Figure 1.

Steps in generating SBP markers. Putative SNPs were identified by (i) SHORE mapping of the 75 bp Nd-0 Solexa reads and Co-0 genome sequence and/or (ii) searching SNPs by comparing batches of 50 Kb Col-0 sequences with the 75 bp Nd-0 Solexa reads. The putative SNPs containing Solexa reads that carried staggered ends were selected for next step. Assembled genome sequences of Col-0 carrying putative SNPs were searched for 100% nucleotide matches with transcript sequences or sequences from multiple BACs. The SNPs were utilized to develop SBP markers if they could be translated to restriction fragment length polymorphisms.