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Overall, we observed a high level of agreement between our linkage groups and one or more unplaced Astyanax genomic scaffolds.
Our map contains a total of 784 links between our linkage groups and the Danio rerio genome and an average of 30.84 links (minimum = 14, maximum = 52) per Danio rerio chromosome (Table 3).
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We identified substantial links between these chromosomes and our linkage groups 9 (n = 21) and 23 (n = 15), respectively.
This revealed very good consistency between our genetic linkage group lengths to the physical lengths of the chromosomes.
As expected, based on the significant divergence between these species, we recovered varying levels of synteny between portions of our Astyanax linkage groups and regions of the Danio genome.
We examined the five strongest syntenic links between single linkage groups in our GBS-based map and single Danio chromosomes and then identified analogous connections between those chromosomes and specific linkage groups in the maps presented by Gross et al. (2008) and O'Quin et al. (2013).
Our 25 Astyanax linkage groups contain markers representing between 12 (linkage groups 8 and 22) and 55 (linkage group 3) genome scaffolds each, with a map-wide average of 27.64 scaffolds/linkage group.
Our data confirm several homeology between linkage groups already reported or hypothesized, namely RT2 RT9, RT2 RT29, RT3 RT25, RT7 RT15, RT10 RT18, RT12 RT16, RT14 RT20 and RT27 RT31 ([ 8- 10]).
Epistatic interactions were detected between markers located in and outside of QTL regions as well as within and between linkage groups, and explained between 11.4 and 13.4% of the variance.
Two rainbow trout linkage groups matched to two sockeye linkage groups, with all remaining matches between single linkage groups.
Gray lines show the boundaries between assembled linkage groups, labeled at the top of the figure.
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