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.
EEA Barrow
Fil: Roncallo, Pablo F. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Roncallo, Pablo F. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Barrow; Argentina
Fil: Achilli, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Achilli, Ana Laura. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Saint Pierre, Carolina. International Maize and Wheat Improvement Center (CIMMYT); México
Fil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Gallo, Cristian Andrés. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Dreisigacker, Susanne. International Maize and Wheat Improvement Center (CIMMYT); México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Echenique, Carmen Viviana. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fuente
BMC Genomics 22 : article number: 233 (April 2021)
Materia
Trigo
Trigo Duro
Triticum durum
Genotipos
Población Vegetal
Wheat
Hard Wheat
Genotypes
Plant Population
Argentina
Trigo Candeal
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
oai:localhost:20.500.12123/9028
Acceder
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oai_identifier_str oai:localhost:20.500.12123/9028
network_acronym_str INTADig
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network_name_str INTA Digital (INTA)
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 VivianaTrigoTrigo DuroTriticum durumGenotiposPoblación VegetalWheatHard WheatGenotypesPlant PopulationArgentinaTrigo CandealBackground: 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.EEA BarrowFil: Roncallo, Pablo F. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Roncallo, Pablo F. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Barrow; ArgentinaFil: Achilli, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Achilli, Ana Laura. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Saint Pierre, Carolina. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Gallo, Cristian Andrés. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Dreisigacker, Susanne. International Maize and Wheat Improvement Center (CIMMYT); MéxicoFil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaFil: Echenique, Carmen Viviana. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; ArgentinaBMC2021-04-06T12:12:42Z2021-04-06T12:12:42Z2021-04-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttp://hdl.handle.net/20.500.12123/9028https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z1471-2164https://doi.org/10.1186/s12864-021-07519-zBMC Genomics 22 : article number: 233 (April 2021)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)2025-09-29T13:45:10Zoai:localhost:20.500.12123/9028instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:45:11.04INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
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
Trigo
Trigo Duro
Triticum durum
Genotipos
Población Vegetal
Wheat
Hard Wheat
Genotypes
Plant Population
Argentina
Trigo Candeal
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 Trigo
Trigo Duro
Triticum durum
Genotipos
Población Vegetal
Wheat
Hard Wheat
Genotypes
Plant Population
Argentina
Trigo Candeal
topic Trigo
Trigo Duro
Triticum durum
Genotipos
Población Vegetal
Wheat
Hard Wheat
Genotypes
Plant Population
Argentina
Trigo Candeal
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.
EEA Barrow
Fil: Roncallo, Pablo F. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Roncallo, Pablo F. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Larsen, Adelina Olga. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Barrow; Argentina
Fil: Achilli, Ana Laura. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Achilli, Ana Laura. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Saint Pierre, Carolina. International Maize and Wheat Improvement Center (CIMMYT); México
Fil: Gallo, Cristian Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Gallo, Cristian Andrés. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Dreisigacker, Susanne. International Maize and Wheat Improvement Center (CIMMYT); México
Fil: Echenique, Carmen Viviana. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro de Recursos Naturales Renovables de la Zona Semiárida; Argentina
Fil: Echenique, Carmen Viviana. Universidad Nacional del Sur. Departamento de Agronomía. Centro de Recursos Naturales Renovables de la Zona Semiárida; 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 2021-04-06T12:12:42Z
2021-04-06T12:12:42Z
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/20.500.12123/9028
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z
1471-2164
https://doi.org/10.1186/s12864-021-07519-z
url http://hdl.handle.net/20.500.12123/9028
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07519-z
https://doi.org/10.1186/s12864-021-07519-z
identifier_str_mv 1471-2164
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
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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 BMC
publisher.none.fl_str_mv BMC
dc.source.none.fl_str_mv BMC Genomics 22 : article number: 233 (April 2021)
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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