1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice
While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Springer
2019
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/164649 |
| _version_ | 1855533577759883264 |
|---|---|
| author | Arbelaez, Juan David Dwiyanti, Maria Stefanie Tandayu, Erwin Llantada, Krizzel Jarana, Annalhea Ignacio, John Carlos Platten, John Damien Cobb, Joshua Rutkoski, Jessica Elaine Thomson, Michael J. Kretzschmar, Tobias |
| author_browse | Arbelaez, Juan David Cobb, Joshua Dwiyanti, Maria Stefanie Ignacio, John Carlos Jarana, Annalhea Kretzschmar, Tobias Llantada, Krizzel Platten, John Damien Rutkoski, Jessica Elaine Tandayu, Erwin Thomson, Michael J. |
| author_facet | Arbelaez, Juan David Dwiyanti, Maria Stefanie Tandayu, Erwin Llantada, Krizzel Jarana, Annalhea Ignacio, John Carlos Platten, John Damien Cobb, Joshua Rutkoski, Jessica Elaine Thomson, Michael J. Kretzschmar, Tobias |
| author_sort | Arbelaez, Juan David |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications. |
| format | Journal Article |
| id | CGSpace164649 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2019 |
| publishDateRange | 2019 |
| publishDateSort | 2019 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1646492024-12-19T14:13:10Z 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice Arbelaez, Juan David Dwiyanti, Maria Stefanie Tandayu, Erwin Llantada, Krizzel Jarana, Annalhea Ignacio, John Carlos Platten, John Damien Cobb, Joshua Rutkoski, Jessica Elaine Thomson, Michael J. Kretzschmar, Tobias agronomy crop science plant science soil science While a multitude of genotyping platforms have been developed for rice, the majority of them have not been optimized for breeding where cost, turnaround time, throughput and ease of use, relative to density and informativeness are critical parameters of their utility. With that in mind we report the development of the 1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~ 1000-SNPs that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs Empirical validation tests performed on the 1k-RiCA showed average marker call rates of 95% with marker repeatability and concordance rates of 99%. These technical properties were not affected when two common DNA extraction protocols were used. The average distance between SNPs in the 1k-RiCA was 1.5 cM, similar to the theoretical distance which would be expected between 1,000 uniformly distributed markers across the rice genome. The average minor allele frequencies on a panel of indica lines was 0.36 and polymorphic SNPs estimated on pairwise comparisons between indica by indica accessions and indica by japonica accessions were on average 430 and 450 respectively. The specific design parameters of the 1k-RiCA allow for a detailed view of genetic relationships and unambiguous molecular IDs within indica accessions and good cost vs. marker-density balance for genomic prediction applications in elite indica germplasm. Predictive abilities of Genomic Selection models for flowering time, grain yield, and plant height were on average 0.71, 0.36, and 0.65 respectively based on cross-validation analysis. Furthermore the inclusion of important trait markers associated with 11 different genes and QTL adds value to parental selection in crossing schemes and marker-assisted selection in forward breeding applications This study validated the marker quality and robustness of the 1k-RiCA genotypic platform for genotyping populations derived from indica rice subpopulation for genetic and breeding purposes including MAS and genomic selection. The 1k-RiCA has proven to be an alternative cost-effective genotyping system for breeding applications. 2019-12 2024-12-19T12:54:08Z 2024-12-19T12:54:08Z Journal Article https://hdl.handle.net/10568/164649 en Open Access Springer Arbelaez, Juan David; Dwiyanti, Maria Stefanie; Tandayu, Erwin; Llantada, Krizzel; Jarana, Annalhea; Ignacio, John Carlos; Platten, John Damien; Cobb, Joshua; Rutkoski, Jessica Elaine; Thomson, Michael J. and Kretzschmar, Tobias. 2019. 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice. Rice, Volume 12, no. 1 |
| spellingShingle | agronomy crop science plant science soil science Arbelaez, Juan David Dwiyanti, Maria Stefanie Tandayu, Erwin Llantada, Krizzel Jarana, Annalhea Ignacio, John Carlos Platten, John Damien Cobb, Joshua Rutkoski, Jessica Elaine Thomson, Michael J. Kretzschmar, Tobias 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title | 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title_full | 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title_fullStr | 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title_full_unstemmed | 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title_short | 1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice |
| title_sort | 1k rica 1k rice custom amplicon a novel genotyping amplicon based snp assay for genetics and breeding applications in rice |
| topic | agronomy crop science plant science soil science |
| url | https://hdl.handle.net/10568/164649 |
| work_keys_str_mv | AT arbelaezjuandavid 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT dwiyantimariastefanie 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT tandayuerwin 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT llantadakrizzel 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT jaranaannalhea 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT ignaciojohncarlos 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT plattenjohndamien 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT cobbjoshua 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT rutkoskijessicaelaine 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT thomsonmichaelj 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice AT kretzschmartobias 1krica1kricecustomampliconanovelgenotypingampliconbasedsnpassayforgeneticsandbreedingapplicationsinrice |