Copy Number and Natural Haplotype Variation At The HvFT1 Locus Is Associated With Accelerated Flowering Time In Barley

The Flowering Locus T (FT1= VRN3) is a central integrator of photoperiod and vernalization signals in the temperate cereals. As a mobile signal, FT1 facilitates the conversion of environmental cues received in the leaves to a plant reproductive response in the apical meristem. In barley (Hordeum vulgare L.), it was hypothesized that natural variation in the HvFT1 promoter and first intron was responsible for the differences in flowering time mapped to this locus.  However, we identified alleles with identical HvFT1 sequences but large differences in heading time.  Here we describe differences in copy number variation at the HvFT1 locus that explain the observed differences in heading time. We found that BGS213, the designated barley genetic stock for the dominant VRN-H3 allele, carries four to five identical copies of HvFT1 gene. The higher HvFT1 copy number is associated with a dominant spring growth habit, which is epistatic to the alleles for winter growth habit present at the VRN-H1 and VRN-H2 loci.  Our results show that higher expression of HvFT1 can overcome the repressed state of the VRN-H1 gene in the winter barley varieties. The more precise quantification of the effect of the series of HvFT1 alleles on flowering time is expected to provide barley breeders the information required to engineer flowering time and improve adaptation of barley to changing environments.