An Arabidopsis Example of Association Mapping in Structured Samples

A potentially serious disadvantage of association mapping is the fact that marker-trait associations may arise from confounding population structure as well as from linkage to causative polymorphisms. Using genome-wide marker data, we have previously demonstrated that the problem can be severe in a global sample of 95 Arabidopsis thaliana accessions, and that established methods for controlling for population structure are generally insufficient. Here, we use the same sample together with a number of flowering-related phenotypes and data-perturbation simulations to evaluate a wider range of methods for controlling for population structure. We find that, in terms of reducing the false-positive rate while…

• NS
  National Science Foundation

  Award: 0115062
• WM
  W. M. Keck Foundation
• FJ
  Fletcher Jones Foundation
• NI
  National Institutes of Health

  Award: HG002790
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/D010799/1, BB/E009662/1, BBS/E/J/000CA305