The marker distances were calculated from the genotype data using MapManager QTX vQTXb20 (Manly et al. 2001) and had a total length of 1,250.4 cM with an average of 2.74 cM between markers.
The molecular map of the 100 SSRs was based on the order of their position on the physical map based on the Nipponbare genomic sequence (www.gramene.org), and the marker distances were calculated by multiplying the Mb positions by a factor of 4 to obtain an equivalent estimate of cM (Supplementary Table 1).
Altogether, these results indicate that the performance of different marker distances is well in consistency.
Additional information about the maps, including the average resolution, and the range and standard deviation of the marker distances, is provided in Table 1.
Scaled population recombination rate between adjacent markers relative to inter marker distances was estimated using the LDhat 2.1 software [ 26] with haplotypes from 17,347 SNPs distributed on the 29 BTAs.
Inter-marker distances are expressed in cR5000 units.
However, considering non-fish groups, the markers' distances are, in most cases, very divergent, evidencing that genomes are suffering rearrangements, despite the maintenance of conserved large genomic blocks as part of the same LG.
The advantage of MABLUP was negligible when the marker distance was large, e.g. 5 cM.
The largest marker distance was 5.8 cM, and only 15 intervals had distances greater than 2.0 cM.
