Allelic variation at the FRI (FRIGIDA) and FLC (FLOWERING LOCUS C) loci are major determinants of flowering time in Arabidopsis accessions. Dominant alleles of FRI confer a vernalization requirement causing plants to overwinter vegetatively. Many early flowering accessions carry loss-of-function fri alleles containing one of two deletions. However, some accessions categorized as early flowering types do not carry these deletion alleles. We have analyzed the molecular basis of earliness in five of these accessions: Cvi, Shakhdara, Wil-2, Kondara, and Kz-9. The Cvi FRI allele carries a number of nucleotide differences, one of which causes an in-frame stop codon in the first exon. The other four accessions contain nucleotide differences that only result in amino acid substitutions. Preliminary genetic analysis was consistent with Cvi carrying a nonfunctional FRI allele; Wil-2 carrying either a defective FRI or a dominant suppressor of FRI function; and Shakhdara, Kondara, and Kz-9 carrying a functional FRI allele with earliness being caused by allelic variation at other loci including FLC. Allelic variation at FLC was also investigated in a range of accessions. A novel nonautonomous Mutator-like transposon was found in the weak FLC allele in Landsberg erecta, positioned in the first intron, a region required for normal FLC regulation. This transposon was not present in FLC alleles of most other accessions including Shakhdara, Kondara, or Kz-9. Thus, variation in Arabidopsis flowering time has arisen through the generation of nonfunctional or weak FRI and FLC alleles.The timing of the floral transition has significant consequences for the reproductive success of plants. Plants need to gauge when both environmental and endogenous cues are optimal before undergoing the switch to reproductive development. To achieve this, a complex regulatory network has evolved consisting of multiple pathways that quantitatively regulate a set of genes (the floral pathway integrators) whose activity causes the transition of the meristem to reproductive development (Simpson and Dean, 2002). As plant varieties spread, there is strong selective pressure for changes in flowering time that confer an advantage in that new environment. Arabidopsis accessions show a range of flowering strategies: Some complete their life cycle very rapidly, whereas others adopt a winter annual habit, overwintering vegetatively and flowering in the favorable conditions of spring. The genetic basis of this has been analyzed in a number of studies (Clarke et al., 1995;Jansen et al., 1995;Mitchell-Olds, 1996; Alonso-Blanco et al., 1998).Allelic variation at FRI (FRIGIDA) was found to be a major determinant of vernalization requirement and flowering time variation (Napp-Zinn, 1985; Burn et al., 1993;Lee et al., 1993;Clarke and Dean, 1994). FRI functions to increase RNA levels of the floral repressor FLC (FLOWERING LOCUS C), which represses the expression of genes required for the transition to flowering (Michaels and Amasino, 1999;Sheldon et al., 1999). FLC RNA l...