Comparison of the restriction enzymes' (HpaII vs. MspI) banding patterns was used to determine alterations in the global methylation status of the DNA.
From these, eighty four SSR that were polymorphic and give clear bands patterns were used for linkage mapping and QTL analysis, resulting in a uniform distribution of markers along the genome.
DNA banding patterns were analyzed using bioNumerics software (Applied Maths) to calculate Dice coefficients of correlation and to generate a dendrogram using the unweighted pair group method of arithmetic averages (UPGMA) clustering.
Amplified Fragment Length Polymorphism (AFLP) banding patterns were generated using a modified version of the protocol described in [30], that allowed for fluorescent detection of labeled AFLP's.
The banding patterns were analysed using the GelCompar II software programme (Applied Maths, Belgium).
Banding patterns were analysed using BioNumerics software, version 6.5 (Applied Maths BVBA, Sint-Martens-Latem, Belgium) following the PulseNet protocol.
Banding patterns were analyzed using Image 3.10b and FPC (Fingerprinted Contigs) V6 software [ 61] to assemble overlapping BACs into contigs [ 62].
PFGE banding patterns were analysed using BioNumerics software version 6.6 (Applied Maths, St-Martens-Latem, Belgium), with the Dice coefficient and unweighted- pair group method with arithmetric averages, at settings of 0.5 % optimization and 1.5 % position tolerance.
Results were analyzed by using the BioNumerics Software version 3.0 (Applied-Maths, Kortrijk, Belgium), and banding patterns were compared by using Dice coefficients with a 1.5% band position tolerance.
Restriction-fragment banding patterns were matched digitally using a Gel doc 1000 System (Bio-Rad, Hercules, CA) and compared using the Molecular Analyst Plus software (Bio-Rad).
