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First published online 22 October 2003
doi: 10.1242/dev.00842

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Dissection of floral induction pathways using global expression analysis

Markus Schmid^1,2, N. Henriette Uhlenhaut^2,*, François Godard^2,, Monika Demar¹, Ray Bressan³, Detlef Weigel^1,2, and Jan U. Lohmann^1,2

¹ Department of Molecular Biology, Max Planck Institute for Developmental Biology, D-72076 Tübingen, Germany
² Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
³ Center for Plant Environmental Stress Physiology, Purdue University, West Lafayette, IN 47907, USA

View larger version (43K): [in a new window]   Fig. 1. Characteristics of expression estimates. (A) Expression of marker genes for the shoot apex. (B) Similarity in expression estimates between arrays of duplicate samples. (C,D) Differences in expression estimates for averages from duplicate Col and Ler arrays. Numbers indicate relative expression levels. d, days; rep, replicate number.

View larger version (90K): [in a new window]   Fig. 2. Scanning electron micrographs. (A-E) Shoot apices of plants grown for 30 days under short days. (F-J) Shoot apices of plants after 7 additional long days. Axils of leaf primordia appear empty before the shift to long days (A). White asterisks indicate shoot apical meristems, crosses lateral shoot meristems that form in the axils of leaves. The oldest flower primordia (f) are labeled in F and H-J. Note that these are much younger in co-2 and ft-2 mutants than in wild type, and that flower-like structures have not yet formed in lfy-12 mutants, although several bracts (b) that surround the shoot apical meristem are apparent. Scale bars: 50 µm (A-E,G,I,J); 100 µm (F,H).

View larger version (21K): [in a new window]   Fig. 3. Expression profiles of known flowering-time and floral genes in wild-type and mutant plants. Signals were normalized to the median for each gene. Numbers on the x axis refer to days after transfer to long days. Numbers on the y axis indicate relative expression levels. Data are from experiment III, and were analyzed by RMA.

View larger version (43K): [in a new window]   Fig. 4. Correlation analysis of the list of `top 500 genes in Col and Ler' (see text for details). d, days; rep, replicate number.

View larger version (19K): [in a new window]   Fig. 5. Effect of FLC on the photoperiod response. Induction of CO is independent of FLC repression. Downstream genes CAL, FUL and SOC1 are differentially affected. At the last time point, there was no sign of flower formation in FRI FLC plants.

View larger version (16K): [in a new window]   Fig. 6. Expression profiles of new LFY candidate targets. Locus identifiers and gene descriptions are listed in Table 2. Signals were normalized to the median for each gene. (A) Expression profiles of genes from Table 2. At2g01520 (tan) At3g04960 (cyan) At4g21590 (brown) At4g27460 (light green) At4g31910 (black) At4g33790 (pink) At5g15150 (red) At5g52390 (purple) At5g57720 (green) At5g24910 (teal). (B) Expression profile of At5g22430, which was identified as a potential AP3 target by Zik and Irish (Zik and Irish, 2003).

View larger version (90K): [in a new window]   Fig. 7. Hierarchical clustering of `top 500 genes in Col and Ler'. Red indicates high expression signal, green low signal. Signals were normalized to the median for each gene.

View larger version (16K): [in a new window]   Fig. 8. Expression profiles for a subset of repressed genes, that are expressed more highly in Ler than Col: At3g58990 (green), At2g43100 (blue), At1g47485 (cyan), At3g03190 (purple), At1g74090 (brown), At4g13770 (teal), At2g39310 (pink), At2g37460 (red), At2g46650 (light green), At5g44480 (tan). Signals were normalized to the median for each gene.

View larger version (18K): [in a new window]   Fig. 9. SMZ and SNZ characterization. (A) Diagram of ALF7 insertion. The cauliflower mosaic virus 35S enhancers are located approximately 1 kb upstream of SMZ, which encodes an AP2-domain protein (2; At3g54990). Other genes in the vicinity of the enhancer are annotated as encoding a putative protein (1; At3g54980), and expressed proteins 3 (At4g55000) and 4 (At3g55005). (B) Expression profiles of SMZ and SNZ. Signals were normalized to the median for each gene. Numbers on the x axis refer to days after transfer to long days. (C) Histogram of flowering times of primary transformants in long days. Range of flowering time of Columbia wild type is indicated below the histogram.

View larger version (28K): [in a new window]   Fig. 10. Expression of putative miRNA target genes and a miRNA precursor in response to photoperiod. (A) AP2 (purple), RAP2.7 (cyan), At5g60120 (green) and At5g67180 (red). Signals were normalized to the median for each gene. (B) Expression of MIR172a-2 analyzed by semi-quantitative RT-PCR. Because of background amplification, quantification using SYBR Green and real-time PCR was not possible. ß-tubulin was used as a control. (C) Expression profiles of SPL2 (cyan), SPL3 (light green), SPL4 (ochre), SPL6 (blue), SPL9 (brown), SPL10 (dark green), SPL11 (purple), SPL13 (teal) and SPL15 (pink). Signals were normalized to the median for each gene. Numbers on the x axis refer to days after transfer to long days.