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To fully evaluate short range LD in this population, marker density needs to be increased.
Since a critical requirement for such studies to be sufficiently powered is that the disequilibrium among the disease allele and neighboring marker alleles be large, marker density needs to be high.
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This determines the genetic distances over which LD will decay back to a random association of alleles and facilitates prediction of marker density needed to effectively associate genotypes with traits [11].
The objectives of the present study was to define the optimal conditions for whole-genome association in the tomato by using cherry tomato accessions and to assess the marker density needed to perform association mapping in this crop.
Therefore, we conducted (i) a GWAS and a pathway-level analysis to identify novel genes responsible for quantitative variation of grain carotenoid levels in a maize inbred panel and (ii) genome-wide, pathway-level, and carotenoid QTL-targeted prediction studies to determine the model parameterizations and extent of marker density needed to accurately predict maize grain carotenoid levels.
Levels of LD were calculated in order to estimate the marker densities needed to perform LD-based mapping in Atlantic salmon.
A notable feature of the 2b-RAD method is its ability to fine tune marker density as needed by constructing RR libraries using less-degenerate adaptors.
To be able to benefit from haplotype-based mapping approaches [ 25- 28] a high marker density is needed to first reliably define haplotype blocks in strains of interest [ 29].
Thus, as the marker density increases the need for BSAM is reduced.
Conversely with LD spanning a longer distance, the resolution will be poor, but the marker density does not need to be high.
Merged maps are attractive since their integration allows for an increase in marker density without the need of additional genotyping, increased marker portability (i.e., polymorphic markers can be used in more than one population), improved marker alignment precision (i.e., congruent anchor maker position), and broader inferential capabilities (i.e., cross-population prognostication).
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