Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection

Autores
Roncallo, Pablo Federico; Beaufort, Valeria; Larsen, Adelina Olga; Dreisigacker, Susanne; Echenique, Carmen Viviana
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.
Fil: Roncallo, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Beaufort, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; Argentina
Fil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maiz y Trigo; México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Materia
GENETIC DIVERSITY
LINKAGE DISSEQUILIBRIUM
SNP/AFLP
DURUM WHEAT
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:11336/99867
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/99867
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collectionRoncallo, Pablo FedericoBeaufort, ValeriaLarsen, Adelina OlgaDreisigacker, SusanneEchenique, Carmen VivianaGENETIC DIVERSITYLINKAGE DISSEQUILIBRIUMSNP/AFLPDURUM WHEAThttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.Fil: Roncallo, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Beaufort, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; ArgentinaFil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maiz y Trigo; MéxicoFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaPublic Library of Science2019-06info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/99867Roncallo, Pablo Federico; Beaufort, Valeria; Larsen, Adelina Olga; Dreisigacker, Susanne; Echenique, Carmen Viviana; Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection; Public Library of Science; Plos One; 14; 6; 6-2019; 1-331932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0218562info:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218562info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:18:51Zoai:ri.conicet.gov.ar:11336/99867instacron: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 10:18:51.619CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
title Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
spellingShingle Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
Roncallo, Pablo Federico
GENETIC DIVERSITY
LINKAGE DISSEQUILIBRIUM
SNP/AFLP
DURUM WHEAT
title_short Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
title_full Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
title_fullStr Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
title_full_unstemmed Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
title_sort Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection
dc.creator.none.fl_str_mv Roncallo, Pablo Federico
Beaufort, Valeria
Larsen, Adelina Olga
Dreisigacker, Susanne
Echenique, Carmen Viviana
author Roncallo, Pablo Federico
author_facet Roncallo, Pablo Federico
Beaufort, Valeria
Larsen, Adelina Olga
Dreisigacker, Susanne
Echenique, Carmen Viviana
author_role author
author2 Beaufort, Valeria
Larsen, Adelina Olga
Dreisigacker, Susanne
Echenique, Carmen Viviana
author2_role author
author
author
author
dc.subject.none.fl_str_mv GENETIC DIVERSITY
LINKAGE DISSEQUILIBRIUM
SNP/AFLP
DURUM WHEAT
topic GENETIC DIVERSITY
LINKAGE DISSEQUILIBRIUM
SNP/AFLP
DURUM WHEAT
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.
Fil: Roncallo, Pablo Federico. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Beaufort, Valeria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; Argentina
Fil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maiz y Trigo; México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Centro de Recursos Naturales Renovables de la Zona Semiárida. Universidad Nacional del Sur. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
description The aim of this work was to analyze the genetic diversity and linkage disequilibrium in a collection of 168 durum wheat accessions (Triticum turgidum L. var. durum) of different origins. Our collection was mainly composed of released and unreleased Argentinian germplasm, with additional genotypes from Italy, Chile, France, CIMMYT, Cyprus, USA and WANA region. To this end, the entire collection was characterized with 85 Single Nucleotide Polymorphism (SNP) markers obtained by Kompetitive Allele Specific PCR (KASP), giving a heterozygosity (He) mean value of 0.183 and a coefficient of genetic differentiation (Gst) value of 0.139. A subset of 119 accessions was characterized with six Amplified Fragment Length Polymorphism (AFLP) primer combinations. A total of 181 polymorphic markers (125 AFLP and 56 SNP) amplified across this subset revealed He measures of 0.352 and 0.182, respectively. Of these, 134 were selected to estimate the genome-wide linkage disequilibrium obtaining low significant values (r2 = 0.11) in the subset, indicating its suitability for future genome-wide association studies (GWAS). The structure analysis conducted in the entire collection with SNP detected two subpopulations. However, the structure analysis conducted with AFLP markers in the subset of 119 accessions proved to have greater degree of resolution and detect six subpopulations. The information provided by both marker types was complementary and showed a strong association between old Argentinian and Italian germplasm and a contribution of CIMMYT germplasm to modern Argentinian, Chilean and Cypriot accessions. The influence of Mediterranean germplasm, mainly from Italy, on part of the modern Argentinian cultivars or breeding lines was also clearly evidenced. Although our analysis yields conclusive results and useful information for association mapping studies, further analyses are needed to refine the number of subpopulations present in the germplasm collection analyzed.
publishDate 2019
dc.date.none.fl_str_mv 2019-06
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/99867
Roncallo, Pablo Federico; Beaufort, Valeria; Larsen, Adelina Olga; Dreisigacker, Susanne; Echenique, Carmen Viviana; Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection; Public Library of Science; Plos One; 14; 6; 6-2019; 1-33
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/99867
identifier_str_mv Roncallo, Pablo Federico; Beaufort, Valeria; Larsen, Adelina Olga; Dreisigacker, Susanne; Echenique, Carmen Viviana; Genetic diversity and linkage disequilibrium using SNP (KASP) and AFLP markers in a worldwide durum wheat (Triticum turgidum L. Var durum) collection; Public Library of Science; Plos One; 14; 6; 6-2019; 1-33
1932-6203
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0218562
info:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0218562
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
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
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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score 13.070432

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