Show simple item record

Developing and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries

dc.contributor.authorOffornedo, Q.N.
dc.contributor.authorMenkir, A.
dc.contributor.authorBabalola, D.
dc.contributor.authorGedil, M.
dc.date.accessioned2023-10-02T21:28:40Z
dc.date.available2023-10-02T21:28:40Z
dc.date.issued2022-08-03
dc.identifier.citationOffornedo, 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.
dc.identifier.issn2572-4754
dc.identifier.urihttps://hdl.handle.net/20.500.12478/8266
dc.description.abstractBackground: 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.
dc.format.extent1-38
dc.language.isoen
dc.subjectBreeding
dc.subjectGenotypes
dc.subjectMarker-Assisted Selection
dc.subjectQuality Control
dc.subjectMaize
dc.titleDeveloping and deploying an efficient genotyping workflow for accelerating maize improvement in developing countries
dc.typeJournal Article
cg.contributor.crpMaize
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.coverage.regionAfrica
cg.coverage.regionWest Africa
cg.coverage.countryNigeria
cg.coverage.hubHeadquarters and Western Africa Hub
cg.researchthemeBiotech and Plant Breeding
cg.identifier.bibtexciteidOFFORNEDO:2023
cg.authorship.typesCGIAR Single Centre
cg.iitasubjectAgronomy
cg.iitasubjectFood Security
cg.iitasubjectMaize
cg.iitasubjectPlant Breeding
cg.iitasubjectPlant Production
cg.journalGates Open Research
cg.notesOpen Access Article; Published online: 17 Jan 2022
cg.accessibilitystatusOpen Access
cg.reviewstatusPeer Review
cg.usagerightslicenseCreative Commons Attribution 4.0 (CC BY 0.0)
cg.targetaudienceScientists
cg.identifier.doihttps://doi.org/10.12688/gatesopenres.13338.3
cg.iitaauthor.identifierQueen Nkem Offornedo: 0000-0002-1317-219X
cg.iitaauthor.identifierAbebe Menkir: 0000-0002-5907-9177
cg.iitaauthor.identifierMelaku Gedil: 0000-0002-6258-6014
cg.futureupdate.requiredNo
cg.identifier.issue3
cg.identifier.volume6


Files in this item

Thumbnail
Name:
Offornedo et al. Genotyping ...
Size:
728.3Kb
Format:
PDF
Description:
Journal Article
View/Open

This item appears in the following Collection(s)

Show simple item record