A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2

Nat Genet. 2001 Dec;29(4):435-40. doi: 10.1038/ng767.


Variation of flowering time is found in the natural populations of many plant species. The underlying genetic variation, mostly of a quantitative nature, is presumed to reflect adaptations to different environments contributing to reproductive success. Analysis of natural variation for flowering time in Arabidopsis thaliana has identified several quantitative trait loci (QTL), which have yet to be characterized at the molecular level. A major environmental factor that determines flowering time is photoperiod or day length, the length of the light period, which changes across the year differently with geographical latitude. We identified the EDI locus as a QTL partly accounting for the difference in flowering response to the photoperiod between two Arabidopsis accessions: the laboratory strain Landsberg erecta (Ler), originating in Northern Europe, and Cvi, collected in the tropical Cape Verde Islands. Positional cloning of the EDI QTL showed it to be a novel allele of CRY2, encoding the blue-light photoreceptor cryptochrome-2 that has previously been shown to promote flowering in long-day (LD) photoperiods. We show that the unique EDI flowering phenotype results from a single amino-acid substitution that reduces the light-induced downregulation of CRY2 in plants grown under short photoperiods, leading to early flowering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles*
  • Amino Acid Sequence
  • Arabidopsis / genetics*
  • Arabidopsis / physiology
  • Arabidopsis Proteins
  • Base Sequence
  • Cryptochromes
  • DNA Primers
  • Drosophila Proteins*
  • Eye Proteins*
  • Flavoproteins / chemistry
  • Flavoproteins / genetics*
  • Molecular Sequence Data
  • Photoreceptor Cells, Invertebrate*
  • Quantitative Trait, Heritable*
  • Receptors, G-Protein-Coupled
  • Sequence Homology, Amino Acid


  • Arabidopsis Proteins
  • CRY1 protein, Arabidopsis
  • Cryptochromes
  • DNA Primers
  • Drosophila Proteins
  • Eye Proteins
  • Flavoproteins
  • Receptors, G-Protein-Coupled
  • cry protein, Drosophila

Associated data

  • GENBANK/AB012626
  • GENBANK/AB012627
  • GENBANK/AB024337
  • GENBANK/AF130423
  • GENBANK/AF130425
  • GENBANK/AY057440
  • GENBANK/S66907
  • GENBANK/U43397
  • GENBANK/X72019