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Since recombination frequency in salmonid fishes differs considerably between sexes (e.g. [ 25, 31, 32]), separate male and female maps were constructed based on segregation data from two full-sib families consisting of 50 segregating INDEL and 77 microsatellite markers using the software package LINKMFEX v.2.3 developed by R. G. Danzmann http://www.uoguelph.ca/~rdanzman/.uoguelph.ca/~rdanzman/
This study was based on segregation data from seven populations DH lines and three populations of RIL.
Our study was based on segregation data from six partially connected mapping populations derived from nine triticale elite breeding lines (Table 1).
They were first checked for identical pairs based on segregation data across the population and on this basis 267 were excluded, always dropping the SNP marker with the lower quality score in each identical pair.
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Each marker was scored individually for each line and compiled into a single excel file based on parental segregation data.
To start the linkage analysis of the sex-averaged map, the LOD score was set at 14.0 in order to generate the linkage groups based on the segregation data.
We inferred a linkage map based on the marker segregation data from 201 F2 hybrid male embryos after discarding individuals for which more than 20% of the markers failed to amplify.
Markers were initially ordered along the seven linkage groups from each parent of the H×T mapping progeny using the maximum likelihood algorithm of JOINMAP 4.0 (Kyasma, NL) to provide a map position based on the raw segregation data obtained from Stacks.
Compared to the PS fiber mat, the D_IBS fiber mat surface adsorbed far more proteins, in spite of a lower hydrophobicity (based on WCA data), due to the segregation of a thin polyisobutylene (PIB) layer to the fiber surface.
Income segregation measures, however, are biased upwards when based on sample data.
Linkage mapping was performed using JoinMap 4.0 [ 90] based on genotype data from the same 90 F2 individuals used in the segregation analysis (above).
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