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Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track.
A Mark Settles1, Alyssa M Bagadion2, Fang Bai2
1Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611 settles@ufl.edu.
G3 (Bethesda, Md.)
|April 22, 2014
Summary
Developing insertion-deletion (Indel) markers from maize (Zea mays) polymorphisms significantly enhances marker development efficiency. This strategy provides high-density genome coverage for precise genetic mapping and positional cloning in maize.
Area of Science:
- Plant genetics
- Genomics
- Maize breeding
Background:
- Positional cloning in maize (Zea mays) relies on efficient marker development.
- Existing marker development strategies can be time-consuming and less efficient.
Purpose of the Study:
- To develop a highly efficient strategy for generating polymorphic markers in maize.
- To leverage insertion-deletion (Indel) polymorphisms for high-density marker coverage.
Main Methods:
- Primers were designed to amplify annotated Indel polymorphisms (≥7 bp) between maize lines B73 and Mo17.
- Polymorphism frequency and co-dominance were assessed for marker development.
- Marker development was evaluated across different mapping populations (B73 x Mo17, B73 x W22, Mo17 x W22).
Main Results:
- Indel-based markers showed a 97% polymorphism frequency between B73 and Mo17.
- Co-dominant fragment length polymorphisms were observed in 49% of markers for B73 x Mo17.
- Co-dominance rates were 22% and 31% for B73 x W22 and Mo17 x W22 populations, respectively.
- Over 38,000 Indel polymorphisms can be converted into markers, offering high-density genome coverage.
Conclusions:
- This Indel polymorphism-based strategy significantly improves marker development efficiency for maize.
- The approach facilitates high-density marker coverage, crucial for fine-mapping and positional cloning in Zea mays.
