Our report that different clustering patterns observed in different mapping population was similar to Hyten et al. study [ 48].
Bridge markers were initially identified as having an identical name and being present in TAMU-ARS and at least one of the other 5 mapping populations and having a similar map position in the different mapping populations concerned.
Detailed instructions on the QTL mapping procedure are found in Additional file 8. QTL mapping has been performed on all three repetitions of phenotyping of the Bay-0 × Sha mapping population independently with similar results.
Results are shown in Fig. 2 for PC 1 and PC 2. The plot shows a distribution of populations similar to a map of Europe (note the axes are inverted) as in [ 9], where the Italian (TSI), Iberian (IBE) and Croatian (KOR) populations are located at the bottom of the plot (south), the Finnish (FIN) and Orcadian (ORK) populations in the top (north) and the rest mostly in the centre.
Given the similar sizes of three mapping populations (189 individuals in DC, 190 in JL, and 188 in NF), we made up a large population of 567 individuals that could include three sets of scoring.
Similar observations have been reported for interspecific F2 mapping populations in tomato, which indicated that chromosome recombination in heterochromatin is strongly suppressed compared with that in euchromatin.
Several of these appear to be common among multiple mapping populations, though they seem to be derived from the same or genetically similar donors.
Similar relationships were seen in our companion study on rice mapping populations derived from Kasalath × Nipponbare (Xu et al. 2009).
For effective linkage map pooling (and bridging) the individual mapping populations should share some common genetic bases (populations possessing a common parent for example) or common statistics (similar linkage information), but genetic map construction also relies on genome variation at loci detectable by molecular markers [ 31].
Interestingly, a similar map density was constructed for the salt tolerant tilapia and the kelp grouper, with mapping populations consisting of 95 and 90 individuals, respectively, compared with 48 in this study (Cnaani et al. 2003; Liu et al. 2013a).
