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The number of changing genes in the microarray experiments in the SAP102 and PSD-95 samples was inversely correlated with the number of backcrosses and active marker selection, suggesting the cis-acting effect, if it exists, only partially contributes.
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The correlation between very restrictive and less restrictive marker selection suggested that inbreeding estimates in more inbred individuals will be similar, while in less inbred individuals the presence of LD will tend to overinflate inbreeding estimates (as seen in the comparison of FEstim M0.1 and FEstim M0.05 in the Figure 2).
Theoretical predictions of allele frequency differences at markers linked to a locus under selection suggest that even for a locus under strong selection, the allele frequency differences between two selected lines will fall off rapidly with distance between the markers and the selected locus [ 28].
Similarly, the corrected correlation coefficients of FEstim with each of the single-point methods (for marker selection M0.05) ranged between 0.60-0.67, suggesthat that correlation coefficients for various homozygosity methods will be higher in more inbred individuals.
These observations suggest that further backcrossing and marker selection would result in a reduction of the E14TG2a DNA.
While our simulation studies suggest that these three SNP marker selection methods have similar performance, we find that the combined SNP marker selection performs best when signal SNPs are in high linkage disequilibrium with noise SNPs.
Results suggest that perhaps 100 selected markers (about two per arm) (see methods section for marker selection scheme) are sufficient for the proposed MABS approach although additional markers will further increase accuracy of the RPG recovery estimates for the selected plants.
As a result, the suggested methods implement at less time than other MSF-based methods in the marker selection step.
However, marker selection is still a fundamental challenge.
The following describes our marker selection criteria.
These different tests guided final marker selection.
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