Because TM-1 and 3 79 are also parents of a permanent RIL mapping population, they are essential for the integrated genome mapping and selection of the core reference markers.
These marker order rearrangements could be real, they could be due to error in one of the small mapping populations or they could be explained by the statistical uncertainty of orders at the cM-scale that is inherent in datasets derived from a limited number of RILs.
Several of these appear to be common among multiple mapping populations, though they seem to be derived from the same or genetically similar donors.
Seven of the 60 markers (including CS3BLCR-06, CS3BLCR-08, CS3BLCR-09. CS3BLCR-11, CS3BLCR-12, CS3BLCR-11 and CS3BLCR-12) detected polymorphism in the mapping population and they all co-segregated with the FCR locus (Fig. 2).
While TrPPD was the only candidate gene to be mapped in both homoeologues, many of the other genes exhibited additional amplicons that were not informative in the mapping population suggesting they may have loci elsewhere in the genome, including other homoeologues and paralogues.
We are attempting to map these candidate genes as EST-PCR markers [ 14] in our mapping populations to determine if they map to the same regions as QTL for these traits.
Flax genotypes CDC Bethune, Macbeth, SP2047 and UGG5-5 were selected because they are parents of mapping populations.
Some previously published QTLs could not be precisely identified due to the lack of common shared markers between the consensus map and the original mapping population and hence they were defined as approximate (Additional file 12).
This combined map offers much more complete genome coverage than would be possible with any individual mapping population, even if they were genotyped with a much denser array, due to the occurrence of regions exhibiting suppressed recombination and/or identity by descent in any particular cross.
The associated QTL alleles need to be checked to see if they are segregated in linkage mapping populations.
