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The highest marker density with an inter-marker distance of 0.84 cM was observed on CcLG02, while CcLG09 had the lowest marker density with average marker spacing 1.79 cM.
Genetic gain was robust to a reduction in marker density, with only moderate reductions, even for very low densities.
PLSR and PCR appeared less responsive to increased marker density with the advantage of 'BayesB' increasing by 17% from a marker density of 1 to 8Ne/M.
Compared to the previous lotus genetic maps, the American lotus map presented here has a longer map distance, and higher marker density, with around 20 folds more markers.
In general, SNP map positions correlated with previous marker density, with more SNP markers mapping to larger or more densely-mapped linkage groups.
For example, mapping of quantitative trait loci (QTL) for late leaf spot, rust [ 16] and seed quality [ 17] traits has only been possible at low marker density with 225 and 45 SSR loci, respectively.
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Therefore, the − log10(P) values were consistent for the three marker densities with those of the LM model.
In contrast, accuracy of IBD-GS was very stable across marker densities, with minimal losses in accuracy even at extremely low densities, and always had considerably greater accuracy than the pedigree-based analysis (even at 10 SNPs/M).
With 100 QTL underlying the trait, average accuracies achieved with the base model that used genomic relationship matrices based on different marker densities, with or without the simulated QTL, are in Figure 3 for the RANDOM scenario (A) and VAR scenario (B).
This high marker density combined with good viability in offspring from crosses with Gifu and with the lack of suppression of recombination at the top of chromosome 1 made L. burttii a promising source of genetic material.
An example is shown in figure 2 with BBU6 illustrating the improvement regarding the marker density obtained with the new RH map.
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