Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock

Abstract

Temperature compensation is a defining feature of circadian oscillators, yet no components contributing to the phenomenon have been identified in plants. We tested 27 accessions of Arabidopsis thaliana for circadian leaf movement at a range of constant temperatures. The accessions showed varying patterns of temperature compensation, but no clear associations to the geographic origin of the accessions could be made. Quantitative trait loci (QTL) were mapped for period and amplitude of leaf movement in the Columbia by Landsberg erecta (CoL) and Cape Verde Islands by Landsberg erecta (CvL) recombinant inbred lines (RILs) at 12 degrees , 22 degrees , and 27 degrees . Six CvL and three CoL QTL were located for circadian period. All of the period QTL were temperature specific, suggesting that they may be involved in temperature compensation. The flowering-time gene GIGANTEA and F-box protein ZEITLUPE were identified as strong candidates for two of the QTL on the basis of mapping in near isogenic lines (NILs) and sequence comparison. The identity of these and other candidates suggests that temperature compensation is not wholly determined by the intrinsic properties of the central clock proteins in Arabidopsis, but rather by other genes that act in trans to alter the regulation of these core proteins.

Figure 1.—

Distribution of accession periods. Frequency histograms of accession mean leaf-movement periods at 12° (A), 22° (B), and 27° (C). Periods were binned into 15-min intervals, labeled with the upper period bound of the interval.

Figure 2.—

Natural variation in temperature compensation. Mean period of accessions plotted against temperature and separated by temperature-compensation response into accessions that show period shortening as temperature increases between 12° and 27° (A); accessions that show period shortening between 12° and 22°, followed by little change between 22° and 27° (B); accessions that show period shortening between 12° and 22° and period lengthening between 22° and 27° (C); and accessions that show little change in period between 12° and 27° (D). See insets for accession identities.

Figure 3.—

Correlations between circadian period and geographical origins of accessions. Correlation of mean circadian period to latitude (A, D, and G), longitude (B, E, and H), and altitude (C, F, and I) recorded for accession collection sites at 12° (A–C), 22° (D–F), and 27° (G–I). Correlation (R²) and probability (P) indicated for significant correlations. Data were plotted at an intermediate value for latitude, longitude, and altitude measurements recorded as ranges (see Table 1).

Figure 4.—

Temperature compensation in Ler, Col, Cvi, and the CvL and CoL RILs. (A) Mean leaf-movement period plotted against temperature for the Ler (open circles), Col (solid triangles), and Cvi (solid circles) accessions. Error bars show SEM for period estimates. (B) Frequency histograms of the CvL (i, iii, and v) and CoL (ii, iv, and vi) RIL mean periods at 12° (i and ii), 22° (iii and iv), and 27° (v and vi). Data are binned into 15-min intervals, labeled with the upper period bound of the interval. Horizontal lines below accession names indicate the SEM interval of parental accession periods.

Figure 5.—

Genetic mapping of circadian period QTL in the CvL and CoL RILs. QTL likelihood (LOD) maps across Arabidopsis chromosomes 1 and 5 in the CvL (A) and CoL (B) RILs. Chromosome numbers are indicated in the upper right corner of each graph. Names on the x-axis correspond to molecular markers. QTL were mapped independently at 12° (open diamonds), 22° (shaded diamonds), and 27° (solid diamonds). Dashed line represents 2.7 LOD significance threshold of P < 0.05 (as calculated from Van Ooijen 1999). Solid boxes on x-axis span the 2-LOD support interval of mapped QTL. Putative QTL designations are indicated in italics. Selected markers used as cofactors in mapping are identified above the x-axis with diamonds shown as open (12°), shaded (22°), and solid (27°) according to temperature.

Figure 6.—

Genetic mapping of leaf-movement amplitude QTL in the CvL and CoL RILs. QTL likelihood (LOD) maps across Arabidopsis chromosomes in CvL and CoL RILs. Population and chromosome number are indicated in the upper right corner of each graph. Names on the x-axis correspond to molecular markers. QTL were mapped independently at 12° (open diamonds), 22° (shaded diamonds), and 27° (solid diamonds). Dashed line represents 2.7 LOD significance threshold of P < 0.05 (Van Ooijen 1999). Solid boxes on the x-axis span the 2-LOD support interval of mapped QTL. Putative QTL designations are indicated in italics. Selected markers used as cofactors in mapping are identified above the x-axis with diamonds shown as open (12°), shaded (22°), and solid (27°) to according to temperature.

Figure 7.—

PerCv1a, PerCv1b, and PerCv5d NILs. Mean leaf-movement period of Ler is compared to NILs for PerCv1a and PerCv1b (A and B) and for PerCv5d (D and E) at 12°, 22°, and 27°. See insets for line identification. Error bars represent SEM of period estimates. NIL genotypes across the five Arabidopsis chromosomes are shown to the right of each graph. Open regions represent the Ler genotype and solid regions represent the Cvi genotype. Detailed view of NIL genotypes around PerCv1a and PerCv1b (C) and PerCv5d (F) regions shows the position of mapping markers (solid diamonds) and candidate genes (open diamonds). Horizontal lines correspond to mapping markers and solid (Cvi) and open (Ler) regions of vertical bars represent the genotype of NILs at the markers. Breakpoints are estimated as the midpoint between mapping markers.