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As high marker densities are essential in studies attempting to finely localize QTL, these findings are significant.
Evaluation of sub-simulations that varied according to the positions of simulated effects relative to the nearest markers showed that the CIM-NPCI method overcomes this bias, offering an explanation for the improved coverage probabilities when marker densities are high.
These marker densities are ∼10X what is needed for BSA or XAM mapping of most RIL and F2 populations, but may be useful for applications that require finer mapping, such as BSA mapping on pools derived from lines with known breakpoints around a candidate loci or mapping of break points in RIL lines [16], [17].
Unlike traditional FCM, marker densities are evaluated by single cell mass spectrometry, hence ruling out live cell sorting applications.
Higher marker densities are expected to be more accurate, with sequence data expected to give the highest accuracy.
The simulated data illustrate the primary benefit of integrating multiple linkage maps, which is that higher marker densities are possible.
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The map lengths and marker densities were positively correlated among the populations (r = 0.73).
The marker densities were 1.47 cM per marker for A-genome, 1.33 for B-genome, and 2.87 for D-genome.
Lower than expected marker densities were observed toward the distal ends of all 12 LGs, whereas greater than expected marker densities were observed in putative centromeric regions of LGs 2, 3, and 12.
In these scenarios, N e was set to 1000 and tested marker densities were d = 2500, 3000 and 3500 SNPs/Morgan.
Two genetic maps with improved marker densities were recently developed for rainbow trout by INRA [ 12] and the NCCCWA [ 15].
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