstemmed ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
title_sort ddRAD-seq para el análisis de asociación genómico de los principales caracteres agronómicos y calidad organoléptica en melocotonero
dc.creator.none.fl_str_mv Ksouri, Najla
Sanchez, Gerardo
Contreras-Moreira, Bruno
Gogorcena Aoiz, Yolanda
author Ksouri, Najla
author_facet Ksouri, Najla
Sanchez, Gerardo
Contreras-Moreira, Bruno
Gogorcena Aoiz, Yolanda
author_role author
author2 Sanchez, Gerardo
Contreras-Moreira, Bruno
Gogorcena Aoiz, Yolanda
author2_role author
author
author
dc.subject.none.fl_str_mv Prunus persica
Genotipado
Replicación
Biotecnología
Durazno
Genotyping
Replication
Genetic Techniques
Biotechnology
Peaches
ddRAD-seq
GWAS
Estudio de Asociación de Genoma Completo
topic Prunus persica
Genotipado
Replicación
Biotecnología
Durazno
Genotyping
Replication
Genetic Techniques
Biotechnology
Peaches
ddRAD-seq
GWAS
Estudio de Asociación de Genoma Completo
dc.description.none.fl_txt_mv Póster
Double-digest RAD sequencing (ddRAD-Seq) is a powerful method for SNP discovery at a genome-wide scale. It relies on breaking the genome into a certain size of DNA fragments using two restriction enzymes: i) one common cutter with a short recognition site and ii) a low frequency cutter having a large recognition motif . Amplification step in library preparation can introduce PCR artefacts. Those are expected to skew allele frequency by increasing homozygosity leading to false genotype calls. In this context, we carried out a comparison study between DNA-variants generated with duplicates and those generated after removing with either "'SAMtools:rmdup" or "Stacks clone filter". On the other hand, the accuracy of genetic variants identification is a crucial step towards understanding phenotypical traits and monitoring breeding programs. Thereby, a good combination of computational tools for alignment and variant calling is crucial to tackle the possible artifacts. In response to this challenge, three variant callers (BCFtools, Freebayes and GATK-HaplotypeCaller) were combined on top of the BWA-mem read mapper. SNPs derived from the intersection of these callers were used for a genome wide association study to genetic variants associated with agronomic and organoleptic traits (In this poster, we illustrate only one study case trait). A diverse set of 90 peach accessions were sampled from the Experimental Station of Aula Dei (CSIC) located at Zaragoza (northern of Spain). This germplasm collection includes landraces and modem breeding lines from different origins.
EEA San Pedro
Fil: Ksouri, Najla. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Sánchez, Gerardo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria San Pedro; Argentina
Fil: Contreras-Moreira, Bruno. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
Fil: Gogorcena Aoiz, Yolanda. Consejo Superior de Investigaciones Científicas (CSIC). Estación Experimental Aula Dei; España
description Póster
publishDate 2022
dc.date.none.fl_str_mv 2022-12-29T12:05:58Z
2022-12-29T12:05:58Z
2022-09
dc.type.none.fl_str_mv info:eu-repo/semantics/conferenceObject
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_5794
info:ar-repo/semantics/documentoDeConferencia
format conferenceObject
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/20.500.12123/13758
url http://hdl.handle.net/20.500.12123/13758
dc.language.none.fl_str_mv eng
language eng
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.publisher.none.fl_str_mv SECH-SEG
publisher.none.fl_str_mv SECH-SEG
dc.source.none.fl_str_mv X Congreso de Mejora Genética de plantas. Sociedad Española de Ciencias Hortícolas (SECH) y Sociedad Española de Genética (SEG). Pontevedra, España. 19-22 de Septiembre de 2022.
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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