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In the same linkage group, EgROP1 co-located with a QTL for S/G.
These studies have shown that the sex determination locus appears to be sited in the same linkage group.
All four SNPs were in the same linkage disequilibrium (LD) block (Figure S1).
SNP-638, SNP -420, SNP-358, and SNP+157 were in the same linkage disequilibrium (LD) block.
The polymorphisms c.3001G>A and c.3455G>A were in the same linkage phase in all tested animals, while the other SNP alleles showed lower correlations with r2<0.8 (Figure S2).
Across all 495 loci, 6,171 possible linked locus pairs (in the same linkage groups) and 116,094 unlinked locus pairs (from different linkage groups) could be detected in both sub-groups.
Similar(17)
Interestingly, the latter scenario is consistent with observations that suggest some salinity tolerance candidate genes occur in clusters within the same linkage group region [ 15], and could singly or in combination contribute to the apparent conserved QTL homeologies that were identified.
It is expected that SNPs belonging to the same scaffolds to be in clusters on the same linkage groups.
When two QTL peaks for the same trait occurred in close proximity on the same linkage group, a drop below the permutation cut-off or a change in the directionality of the QTL effect was used to determine whether each peak represented different QTL.
Of the shared 3817 RAD-tag loci between this study and Miller et al. (2012), 58 were mapped in both, all of which were assigned to the same linkage group in both studies.
In different Angiosperms, similar observations could be made where some of the QTLs detected for spring flush, stem height, basal area, and sylleptic branch number in poplar, for bud flush and height growth in oak, or for bunch number and bunch weight in palms, were overlapping on the same linkage groups and could be related to significant correlations among these traits [ 41, 45, 77].
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