Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection

Autores
Olmos, Sofía Eugenia; Lía, Verónica Viviana; Eyherabide, Guillermo
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Knowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.
Inst. de Biotecnología
Fil: Olmos, Sofí­a Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Eyherabide, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
Fuente
Plant genetic resources 5 (6) : 515-526. (December 2017)
Materia
Genética
Maíz
Variación Genética
Lineas Consanguíneas
Genetics
Maize
Genetic Variation
Inbred Lines
Diversidad Genética
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/955
Acceder
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oai_identifier_str oai:localhost:20.500.12123/955
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network_name_str INTA Digital (INTA)
spelling Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collectionOlmos, Sofía EugeniaLía, Verónica VivianaEyherabide, GuillermoGenéticaMaízVariación GenéticaLineas ConsanguíneasGeneticsMaizeGenetic VariationInbred LinesDiversidad GenéticaKnowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.Inst. de BiotecnologíaFil: Olmos, Sofí­a Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; ArgentinaFil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; ArgentinaFil: Eyherabide, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina2017-08-11T13:34:18Z2017-08-11T13:34:18Z2017info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/955https://www.cambridge.org/core/journals/plant-genetic-resources/article/genetic-diversity-and-linkage-disequilibrium-in-the-argentine-public-maize-inbred-line-collection/A2B509D9C6A37824E41B40F6D92805D81479-2621 (Print)1479-263X (Online)https://doi.org/10.1017/S1479262116000228Plant genetic resources 5 (6) : 515-526. (December 2017)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología AgropecuariaengArgentina (nation)info:eu-repo/semantics/restrictedAccess2025-09-04T09:46:57Zoai:localhost:20.500.12123/955instacron: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 09:46:58.262INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
title Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
spellingShingle Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
Olmos, Sofía Eugenia
Genética
Maíz
Variación Genética
Lineas Consanguíneas
Genetics
Maize
Genetic Variation
Inbred Lines
Diversidad Genética
title_short Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
title_full Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
title_fullStr Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
title_full_unstemmed Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
title_sort Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
dc.creator.none.fl_str_mv Olmos, Sofía Eugenia
Lía, Verónica Viviana
Eyherabide, Guillermo
author Olmos, Sofía Eugenia
author_facet Olmos, Sofía Eugenia
Lía, Verónica Viviana
Eyherabide, Guillermo
author_role author
author2 Lía, Verónica Viviana
Eyherabide, Guillermo
author2_role author
author
dc.subject.none.fl_str_mv Genética
Maíz
Variación Genética
Lineas Consanguíneas
Genetics
Maize
Genetic Variation
Inbred Lines
Diversidad Genética
topic Genética
Maíz
Variación Genética
Lineas Consanguíneas
Genetics
Maize
Genetic Variation
Inbred Lines
Diversidad Genética
dc.description.none.fl_txt_mv Knowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.
Inst. de Biotecnología
Fil: Olmos, Sofí­a Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología; Argentina
Fil: Eyherabide, Guillermo. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino; Argentina
description Knowledge of linkage disequilibrium (LD) patterns is considered a prerequisite for effective association mapping studies. However, no LD analysis in the Argentine public temperate maize collection has been reported to date. In this study, a panel of 111 temperate maize inbreds genotyped at 74 single sequence repeats (SSRs) loci was used to assess LD, genetic diversity and population structure to evaluate the suitability of the panel for association mapping. Mini-core sets were also designed for in-depth phenotyping and allele mining purposes. The panel consisted of: (1) locally developed orange flint germplasm; (2) temperate inbred lines with Iowa Stiff Stalk Synthetic background; and (3) eight historic flint lines, some of them from the Cuarentín race. As a result, four subpopulations were defined. Joint analysis of population structure and combining ability allowed identifying two main heterotic patterns. High molecular diversity, a low extent of LD and a high ratio of linked to unlinked SSR loci pairs in significant LD were detected indicating the suitability of the entire collection for association mapping. The fact that the LD extent in the mini-core sets was similar to that observed in the entire collection and that only a small percentage of allelic richness was reduced suggests that these mini-core sets are suitable to capture diversity, exploit phenotypic variance and discover useful variants representative of the entire collection.
publishDate 2017
dc.date.none.fl_str_mv 2017-08-11T13:34:18Z
2017-08-11T13:34:18Z
2017
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/20.500.12123/955
https://www.cambridge.org/core/journals/plant-genetic-resources/article/genetic-diversity-and-linkage-disequilibrium-in-the-argentine-public-maize-inbred-line-collection/A2B509D9C6A37824E41B40F6D92805D8
1479-2621 (Print)
1479-263X (Online)
https://doi.org/10.1017/S1479262116000228
url http://hdl.handle.net/20.500.12123/955
https://www.cambridge.org/core/journals/plant-genetic-resources/article/genetic-diversity-and-linkage-disequilibrium-in-the-argentine-public-maize-inbred-line-collection/A2B509D9C6A37824E41B40F6D92805D8
https://doi.org/10.1017/S1479262116000228
identifier_str_mv 1479-2621 (Print)
1479-263X (Online)
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.coverage.none.fl_str_mv Argentina (nation)
dc.source.none.fl_str_mv Plant genetic resources 5 (6) : 515-526. (December 2017)
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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