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Design of PCR methods
Sequence data used
Determination of gene models
- in silico GeneSeqer-facilitated MAGI/EST alignments
- ab initio FgeneSH predictions (Yao et al., Plant Mol. Biol.,2005)
Primer positions
Primers were designed to amplify 3' UTRs (~300 bp upstream of polly A sites) or introns (Fig. 1)
Figure 1: The locations of primer pairs (amplicons <= 800bp)
Detection of Polymorphisms
Gel-based [A] and Temperature Gradient Capillary Electrophoresis TGCE (Hsia et al., 2005, TAG) - [B] based detection of polymorphisms between B73
and Mo17. Polymorphism data are available at the project website.
- Survey PCR: Identify potential markers that are polymorphic between B73 and Mo17 via gel or TGCE
- Gradient PCR: Optimize annealing Tm for markers selected in the survey
- Mapping PCR: Selected markers are mapped using 91 of the 94 IBM.
Map Construction and Display
- Mapping score data entry: Gel-based mapping scores were recorded manually and TGCE data were directly curated
and analyzed using GRAMA (Genetic Recombinant Analysis and Mapping
Assistant; Maher et al.)
- MultiMap (Mester et al., 2003) was used to generate genetic maps with or without MMP markers. Genetic maps are displayed
using CMap/GMOD. Chromosome assignments are available at the project website.
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