Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries
Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of mo...
| Main Authors: | , , , |
|---|---|
| Format: | Journal Article |
| Language: | Inglés |
| Published: |
F1000 Research Ltd
2022
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/132017 |
| _version_ | 1855520889695633408 |
|---|---|
| author | Offornedo, Q.N. Menkir, A. Babalola, D. Gedil, M. |
| author_browse | Babalola, D. Gedil, M. Menkir, A. Offornedo, Q.N. |
| author_facet | Offornedo, Q.N. Menkir, A. Babalola, D. Gedil, M. |
| author_sort | Offornedo, Q.N. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities.
Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory.
Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines.
Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement. |
| format | Journal Article |
| id | CGSpace132017 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | F1000 Research Ltd |
| publisherStr | F1000 Research Ltd |
| record_format | dspace |
| spelling | CGSpace1320172025-11-11T10:10:59Z Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries Offornedo, Q.N. Menkir, A. Babalola, D. Gedil, M. breeding genotypes marker-assisted selection quality control maize Background: Molecular breeding is an essential tool for accelerating genetic gain in crop improvement towards meeting the need to feed an ever-growing world population. Establishing low-cost, flexible genotyping platforms in small, public and regional laboratories can stimulate the application of molecular breeding in developing countries. These laboratories can serve plant breeding projects requiring low- to medium-density markers for marker-assisted selection (MAS) and quality control (QC) activities. Methods: We performed two QC and MAS experiments consisting of 637 maize lines, using an optimised genotyping workflow involving an in-house competitive allele-specific PCR (KASP) genotyping system with an optimised sample collection, preparation, and DNA extraction and quantitation process. A smaller volume of leaf-disc size plant samples was collected directly in 96-well plates for DNA extraction, using a slightly modified CTAB-based DArT DNA extraction protocol. DNA quality and quantity analyses were performed using a microplate reader, and the KASP genotyping and data analysis was performed in our laboratory. Results: Applying the optimized genotyping workflow expedited the QC and MAS experiments from over five weeks (when outsourcing) to two weeks and eliminated the shipping cost. Using a set of 28 KASP single nucleotide polymorphisms (SNPs) validated for maize, the QC experiment revealed the genetic identity of four maize varieties taken from five seed sources. Another set of 10 KASP SNPs was sufficient in verifying the parentage of 390 F1 lines. The KASP-based MAS was successfully applied to a maize pro-vitamin A (PVA) breeding program and for introgressing the aflatoxin resistance gene into elite tropical maize lines. Conclusion: This improved workflow has helped accelerate maize improvement activities of IITA's Maize Improvement Program and facilitated DNA fingerprinting for tracking improved crop varieties. National Agricultural Research Systems (NARS) in developing countries can adopt this workflow to fast-track molecular marker-based genotyping for crop improvement. 2022 2023-09-26T14:02:36Z 2023-09-26T14:02:36Z Journal Article https://hdl.handle.net/10568/132017 en Open Access application/pdf F1000 Research Ltd Offornedo, Q.N., Menkir, A., Babalola, D. & Gedil, M. (2022). Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries. Gates Open Research, 6(3), 1-38. |
| spellingShingle | breeding genotypes marker-assisted selection quality control maize Offornedo, Q.N. Menkir, A. Babalola, D. Gedil, M. Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title | Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title_full | Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title_fullStr | Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title_full_unstemmed | Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title_short | Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| title_sort | developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries |
| topic | breeding genotypes marker-assisted selection quality control maize |
| url | https://hdl.handle.net/10568/132017 |
| work_keys_str_mv | AT offornedoqn developinganddeployinganefficientgenotypingworkflowforacceleratingmaizeimprovementindevelopingcountries AT menkira developinganddeployinganefficientgenotypingworkflowforacceleratingmaizeimprovementindevelopingcountries AT babalolad developinganddeployinganefficientgenotypingworkflowforacceleratingmaizeimprovementindevelopingcountries AT gedilm developinganddeployinganefficientgenotypingworkflowforacceleratingmaizeimprovementindevelopingcountries |