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Results obtained in some studies suggest that the method that accounts both for subpopulations and kinship (also called the "QK method") is the most appropriate for association mapping [10].
These results indicated that the K approach was less appropriate for association mapping than the approaches based on the integration of fixed effects in the statistical model.
Our study suggests that the QK method [ 15] is not only appropriate for association mapping in humans, maize, and Arabidopsis but also in rapeseed, potato, and sugar beet.
Therefore, marker-based kinship estimates might be more appropriate for association mapping approaches than coancestry coefficients calculated from pedigree records [ 15, 17].
Population structure and LD decay were finely analyzed at different levels of organization to assess to what extent the panel is appropriate for association mapping studies and will eventually enable the identification of new agronomically relevant alleles.
We then thinned the SNP dataset to generate two genetic mapping marker sets, one appropriate for association (retaining SNPs with pairwise r<=0.9) and one appropriate for linkage mapping (retaining SNPs with pairwise r<=0.4).
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The diversity of photoperiod response of our panel of accessions made it an appropriate choice for association analysis for candidate flowering genes.
Clearly, the genomes of conifers are less than homogenous with regards to patterns of LD, and more data on the variability of LD across species and the genome are needed to fully evaluate the appropriate method for association mapping studies.
Nevertheless, the MSD values observed for the association mapping methods, which include fixed effects such as the Q 1 K T o p t, Q 2 K T o p t, or PK T o p t, were lower than that of the K T o p t. Therefore, in our study the Q 1 K T o p t, Q 2 K T o p t or PK T o p t are the most appropriate methods for association mapping.
The question of what significance threshold is appropriate for genomewide association studies is somewhat unresolved.
Whether such thinking is appropriate for the association of the regulatory GMS proteins with the PVM is not clear.
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