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Genetics and Molecular Biology |
Department of Biology, PO Box 3000, FIN-90014 University of Oulu, Finland
Received for publication June 24, 2003. Accepted for publication February 17, 2004.
| ABSTRACT |
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Key Words: adaptation Arabidopsis lyrata Brassicaceae day length flowering time vernalization
| INTRODUCTION |
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The plant molecular biology model organism Arabidopsis thaliana L. Heynh. also exhibits extensive flowering time variation, as has been shown in studies of sets of accessions (Napp-Zinn, 1957
, 1962
; Karlsson et al., 1993
; Nordborg and Bergelson, 1999
; Alonso-Blanco and Koornneef, 2000
; Maloof et al., 2001
). In a developmental genetics research tradition, the genetic pathways potentially influencing flowering time variation have been thoroughly explored mainly using mutants (Koornneef et al., 1998
; Simpson et al., 1999
; Reeves and Coupland, 2000
; Mouradov et al., 2002
). These studies have discovered multiple genetic pathways that lead to flowering. The photoperiodic pathway genes promote flowering in long days; those in the autonomous pathway promote flowering independent of day length. The vernalization pathway genes are responsive to cold treatments. Other pathways include genes related to nutrient level and gibberellins (see Blásquez, 2000
). Once new late flowering mutants are discovered, the locus of the mutant gene can be initially assigned to a pathway by examining the phenotype in different conditions. For instance, wild type plants flower early in long days, late in short days. If a mutant differs from the wild type in being late flowering in long days but does not differ in other conditions, the mutation may have occurred in one of the genes of the photoperiodic pathway promoting flowering in long days. Likewise, a mutant phenotype responding to cold treatment in a different way than the wild type plant may be due to an alteration in the vernalization responsive loci. These kinds of approaches have detected and assigned to pathways dozens of loci that can potentially influence flowering time (e.g., Koornneef et al., 1991
).
The existence of a large number of loci in the genome that can influence flowering time does not mean that all of these loci govern the variation between natural plant populations. For this purpose, natural populations, not mutant strains, need to be studied. In A. thaliana, the large flowering time differences between winter and summer annual accessions have been found to be due to differences in response to cold treatment (Napp-Zinn, 1957
; Clarke and Dean, 1994
; Johanson et al., 2000
). The molecular work until now suggests that much of the variation is due to the locus FRI (FRIGIDA) and some to the locus FLC (FLOWERING LOCUS C) (Johanson et al., 2000
; Gazzani et al., 2003
). Further, variation in flowering time even within British populations seems to be due to a major gene, possibly FRI (Westerman and Lawrence, 1970
; Jones, 1971a
, b
).
Natural populations of A. thaliana, however, differ from many other plant species in having no evidence of north-south clinal variation in flowering time (Stenøien et al., 2002
). We have started studying flowering time variation in populations of Arabidopsis lyrata (L.) O'Kane and Al-Shehbaz, a close outcrossing relative of A. thaliana (Price et al., 1994
; Koch et al., 2000
; Mitchell-Olds, 2001
). Based on 12 plants per population, from four northern and two southern populations, we found that southern populations flowered earlier than the northern ones (Riihimäki et al., 2004
). Here the goal is to examine those differences within a smaller set of populations but with larger samples sizes with respect to flowering probabilities and flowering times. We also examine the effect of different environmental conditions, specifically with respect to day length and temperature. Further, we test whether the perennial A. lyrata has a similar high correlation between flowering time and leaf number as does the annual A. thaliana. In order to relate the variation to more natural light and temperature environments than are available in growth chambers, the flowering traits of A. lyrata and A. thaliana are also compared in a shared common garden experiment. Further, as A. lyrata is so similar to A. thaliana, we can also interpret the results in the light of the likely importance of the photoperiod- and temperature-related pathways in governing the differences, using the same principles as were described above for assigning mutations to pathways. The genetic architecture of adaptation can be compared between the selfing A. thaliana and the outcrossing A. lyrata. These experiments provide initial evidence on the involvement of the cold and photoperiodic response pathways in the between-population differences of A. lyrata.
| MATERIALS AND METHODS |
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Arabidopsis lyrata populations from the following locations were included in this study: Plech, Germany (49°39' N); Poteply (Bohemia), Czech Republic (50°03' N); Spiterstulen, Norway (61°38' N, 1100 m above sea level [a.s.l.]); Stubbsand (63°13' N) and Mjällom (62°55' N), Sweden; Karhumäki, Russia (62°55' N); and Reykjavik, Iceland (64°09' N). Field-collected seed from individual plants (Spiterstulen and Stubsand) were collected and kept separately as families. The Bohemia seeds were a pooled population sample. The Plech seeds were from crosses made in the laboratory. In addition, we used A. thaliana material collected from natural populations of Naantali, (60°40' N) and Nurmes (63°32' N), Finland, Ruds Vedby, Denmark (55°33' N) (for details, see Kuittinen et al., 1997
), and an accession (Li-5) originally collected from Limburg an der Lahn, Germany (50°35' N).
Photoperiod and vernalization response in climate chambers
We studied the effect of vernalization at the rosette stage and day length (long vs. short day) on flowering time in four Arabidopsis lyrata populations in controlled environment climate chambers at the University of Oulu, Oulu, Finland. We utilized a factorial design with two southern and two northern populations: southern Bohemia and Plech and northern Spiterstulen and Stubbsand. From Spiterstulen and Stubbsand, there were 15 open-pollinated (half-sib) families, and four individuals per family in each treatment. From Plech, there were 15 independent full-sib families from different crosses. The aim was to have 60 plants per population per treatment. If this was not possible, the remaining space was used for additional plants of other populations.
The plants were germinated under two day-length conditions, same as the photoperiod treatments: long days (LD) consisted of 20 h light and 4 h dark, while short days (SD) were 14 h light and 10 h of darkness. Fifteen seeds from each of 15 families from Plech, Spiterstulen, and Stubbsand were sown on petri dishes on moist filter paper in both LD and SD treatments. From Bohemia, 60 seeds (two dishes x 30) were sown per day-length treatment. In order to estimate flowering time as the number of days from germination to flower emergence, we recorded germination in each petri dish daily at noon. To characterize individual plants, we used family median germination dates, and from Bohemia, the population median. Two weeks after sowing the seedlings were transferred into pots filled with gravelpeat mixture (1 : 1). A few additional transfers occurred for another 9 d. The final numbers of plants per population per treatment are presented in Table 1. The populations were represented by 1415 families in each treatment, except for Stubbsand, where the number of families in two cases was 10 and 12.
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Response to seed cold treatment and natural winter in a common garden experiment
The common garden experiment was planted in the Botanical Garden at the University of Oulu, Finland (65°01' N) in June 1996. Seeds from three northern Arabidopsis lyrata subsp. petraea populations (Karhumäki, Russia; Mjällom, Sweden; and Reykjavik, Iceland), and four northern A. thaliana populations/accessions (Limburg, Germany; Ruds Vedby, Denmark; Naantali, Finland; and Nurmes, Finland) were planted in the outside common garden experiment. The Finnish A. thaliana populations, Naantali and Nurmes, were previously classified as late-flowering winter annuals while Limburg-5 is an early-flowering strain (Kuittinen et al., 1997
). Half of the seeds were cold treated (stratified). These seeds were sown in the middle of May in peat pots, filled with a peatvermiculite mixture (1 : 1), 23 seeds per pot. The cold treatment took place in 24 h dark at 4°C for 3 wk. After the cold treatment, we moved the pots into a greenhouse. The remaining seeds were sown 2 wk after the cold treatment started, in pots placed in the garden. After germination all plants were thinned to one seedling per pot. In the garden, we used a split plot design, where cold-treated seeds and untreated ones were placed in separate parts of the experiment, for practical reasons of planting. Within each treatment, pots were placed in a randomized block design in five blocks and six individuals per population in each block, resulting in a total of 30 plants per population and treatment. Additional randomly chosen individuals were planted at the edges of each block to prevent edge effects. No additional nutrients were added during the course of the experiment. The plants were watered as required during dry periods in the summer. We made daily observations of flowering, defined as expansion of petals, during the summer in 1996 and after the spring in 1997.
Field study of flowering time variation in a natural population
Flowering time variation in a natural population in Spiterstulen, Norway, along a rocky riverbank was studied during three summers, 20002002. The habitat of this large, natural population is situated at the lower oroarctic vegetation zone (Ahti et al., 1968
) i.e., middle alpine belt (Jonsell et al., 1995
) at 1106 m a.s.l. Arabidopsis lyrata grows a thick main root that sends few (<10) ramets to a small area. Other vegetation at the area is scarce.
In the beginning of June 2000, 150 rosettes representing different individuals (at least 0.5 m apart) were marked. We checked the marked rosettes for flowering at least twice per week during peak onset of flowering in June, and approximately once per week later in the season (July, August). In 2001 the study site was visited only three times: at the beginning of the season when plants were starting to flower (early June), at the time when most plants were flowering (beginning of August), and at the end of the season (middle of September). In 2002, flowering of the permanently marked plants was recorded every second day throughout the season. The procedure varied between years, but all methods allowed following the progress of flowering. On every visit we recorded the stage of the marked individuals as flowering, non-flowering, dead, or missing. The proportion of flowering plants was the percentage of plants that had produced fully open flowers at any time in the season.
Data analyses
For the growth chamber experiments, we analyzed the proportion of plants that flowered using a generalized linear model (GLM) including a logit-function in the model. The number of days until flowering and the number of leaves at the beginning of the flowering were analyzed using a linear model (lm). Flowering time and leaf number were not normally distributed and transformations did not improve the normality of the distributions. However, residuals were normally distributed and were therefore not transformed prior to the analyses.
Population, vernalization, and day length were all treated as fixed effects. Even though we knew the family origin of seeds for most populations, we did not include this effect because of the small number of samples per family. The effect of vernalization within long day on all dependent variables was tested with a generalized linear mixed model. Population and day length were treated as fixed effects, the growth chamber as a random effect. All the analyses were performed using the free software R (R Development Core Team, 2002).
We employed similar analyses of the data obtained from the garden and field experiments. The proportion of flowering plants and flowering time in the common garden in the first and second year were analyzed with a general linear mixed model in R. Population and cold treatment were treated as fixed effects, block as a random effect. Population and block were nested within treatment in the analysis of 1996. The effects of flowering in 1996, vernalization, and population (nested within vernalization) on the probability of flowering in 1997 were examined with GLM. There was no influence of flowering in 1996 or of vernalization. In the later analysis, the data from different vernalization treatments were pooled.
| RESULTS |
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Probability of flowering in controlled conditions
The proportion of plants flowering by the end of the experiment differed between southern and northern populations in all different environmental treatments. In LD, the differences were smaller than in SD. Nearly all plants of the southern populations Bohemia and Plech flowered in the LD treatment (always >92%). Flowering in LD was nearly complete also in the northern Spiterstulen population (87100%) (Table 1). In the Swedish Stubbsand population the proportion of flowering in LD was between 36 and 72%. It differed from the others in that even in the LD the proportion of flowering plants was clearly below 100%. None of the environmental conditions we used were fully conducive to flowering for the Stubbsand population, whereas LD eventually led to full flowering in the other populations. In SD, the probability of flowering was much lower for all populations. However, in the SD conditions, the differences between southern and northern populations were larger than in LD. On average, 55% of the southern Plech and 73% of the southern Bohemia flowered, whereas less than 14% of the northern Spiterstulen or Stubbsand populations flowered.
As the LD conditions that we used did not lead to full flowering in the Stubbsand population, the statistical analyses are conducted in two ways: with the Stubbsand population included and excluded. Furthermore, as we had two LD rooms and only one SD room, we contrasted each of these against the SD room in separate analyses.
In the overall logit analysis of variance of the three populations, there were highly significant differences between the populations and day length (Table 2). The question at the outset was whether the southern and northern populations respond differently to the different photoperiods. In our analysis of the three populations, the interaction of population and day length is significant (Table 2). This suggests a role for the photoperiodic pathway in governing the probability of flowering, for this set of populations. However, if the Swedish Stubbsand population is included in the analysis, the interaction effect is no longer statistically significant. Flowering of Stubbsand clearly is inhibited by other factors in addition to SD.
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The size of plant at flowering was estimated as number of rosette leaves. The northern Spiterstulen and Stubbsand populations had much higher numbers of rosette leaves at flowering (around 100) than the southern ones (about 50), varying in different conditions (Table 1, Fig. 3). The number of leaves at flowering was greater in SD than in LD, concordant with the delay in flowering time in those conditions (Table 1). Plants were able to change from the vegetative to the flowering stage with very different rosette sizes (Fig. 3). In Spiterstulen, for instance, plants flowered with leaf numbers ranging from <50 to >150. In the Bohemia population plants tended to flower with <50 leaves, whereas plants from the southern Plech population flowered with more variable leaf number, ranging from <50 to >100. Vernalization did not have an effect on the number of leaves at the onset of flowering (Tables 1 and 2). In all populations and environments, there was a positive correlation between the number of leaves and days to flowering. However, the correlation was lower than in A. thaliana. The squared correlation coefficients were less than 0.4 except for in the Stubbsand population (r2 = 0.8).
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There were significant differences in flowering times between the A. thaliana populations within each treatment (no cold treatment, F1,37 = 108.42, P < 0.0001; cold treated F3,95 = 72.41, P < 0.0001; Table 3) and in an overall analysis. In the overall analysis, the interaction of population and vernalization was also significant, providing evidence of a differential reaction of the populations also with respect to flowering time (F1,142 = 16.05, P < 0.0001).
Progression of flowering in the field and garden experiments
Most of the marked plants in the field flowered in each year, with only 8%, 19%, and 13% remaining vegetative in 2000, 2001, and 2002, respectively. Flowering in the field in Spiterstulen progressed rapidly, such that nearly all of the plants that did flower had started flowering within 2 wk of the first plant flowering, in both 2000 and 2002 when flowering was followed in detail (Fig. 4A). The start of the flowering varied between the years, depending on the melting of snow and temperatures. The onset of flowering was also rapid in the common garden experiments. The Karhumäki population started flowering 3 d earlier than Swedish Mjällom or Reykjavik, Iceland, but nearly all plants bloomed within 2 wk. These data can be compared to the progression of flowering in the conditions most permissive to flowering in our growth chamber experiment (Fig. 4). Flowering in all populations proceeded more slowly in the LD, vernalized plants grown in the chambers than in the field.
| DISCUSSION |
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Populations are genetically differentiated with respect to probability to flower and flowering time
There were statistically highly significant differences in the probability to flower and flowering time between the populations in all environmental conditions in the growth chambers. The probability to flower differed between populations in the first year in the common garden, and the time to flowering differed in the second year. Thus, there is likely to be ample genetic variation between populations. Further, this study and the earlier pilot study by Riihimäki et al. (2004)
, which included additional northern populations, show that there are consistent differences between the northern and southern populations. This is a small number of populations, but our group has also found similar differences between northern and southern populations of A. lyrata subsp. lyrata from North America (A. Baker, University of Oulu, personal communication). Northern populations are less likely to flower in short days than the southern populations. In the growth chambers, they also flowered more slowly than southern populations. Thus the populations differ genetically with respect to these traits.
The experiments were based partly on seeds collected in the field and could thus include some effects due the environment where the seed developed. It is known that the parental environment can influence offspring traits (Lacey, 1996
; Munir et al., 2001
), but the genotype of the zygote still has the most influence. Here the field-collected southern Bohemia seeds and the laboratory-grown southern Plech seeds had similar responses. Ongoing work on seeds generated in constant conditions will resolve this issue.
Similar patterns of population differentiation between north and south have been documented for many species (Thomas and Vince-Prue, 1997
). They are consistent with adaptation by natural selection to the local environmental conditions. In some species, such as long-lived trees, the clines for timing of growth or reproduction can be very steep (Mikola, 1982
). It is also likely that natural selection has given rise to the pattern of population differences in A. lyrata, a perennial species. The view of the relative stablility of the populations is supported by the large-scale correlations of geographical and genetic distances between populations (Jonsell et al., 1995
; Van Treuren et al., 1997
).
However, a recent study of flowering time in Arabidopsis thaliana, based on samples from natural populations in this same area, did not find any clinal variation in flowering time (Stenøien et al., 2002
). Other studies, based on accessions of A. thaliana, have also not provided evidence for this kind of clinal pattern in any environmental conditions (Karlsson et al., 1993
; Nordborg and Bergelson, 1999
; Johanson et al., 2000
). The reasons for the lack of strong clinal variation in A. thaliana could be manifold. It is a general finding in A. thaliana that correlations between genetic and geographical distance are weak (Sharbel et al., 2000
), and many times no correlation is found (Kuittinen and Aguadé, 2000
; Aguadé, 2001
). Thus, the difference could be partly due to the general patterns of differentiation in the genome, accounted for by historical migration and colonization. It is also possible that selection would not favor clinal adaptation in this weedy species or that drift and bottlenecks could override its effects. Instead, selection for flowering time could also vary more locally. In fact, molecular evolution studies do provide evidence of local adaptation at the FRI locus (LeCorré et al., 2002).
Effect of day length on flowering of A. lyrata
We can begin to examine the genetics underlying the between population differences by comparing the results in the two different day lenghts. Like Arabidopsis thaliana, A. lyrata is a long-day plant, and all populations were more likely to flower and flowered sooner in long than in short days. Short days of 14 h resulted in significantly fewer plants flowering in all populations compared to long days, but the effect was strongest in the northern Spiterstulen population. Riihimäki et al. (2004)
also found that an interaction of day length by south-north region influenced flowering probability. This significant difference between the populations in response to day length, i.e., the population by day length interaction, suggests that the populations differ with respect to a specific physiological response to photoperiod. These patterns were not as apparent for the time to flowering. Southern populations flowered first, and all populations flowered faster in long than in short days, but the interaction term was significant in only one of the two comparisons between long and short days. As seen in Table 1, the flowering times within populations and treatments were quite variable, resulting in reduced power. In all, the results do suggest that the critical threshold day lengths for flowering are shorter in the southern than in the northern populations and that there may be genetic differences between the northern and southern populations in genes of the photoperiodic pathway involved in promoting flowering.
Studies of accessions of A. thaliana (Karlsson et al., 1993
; Nordborg and Bergelson, 1999
) can be searched for a latitude-related variation response to day length, in this case the difference between flowering time in short and long days, just as we found for A. lyrata. Figure 5 plots the results of Karlsson et al. (1993)
. It shows, on the vertical axis, the difference between flowering time (measured as basal rosette leaf number at flowering) in short (8 h) and long (20 h) days, for different accessions, with their latitude of origin (as close as possible) on the horizontal axis. These data, even if limited, suggest that there is no latitudinal cline in the strength of the photoperiodic response. Differences between northern and southern populations of the same species are quite common otherwise (Thomas and Vince-Prue, 1997
). The lack of a cline in photoperiodic reactions may be related to the weedy life style of A. thaliana, as discussed above. Local adaptation, with respect to other quantitative traits, has been described in another partly outcrossing relative of A. thaliana, Arabis fecunda (McKay et al., 2001
).
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The results of the different cold treatments varied between experiments. The common garden experiment provided evidence for differences between populations in response to cold treatment, in both A. lyrata and A. thaliana. The lack of a vernalization response in the growth chambers was surprising, given the other results. In A. thaliana, it is known that both seed and rosette cold treatment can promote flowering. Seed vernalization for just 2 wk will cause a marked acceleration of flowering in the strain St (Napp-Zinn, 1969
). For instance Karlsson et al. (1993)
used 24 d of cold treatment. Nordborg and Bergelson (1999)
found that a cold treatment of 1 mo at the seed or the rosette stage decreased flowering times. Thus, the treatments we chose were rather standard conditions for A. thaliana, but it will be necessary to examine the A. lyrata vernalization conditions in more depth in future studies.
Still, we conclude that in this set of populations, there were differences between populations in their reaction to the cold treatment in the first year in the garden. In the second year, all populations flowered, but there remained difference in the time to flowering. Because the common garden study did not include a northsouth comparison, we do not know whether clinal patterns exist between the populations of A. lyrata. Many other species, such as Beta vulgaris (Boudry et al., 2002
) do show latitudinal variation with regard to vernalization requirement. As shown above, the earlier results of A. thaliana accessions (Karlsson et al., 1993
; Nordborg and Bergelson, 1999
) can be examined to search for a latitude-related pattern in response to vernalization (Fig. 5B). Even if there was much variation in terms of the response, it was not related to latitude of origin, as has been found also in other studies (Johanson et al., 2000
).
Flowering responses in relation to A. thaliana flowering pathways
The growth chamber experiments demonstrate that it is likely that the genes of the photoperiodic response pathway are involved in the differences between populations. The experiments in the garden showed that populations respond differently to the seed-stage cold treatment. The earlier experiments of Riihimäki et al. (2004)
also showed a small differential response for vernalization in growth chambers, suggesting the involvement of the temperature-related pathway to flowering. Thus, it is likely that genes in both pathways are involved in the differences between this small set of populations. In A. thaliana, molecular and developmental studies have identified dozens of loci that can influence flowering time. Many loci in the photoperiodic and autonomous or vernalization pathways have been described (Simpson et al., 1999
; Blásquez and Weigel, 2000
; Reeves and Coupland, 2000
; Simpson and Dean, 2002
). However, only a few loci are known to account for differences between natural populations. Most often it is FRI, sometimes also another cold responsive gene, FLC (Johanson et al., 2000
; Le Corré et al., 2002
; Gazzani et al., 2003
). The photoperiodic pathway gene (CRY2) has been found to be responsible for some of the variation segregating in the cross between the Cape Verde Island accession (Cvi) and the Landsberg erecta (Ler) strain (El-Assal et al., 2001
). The Cvi accession also has an allele causing late flowering at the FRI locus (Gazzani et al., 2003
).
Most work in A. thaliana has centered on the large differences between summer and winter annuals, corresponding to early and late flowering accessions. Differences in flowering time within these groups are smaller than between the groups and have attracted less attention and the loci have not been characterized yet (Härer, 1950
; Jansen et al., 1995
).
We do not yet know about the details of genetics of between population differences in A. lyrata, but the genetic architecture seems to differ from A. thaliana. The temperature-related pathway has a role in A. lyrata as in A. thaliana, but in addition the photoperiodic pathway is also important. Further studies will be needed to examine the effects of these two pathways in more depth.
Here we have limited the studies to examining the effects of just the temperature and light environment. In a perennial plant, the age and size of the plant can also have a more complex effect than in an annual. In A. thaliana, there is a high positive correlation between flowering time and the number of rosette leaves (Koornneef et al., 1991
), across different mutant strains. Mutations that cause late flowering also cause an increase in leaf number. In A. lyrata, there is a positive correlation between size and flowering time (Fig. 3). However, the correlation is much weaker, and it differs between populations. Thus, the populations are differentiated for flowering characteristics, but also with respect to the size and flowering time relationship. Other environmental factors that could influence flowering time, as in A. thaliana, are variation in nutrients and plant hormone levels (Napp-Zinn, 1969
; Chandler et al., 1996
; Michaels and Amasino, 2000
). Light quality is also known to influence flowering times (Martinez-Zapater and Somerville, 1990
).
The differentiation between populations can be examined further with genetic methods adopted from A. thaliana. Crosses between the northern and southern populations described here, along with a recently completed genetic map (H. Kuittinen et al., unpublished data), will allow more detailed studies of the loci involved in this adaptive differentiation.
| FOOTNOTES |
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2 E-mail: outi.savolainen{at}oulu.fi ![]()
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