Sequence information from datasets of 776 and 840 accessions, respectively, have been available that were used in this study. The genomic sequences of a comprehensive set of 1135 Arabidopsis accessions have just recently been released and were used for concluding analyses (The 1001 Genomes Consortium, 2016). Genomic FLM sequences (7 kb; Chr1: 28953637–28960296; including 2 kb upstream and 0.2 kb downstream sequence) were extracted from 776 accessions from the 1001 Genomes portal (http://1001genomes.org/datacenter/) using the Wang dataset (343 accessions), the GMI dataset (180 accessions), the Salk dataset (171 accessions) and the MPI dataset (80 accessions) (The 1001 Genomes Consortium, 2016; Schmitz et al., 2013; Long et al., 2013; Cao et al., 2011). 45 SNPs with a MAF>5% were extracted and used for haplotype analysis of the FLM locus (Figure 3A and Figure 3—figure supplement 1). 31 SNPs were polymorphic between the 54 selected accessions represented in the FLM haplotype set (Supplementary file 1).