Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection
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...
| Autores principales: | , , |
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| Formato: | info:ar-repo/semantics/artículo |
| Lenguaje: | Inglés |
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2017
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| Acceso en línea: | 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 |
| _version_ | 1855034735353397248 |
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| author | Olmos, Sofía Eugenia Lía, Verónica Viviana Eyherabide, Guillermo |
| author_browse | Eyherabide, Guillermo Lía, Verónica Viviana Olmos, Sofía Eugenia |
| author_facet | Olmos, Sofía Eugenia Lía, Verónica Viviana Eyherabide, Guillermo |
| author_sort | Olmos, Sofía Eugenia |
| collection | INTA Digital |
| 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. |
| format | info:ar-repo/semantics/artículo |
| id | INTA955 |
| institution | Instituto Nacional de Tecnología Agropecuaria (INTA -Argentina) |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| record_format | dspace |
| spelling | INTA9552019-03-22T12:51:09Z Genetic diversity and linkage disequilibrium in the Argentine public maize inbred line collection Olmos, Sofía Eugenia Lía, Verónica Viviana Eyherabide, Guillermo Genética Maíz Variación Genética Lineas Consanguíneas Genetics Maize Genetic Variation Inbred Lines Diversidad Genética 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 2017-08-11T13:34:18Z 2017-08-11T13:34:18Z 2017 info:ar-repo/semantics/artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion 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 eng info:eu-repo/semantics/restrictedAccess application/pdf Argentina (nation) Plant genetic resources 5 (6) : 515-526. (December 2017) |
| spellingShingle | Genética Maíz Variación Genética Lineas Consanguíneas Genetics Maize Genetic Variation Inbred Lines Diversidad Genética Olmos, Sofía Eugenia Lía, Verónica Viviana Eyherabide, Guillermo 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 |
| 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_short | 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 |
| topic | Genética Maíz Variación Genética Lineas Consanguíneas Genetics Maize Genetic Variation Inbred Lines Diversidad Genética |
| 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 |
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