To detect variants with significant effects on FLM transcript levels (simple single locus association test), 119 variants of a 7 kb FLM locus were extracted from a set of 840 sequences retrieved from the GEBrowser 3.0, as described above. To examine whether a variant showed a significant effect on FLM expression, the qRT-PCR expression values of the 54 accessions from the FLM haplotype set were used as input data (Supplementary file 4) to run Kruskal-Wallis tests using R (http://www.r-project.org/). p-values from all comparisons were corrected following the Benjamini-Hochberg multiple testing correction and resulting values were -log(10) transformed and plotted along the gene model (Figure 3—figure supplement 5 and Supplementary file 5).