Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum L.) was developed using the DArTag technology and later expa...
| Main Authors: | , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Wiley
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/148702 |
| _version_ | 1855525748715028480 |
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| author | Endelman, J.B. Kante, M. Lindqvist‐Kreuze, H. Kilian, A. Shannon, L.M. Caraza‐Harter, M.V. Vaillancourt, B. Mailloux, K. Hamilton, J.P. Buell, C.R. |
| author_browse | Buell, C.R. Caraza‐Harter, M.V. Endelman, J.B. Hamilton, J.P. Kante, M. Kilian, A. Lindqvist‐Kreuze, H. Mailloux, K. Shannon, L.M. Vaillancourt, B. |
| author_facet | Endelman, J.B. Kante, M. Lindqvist‐Kreuze, H. Kilian, A. Shannon, L.M. Caraza‐Harter, M.V. Vaillancourt, B. Mailloux, K. Hamilton, J.P. Buell, C.R. |
| author_sort | Endelman, J.B. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum
L.) was developed using the DArTag technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium single nucleotide polymorphism (SNP) array to maximize genome coverage and polymorphism rates. The
DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root mean squared error) <0.5. DArTag is suited for
genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the
RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N = 85), which was significantly lower than the RMSE of 0.42 with the random forest method. Regarding high-value traits, the DArTag markers for resistance to potato
virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato
breeding and genetics. |
| format | Journal Article |
| id | CGSpace148702 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | Wiley |
| publisherStr | Wiley |
| record_format | dspace |
| spelling | CGSpace1487022025-12-08T09:54:28Z Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR Endelman, J.B. Kante, M. Lindqvist‐Kreuze, H. Kilian, A. Shannon, L.M. Caraza‐Harter, M.V. Vaillancourt, B. Mailloux, K. Hamilton, J.P. Buell, C.R. genotypes potatoes marker-assisted selection Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato (Solanum tuberosum L.) was developed using the DArTag technology and later expanded to 4K targets. Genomic markers were selected from the potato Infinium single nucleotide polymorphism (SNP) array to maximize genome coverage and polymorphism rates. The DArTag and SNP array platforms produced equivalent dendrograms in a test set of 298 tetraploid samples, and 83% of the common markers showed good quantitative agreement, with RMSE (root mean squared error) <0.5. DArTag is suited for genomic selection candidates in the clonal evaluation trial, coupled with imputation to a higher density platform for the training population. Using the software polyBreedR, an R package for the manipulation and analysis of polyploid marker data, the RMSE for imputation by linkage analysis was 0.15 in a small half-diallel population (N = 85), which was significantly lower than the RMSE of 0.42 with the random forest method. Regarding high-value traits, the DArTag markers for resistance to potato virus Y, golden cyst nematode, and potato wart appeared to track their targets successfully, as did multi-allelic markers for maturity and tuber shape. In summary, the potato DArTag assay is a transformative and publicly available technology for potato breeding and genetics. 2024-09 2024-06-25T16:51:20Z 2024-06-25T16:51:20Z Journal Article https://hdl.handle.net/10568/148702 en Open Access Wiley Endelman, J.B.; Kante, M.; Lindqvist‐Kreuze, H.; Kilian, A.; Shannon, L.M.; Caraza‐Harter, M.V.; Vaillancourt, B.; Mailloux, K.; Hamilton, J.P.; Buell, C.R. 2024. Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR. The Plant Genome. ISSN 1940-3372. 13 p. https://doi.org/10.1002/tpg2.20484 |
| spellingShingle | genotypes potatoes marker-assisted selection Endelman, J.B. Kante, M. Lindqvist‐Kreuze, H. Kilian, A. Shannon, L.M. Caraza‐Harter, M.V. Vaillancourt, B. Mailloux, K. Hamilton, J.P. Buell, C.R. Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title | Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title_full | Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title_fullStr | Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title_full_unstemmed | Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title_short | Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR |
| title_sort | targeted genotyping by sequencing of potato and data analysis with r polybreedr |
| topic | genotypes potatoes marker-assisted selection |
| url | https://hdl.handle.net/10568/148702 |
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