Novel natural alleles at FLC and LVR loci account for enhanced vernalization responses in Arabidopsis thaliana

ABSTRACT Vernalization, the induction of flowering by low winter temperatures, is likely to be involved in plant climatic adaptation. However, the genetic, molecular and ecological bases underlying the quantitative variation that tunes vernalization sensitivity to natural environments are largely unknown. To address these questions, we have studied the enhanced vernalization response shown by the Ll‐0 accession of Arabidopsis thaliana. Quantitative trait locus (QTL) mapping for several flowering initiation traits in relation to vernalization, in a new Ler × Ll‐0 recombinant inbred line (RIL) population, identified large effect alleles at FRI, FLC and HUA2, together with two small effect loci named as Llagostera vernalization response (LVR) 1 and 2. Phenotypic analyses of near isogenic lines validated LVR1 effect on flowering vernalization responses. To further characterize the FLC allele from Ll‐0, we carried out genetic association analyses using a regional collection of wild genotypes. FLC‐Ll‐0 appeared as a low‐frequency allele that is distinguished by polymorphism Del(‐57), a 50‐bp‐deletion in the 5′‐UTR. Del(‐57) was significantly associated with enhanced vernalization responses and FLC RNA expression, as well as with altitude and minimum temperatures. These results are consistent with Del(‐57) acting as a novel cis‐regulatory FLC polymorphism that may confer climatic adaptation by increasing vernalization sensitivity. Although vernalization is likely to be involved in plant climatic adaptation, the molecular bases of its natural quantitative variation still remain mostly unknown. QTL analysis of the enhanced vernalization response shown by the Ll‐0 wild genotype of Arabidopsis thaliana identified the large effect loci FRI, FLC and HUA2, as well as two new small effect loci named as Llagostera vernalization response (LVR) 1 and 2. In addition, molecular and environmental characterization of the FLC allele from Ll‐0 revealed Del(‐57), a deletion in the untranslated leader, as a potential cis‐regulatory FLC polymorphism that might confer climatic adaptation by increasing vernalization sensitivity.