Figure 1

Schematic display of the deconvolution of 5-D clone pools with the Illumina GoldenGate assay and a contig map. A total of 302,976 BAC clones of Ae. tauschii were screened for the SNP marker BE442608. In the super pool screening step, 5 row hits and 6 column hits were observed and thus 30 potential plate hits were obtained. To screen plate rows and plate columns, the entire stack of plates was split into 5 smaller stacks (sub-pools) with only 1~2× coverage based on individual BAC libraries (see Table 2) and those sub-pools (RP_HB and CP_HB, RP_HI and CP_HI, RP_HD and CP_HD, and RP_BB and CP_BB) were screened separately, dramatically decreasing the number of candidate positive clones and F+ clones. By combining observed plate hits and row/column hits for each sub-pools, a total of 546 candidate clones (144, 24, 42 and 336 candidate clones for HB, HI, HD and BB sub-pools, respectively) were obtained. Of the candidate clones, 362 were located in 336 contigs, 336 clones were not included in contig assembly because of substandard or failed fingerprints, and the remaining 23 clones were singletons. The deconvolution algorithm was used to detect truly positive (TP) clones among the 362 candidate clones. Five TP clones, BB092N18, BB070C1, HB086J7, HI137N13, and HB006B8 were detected in ctg4985. The SNP marker derived from EST BE442608 was previously mapped on the genetic map of Ae. tauschii chromosome 2D, hence contig ctg4985 was anchored at this locus on the 2D genetic map. This inference agrees with the previous anchoring of contig ctg4985 [9].