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However, the map distances and marker orders of the common SSR markers differed, possibly due to the intraspecific nature of our mapping population.
For chromosomes SCC2, SSC4 and SSC6, the estimated marker orders of their linkage maps were consistent with those of the published USDA-MARC linkage maps http://www.marc.usda.gov/genome/swine/swine.html and their sex-averaged lengths were 149 cM, 116 cM and 166 cM, respectively.
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The accuracy of marker orders on the present consensus map is also improved over the previous one [ 44].
Consequently, we chose to use the marker order of the physical map and the physical distance between markers as explained above.
Two small linkage fragments containing the anchor markers CMBR120 and GCM181 and the unlinked marker CMBR154 were incorporated into LG2, LG7, and LG4, respectively, according to the marker order of the melon consensus map (Diaz et al. 2011).
The marker order of each linkage group was determined as described previously [ 40].
We compared the marker order of genes previously mapped in loblolly pine and found high agreement.
The final marker order of each linkage group was verified by the software program RECORD [ 53].
The robustness of the marker order obtained in our final interpolated map is demonstrated by the overall high rank correlations between the marker order of linkage groups from single component maps and the marker order of the consensus linkage groups.
The marker order of the estimated linkage map (see Additional file 1) is in good agreement with other maps.
The marker order of each linkage group was further optimized by JoinMap 4.1 with the maximum-likelihood algorithm.
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