Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice
Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding c...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2019
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/164650 |
| _version_ | 1855538677259698176 |
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| author | Arbelaez, Juan David Tandayu, Erwin Reveche, Maria Ymber Jarana, Annalhea van Rogen, Petra Sandager, Line Stolt, Patrik Ng, Enghwa Varshney, Rajeev K. Kretzschmar, Tobias Cobb, Joshua |
| author_browse | Arbelaez, Juan David Cobb, Joshua Jarana, Annalhea Kretzschmar, Tobias Ng, Enghwa Reveche, Maria Ymber Sandager, Line Stolt, Patrik Tandayu, Erwin Varshney, Rajeev K. van Rogen, Petra |
| author_facet | Arbelaez, Juan David Tandayu, Erwin Reveche, Maria Ymber Jarana, Annalhea van Rogen, Petra Sandager, Line Stolt, Patrik Ng, Enghwa Varshney, Rajeev K. Kretzschmar, Tobias Cobb, Joshua |
| author_sort | Arbelaez, Juan David |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development. |
| format | Journal Article |
| id | CGSpace164650 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1646502024-12-20T06:19:39Z Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice Arbelaez, Juan David Tandayu, Erwin Reveche, Maria Ymber Jarana, Annalhea van Rogen, Petra Sandager, Line Stolt, Patrik Ng, Enghwa Varshney, Rajeev K. Kretzschmar, Tobias Cobb, Joshua biotechnology genetics plant science Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers’ nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7–8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost–benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development. 2019-12 2024-12-19T12:54:08Z 2024-12-19T12:54:08Z Journal Article https://hdl.handle.net/10568/164650 en Open Access Springer Arbelaez, Juan David; Tandayu, Erwin; Reveche, Maria Ymber; Jarana, Annalhea; van Rogen, Petra; Sandager, Line; Stolt, Patrik; Ng, Enghwa; Varshney, Rajeev K.; Kretzschmar, Tobias and Cobb, Joshua. 2019. Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice. Plant Methods, Volume 15, no. 1 |
| spellingShingle | biotechnology genetics plant science Arbelaez, Juan David Tandayu, Erwin Reveche, Maria Ymber Jarana, Annalhea van Rogen, Petra Sandager, Line Stolt, Patrik Ng, Enghwa Varshney, Rajeev K. Kretzschmar, Tobias Cobb, Joshua Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title | Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title_full | Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title_fullStr | Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title_full_unstemmed | Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title_short | Methodology: ssb-MASS: a single seed-based sampling strategy for marker-assisted selection in rice |
| title_sort | methodology ssb mass a single seed based sampling strategy for marker assisted selection in rice |
| topic | biotechnology genetics plant science |
| url | https://hdl.handle.net/10568/164650 |
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