Role of FRIGIDA and FLOWERING LOCUS C in determining variation in flowering time of Arabidopsis

Abstract

Arabidopsis (Arabidopsis thaliana) accessions provide an excellent resource to dissect the molecular basis of adaptation. We have selected 192 Arabidopsis accessions collected to represent worldwide and local variation and analyzed two adaptively important traits, flowering time and vernalization response. There was huge variation in the flowering habit of the different accessions, with no simple relationship to latitude of collection site and considerable diversity occurring within local regions. We explored the contribution to this variation from the two genes FRIGIDA (FRI) and FLOWERING LOCUS C (FLC), previously shown to be important determinants in natural variation of flowering time. A correlation of FLC expression with flowering time and vernalization was observed, but it was not as strong as anticipated due to many late-flowering/vernalization-requiring accessions being associated with low FLC expression and early-flowering accessions with high FLC expression. Sequence analysis of FRI revealed which accessions were likely to carry functional alleles, and, from comparison of flowering time with allelic type, we estimate that approximately 70% of flowering time variation can be accounted for by allelic variation of FRI. The maintenance and propagation of 20 independent nonfunctional FRI haplotypes suggest that the loss-of-function mutations can confer a strong selective advantage. Accessions with a common FRI haplotype were, in some cases, associated with very different FLC levels and wide variation in flowering time, suggesting additional variation at FLC itself or other genes regulating FLC. These data reveal how useful these Arabidopsis accessions will be in dissecting the complex molecular variation that has led to the adaptive phenotypic variation in flowering time.

Figure 1.

Variation of flowering time among Arabidopsis accessions. Flowering time was assayed by the FLN. A, The relationship between FLN of nonvernalized plants and latitude of collection site. B, FLN of vernalized plants. For white diamonds, see details in the main text. C, Plants grown in long-day conditions without vernalization. A very-late-flowering accession from Sweden (left) compared to an early-flowering Col-0 (right). D, FLN without vernalization plotted against FLN with vernalization to show variation in vernalization response. DNF represents accessions that did not flower without vernalization.

Figure 2.

A, Expression levels of FLC and FRI genes detected by northern hybridization in total RNA from nonvernalized plants. Expression levels were shown as relative to our standard accession H51. *, Very low level of FRI transcripts in the accessions that carry the Ler-type deletion, as reported by Johanson et al. (2000). B, Relationship between FLC expression level and flowering time of nonvernalized plants. The regression line was calculated without DNF accessions (y = 16.233x + 17.628; R² = 0.331; P < 0.001). The white diamond shows the value of the control accession H51. 1, Kno-18; 2, Cvi-0; 3, Ag-0; 4, Ra-0; 5, Br-0; 6, N6034. C, Relationship between vernalization response and FLC expression level in nonvernalized plants. Vernalization response was measured as the ratio of flowering time without and with an 8-week cold treatment. For DNF plants, we calculated the value by assigning FLN = 150.0. The regression line was y = 1.0662x + 1.0864; R² = 0.3771; P < 0.001.

Figure 3.

A, Polymorphisms in the amino acid sequence of the FRI protein. The protein sequence of each accession is compared to that of H51. The letters (a–t) above the sequence show the major mutations that disrupt protein function. Single substitutions of amino acids within the sequence are indicated with numbers (1–31). The underlined sequences indicate the two coiled-coil domains. ↓, Amino acid substitutions; ▴ and ▾, insertion and deletion of nucleotides, respectively; and STOP, the premature stop codons. Accessions containing each polymorphism are shown in Supplemental Figure 4, A and B. B, Variation in FLC expression level among accessions with putative nonfunctional FRI haplotypes. ○, Accessions with Ler-type deletion (b–e in A); □, accessions with the Col-type deletion (l in A); ▵, accessions with the other nonfunctional haplotypes. Black symbols indicate the very-late-flowering accessions.

Figure 4.

Number of accessions with functional or nonfunctional FRI and their FLC expression level and flowering time.

Figure 5.

The effect of the FRI and FLC allelic types on the relationship between flowering time and latitude. A and B, Variation of flowering time in nonvernalized and vernalized accessions carrying the functional FRI and FLC alleles. C and D, Variation in flowering time in nonvernalized and vernalized accessions with nonfunctional FRI alleles or weak FLC alleles. ♦, Accessions with functional FRI/FLC alleles; ○, with Ler-type FRI alleles; □, with Col-type FRI allele; ▵, with other nonfunctional FRI alleles; gray diamonds, with the putative weak FLC allele.

Figure 6.

The geographical distribution of the nonfunctional FRI and weak FLC alleles. ○, Accessions with Ler-type deletion; □, accessions with the Col-type deletion; ▵, accessions with other nonfunctional FRI alleles; gray diamonds, accessions with putative weak FLC alleles.