Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes
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...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Artículo |
| Lenguaje: | Inglés |
| Publicado: |
BMC
2021
|
| Materias: | |
| Acceso en línea: | 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 |
| _version_ | 1855484315432910848 |
|---|---|
| author | Roncallo, Pablo Federico Larsen, Adelina Olga Achilli, Ana Laura Saint Pierre, Carolina Gallo, Cristian Andrés Dreisigacker, Susanne Echenique, Carmen Viviana |
| author_browse | Achilli, Ana Laura Dreisigacker, Susanne Echenique, Carmen Viviana Gallo, Cristian Andrés Larsen, Adelina Olga Roncallo, Pablo Federico Saint Pierre, Carolina |
| author_facet | Roncallo, Pablo Federico Larsen, Adelina Olga Achilli, Ana Laura Saint Pierre, Carolina Gallo, Cristian Andrés Dreisigacker, Susanne Echenique, Carmen Viviana |
| author_sort | Roncallo, Pablo Federico |
| collection | INTA Digital |
| 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. |
| format | Artículo |
| id | INTA9028 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2021 |
| publishDateRange | 2021 |
| publishDateSort | 2021 |
| publisher | BMC |
| publisherStr | BMC |
| record_format | dspace |
| spelling | INTA90282021-04-06T12:16:05Z Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes Roncallo, Pablo Federico Larsen, Adelina Olga Achilli, Ana Laura Saint Pierre, Carolina Gallo, Cristian Andrés Dreisigacker, Susanne Echenique, Carmen Viviana Trigo Trigo Duro Triticum durum Genotipos Población Vegetal Wheat Hard Wheat Genotypes Plant Population Argentina Trigo Candeal 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 2021-04-06T12:12:42Z 2021-04-06T12:12:42Z 2021-04-05 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng 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) application/pdf BMC BMC Genomics 22 : article number: 233 (April 2021) |
| spellingShingle | Trigo Trigo Duro Triticum durum Genotipos Población Vegetal Wheat Hard Wheat Genotypes Plant Population Argentina Trigo Candeal Roncallo, Pablo Federico Larsen, Adelina Olga Achilli, Ana Laura Saint Pierre, Carolina Gallo, Cristian Andrés Dreisigacker, Susanne Echenique, Carmen Viviana 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 |
| 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_short | 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 |
| topic | Trigo Trigo Duro Triticum durum Genotipos Población Vegetal Wheat Hard Wheat Genotypes Plant Population Argentina Trigo Candeal |
| 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 |
| work_keys_str_mv | AT roncallopablofederico linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT larsenadelinaolga linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT achillianalaura linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT saintpierrecarolina linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT gallocristianandres linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT dreisigackersusanne linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes AT echeniquecarmenviviana linkagedisequilibriumpatternspopulationstructureanddiversityanalysisinaworldwidedurumwheatcollectionincludingargentiniangenotypes |