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Hybridization of these genetically mapped markers to switchgrass chromosomes would lead to definitive assignment of linkage groups.
These common markers enabled the determination of linkage group orientation and assignment of linkage group numbers for the Pop-DG map.
As expected, the assignment of linkage groups within the two salmonid species to the ancestral ray-finned fish karyotype indicates that most ancestrally derived 3R linkage groups are represented by approximately 4 whole or partial arm affinities in the salmonids (Table 1 and Figures 1, 2 and 3).
Assignment of linkage group to At or Dt subgenome was based on comparison of sequences containing RNA-seq−derived SNPs with those of the A2 genome (G. arboretum, our own unpublished callus transcriptome data; data not shown) and the D5 reference genome (G. raimondii; Paterson et al. 2012).
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Note also that only two triple crossovers were found instead of 15 (1/8 × 120 individuals) when RT2A and RT2B are grouped, suggesting that these two fragments could be linked in our DH families as in [ 8, 9, 23] Assignment of each linkage group to a specific chromosome[ 23] will allow to replace the current linkage group numbering by a nomenclature based on chromosome size as in other species.
These results allowed for the assignment of each linkage group to an individual chromosome in cultivated sunflower.
The quality of the MS data allowed confident assignment of 224 linkage sites and revealed a further 178 sites with lower confidence.
The total length of the map was 1259.8 cM spanning 37 linkage groups, exceeding the 28 expected groups for an integrated map of the species; however, all the LGs included a marker present in the reference map (FV×FB) allowing the assignment of each linkage group fragment to one of the seven diploid LGs and permitting further map comparisons between the diploid and octoploid maps to be performed.
We report the assignment and orientation of linkage groups to each chromosome pair in Chinook salmon and the comparison of the resulting Chinook salmon chromosome map with that of rainbow trout (Phillips et al. 2006).
The assignment and orientation of linkage groups to wheat chromosomes were carried out by checking for SSR loci common to the hexaploid wheat consensus map Ta-SSR-2004 Ta-SSR-2004 Ta-SSR-2004gov/GG2/index.shttp) and//wheat.pw.usda.gov/GG2/index (http://www.shtmlcand/orom.au).
Assignment of markers to linkage groups was achieved using logarithm of the odds (LOD) threshold values ranging from 3.0 to 10.0.
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