CAPS-Based SNP Genotyping for Nitrogen-Response Phenotypes in Maize Hybrids.
Jannis Jacobs1,2, Linsey Newton2,3, Brian McSpadden Gardener4
1Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
Bio-Protocol
|December 26, 2025
Summary
A new method identifies genetic markers for maize yield response to nitrogen fertilizer. This approach uses genome-wide association studies and molecular assays to predict nitrogen response, optimizing fertilizer use.
Area of Science:
- Agricultural Science
- Genetics
- Plant Breeding
Background:
- Optimizing nitrogen (N) fertilizer application in maize is crucial for yield and environmental sustainability.
- Identifying genetic markers for N-responsive maize hybrids is essential for targeted breeding and efficient N management.
Purpose of the Study:
- To develop and detail a methodology for identifying genetic markers associated with maize yield response to nitrogen fertilizer.
- To create robust molecular assays for predicting N-response in diverse maize germplasm.
Main Methods:
- Utilized an in silico workflow to identify high-priority single-nucleotide polymorphism (SNP) markers from genome-wide association studies (GWAS).
- Developed cleaved amplified polymorphic sequences (CAPS) and derived CAPS (dCAPS) assays for efficient genetic marker testing.
Main Results:
- The study presents a detailed protocol for marker identification and assay development.
- The methodology effectively identifies genetic markers for predicting nitrogen use efficiency in maize.
Conclusions:
- This protocol offers a robust approach to determine N-response types in maize germplasm, including commercial varieties.
- Implementation allows for more precise on-farm nitrogen application, reducing fertilizer waste and improving crop productivity.
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