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As recombination information is not used, association mapping cannot give a position estimation of the identified QTL, which is essential for gene fine-mapping and map-based cloning, especially under moderate marker density.
GWASs can be implemented with moderate marker density in barley and alfalfa because these populations contain extensive admixture LD, as does watermelon [ 27, 39].
Including multiple markers per haplotype and IBD information, with a moderate marker density generally yields more accurate results than models that include haplotypes based on two marker alleles but not relations between haplotypes, or models that include marker alleles instead of haplotypes [ 3].
As few as 5 K SNPs gives close to maximal accuracy within population, suggesting that only moderate marker density is likely to be suitable for GS breeding programs for similar highly heritable but polygenic traits where the discovery populations have close relationships with the selection candidates.
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These maps of moderate marker densities have proved valuable for mapping QTL to broad genome regions.
Genetic gain was robust to a reduction in marker density, with only moderate reductions, even for very low densities.
However, using a high or medium high marker density in an F2 population provides only a moderate improvement in the resolution because the population has undergone only one generation of recombination [ 5].
Small sample size and low marker density limit our power to detect risk-associated alleles, especially those with moderate effects on CWD prevalence.
The average marker density was 5.6 SNP markers per cM or 3.3 SNP markers per recombination point.
Fig. 3 Effect of the marker density on the predictability.
Chromosome wise marker density varied from 6.21 cM/marker in chromosome 11 to 19.25 cM/marker on chromosome 3 (Table 3).
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