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The marker density has lower influence on predicting rice hybrid performance compared with the size of training population.
Current investigation of sugarbeet genome marker density has direct implications in increasing mapping marker density.
Increasing the marker density has been demonstrated to improve the power of genomic prediction [ 10] and GWAS [ 6].
The results in Table 2 show that improved IBD detection due to increased marker density has the potential to significantly expand the range of scenarios in which IBD mapping has more power than standard single-marker association testing.
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Several large panels of rice varieties genotyped with high marker density have been developed for GWAS (e.g., Huang et al. (2010), Zhao et al. (2011), McCouch et al. (2016)).
For this case, increasing marker density had no effect on accuracy.
The marker density had only a very slight influence on the MSE value.
Regardless of trait, marker density had only small effects on the genetic gain down to the density of 12 markers per Morgan.
To test if SNP marker density had an effect on recombination frequency, we calculated marker densities along each of the chromosomes using a 10 Kb window, and graphically plotted the total number of COs against their corresponding marker density values.
We also confirmed that the sex locus is situated downstream of SSR marker VVIB23, while previous studies, based on a lower marker density, had placed it upstream [ 17, 20].
In general, however, genome scans with an insufficient marker density have proved unsatisfactory to identify adaptation during marine invasion [ 24, 28], and the study of phenotypic differentiation has been proposed as a more promising approach [ 29, 30].
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