An imputation platform to enhance integration of rice genetic resources
As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of inte...
| Autores principales: | , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2018
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164815 |
| _version_ | 1855523198162960384 |
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| author | Wang, Diane R. Agosto-Pérez, Francisco J. Chebotarov, Dmytro Shi, Yuxin Marchini, Jonathan Fitzgerald, Melissa McNally, Kenneth L. Alexandrov, Nickolai McCouch, Susan R. |
| author_browse | Agosto-Pérez, Francisco J. Alexandrov, Nickolai Chebotarov, Dmytro Fitzgerald, Melissa Marchini, Jonathan McCouch, Susan R. McNally, Kenneth L. Shi, Yuxin Wang, Diane R. |
| author_facet | Wang, Diane R. Agosto-Pérez, Francisco J. Chebotarov, Dmytro Shi, Yuxin Marchini, Jonathan Fitzgerald, Melissa McNally, Kenneth L. Alexandrov, Nickolai McCouch, Susan R. |
| author_sort | Wang, Diane R. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel. To address these challenges, we develop the Rice Imputation Server, a publicly available web application leveraging genetic information from a globally diverse rice reference panel assembled here. This resource allows researchers to benefit from increased marker density without needing to perform imputation on their own machines. We demonstrate improvements that imputed data provide to rice genome-wide association (GWA) results of grain amylose content and show that the major functional nucleotide polymorphism is tagged only in the imputed data set. |
| format | Journal Article |
| id | CGSpace164815 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2018 |
| publishDateRange | 2018 |
| publishDateSort | 2018 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1648152024-12-19T14:12:27Z An imputation platform to enhance integration of rice genetic resources Wang, Diane R. Agosto-Pérez, Francisco J. Chebotarov, Dmytro Shi, Yuxin Marchini, Jonathan Fitzgerald, Melissa McNally, Kenneth L. Alexandrov, Nickolai McCouch, Susan R. apparent amylose content genetic resources genomics genotypes germplasm As sequencing and genotyping technologies evolve, crop genetics researchers accumulate increasing numbers of genomic data sets from various genotyping platforms on different germplasm panels. Imputation is an effective approach to increase marker density of existing data sets toward the goal of integrating resources for downstream applications. While a number of imputation software packages are available, the limitations to utilization for the rice community include high computational demand and lack of a reference panel. To address these challenges, we develop the Rice Imputation Server, a publicly available web application leveraging genetic information from a globally diverse rice reference panel assembled here. This resource allows researchers to benefit from increased marker density without needing to perform imputation on their own machines. We demonstrate improvements that imputed data provide to rice genome-wide association (GWA) results of grain amylose content and show that the major functional nucleotide polymorphism is tagged only in the imputed data set. 2018-08-29 2024-12-19T12:54:20Z 2024-12-19T12:54:20Z Journal Article https://hdl.handle.net/10568/164815 en Open Access Springer Wang, Diane R.; Agosto-Pérez, Francisco J.; Chebotarov, Dmytro; Shi, Yuxin; Marchini, Jonathan; Fitzgerald, Melissa; McNally, Kenneth L.; Alexandrov, Nickolai and McCouch, Susan R. 2018. An imputation platform to enhance integration of rice genetic resources. Nat Commun, Volume 9, no. 1 |
| spellingShingle | apparent amylose content genetic resources genomics genotypes germplasm Wang, Diane R. Agosto-Pérez, Francisco J. Chebotarov, Dmytro Shi, Yuxin Marchini, Jonathan Fitzgerald, Melissa McNally, Kenneth L. Alexandrov, Nickolai McCouch, Susan R. An imputation platform to enhance integration of rice genetic resources |
| title | An imputation platform to enhance integration of rice genetic resources |
| title_full | An imputation platform to enhance integration of rice genetic resources |
| title_fullStr | An imputation platform to enhance integration of rice genetic resources |
| title_full_unstemmed | An imputation platform to enhance integration of rice genetic resources |
| title_short | An imputation platform to enhance integration of rice genetic resources |
| title_sort | imputation platform to enhance integration of rice genetic resources |
| topic | apparent amylose content genetic resources genomics genotypes germplasm |
| url | https://hdl.handle.net/10568/164815 |
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