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.
Sahu et al. BMC Genomics 2012 13:20 doi:10.1186/1471-2164-13-20