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The expected resolution of the association mapping panel was evaluated by calculating the linkage disequilibrium (LD) as the correlation (R2) between loci on each chromosome, after filtering the SNP markers with the following threshold values: call rate > 95%; MAF > 5%.

The association mapping panel was characterized by strong population substructure.

The quality genomic DNA of the gametophyte clones of mapping panel was used for RAD sequencing.

The mapping panel developed for this study, the Porosus Mapping Panel, was therefore derived from a simple two-generation pedigree.

The mapping panel was made from offspring of P. maniculatus (BW) × P. polionotus (PO) F1 hybrid males backcrossed to BW females.

Our findings are probably not due to a lack of power for detecting distortion, because we mapped a similar number of markers per linkage group as the studies above, although the number of individuals per mapping panel was less than these studies, except Woram et al.[ 55].

It is to address this point that a second HAPPY mapping panel is created (Figure 1f), this time constructed using HMW fragments of genomic DNA.

In 2005, a subset of 115 inbred genotypes from the full association mapping panel were used as seed parents in crosses with both B73 and Mo17.

The inbred lines from an association mapping panel were crossed to a common inbred line, B73, to generate nearly 300 hybrid genotypes.

With smaller effects of QTL, a large mapping panel is required [ 37].

All candidate alleles identified among gametophyte clones of mapping panel were clustered for SNP and SNP genotype calling.