Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

Autores
Roncallo, Pablo Federico; Larsen, Adelina Olga; Achilli, Ana Laura; Saint Pierre, Carolina; Gallo, Cristian Andrés; Dreisigacker, Susanne; Echenique, Carmen Viviana
Año de publicación
2021
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.
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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; Argentina
Fil: Achilli, Ana Laura. 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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Saint Pierre, Carolina. Centro Internacional de Mejoramiento de Maíz y Trigo; México
Fil: Gallo, Cristian Andrés. 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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maíz y Trigo; México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Materia
DIVERSITY
DURUM
LINKAGE DISEQUILIBRIUM
POPULATION STRUCTURE
RARE ALLELES
SNP
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/134858
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/134858
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network_name_str CONICET Digital (CONICET)
spelling Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypesRoncallo, Pablo FedericoLarsen, Adelina OlgaAchilli, Ana LauraSaint Pierre, CarolinaGallo, Cristian AndrésDreisigacker, SusanneEchenique, Carmen VivianaDIVERSITYDURUMLINKAGE DISEQUILIBRIUMPOPULATION STRUCTURERARE ALLELESSNPhttps://purl.org/becyt/ford/4.4https://purl.org/becyt/ford/4Background: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.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. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; ArgentinaFil: Achilli, Ana Laura. 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. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Saint Pierre, Carolina. Centro Internacional de Mejoramiento de Maíz y Trigo; MéxicoFil: Gallo, Cristian Andrés. 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. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaFil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maíz y Trigo; MéxicoFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; ArgentinaBioMed Central2021-04-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/134858Roncallo, Pablo Federico; Larsen, Adelina Olga; Achilli, Ana Laura; Saint Pierre, Carolina; Gallo, Cristian Andrés; et al.; Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes; BioMed Central; BMC Genomics; 22; 5-4-2021; 1-171471-2164CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-zinfo:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-021-07519-zinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:38:19Zoai:ri.conicet.gov.ar:11336/134858instacron: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 09:38:20.178CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
title Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
spellingShingle Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
Roncallo, Pablo Federico
DIVERSITY
DURUM
LINKAGE DISEQUILIBRIUM
POPULATION STRUCTURE
RARE ALLELES
SNP
title_short Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
title_full Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
title_fullStr Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
title_full_unstemmed Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
title_sort Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
dc.creator.none.fl_str_mv Roncallo, Pablo Federico
Larsen, Adelina Olga
Achilli, Ana Laura
Saint Pierre, Carolina
Gallo, Cristian Andrés
Dreisigacker, Susanne
Echenique, Carmen Viviana
author Roncallo, Pablo Federico
author_facet Roncallo, Pablo Federico
Larsen, Adelina Olga
Achilli, Ana Laura
Saint Pierre, Carolina
Gallo, Cristian Andrés
Dreisigacker, Susanne
Echenique, Carmen Viviana
author_role author
author2 Larsen, Adelina Olga
Achilli, Ana Laura
Saint Pierre, Carolina
Gallo, Cristian Andrés
Dreisigacker, Susanne
Echenique, Carmen Viviana
author2_role author
author
author
author
author
author
dc.subject.none.fl_str_mv DIVERSITY
DURUM
LINKAGE DISEQUILIBRIUM
POPULATION STRUCTURE
RARE ALLELES
SNP
topic DIVERSITY
DURUM
LINKAGE DISEQUILIBRIUM
POPULATION STRUCTURE
RARE ALLELES
SNP
purl_subject.fl_str_mv https://purl.org/becyt/ford/4.4
https://purl.org/becyt/ford/4
dc.description.none.fl_txt_mv Background: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.
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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Barrow; Argentina
Fil: Achilli, Ana Laura. 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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Saint Pierre, Carolina. Centro Internacional de Mejoramiento de Maíz y Trigo; México
Fil: Gallo, Cristian Andrés. 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. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
Fil: Dreisigacker, Susanne. Centro Internacional de Mejoramiento de Maíz y Trigo; México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Universidad Nacional del Sur. Departamento de Agronomía; Argentina
description Background: Durum wheat (Triticum turgidum L. ssp. durum Desf. Husn) is the main staple crop used to make pasta products worldwide. Under the current climate change scenarios, genetic variability within a crop plays a crucial role in the successful release of new varieties with high yields and wide crop adaptation. In this study we evaluated a durum wheat collection consisting of 197 genotypes that mainly comprised a historical set of Argentinian germplasm but also included worldwide accessions. Results: We assessed the genetic diversity, population structure and linkage disequilibrium (LD) patterns in this collection using a 35 K SNP array. The level of polymorphism was considered, taking account of the frequent and rare allelic variants. A total of 1547 polymorphic SNPs was located within annotated genes. Genetic diversity in the germplasm collection increased slightly from 1915 to 2010. However, a reduction in genetic diversity using SNPs with rare allelic variants was observed after 1979. However, larger numbers of rare private alleles were observed in the 2000–2009 period, indicating that a high reservoir of rare alleles is still present among the recent germplasm in a very low frequency. The percentage of pairwise loci in LD in the durum genome was low (13.4%) in our collection. Overall LD and the high (r2 > 0.7) or complete (r2 = 1) LD presented different patterns in the chromosomes. The LD increased over three main breeding periods (1915–1979, 1980–1999 and 2000–2020). Conclusions: Our results suggest that breeding and selection have impacted differently on the A and B genomes, particularly on chromosome 6A and 2A. The collection was structured in five sub-populations and modern Argentinian accessions (cluster Q4) which were clearly differentiated. Our study contributes to the understanding of the complexity of Argentinian durum wheat germplasm and to derive future breeding strategies enhancing the use of genetic diversity in a more efficient and targeted way.
publishDate 2021
dc.date.none.fl_str_mv 2021-04-05
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/11336/134858
Roncallo, Pablo Federico; Larsen, Adelina Olga; Achilli, Ana Laura; Saint Pierre, Carolina; Gallo, Cristian Andrés; et al.; Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes; BioMed Central; BMC Genomics; 22; 5-4-2021; 1-17
1471-2164
CONICET Digital
CONICET
url http://hdl.handle.net/11336/134858
identifier_str_mv Roncallo, Pablo Federico; Larsen, Adelina Olga; Achilli, Ana Laura; Saint Pierre, Carolina; Gallo, Cristian Andrés; et al.; Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes; BioMed Central; BMC Genomics; 22; 5-4-2021; 1-17
1471-2164
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://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z
info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-021-07519-z
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
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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