An Arabidopsis example of association mapping in structured samples.

Naive analyses using standard linear methods without correction for population structure (as in the original papers) often identified what appeared to be highly significant associations.

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Nominally significant associations, in contrast, although far from uniformly distributed, were found across the genome, indicating that most are likely to be spurious even after confounding has been reduced statistically.

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The PHYC by Latitude interaction term was very significant for ±V (SD), and weakly significant for ±V (LD) and VERN.

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Using the various mixed-model approaches, PHYC was marginally significant for ±V (LD) and VERN ( p -values ranged from 0.01 to 0.07 depending on the method used, see Table S1 ), while FLC showed a tendency towards significance ( p -values ranged from 0.03 to 0.13) for SD, SD/LD (V), and FLC.

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