Figure 1

Pearl millet consensus function map based on gene-based SNPs, CISPs and EST-SSRs. Distances are given in Haldane cM on the left side of each linkage bar. Candidate genes integrated as SNP and CISP markers are shown as underlined. Major QTLs of drought tolerance added onto the consensus map from Yadav et al. [4, 5] and Bidinger et al. [9] are indicated as hatched boxes on the right side of LG2. Six SNP markers, Xibmsp60, Xibmsp34, Xibmsp14, Xibmsp24, Xibmsp11 and Xibmsp31, showed complete linkage on LG2. Similarly, on LG3 three pairs of SNP loci Xibmsp46 and Xibmsp33, Xibmsp35 and Xibmsp30, and Xibmsp41 and Xibmsp28 showed complete linkage. On LG5, the SNP markers Xibmsp13 and Xibmsp16 were completely linked. Complete linkage between gene-based SNPs and framework markers was observed on LG3 (Xibmsp1 and Xipes0166), LG4 (Xibmsp32, Xibmsp10 and Xicmp3029), LG5 (Xicmp3027 and Xibmsp49, and Xpsmp2078 and Xibmsp47) and LG6 (Xibmsp8 and Xipes0176). In agreement with the previous studies [6], genomic SSR marker Xpsmp2086 showed weak linkage and/or aberrant behaviour i.e. tripled the length of LG4 when incorporated based on its expected position (shown as dashed line in Figure 1). Four CISP markers, Xibmcp5, Xibmcp6, Xibmcp7 and Xibmcp12, and two SNP markers Xibmsp20 and Xibmsp56 remained ungrouped.