Changes in synteny were validated on a second mapping population available for each species whenever necessary.
Full genotyping information for both mapping populations is available (Supporting Information, File S1).
Although, currently no mapping populations are available for the barley variety used here, a sequence based strategy for assigning Ds insertions in Golden Promise to linkage map coordinates on the existing Oregon Wolfe Barley map has been reported [ 13].
For both species a mapping population is available, in lily, an inter-sectional F1 population (100 progenies) 'White Fox' × 'Connecticut King' [ 57] and in tulip, an inter-sectional F1 population (125 progenies) 'Kees Nelis' × 'Cantata'.
G × E is frequently evaluated by year year and/or location location variations using mapping populations that are available for replication, such as doubled haploid lines (DHLs), RILs or BILs.
High-density marker maps (with marker intervals smaller than 1 cM in mapping populations) have been available to an increasing number of plant species, such as in Arabidopsis thaliana (Kover et al. 2009; Huang et al. 2011), maize (Swarts et al. 2014), rice (Yu et al. 2011), and sorghum (Zou et al. 2012).
The extensible nature of the method means that any number of available mapping populations can be added to further improve the results.
Acting on this expectation, we tested for Mendelian segregation of these loci within the two available mapping populations for loblolly pine with 90 progeny each, as well as families of the FBRC-family based association population of loblolly pine (∼16 progeny per family on average).
Between 176 and 198 of the assays were informative in at least one of the three available mapping populations.
We analyzed the segregation of the 80 genotyped SNPs in four available mapping populations (Additional file 3).
