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Genetic Interactions Among Late-Flowering Mutants of Arabidopsis
M. Koornneefa, C. Alonso-Blancoa, H. Blankestijn-de Vriesa, C. J. Hanharta, and A. J. M. Peetersaa Laboratory of Genetics, Graduate School Experimental Plant Sciences,Wageningen Agricultural University, NL-6703 HA, Wageningen, The Netherlands
Corresponding author: M. Koornneef, Laboratory of Genetics, Wageningen Agricultural University, 2 Dreijenlaan, NL-6703 HA, Wageningen, The Netherlands, maarten.koornneef{at}botgen.el.wau.nl (E-mail).
Communicating editor: J. CHORY
| ABSTRACT |
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Flowering time in Arabidopsis is controlled by a large number of genes, identified by induced mutations. Forty-two double mutants involving 10 of these loci were obtained and analyzed for their flowering behavior under long-day conditions, with and without vernalization, and under short-day conditions. The genetic interactions between the various mutants proved to be complex, although a major epistatic group (called group A) could be identified corresponding to the mutants, which are relatively insensitive to vernalization and daylength. In contrast, the genetic behavior of the mutants much more responsive to these environmental factors (group B) is more complex. The vernalization responsiveness of the group B mutants did not compensate for the lateness of the group A mutants. This indicated that these genes do not control vernalization sensitivity as such, but provide a factor that becomes limiting in short days. The classification of these mutants in different physiological groups is discussed in relation to the detected genetic interactions, and based on these interactions a more detailed model of their role in flowering initiation is proposed.
THE genetic control of the transition to flowering in Arabidopsis is complex. This is indicated by the large number of loci identified by the analysis of both mutants and natural variants (reviewed by ![]()
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One of the best characterized groups of flowering mutants in Arabidopsis are the late mutants reviewed by ![]()
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The analysis of genetic relationships among a large number of mutants with quantitative effects has not often been described. The availability of flowering-time mutants such as those of Arabidopsis provides an attractive system for this type of analysis. Examples of clear epistatic relationships among flowering-time genes in Arabidopsis are the interactions between FLC and, respectively, the FR I and L D loci, which could be interpreted in a model where the L D gene inhibits the FLC gene, which together with FRI, is required for the inhibition of flowering (![]()
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In the present article, a systematic and quantitative comparison of double mutants of representative alleles at 10 of the late-flowering mutant loci has been made, and thus epistatic groups have been established. Preliminary data on the epistatic groups were given in ![]()
| MATERIALS AND METHODS |
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The mutant alleles, all in the Landsberg erecta (Ler) genetic background, that were used are the following: fca-1, fve-1, fy-1, fpa-1, fe-1, ft-1, fha-1, fwa-1, co-3, and gi-3. These mutant alleles have been described in ![]()
Flowering time (FT) was recorded as the number of days from the date the seeds were imbibed at 25° to the opening of the first flower. Total leaf number (LN) was scored as the number of leaves in the rosette plus the number of cauline leaves on the main stem, which has been shown to correlate highly with flowering time (![]()
The interaction between each pair of mutations was tested by two-way anova. Given the correlation between means of leaf number and the corresponding variances, logarithmic transformation was applied to the leaf number data. The latter implies that interaction is based on the absence of additivity in a multiplicative scale. Long-day (LD) experiments were performed in an air-conditioned greenhouse supplemented with additional light from the middle of September until the beginning of April, providing a daylength of at least 14 hr and a light intensity sufficient to allow growth. Day temperature was 2225° and night temperature 1619°. Per genotype, groups of six plants were grown in a row. These groups were randomized over four blocs. The vernalization treatment was tested in the same LD experiments. This treatment was given as described by ![]()
Short-day (SD) experiments were carried out in a single climate chamber with 8 hr of light as described by ![]()
| RESULTS |
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The isolation of double mutants:
In most cases double mutants could be readily identified by the procedure described in MATERIALS AND METHODS. However, three double mutant combinations were not obtained. Because of close linkage between co and fy (![]()
The genetic relationships among late-flowering mutants:
The various confirmed double mutants were grown in the greenhouse under LD conditions in three different experiments. Because the most complete collection of double mutants was present in the last experiment and the correlation between the various experiments was high, the data of this experiment (Table 1) are presented and discussed. Table 1 shows the total leaf number of all single and double mutants tested.
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The double mutants can be classified in a qualitative manner, according to their phenotype (total leaf number) in comparison to the parental mutants in the following three classes: (1) double mutants with a flowering time approximately similar to the addition of the delay produced by each mutant (and therefore both mutations do not interact but behave additively), and (2) double mutants with earlier flowering time than the addition of the effects of both single mutations. In this case, the double mutants are considered as showing epistasis in the sense of less-than-additive interaction. The extreme situation of this type of interaction is when a double mutant shows similar flowering time to one of the parental mutants, usually the latest one. (3) Those double mutants showing a later flowering time than the simple addition of both mutations, for example, a more-than-additive effect, the mutations interacting synergistically. Mutants belonging to the same epistatic group are expected to have double mutants, which among them are epistatic and which will show a relatively similar behavior, either additive or synergistic, with the mutants outside the group. The significance of the interaction between two mutations was estimated from the interaction term of a two-way ANOVA for each pair of mutants (Table 1).
According to these criteria, taking into account not only the significance of the interaction but also the size of the interaction effect (Table 1), the most remarkable interactions detected among the 42 double mutants can be summarized as follows:
On one hand, gi behaves as epistatic with co, fwa, fha, fe, and f t ; the co mutant behaves as epistatic with fwa, ft, and fe ; and fwa shows epistasis with ft. In general, when considering the interactions among these mutants, the later mutants give rise to clear epistasis, whereas the earlier ones have a slightly additive effect. Therefore, these six mutants can be classified as one epistatic group, in agreement with the established physiological classification of these loci in a common group, which from here on will be referred to as group A.
On the other hand, the genetic relationships among fca, fve, f y, and fpa, which belong to the so-called responsive physiological group, seem more complex. This group will be referred to as group B. The only clear epistatic behavior was observed between fca and f y and between fve and fpa. The fpa mutant is the most deviating one as shown by the more-than-additive effect observed in the double mutant with fca.
When considering the interactions between mutants of group A and group B, in general an additive effect was observed, although strong synergistic interactions appeared in several double mutants. Particular complex interactions are shown by the double mutants involving fpa, which interacts synergistically with ft and fe, as shown by the extreme lateness of the double mutants. In contrast, the double mutants of fpa with fha, fwa, co, and gi are relatively early. The gi mutant is in fact epistatic with fpa. A last intriguing interaction is shown between fha and fca, which seem to interact synergistically as well. From this analysis it appears that genetic relations can be complex, and that this complexity depends on the mutant.
Vernalization responsiveness in the double mutants:
Because the mutants differ strongly in the effect of a 3-wk vernalization treatment it was tested for all single and double mutants (Table 1, Figure 1). The vernalization response of the single mutants was similar to previous reports (![]()
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A number of mutants from group A (co, gi, fwa, and fe) and from group B (fca and fve) were selected to test different periods of vernalization treatment (Figure 2). The comparisons of the double mutants with different periods of vernalization show a similar pattern, as with the 3-wk treatment. Double mutants within group A did not increase their response when increasing the vernalization treatment to 5 wk (Figure 2A). It appears that the vernalization responsiveness of fca and fve is additive. In combinations where one of the mutants is vernalization-responsive and the second one is not, the additional lateness due to the vernalization-responsive mutant (fca and fve) can be overcome by vernalization, but this treatment cannot compensate for the lateness of the second unresponsive mutant. In other words, vernalization cannot compensate for the lateness conferred by the nonresponsive mutants, as it can do for the responsive parent.
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The effect of short days (SD):
A number of mutants from group A (co, gi, fwa, and fe) and from group B (fca and fve) and all the corresponding double mutants were analyzed under SD light conditions (Figure 3). Two different greenhouse experiments (LD conditions) that are used for comparison show a considerable difference, where the plants in the summer experiment flowered earlier and with fewer leaves than in the autumn. This difference is probably mainly due to differences in light intensity, as has been reported before (![]()
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The relationship between rosette and cauline leaf number and flowering time:
In earlier analyses it appeared that the late-flowering mutants differ in the relative numbers of rosette and cauline leaves. Analysis of the ratio of cauline/total leaf number (Figure 4) indicated that a high ratio is present among single and double mutants of the group A and relatively lower ratios within the group B mutants, as it was described previously for the single mutants (![]()
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The ratio between LN and flowering time showed a relatively low variation among the genotypes, although the group A mutants flowered slightly later at the same number of leaves than the double mutants involving the B group, indicating a slightly faster rate of leaf initiation in the latter (data not shown).
| DISCUSSION |
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The large number of flowering-time loci in Arabidopsis (![]()
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The analysis of 42 double mutants involving 10 different loci show that genetic relationships among these genes are complex. This can be interpreted by assuming that these genes interact in a complex way and cannot be grouped into a few parallel pathways, each with a number of genes acting in a linear way. However, a complication in the interpretation of this type of genetic analysis is that some of the mutants might be "leaky." Leaky mutants in a linear pathway often show additive or even more-than-additive effects, which normally are interpreted as the genes controlling different pathways. Nevertheless, in most cases several alleles have been found, and mostly the more extreme alleles were included in the present analysis. The available sequence information for the alleles co-3 (![]()
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When small differences between double mutants, which might be explained by differences in leakiness, are neglected, the group A mutants (co, gi, fe, fha, ft, and fwa) behave as one epistatic group, which corresponds with their physiological properties. Their relatively limited responsiveness to environmental factors is also observed in the double mutants among the group A mutants. Moreover, these mutants have a relatively high proportion of cauline leaves and a slightly reduced leaf-initiation rate compared with the group B mutants. The fe and ft mutants can be considered a subgroup within group A, based on their similar genetic behavior with most late-flowering mutants, and particularly on their synergistic interaction in combination with the fpa mutant. This similarity between ft and fe may be surprising because the fe mutant has been described as a mutant somewhat intermediate in its response to environmental factors (![]()
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The vernalization and daylength-responsive mutants (group B) behave more variably in their genetic relations with other mutants. Within this group the two mutants with the largest effect (fca and fve) show a clear additive effect even for their increased responsiveness to vernalization (Figure 2). On the other hand, fpa is epistatic with fve, and fca also shows less-than-additive interaction with fy. Thus, it is suggested that there might be two subgroups within group B. The more-than-additive effect observed between fca and fpa and the additivity between fca and fve suggests a redundant role for FPA and FC A and would locate FPA upstream to FV E. The possible lethality of the fpa fy double mutant would locate FY upstream to FCA, because otherwise the double fpa fca also would be expected to be lethal.
Several interactions between the two groups of late-flowering mutants are very interesting and might be interpreted in terms of interactions among the different pathways controlling flowering initiation (Figure 5). One of these is the extreme lateness of the double mutants fpa ft and fpa fe. To explain these synergistic interactions, we assume that FPA has a function in flowering similar to FE and FT, and in this way they may replace each other; only when both are absent is flowering strongly delayed. Taking into account that this extreme lateness is not observed in the double mutants between fpa and the rest of the group A mutants, then CO, GI, and probably FHA are likely to locate downstream of FE and FT. Nevertheless, some of these loci, although affecting specifically the same pathway, might be placed as branches from the LD-promotion pathway, as suggested for F WA. The interactions shown between FPA and genes from both groups FCA, FE, and FT suggest that the fpa mutation would affect flowering time through both the LD and the constitutive promotion pathways. This would explain the reduced responsiveness to vernalization observed in the fpa fca double mutants, because part of the lateness might come from an effect in the LD-promotion pathway through the interaction with FE and FT, and similarly would explain the large responsiveness to vernalization shown by the fpa fe and fpa ft double mutants. A last intriguing interaction between both groups of mutants is the very late phenotype of the f h a fca double mutant. Because this extreme interaction is not observed between fca and the other group A mutants, this might locate FHA upstream in the LD promotion or, as discussed above, might determine a branching point of this pathway.
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In the present study we observed that the vernalization responsiveness is not abolished in double mutants involving responsive and nonresponsive mutants, which indicates that the group A genes are not required for the vernalization responsiveness of the group B mutants. However, vernalization does not compensate for the lateness due to the group A mutants, in agreement with the observation that a saturating vernalization treatment of wild type in SD greatly reduced flowering time but did not compensate fully for the SD delay (![]()
The model that in group A mutants the LD promotive pathway is blocked leads to the expectation that in SD the effect of the group A mutants will not be observed as was found (Figure 3). However, the observation that the co fve double mutant in SD is somewhat earlier than the monogenic fve mutant suggests that CO not only promotes flowering under LD but somehow also promotes the inhibition by SD. A scheme summarizing the relations among the various late-flowering genes is shown in Figure 5, which can be considered a refinement of the MCDK model.
One important gene, FLC, was not included in the present analysis because all mutants were isolated in the Ler genetic background which probably carries a loss-of-function allele at this locus (![]()
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The present genetic analysis has shown that the physiological pathways thought to control flowering promotion in Arabidopsis also interact. In the near future more genes affecting flowering time and further genetic interactions probably will show a larger complexity in the flowering gene network. Some of the genes already have been cloned (![]()
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| ACKNOWLEDGMENTS |
|---|
We thank J.M. MARTINEZ-ZAPATER for critical comments on an early version of the manuscript and PATTY VAN LOENEN-MARTINET for assistance at the start of the project. This work was supported by the BRIDGE program of the European Union (contract BIOT-CT90-0207 and BIOT-CT92-05290). C.A-B. is supported by the TDR Biotechnology program BIO4-CT96-5008 and A.J.M.P. by BIO4-CT96-0062).
Manuscript received July 29, 1997; Accepted for publication November 3, 1997.
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H. Zhang, C. Ransom, P. Ludwig, and S. van Nocker Genetic Analysis of Early Flowering Mutants in Arabidopsis Defines a Class of Pleiotropic Developmental Regulator Required for Expression of the Flowering-Time Switch Flowering Locus C Genetics, May 1, 2003; 164(1): 347 - 358. [Abstract] [Full Text] [PDF] |
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O. J. Ratcliffe, R. W. Kumimoto, B. J. Wong, and J. L. Riechmann Analysis of the Arabidopsis MADS AFFECTING FLOWERING Gene Family: MAF2 Prevents Vernalization by Short Periods of Cold PLANT CELL, May 1, 2003; 15(5): 1159 - 1169. [Abstract] [Full Text] |
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M. Suzuki, S. Yamaguchi, T. Iida, I. Hashimoto, H. Teranishi, M. Mizoguchi, F. Yano, Y. Todoroki, N. Watanabe, and M. Yokoyama Endogenous {alpha}-Ketol Linolenic Acid Levels in Short Day-Induced Cotyledons are Closely Related to Flower Induction in Pharbitis nil Plant Cell Physiol., January 15, 2003; 44(1): 35 - 43. [Abstract] [Full Text] [PDF] |
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S. M. Welch, J. L. Roe, and Z. Dong A Genetic Neural Network Model of Flowering Time Control in Arabidopsis thaliana Agron. J., January 1, 2003; 95(1): 71 - 81. [Abstract] [Full Text] [PDF] |
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H. Yu, Y. Xu, E. L. Tan, and P. P. Kumar AGAMOUS-LIKE 24, a dosage-dependent mediator of the flowering signals PNAS, December 10, 2002; 99(25): 16336 - 16341. [Abstract] [Full Text] [PDF] |
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M. B. Bitonti, R. Cozza, A. Chiappetta, D. Giannino, M. R. Castiglione, W. Dewitte, D. Mariotti, H. Van Onckelen, and A. M. Innocenti Distinct nuclear organization, DNA methylation pattern and cytokinin distribution mark juvenile, juvenile-like and adult vegetative apical meristems in peach (Prunus persica (L.) Batsch) J. Exp. Bot., May 1, 2002; 53(371): 1047 - 1054. [Abstract] [Full Text] [PDF] |
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A. Mouradov, F. Cremer, and G. Coupland Control of Flowering Time: Interacting Pathways as a Basis for Diversity PLANT CELL, May 1, 2002; 14(90001): S111 - 130. [Full Text] [PDF] |
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N. A. Eckardt Alternative Splicing and the Control of Flowering Time PLANT CELL, April 1, 2002; 14(4): 743 - 747. [Full Text] [PDF] |
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P. H. Reeves, G. Murtas, S. Dash, and G. Coupland early in short days 4, a mutation in Arabidopsis that causes early flowering and reduces the mRNA abundance of the floral repressor FLC Development, January 12, 2002; 129(23): 5349 - 5361. [Abstract] [Full Text] [PDF] |
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M.-a. Ohto, K. Onai, Y. Furukawa, E. Aoki, T. Araki, and K. Nakamura Effects of Sugar on Vegetative Development and Floral Transition in Arabidopsis Plant Physiology, September 1, 2001; 127(1): 252 - 261. [Abstract] [Full Text] [PDF] |
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P. H. Reeves and G. Coupland Analysis of Flowering Time Control in Arabidopsis by Comparison of Double and Triple Mutants Plant Physiology, July 1, 2001; 126(3): 1085 - 1091. [Abstract] [Full Text] [PDF] |
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F. M. Schomburg, D. A. Patton, D. W. Meinke, and R. M. Amasino FPA, a Gene Involved in Floral Induction in Arabidopsis, Encodes a Protein Containing RNA-Recognition Motifs PLANT CELL, June 1, 2001; 13(6): 1427 - 1436. [Abstract] [Full Text] [PDF] |
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O. J. Ratcliffe, G. C. Nadzan, T. L. Reuber, and J. L. Riechmann Regulation of Flowering in Arabidopsis by an FLC Homologue Plant Physiology, May 1, 2001; 126(1): 122 - 132. [Abstract] [Full Text] |
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N. A. Eckardt Giving Rice the Time of Day: Molecular Identification of a Major Photoperiod Sensitivity Quantitative Trait Locus PLANT CELL, December 1, 2000; 12(12): 2299 - 2301. [Full Text] |
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A. Samach, H. Onouchi, S. E. Gold, G. S. Ditta, Z. Schwarz-Sommer, M. F. Yanofsky, and G. Coupland Distinct Roles of CONSTANS Target Genes in Reproductive Development of Arabidopsis Science, June 2, 2000; 288(5471): 1613 - 1616. [Abstract] [Full Text] |
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H. Onouchi, M. I. Igeno, C. Perilleux, K. Graves, and G. Coupland Mutagenesis of Plants Overexpressing CONSTANS Demonstrates Novel Interactions among Arabidopsis Flowering-Time Genes PLANT CELL, June 1, 2000; 12(6): 885 - 900. [Abstract] [Full Text] |
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I. Kardailsky, V. K. Shukla, J. H. Ahn, N. Dagenais, S. K. Christensen, J. T. Nguyen, J. Chory, M. J. Harrison, and D. Weigel Activation Tagging of the Floral Inducer FT Science, December 3, 1999; 286(5446): 1962 - 1965. [Abstract] [Full Text] |
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T. Mockler, H Guo, H Yang, H Duong, and C Lin Antagonistic actions of Arabidopsis cryptochromes and phytochrome B in the regulation of floral induction Development, January 5, 1999; 126(10): 2073 - 2082. [Abstract] [PDF] |
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Y. Y. Levy and C. Dean The Transition to Flowering PLANT CELL, December 1, 1998; 10(12): 1973 - 1990. [Full Text] |
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O. Nilsson, I. Lee, M. A. Blazquez, and D. Weigel Flowering-Time Genes Modulate the Response to LEAFY Activity Genetics, September 1, 1998; 150(1): 403 - 410. [Abstract] [Full Text] |
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C. Alonso-Blanco, S. E.-D. El-Assal, G. Coupland, and M. Koornneef Analysis of Natural Allelic Variation at Flowering Time Loci in the Landsberg erecta and Cape Verde Islands Ecotypes of Arabidopsis thaliana Genetics, June 1, 1998; 149(2): 749 - 764. [Abstract] [Full Text] [PDF] |
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, parents and mutants of group B;
, double mutants combining group A and B mutants;
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