FIGURE 3.

The first SNP-based linkage map in C. intybus. Tags underlined represent those mapped sequences showing a significant match (BLASTN, similarity >90%, E-value < 1E-50) with contigs from the first genome draft of chicory (Galla et al., 2016) that in turn aligned against protein from the TAIR database (BLASTX, E-value < 1E-5). The correspondence between each underlined tag and the best TAIR match is reported in Supplementary Table S3. The male-sterility locus (ms1) was assessed by recording the target locus as a putative gene fully co-segregating with the trait. Four SSR markers, M4.10b, M4.12 [from linkage group 4 of Cadalen et al. (2010)], M2.6 and M2.4 [from linkage group 2 of Cadalen et al. (2010)] were used to genotype the same samples employed for the SNP-based map and integrated in the linkage map. M4.10b and M4.12 were chosen because co-segregating with the ms1 (Barcaccia and Tiozzo Caenazzo, 2012, 2014), M2.6 and M2.4 were selected because were found to be associated with the sporophytic self-incompatibility (SSI) locus by Gonthier et al. (2013).