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PLoS One. 2010; 5(4): e10065.
Published online Apr 19, 2010. doi:  10.1371/journal.pone.0010065
PMCID: PMC2856676

Comparative Genomics of Flowering Time Pathways Using Brachypodium distachyon as a Model for the Temperate Grasses

Samuel P. Hazen, Editor

Abstract

Brachypodium distachyon (Brachypodium) is a model for the temperate grasses which include important cereals such as barley, wheat and oats. Comparison of the Brachypodium genome (accession Bd21) with those of the model dicot Arabidopsis thaliana and the tropical cereal rice (Oryza sativa) provides an opportunity to compare and contrast genetic pathways controlling important traits. We analysed the homologies of genes controlling the induction of flowering using pathways curated in Arabidopsis Reactome as a starting point. Pathways include those detecting and responding to the environmental cues of day length (photoperiod) and extended periods of low temperature (vernalization). Variation in these responses has been selected during cereal domestication, providing an interesting comparison with the wild genome of Brachypodium. Brachypodium Bd21 has well conserved homologues of circadian clock, photoperiod pathway and autonomous pathway genes defined in Arabidopsis and homologues of vernalization pathway genes defined in cereals with the exception of VRN2 which was absent. Bd21 also lacked a member of the CO family (CO3). In both cases flanking genes were conserved showing that these genes are deleted in at least this accession. Segmental duplication explains the presence of two CO-like genes in temperate cereals, of which one (Hd1) is retained in rice, and explains many differences in gene family structure between grasses and Arabidopsis. The conserved fine structure of duplications shows that they largely evolved to their present structure before the divergence of the rice and Brachypodium. Of four flowering-time genes found in rice but absent in Arabidopsis, two were found in Bd21 (Id1, OsMADS51) and two were absent (Ghd7, Ehd1). Overall, results suggest that an ancient core photoperiod pathway promoting flowering via the induction of FT has been modified by the recruitment of additional lineage specific pathways that promote or repress FT expression.

Introduction

The switch from vegetative growth (the production of stems and leaves) to reproductive growth (the production of flowers) is an important developmental step in the life cycle of plants. Flowering needs to occur when conditions for pollination and seed development are optimal and consequently most plants restrict flowering to a specific time of year. They commonly achieve this by using reliable environmental cues such as day length (photoperiod) and temperature. In addition, nutrient and water availability and plant size can be important.

The genes and molecular mechanisms controlling flowering have been extensively studied in the model dicot Arabidopsis thaliana, subsequently Arabidopsis (reviewed by [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]). As part of this study the Arabidopsis flowering pathways were curated in Arabidopsis Reactome (http://www.arabidopsisreactome.org [15]) to provide an electronic knowledge resource allowing for further developments such as integration with protein-protein interaction datasets, overlaying with microarray data and electronic projection into all newly sequenced plant genomes. Using this we compiled a list of genes and gene families with a known role in flowering time in Arabidopsis.

Flowering time has also been extensively studied in crop species (reviewed by [5], [6], [9], [11], [12], [13], [16], [17], [18], [19]). Flowering time is important for adaptation to specific environments and the world's major crop species provide a particularly interesting opportunity for study because they are grown in areas outside the ecogeographical limits of their wild ancestors. In addition, they are adapted to different farming practices such as fall (autumn) sowing or spring sowing in temperate regions. Adaptation to different environments and practices has been achieved by manipulation of flowering time responses and this makes flowering pathways an excellent system for comparison between and within domestic and wild species.

Comparative studies between Arabidopsis and the tropical cereal rice (Oryza sativa) have shown that rice has homologues of many flowering-time genes and that aspects of the photoperiod and autonomous pathway are well conserved (reviewed by [6], [9], [11], [12], [13], [16], [17], [19] Experimental studies have also shown that a gene may retain a role in flowering but with important changes of action. For example the CONSTANS (CO) gene of Arabidopsis promotes flowering in long days while the equivalent gene in rice (Hd1 [20]) promotes flowering in short days but represses flowering in long days [9]. In addition, novel flowering-time genes have been found in rice, showing that different plant lineages have evolved new flowering controls. Examples are the rice Ghd7, OsID1, Ehd1 and OsMADS51 genes that are discussed individually in the results section.

Vernalization pathways are significantly different between Arabidopsis and the grasses as the key flowering repressors (FLC in Arabidopsis and VRN2 in cereals) are not conserved (reviewed by [5], [11], [12], [13], [16], [17], [18], [19]). Understanding the control of flowering time in a range of plant species therefore gives us insights into the ancestral control of flowering time and the evolution of alternative mechanisms in different plant lineages.

The wild grass Brachypodium distachyon (subsequently Brachypodium) has emerged as an important model for temperate species which include important grain crops such as wheat (Triticum monococcum, T. durum and T. aestivum), barley (Hordeum vulgare) and oats (Avena sativa) and forage grasses such as Lolium and Festuca species. The availability of a complete genome sequence for Brachypodium enables the evolutionary relationships of chromosomes to be revealed [21], [22] and is a powerful method for identifying candidates for QTLs identified in individual crop species.

In this paper we used the complete genome sequences of Arabidopsis, rice and Brachypodium to find homologues of genes known to have a role in flowering time in Arabidopsis or other species. For our purposes the genes of interest were those known to affect flowering time measured as leaf number or days to bolting or flowering in Arabidopsis, or as days to panicle emergence, ear emergence or anthesis in cereals. Genes may have been identified from mutation screens or from studies of natural variation. Our aim was to analyse a range of genes involved in known pathways rather than to complete an exhaustive study of all possible flowering-time genes. From this basis phylogenetic analyses of gene families were used to investigate the evolutionary relationships of genes and the impact of segmental duplications on the number of genes in families. Segmental duplications are collinear regions containing paralogous genes that derive from likely whole genome duplication events that occurred in the ancestors of modern species (recently reviewed by [23]). Tandem duplications are instances in which paralogous genes reside side by side along a chromosome and these are likely to result from evolutionarily recent amplification events. The results give us an insight into the evolution of flowering-time genes at the monocot/dicot divide and the relationship between temperate cereals (long-day plants with a vernalization requirement) and tropical cereals (short-day plants with no vernalization requirement).

Results

The genes and pathways selected are shown in Figure 1 and are listed with names and genomic identifiers in Tables 1 and S1. For clarity, we prefix the gene name with two letters showing the species when more than one species is being discussed: At for Arabidopsis thaliana, Bd for Brachypodium distachyon, Os for Orzya sativa (rice), Hv for Hordeum vulgare (barley), Ta for Triticum aestivum (bread wheat); Tm for T. monococcum (einkorn wheat); Sb for Sorghum bicolor (sorghum) and Zm for Zea mays (maize). Following Arabidopsis nomenclature, we use italics when referring to genes and non-italic uppercase to refer to proteins in the text.

Figure 1
Genetic pathways controlling flowering in Arabidopsis, rice and temperate grasses.
Table 1
Flowering-time genes in Arabidopsis and rice and their Brachypodium homologues.

Brachypodium homologues were identified by BLASTP and TBLASTN searches using Arabidopsis, rice, barley or cereal predicted proteins. The approaches and stringencies are described in full in the materials and methods section. Putative orthologues in Brachypodium were confirmed by reciprocal BLAST searches (Table S1). In cases where flowering-time genes and their close homologues belonged to large gene families, searches were performed using profile Hidden Markov Models (HMMs) [24]. Homologous proteins were aligned using the Probabilistic Alignment Kit (PRANK) [25] which recognises insertions and deletions as individual evolutionary events and takes into account the evolutionary distances between sequences. Phylogenetic trees for each family were estimated from these alignments using distance matrix methods.

It is well known that the Arabidopsis, rice and Brachypodium genomes contain segmental duplications as a result of whole genome duplication events in relatively recent ancestors [26]. The genes residing in these regions may exhibit some functional redundancy which is important to recognise in the present study. We used information on flowering-time genes from the Plant Genome Duplication Database (http://chibba.agtec.uga.edu/duplication) and the segmental duplications function of Rice annotation 6.1 (http://rice.plantbiology.msu.edu/). We also carried out additional TBLASTN searches to compare genomic sequences. Paralogues arising from segmental duplications are shown in the phylogenetic tree diagrams. Paralogues that are tandem duplications on individual chromosomes are shown separately on the phylogenetic trees because they are a result of more recent and localised duplication events and the genes are more likely to be functionally redundant.

As an additional check against rice or, where available, other cereals, flanking genes around the gene of interest were also identified and compared. This provided a genomic context that helped support the orthology of individual genes. Where genes were not found in Brachypodium, the presence of conserved flanking genes and intervening continuous sequence provided evidence that the gene was deleted.

1. Light signalling pathways

1.1 Photoreceptors

Light perception by the plant is primarily by the PHOTOTROPIN (PHOT) and CRYPTOCHROME (CRY) blue light receptors and the PHYTOCHROME (PHY) red/far red light receptors. PHOT genes do not have a known flowering role and were not analysed. Brachypodium CRY genes were similar to genes previously described in rice, with two CRY1 like genes and one CRY2 like gene (Table 1). The ZEITLUPE (ZTL) protein is also a blue light receptor (see section 1.2). Three phytochrome genes (PHYA, PHYB and PHYC) were found in Brachypodium, as in rice. Three additional PhyA loci are known in barley from RFLP mapping but these may be pseudogenes [27]. This is supported by the absence of the additional copies in Brachypodium. Comparison of flanking genes showed the PhyA gene in Brachypodium to be colinear to the rice PhyA gene and the likely functional copy on the barley and wheat group 4 chromosomes.

1.2 Circadian clock components

Light and temperature inputs entrain the circadian clock, allowing plants to coordinate metabolic pathways that need to be attuned to the day. The circadian clock also provides the time piece against which day length is measured, allowing flowering to be induced by specific inductive day length conditions (reviewed by [3], [4], [7], [14]).

In Arabidopsis, two genes encoding related myb transcription factors (CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY)) are expressed in the morning and PSEUDO-RESPONSE REGULATOR 1 (PRR1, also called TOC1) is expressed in the evening, forming a feedback loop. These three genes form the central oscillator of the circadian clock (Figure 1). The Arabidopsis CCA1 and LHY genes have a single counterpart in rice (OsCCA1 [28]) and Brachypodium (called BdCCA1 here). A single homologue of PRR1(TOC1) is present in Brachypodium, rice and barley. The PRR1-like genes could clearly be recognized as an outgroup of the PRR gene family. All PRR1 homologues had a conserved 6 exon structure and were the only PRR genes lacking an intron in the CCT domain.

In rice, the Heading date6 (Hd6) gene was identified as the α subunit of CASEIN KINASE 2 (CK2) which is thought to have a role in CCA1 protein regulation by phosphorylation [29]. The Brachypodium orthologue of Hd6 was identified as Bradi1g07810. Paralogous genes exist in rice and Brachypodium as a result of segmental duplication (Figure 2A).

Figure 2
Phylogenetic relationships within gene families containing circadian clock associated proteins.

CCA1 HIKING EXPEDITION (CHE) interacts with TOC1 to repress CCA1 [30]. CHE is a TCP family protein. There are 11 high homology matches in Brachypodium to this protein but the amino acid sequence outside the TCP domain was conserved sufficiently between CHE and the Bradi3g60350 protein to suggest that the latter protein was a Brachypodium orthologue (Figure S1).

In Arabidopsis, the circadian clock has additional feedback loops. A morning loop contains members of the PRR family and an evening loop contains EARLY FLOWERING 3 (ELF3), EARLY FLOWERING 4 (ELF4), LUX ARRHYTHMO (LUX) and GIGANTEA (GI) (Figure 1 [3], [7], [14], [31], [32]). CYCLING DOF FACTOR (CDF), CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), ZTL and LOV KELCH PROTEIN 2 (LKP2) proteins all interact with these feedback loops. ZTL, the highly homologous LKP2 and the closely related FLAVIN-BINDING, KELCH REPEAT, F BOX 1 (FKF1) gene encode ubiquitin-ligase proteins. The COP1 and ELF3 proteins interact and regulate GI by promoting the degradation of GI protein in the dark [33]. Interactions between GI and other proteins allow different functions to be performed. In the circadian clock, the ZTL gene is constitutively expressed but blue light enhanced interaction between clock controlled GI and ZTL is required to stabilize the latter. This provides circadian oscillation of ZTL that directs the degradation of TOC1 [34]. In the photoperiod pathway, blue light enhanced interaction of GI and FKF1 are involved in the induction of CONSTANS (CO) expression (see section 1.3). Arabidopsis ZTL, LKP2 and FKF1 also act to regulate CDF transcription factors (section 1.3; Figure 1 [35]).

GI is a highly conserved single copy gene in Arabidopsis, rice and Brachypodium (where it has a proven roles in flowering time [36], [37] and in barley (Table 1). Rice and Brachypodium have two paralogous ZTL-like genes with similar homologies to AtZTL and the closely related AtLKP2. This suggests independent gene duplication in the monocot and dicot lineages after divergence. One additional gene in rice and Brachypodium was more similar to AtFKF1 (Figure 2B). Arabidopsis COP1 had a single orthologue in rice and Brachypodium (Table 1). Arabidopsis ELF3 and SIMILAR TO ELF3 (At3g21320) identified two rice genes both of which were most closely related to AtELF3 (Figure 2C). At least one rice gene has a role in flowering as an Os01g38530 loss of function mutation causes late flowering in short or long days [38]. Two genes were also found in sorghum, one of which was in the same sub-group as the two rice genes. One Brachypodium homologue was found, but flanking genes surrounding the OsELF3-like genes did not identify the same Brachypodium location. This suggests that two genes were originally present in grasses, one of which was lost from the temperate grasses. The other gene was lost from rice and the remaining rice gene was subsequently duplicated.

Overall, the results suggest that GI and its various interactors are well conserved but that independent duplications affect the ZTL/LKP2 homologues giving the same numbers of genes in Arabidopsis and grasses by different routes.

Two other Arabidopsis genes (ELF4 and LUX) that are involved in the regulation of CCA1 and LHY were also investigated. A single orthologue of the Arabidopsis LUX gene was identified in rice and Brachypodium (Table 1). Four rice and three Brachypodium genes were found with homology to Arabidopsis ELF4 gene, but homology was closest to related members of the Arabidopsis gene family and no convincing orthologue of ELF4 was identified (Figure 2D).

The Pseudo-Response Regulator (PRR) family consists of five genes in Arabidopsis (PRR1 (TOC1), PRR3, PRR5, PRR7 and PRR9) and five PRR genes in rice (OsPRR1, OsPRR37, OsPRR73, OsPRR59, OsPRR95) [28]. Five genes were found in Brachypodium and these were closely related to the respective rice genes (Figure 3A). The PRR1 (TOC1) genes were clearly recognizable across all species but the relationships of the remaining grass and Arabidopsis genes was less clear, as reflected in the rice nomenclature.

Figure 3
Phylogenetic relationship of PRR proteins.

PRR37 and PRR73 are paralogues arising from a segmental duplication (Figure 3B). The gene content of the two segments is consistent with a model in which duplication occurred and experienced a period of gene loss so that the majority of the genes remaining were present in one copy. The derived chromosomes were largely stable and retained a well conserved gene order during the divergence of the major grass lineages. All the duplicated regions we examined were consistent with this model, but the example in Figure 3B was unusual in that the rice 7 region and its Brachypodium equivalent contained many fewer genes, suggesting preferential gene loss from one of the duplicated segments.

PRR37 and PRR73 are most similar to AtPRR7. PRR37 is also known as PHOTOPERIOD 1 (Ppd1) as mutations in this gene provide important flowering time variation in barley (Ppd-H1 [39]) and wheat (Ppd-A1, Ppd-B1, Ppd-D1 [40], [41]). PRR37 in rice has been identified as the Heading date 2 (Hd2) locus [42]. The paralogue (PRR73) is not known to provide flowering time variation in any of these species. This may reflect subfunctionalization, and the genes are known to have different expression profiles in rice [43]. AtPRR7 is thought to have roles in clock function and photoperiod response (Figure 1A), but the cereals genes may have partly separated these functions, allowing photoperiod response to be manipulated by mutation of the PRR37 gene without compromising clock function.

The two other PRR genes in grasses are more similar to AtPRR5 and AtPRR9 (Figure 3A). The relationship between these genes is not clear and a further ambiguity is that AtPRR5 has six exons and AtPRR9 has seven while the cereal PRR59 and PRR95 genes have the same eight exon structure as OsPRR37, OsPRR73 and AtPRR7. Therefore, while the PRR family has the same number of genes in Arabidopsis and grasses, they may have achieved this number by different routes and the genes in grasses do not relate to the Arabidopsis genes in a simple one to one manner.

1.3 Photoperiod pathway genes

In Arabidopsis the CONSTANS (CO) gene plays a key role in photoperiod response (reviewed by [9]), but other members of the family are also likely to be involved in flowering (e.g. COL5 [44]). CO is characterized by two B-boxes (a class of zinc-finger domain) near the amino-terminus and a CCT domain at the COOH-terminus. Its transcription is regulated by outputs from the circadian clock and peaks late in the day. CO transcription at the start of the day is directly repressed by binding of the Dof transcription factor CDF1 [45]. CDF1 transcription is repressed by PRR genes [46] and the CDF1 protein is removed from the CO gene by a blue light activated complex of GI and FKF1 proteins [47]. In this way GI acts as a positive regulator of CO expression. CO expression is also repressed by CDF2, CDF3 and CDF5 [35]. CDF2 is known to be regulated by FKF1 and the related ZTL and LKP2 genes [35]. The activity of the CO protein is also regulated. In short days the expression peak occurs in the dark where CO protein is rapidly degraded. PHYB and SUPPRESSOR OF PHYA-105 (SPA) proteins remove CO protein at the start of the day. If the expression peak coincides with light, which occurs in long days, the CO protein is stabilized by a mechanism involving PHYA and CRY proteins and can then activate FLOWERING LOCUS T (FT) (section 2.1 [48], [49]).

Four Brachypodium and four rice genes were most closely related to AtCDF1, 2 and 3 but the grass and Arabidopsis genes formed separate subgroups (Figure 4) suggesting that the CDF family has increased in size after monocot/dicot divergence. Conserved domains were highly conserved between all these proteins while other regions were diverged. Therefore, the relationships between them were ambiguous and a role for individual CDF genes in the photoperiod pathway in grasses would need to be established by experimental approaches.

Figure 4
Phylogenetic relationship of CDF proteins.

CONSTANS (CO) is a member of a gene family [50] which can be divided into four sub-groups based on conserved domains [51]. The gene family has the same overall structure in Brachypodium as previously shown in rice and barley (Figure 5A [51]). However, barley was previously shown to differ from rice in having two highly CO-like genes (HvCO1 on chromosome 7H and HvCO2 on chromosome 6H). Barley HvCO1 is colinear with the rice CO homologue Heading date 1 (Hd1) which is an important source of flowering time variation in rice [20]. The wheat TaCO2 gene (TaHd1) is implicated in flowering control as it can complement the rice hd1 mutation [52].

Figure 5
Phylogenetic relationship of CO proteins and physical maps of the CO1 and CO2 gene regions.

Brachypodium has two highly CO-like genes and comparison with rice shows that these are paralogues arising from segmental duplication. Barley and Brachypodium have retained both copies of the gene while the HvCO2/BdCO2 equivalent has been lost from rice (Figure 5B). The presence of the HvCO2/BdCO2 gene is not specific to temperate grasses because an orthologous gene is present in sorghum (SbCO2). However, SbCO2 is unusual in grasses in lacking highly conserved C and H residues from B-box 1 (red arrows, Figure 5C) suggesting it may be non functional. Griffiths et al. [51] showed that HvCO1 lacks conserved C residues at the start of B-box 2 and this is conserved in Brachypodium (blue arrows, Figure 5C) suggesting that temperate grasses have a CO1 protein with a modified or non-functional second B-box.

The barley HvCO3 gene and its rice counterpart (OsCO3; Os09g06464, a known flowering-time gene [53]) are unusual in having a single B-box that is likely to have arisen from a two B-box ancestor by internal deletion [51]. No homologue of HvCO3 was found in Brachypodium. Genes flanking OsCO3 had clear orthologues on Brachypodium chromosome 4 which were separated by three additional genes with different rice locations, suggesting BdCO3 may have been lost by a complex rearrangement (Figure 5D). Other CO family genes were well conserved between Brachypodium, barley and rice. The CO4 and CO5 genes are paralogues arising from segmental duplication as are the CO6 and CO7 genes (Figure 5A).

In Arabidopsis, SUPPRESSOR OF PHYA-105 (SPA) proteins interact with the CO protein to reduce its stability, inhibiting flowering in short days (Figure 1). Mutations in SPA1 cause early flowering under short-day (SD) but not long-day (LD) conditions and this is independent of PHYA. Mutations of SPA1, SPA3 and SPA4 in combination have an enhanced phenotype and flower at the same time in LD and SD [48]. The spa1 mutation is also reported to have an effect on the circadian clock, slightly shortening the circadian period of CCA1, TOC1 and SPA1 transcript accumulation under constant light conditions [54].

Rice and Brachypodium each had three genes with homology to AtSPA. One was the COP1 orthologue which has a similar WD repeat domain to SPA in the C-terminal region of the protein and which also has a role in degrading CO protein [55]. The related Os05g49590 and Bradi2g15900 genes lacked a protein kinase domain found in AtSPA1,3 and 4 so that only one rice and one Brachypodium gene (Os01g52640 and Bradi2g48660; Table 1) were identified as likely orthologues of AtSPA.

In addition to activation by CO, FT is regulated by GI through an independent pathway in Arabidopsis where GI upregulates microRNA172 which acts as a repressor of the APETALA 2 (AP2) domain gene TARGET OF EAT1 (TOE1) which in turn encodes a repressor of FT [56]. TOE1 is a member of a gene family characterized by two AP2 domains. Other members include APETALA 2 itself, involved in inflorescence development. The TOE1 subfamily members have a smaller first AP2 domain due to an internal deletion of 10 amino acids and all contain a miR172 target site. Genes of this subfamily are present in grasses (Figure 6A) and include the Q gene of wheat and the INDETERMINATE SPIKELET 1 (IDS1) gene of maize, both affecting inflorescence structure [57]. However, TOE1 is unusual in having a deletion of 15 amino acids in the second AP2 domain. No gene with this deletion was found in Brachypodium or rice but the maize VEGETATIVE 1 (RAP2.7_Vgt1) gene, which affects flowering time [58], has the 15 amino-acid deletion (Figure 6A). It is unlikely that identical deletions would occur independently in Arabidopsis and maize so it is possible that this type of gene has been lost from the rice/Brachypodium lineage. Genes flanking Vgt1 in maize were found on rice chromosome 1 and Brachypodium chromosome 2 (Figure 6B). These regions contained a distantly related AP2 domain gene related to Arabidopsis BABYBOOM that is too dissimilar to Vgt1 to appear in the clade of AP2 domain proteins shown in Figure 6A.

Figure 6
Phylogenetic relationship of TOE1 and related AP2 family genes a physical maps of the maize Vgt1 region.

TOE2 and SCHLAFMUTZE (SMZ) also have diverged second AP2 domains. SMZ is an additional factor repressing FT, and this repression requires the MADS-box transcription factor MADS AFFECTING FLOWERING 1 (MAF1) gene [59]. No homologue of SMZ was identified in rice or Brachypodium (Figure 6A) nor was a homologue of MAF1 found (see section 5).

In Arabidopsis, TEMPRANILLO 1 and 2 (TEM1 and TEM2) have been identified as additional repressors of FT [60]. TEM proteins have one AP2 domain and a B3 domain. TEM-like genes were found in rice and Brachypodium but no clear orthologues of TEM1 or TEM2 were found (Figure 7A). This suggests that TEM1 and TEM2, with two RAV genes, may have originated by gene duplication after the monocot/dicot divergence.

Figure 7
Phylogenetic relationships of TEM, ID1 and Ehd1 proteins.

Early heading date (Ehd1) is a B-type response regulator identified in rice which has no counterpart in Arabidopsis [61]. Its role is to upregulate Hd3a (FT) in inductive conditions (short days) and it acts independently of Hd1(CO) (Figure 1B). No orthologue was identified in Brachypodium, although flanking genes were well conserved (Figure 7B), or in temperate grass ESTs suggesting that this is likely to be an additional flowering component that evolved within the rice lineage or was deleted from the temperate grasses.

The rice MADS-box transcription factor OsMADS51 is regulated by OsGI and upregulates Ehd1 in short days, providing an alternative route for the upregulation of Hd3a (FT) in inductive conditions (Figure 1B [62]). OsMADS51 has no clear Arabidopsis orthologue but in contrast to Ehd1 there were Brachypodium and wheat (AGL41) orthologues. The relationship of the OsMADS51 group to other MADS-box proteins is shown in Figures S7 and and9B.9B. The lack of an Ehd1 gene in temperate grasses suggests either that the OsMADS51 orthologue has a different function or that there are additional targets linking it to flowering control.

Figure 9
Phylogenetic relationship of 14-3-3 and SOC1 proteins.

INDETERMINATE 1 (ID1) was first identified in maize (Zea mays) where loss of function mutation causes extremely late flowering [63]. ID1 encodes a C2H2 zinc-finger transcription factor which has no clear Arabidopsis orthologue. In rice, loss of function mutations of the ID1 orthologue (RID1; Os10g28330, also called Early heading date2 (Ehd2)) show extremely late flowering under short- or long-day conditions [64], [65], [66]. The expression of ID1 and RID1 is independent of photoperiod and is necessary for the expression of genes such as Ehd1 and Ghd7 involved in regulating the switch from vegetative to floral development (Figure 1B). A phylogenetic tree was constructed for ID1-like proteins in rice and Brachypodium which form a distinct grass specific clade of the C2H2 proteins (Figure 7C). In Brachypodium Bradi3g26910 was identified as the closest equivalent by sequence and the presence of flanking genes. The BdID1 genomic sequence had a 1 bp insertion giving a frame shift mutation. This could be a feature of the Bd21 accession or a sequencing error.

In Arabidopsis, FT expression is also promoted independently of CO by CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1) in a blue light dependent interaction with CRY2 [67]. Weak homologies to CIB1 were found in rice and Brachypodium in the bHLH domain but no convincing orthologue could be identified (Figure S4)

2. Flowering pathway integrators

2.1 The FLOWERING LOCUS T (FT) family

The induction of FT expression is a key step in flowering. Long-day and short-day plants differ in how FT expression is regulated but in both cases flowering is associated with increased FT expression, suggesting that FT is a conserved activator of flowering (reviewed by [9]). In Arabidopsis, FT protein is a mobile signal that moves from leaf to apex where it interacts with the FD protein to activate the APETALA 1 (AP1) gene and initiate the transition to reproductive growth [9], [68], [69]. FT and its close homologue TWIN SISTER OF FT (TSF) are members of a phosphatidylethanolamine binding domain (PEBP) gene family that is more extensive in grasses [70], [71].

The clade of PEBP proteins most similar to FT and TSF is encoded by two sub groups of genes in the grasses (Figure 8A). The first comprised OsFTL1 and its orthologues BdFTL1 and HvFT2. The second comprised two rice genes (OsFTL2 and OsFTL3) that are arranged in tandem and are likely to be a recent duplication so that both can be regarded as orthologues of HvFT1 and BdFTL2. The rice numbering follows Chardon and Damerval [70] and we have also used this for orthologous Brachypodium genes. OsFTL2 (Hd3a) and OsFTL3 (RFT1) promote flowering [72], [73], [74]. HvFT1 and HvFT2 are also likely to be flowering promoters because they can act as such in rice [75] but HvFT1 was thought to be the most likely orthologue of FT because it is upregulated at the floral transition [71].

Figure 8
Phylogenetic relationship of FT and HAP family proteins.

Generally, other rice and Brachypodium genes grouped as recognizable orthologues. However, rice OsFTL8 and 11 had no counterpart in Brachypodium. HvFT5 had no detectable expression in barley and may be a pseudogene [71]. It had no counterpart in Brachypodium. The HvFT3 gene, which is a candidate for the Ppd-H2 flowering-time locus [71], [75] was present in Brachypodium. The OsFTL7 orthologue in Brachypodium was present as a tandem triplication (Figure 8A).

In Arabidopsis the TERMINAL FLOWER 1 (TFL1) gene is important in regulating meristem determinacy. Three TFL1-like genes were found in Brachypodium. Two had rice orthologues while the third was orthologous to two rice genes known to be part of a recent segmental duplication involving rice chromosomes 11 and 12 [76]. The rice MOTHER OF FT 1 (OsMFT1) gene has two counterparts in Brachypodium (Figure 8A). The Brachypodium FT/TFL family was therefore similar to barley and rice with differences attributable to the fate of genes in segmental duplications and to different tandem duplications.

2.2 The HEME ACTIVATOR PROTEIN (YEAST) HOMOLOG (HAP) family

The CO protein is thought to act as a transcription factor but has no direct DNA binding activity. Recently it has been shown to form a complex with proteins similar to yeast HAP proteins and it is this complex that activates FT expression in Arabidopsis [77]. HAP proteins are present as large families in cereals (Figure S5 [18]) and there were several possible counterparts for the HAP3 and HAP5 proteins involved in CO interaction in Arabidopsis (Figures 8B and 8C, respectively). This suggests diversification of the HAP family following monocot/dicot divergence and further clarification of the relationships will require experimental approaches. The HAP family is of interest in grasses because key photoperiod (Hd1, Ppd-H1) and vernalization (VRN2) proteins belong to the CCT family (sections 1.3 and 3.2) and are likely to act in complexes with HAP proteins. Variation in HAP proteins or complexes could therefore provide functional variation.

FT is also regulated at the protein level by interaction with 14-3-3 proteins (PF00244) that typically modulate the activity of phosphorylation-dependent protein–protein interactions [78]. In rice, the GF14c Os08g0430500 protein (Os08g33370) acts as an inhibitor of flowering by binding to the Hd3a protein and thereby preventing activation of its targets [79]. GF14c falls in a clade containing six closely related rice proteins (Figure 9A); putative orthologs are present in Brachypodium suggesting that this type of control also exists in the temperate grasses. In Arabidopsis, 14-3-3 proteins are also implicated in the regulation of CO activity [80].

2.3 SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1)

In Arabidopsis, FT upregulates the MADS-box transcription factor SOC1 (AGL20) which is also controlled by the gibberellic acid pathway (not investigated in this paper) and repressed by FLOWERING LOCUS C (FLC) (Figure 1A). SOC1 is also controlled post-transcriptionally by EARLY FLOWERING 9 (ELF9) (Figure 1 [81]). SOC1-like genes have been reported from rice and wheat but although the wheat gene can partially complement an Arabidopsis soc1 mutation, its expression was not found to be regulated by photoperiod or vernalization [82]. However, two paralogous rice genes (OsMADS50 and 56) have been shown to be involved in flowering in long days by regulating Ehd1 via antagonistic regulation of LEC2 and FUSCA3 Like 1 (LFL1) (Figure 1 [83], [84]). Brachypodium orthologues of OsMADS50 and 56 were found from the phylogenetic analysis but their relationship to Arabidopsis is complicated by the observation that the grass genes also resemble other Arabidopsis genes (AGL14, 19, 42, 71 and 72; Figure 9B).

2.4 LEAFY (LFY)

RFL (Os04g51000), the rice homologue of Arabidopsis LFY, has been shown to have a dual role. RFL acts as a regulator of plant architecture through its effects on apical and axillary meristems throughout the growth of the rice plant, but it appears to have a different expression profile compared to other grasses [85]. RFL affects flowering time and acts upstream of OsMADS50 (OsSOC1) and RFT1 to promote flowering [85]. This contrasts with Arabidopsis where LFY functions downstream of SOC1 (Figure 1). The protein is well conserved and a Brachypodium homologue was found (Bradi5g20340) so differences in function may reflect changes in expression profile.

3. Vernalization pathways

In contrast to photoperiod, the control of flowering by exposure to extended periods of cold (vernalization) is generally thought to have evolved independently in Arabidopsis and grasses (reviewed by [11], [12], [16], [17], [18], [19]). However, in both cases there is repression of FT expression (Figure 1) and there are common components of epigenetic regulation [86]. Three genes determining vernalization requirement (VERNALIZATION-1 (VRN-1), VRN-2 and VRN-3) have been identified in wheat and barley using mutations that distinguish “winter” types (requiring vernalization) from “spring” types (no vernalization requirement). (N.B. the cereal VRN genes are unrelated to the VRN genes of Arabidopsis).

3.1 VERNALIZATION-1 (VRN-1)

The grass VRN-1 gene is related to the FRUITFUL (FUL)/APETALA1 (AP1) subgroup of the MADS-box transcription factors in Arabidopsis [87], [88]. AP1 is expressed in the shoot apex but the role of the grass VRN-1 is more complex as it is expressed in vegetative tissues (leaf) as well as in the apex and may have different roles in these tissues [88].

In contrast to the Arabidopsis major flowering repressor FLC (section 5), VRN-1 increases in expression during vernalization as plants move towards flowering competence [12], [18], [19], [87]. In cereals, mutations in the promoter or first intron of VRN-1 create “spring” alleles that do not require vernalization, suggesting that they remove regulatory domains normally required for repressing gene expression (summarized in [16], [18]). In polyploid wheats, the presence of a single spring allele is sufficient to allow flowering without vernalization. Plants of diploid wheat (T. monococcum) which are homozygous for a deletion of VRN-1 cannot flower, suggesting that VRN-1 is essential for the transition from vegetative to reproductive growth [89], although it is not clear whether additional genes are also deleted. A VRN-1 homologue is present in Brachypodium (BdVRN1 or BdFUL1) in a colinear position with respect to rice (OsMADS14) and wheat (Vrn-1) genes (Figure 10B).

Figure 10
Phylogenetic relationship of FUL/AP1/VRN1 type MADS-box proteins and physical maps of the FUL1 and FUL2 regions.

The FUL/AP1 clade includes four genes in the grasses (Figure 10A). The VRN-1/FUL1/OsMADS14 gene is a paralogue of the FUL2/OsMADS15 gene arising from a segmental duplication (Figure 10B [88]). Both genes have been identified as controllers of flowering in rice but only VRN-1 is currently known to have a role in temperate grasses. There is likely to be some diverged function for the two genes as they have differences in expression pattern [88]. The third gene and fourth rice genes, OsMADS18 and OsMADS20 both had temperate grass orthologues.

3.2 VERNALIZATION-2 (VRN-2)

VRN-2 is a dominant repressor of flowering that behaves genetically in a similar way to the Arabidopsis FLC gene [90]. In contrast to FLC (encoding a MADS-box protein), VRN-2 encodes a zinc-finger and CCT domain protein also called ZCCT1 [90]. VRN-2 is a member of the group IV subfamily of CO-like CCT domain genes [51]. This subfamily is not found in Arabidopsis [51], [90]. Cereals have two or three ZCCT genes arranged in tandem (Figure 11A) but experimental evidence suggest that ZCCT1 plays the important role in vernalization [90]. In contrast to FLC, VRN-2 is controlled by day length as well as temperature and is only expressed in long days [91], [92]. The group IV subfamily of CCT genes also contains a long- day repressor in rice (Ghd7 [93]) suggesting that long-day repression might be an ancestral feature and that regulation by cold was recruited to the cereal flowering pathway at a later date.

Figure 11
Phylogenetic relationship of VRN2/ZCCT proteins and physical maps of the VRN2 region.

Brachypodium Bd21 resembled rice in having no VRN-2 gene. Flanking genes from sequenced wheat BAC clones were present in collinear order suggesting that the gene is deleted (Figure 11A). This could mean that Brachypodium does not use vernalization as a flowering control in the same way as temperate cereals. However, Brachypodium accessions vary in flowering characteristics and Bd21 is a rapid flowering form with no requirement for vernalization [94]. This suggests that Bd21 resembles the vrn-2 mutant of spring barley in having a complete deletion of the gene and that a VRN-2 orthologue will be present in Brachypodium accessions with a vernalization requirement. Genetic mapping and sequencing of additional accessions will show if this is the case.

Although no VRN-2 gene was found, Brachypodium did have two group IV CCT genes (Figure 11B). Bradi3g33340 is orthologous to HvCO9. A role for CO9 in flowering has not been shown but is plausible as this gene is a paralogue of VRN-2 arising from segmental duplication (Figure 11A). The absence of VRN-2 in Bd21 and the segmental relationship to HvCO9 has also been described by Cockram et al. [95]. The second Brachypodium gene (Bradi3g10010) was intermediate between HvCO9 and VRN-2 in the phylogenetic tree (Figure 11B) and had a diverged first exon compared to the latter. Brachypodium had no Gdh7 homologue although genes flanking Ghd7 in rice were well conserved and in collinear order (Figure 11C).

3.3 VERNALIZATION-3 (VRN-3)

VRN-3 is the FT1 gene (section 2.1). The spring mutation in wheat is a transposon insertion in the promoter but the basis in barley is less clear. However, in both cases it is likely that there is loss of a regulatory region that normally allows repression by the vernalization pathway [96].

4. Meristem identity genes

A key stage in flowering is the transition of the apical meristem from the vegetative phase (the production of leaves) to the reproductive phase (the production of flowers). In Arabidopsis the activation of LFY, FUL and AP1 are important in this change (Figure 1). A protein complex containing FT and the basic leucine zipper (bZIP) domain protein FD activates AP1 expression [68], [69] and this is likely to be conserved in other species including temperate grasses [97]. The bZIP clade (Figure 12) was identified using an online interrogatory tree [98] with Arabidopsis FD as the query sequence. This clade has several gene duplication events, complicating the interpretation of relationships.

Figure 12
Phylogenetic relationship of FD and related bZIP proteins.

Delayed flowering1 (DFL1) in maize encodes a bZIP protein that acts downstream of ID1 and mediates floral inductive signals at the shoot apex [99]. DFL1 is closely related to Arabidopsis FD in the phylogenetic tree; putative orthologues of DFL1 are present in Brachypodium and rice (Figure 12).

Five FD-like proteins have been identified in wheat of which TaFDL2 has been identified as a functional homologue of Arabidopsis FD because it interacts with both TaFT and the promoter of the wheat meristem identity gene VRN-1 and is expressed in vegetative and reproductive apices [97]. In contrast to DFL1, TaFDL2 is not among the temperate grass proteins closely related to FD (Figure 12). These results suggest temperate grass genes more closely related to FD and DFL1 would be of interest for study.

VRN-1 and its paralogue FUL2 (section 3.1) are likely to have roles in meristem identity [88]. In Arabidopsis, the LFY, FUL and AP1 genes are activated by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3) (Figure 1) which is regulated by FT and microRNA156 [100]. This control might also apply to VRN-1 and/or FUL2 in grasses. However, SPL3 is a member of a large gene family in Arabidopsis and this was also the case in rice and Brachypodium, making identification of likely orthologues difficult (Figure S8).

5. The Arabidopsis vernalization and autonomous pathways

5.1 FLOWERING LOCUC C (FLC)

In Arabidopsis, the major flowering repressor in the vernalization pathway is the MADS-box gene FLC which represses FT and FD (Figure 1A; reviewed by [5]). Arabidopsis also has five MADS AFFECTING FLOWERING (MAF) genes which are homologous to FLC (Figure 13A). Vernalization represses MAF1 (FLM), MAF2 and MAF3 but induces MAF5 and does not affect MAF4 [1], [101]. MAF1 is a flowering repressor and MAF2 functions in preventing short cold periods from inducing the vernalization response [1]. FLC and the MAFs formed a MADS-box subgroup lacking rice or Brachypodium members (Figure 13A), consistent with previous findings in the grasses (reviewed by [11], [12], [16], [17], [18], [19]). The FLC/MAF group of MADS-box genes is therefore likely to have evolved after the dicot/monocot divergence.

Figure 13
Phylogenetic relationships of FLC, SVP, FRI, VRN5 and polycomb-like proteins.

5.2 AGAMOUS-LIKE 19 (AGL19)

In Arabidopsis, AGL19 (related to SOC1) is regulated by vernalization (Figure 1A) but in contrast to FLC it is upregulated and acts as a floral promoter (reviewed by [1]). Rice and Brachypodium genes related to SOC1 and AGL19 were found and are described in section 2.3 (Figure 9B).

5.3 SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24 (AGL24)

In Arabidopsis, the MADS-box transcription factor SVP has a role in repressing FT, TSF and SOC1 (Figure 1 [102]) and is likely to do this by interaction with FLC [103]. SVP also has a role in ambient temperature regulation [104]. SVP protein level is affected in lhy/cca1 double mutants, suggesting that the clock also influences flowering by an additional route (not shown in Figure 1 [105]) which is also thought to involve ELF3 [106]. AGL24 is upregulated by vernalization and acts as a flowering promoter (reviewed by [1]).

SVP/AGL24 like genes were found in rice and Brachypodium (Figure 13B) and have also been described in barley and wheat. In view of the lack of an FLC homologue in grasses the potential for SVP/AGL24-like genes to be involved in vernalization in grasses needs to be considered. Wheat VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (TaVRT2) is a member of this group that has been reported to be down regulated by vernalization and to interact with VRN2 protein to repress VRN1 [107], [108]. However, other researchers disagree. Trevaskis et al. [109] did not find VRT2 to be downregulated by vernalization and their studies of transgenic barley showed SVP-like genes to have roles in meristem development. VRT2 is therefore shown in two possible positions in Figure 1C.

5.4 FRIGIDA (FRI)

FRI, FRI-like (FRL1, FRL2), FRIGIDA ESSENTIAL 1 (FES1) and SUPPRESSOR OF FRIGIDA4 (SUF4) act to establish FLC expression (Figure 1A [110]). Genes with the closest homology to FRI in rice and Brachypodium were Os03g63440 and Bradi1g01520, respectively (Figure 13C). However, the sequences are considerably diverged from the Arabidopsis protein and it is unclear whether they are functionally related. For example, Arabidopsis FRI has two predicted coiled-coil domains [111] but neither was found in the rice or Brachypodium proteins. The relationships of the FRI-like genes are therefore ambiguous and functional assays of the rice and Brachypodium genes are needed to assess their function.

5.5 Autonomous pathway genes

In Arabidopsis, FLC is downregulated by genes of the autonomous pathway (Figure 1A). In contrast to FLC and FRI, autonomous pathway genes are well conserved and are found in rice and Brachypodium (Table 1). FCA and FY interact and FCA transcript levels are controlled by alternative splicing which is conserved in grasses [112], [113]. Genes of the autonomous pathway are not solely concerned with the regulation of FLC and have functions in RNA-mediated chromatin silencing that affect other developmental processes [114], [115], [116]. These are plausible functions in other species and may include roles in flowering. FCA has also been shown to affect the level of miRNA172, providing a link to the photoperiod pathway in Arabidopsis [56]. FCA, FY, FLOWERING LOCUS D (FLD), FPA, FVE and LUMINIDEPENDENS (LD) were represented by orthologous single copy genes in rice and Brachypodium while FLK had two orthologues in rice and in Brachypodium (Table S1).

5.6 Other genes repressing FLC

In Arabidopsis, FLC is repressed by vernalization in two phases, first by a repression of expression by cold and secondly by a stable maintenance of repression that persists after the plant returns to warm temperatures [5], [114]. These processes overlap and several genes function in both. The initial downregulation is thought to involve VERNALIZATION INSENSITIVE 3 (VIN3) and VERNALIZATION 5 (VRN5) which are related PHD-FNIII-VID (PHD) domain genes. Two additional members of this family, VERNALIZATION5/VIN3-LIKE (VEL1) and VEL2 are also found in Arabidopsis. Four PHD genes from rice and three from T. monococcum were described previously, with the T. monococcum genes shown to be upregulated by vernalization [117]. Five genes were found in Brachypodium, four corresponding to the known rice genes with the fifth being related to OsVIL2 (Figure 13D). As previously found [117], the grass genes are most closely related to VRN5 and could play roles in gene regulation through chromatin changes. There were no genes highly homologous to VIN3, VEL1, VEL2 or VEL3.

Stable repression of FLC involves a protein complex containing VRN5, VIN3, VEL1 and polycomb repressive complex 2 (PRC2) components VERNALIZATION 2 (VRN2; polycomb group protein), SWINGER (SWN; SET domain protein), FERTILIZATION INDEPENDENT ENDOSPERM 1 (FIE1; polycomb group) and MULTICOPY SUPRESSOR OF IRA1 (MSI1; WD repeat domain proteins) [118], [119]. Arabidopsis VERNALIZATION 1 (VRN1; a class VI REM type B3 domain protein [120]) was not found in rice or Brachypodium. Genes related to the PRC2 components were found in grasses and may have roles in gene regulation that involve changes to chromatin structure. This could include vernalization which, as in Arabidopsis, has an epigenetic “memory”. However, other flowering processes may also be regulated since FT has also been shown to have PRC2 control [121].

No convincing homologue of Arabidopsis VRN2 was found in rice. Two genes of the polycomb type were found (Os09g13630 and Os04g08034) but they were more closely related to Arabidopsis EMBRYONIC FLOWER 2 (EMF2). One gene was found in Brachypodium (Figure 13E). This was also EMF2 like and was orthologous to Os09g13630. A second Brachypodium gene may be present on chromosome 4 but is not currently annotated.

Two SET domain genes SWINGER (SWN) and CURLY LEAF (CLF) have a role in vernalization in Arabidopsis; putative orthologs were found in both rice and Brachypodium (Table S1). Two WD repeat genes resembling AtFIE1 were found in rice, positioned closely on chromosome 8 and separated only by a putative actin gene. Four possible genes were found in Brachypodium of which Bradi3g14520 was the closest relative. These results suggest that grasses contain chromatin regulatory genes related to PRC2 complexes, as might be expected, but lack convincing orthologues of key FLC regulators such as VRN2.

6. Ambient temperature pathways

In addition to control by vernalization, flowering in Arabidopsis is strongly affected by changes in ambient temperature. For example, a change in temperature from 23°C to 27°C (thermal induction) in short days promotes flowering as effectively as changing from short to long days [122]. Thermal induction is dependent on FT and FD but does not depend on CRY1, CRY2, CO, GI or SOC1, showing that FT is activated independently of the photoperiod pathway. Thermal induction is suppressed by FLC and by mutations of FCA, FVE and FLD that increase FLC expression [122].

Recent work in Arabidopsis shows that an important component of temperature response is the presence of histone H2A in place of H2A.Z in nucleosomes at higher temperatures (17°C vs. 27°C [123]). H2A.Z was depleted from the FT promoter at higher temperature, explaining the photoperiod independent induction of expression. ACTIN-RELATED PROTEIN 6 (APR6; Table 1) is part of the SWR1 complex that incorporates H2A.Z in nucleosomes. The arp6 mutant cannot incorporate H2A.Z, constitutively behaves as if at a higher temperature and is early flowering, especially in short days, consistent with higher FT expression [123]. SWR1 is also required for FLC expression suggesting that nucleosome changes may affect multiple flowering-time genes. Cereals show a degree-day response and it would be of interest to quantify effect of temperature in relation to FT expression. Also, given the lack of an FLC equivalent and the day length dependent expression of the flowering repressor VRN2 (ZCCT; section 3.2) it would be interesting to compare cereal temperature responses in short and long days.

Discussion

We analyzed the genome of Brachypodium distachyon to identify homologues of genes likely to be involved in the control of flowering time. As well as using flowering-time genes, we used flanking genes from rice or other cereals, where available, to clarify the relationships of putative orthologues. The use of flanking genes or “genomic context” was especially useful for understanding cases where a gene was absent from Brachypodium. A prominent example of this was the absence of the VRN2 gene which acts as a flowering repressor in the cereal vernalization pathway.

The FT hub

The core photoperiod pathway (circadian clock-GI-CO-FT) defined in Arabidopsis is well conserved as are components of the autonomous pathway. However, there is good evidence that additional components and regulatory pathways have been added during the evolution of different lineages and a common feature of these, illustrated in Figure 1, is that they provide additional promoting or repressing controls of the floral pathway integrator FT. As FT is a key signalling molecule moving from the leaves to the apical meristem (reviewed by [9]) this suggests that adjustment of FT levels provides a convenient evolutionary solution when alteration of flowering time is needed. However, care must be taken in this interpretation because FT is studied in many experiments and other significant hubs might emerge as additional genes, and other species, are studied in more depth.

Segmental duplications

The number of genes in a family is affected by the segmental duplications that are well characterized in rice and Brachypodium [124], [125]. The overall structure of the duplications we examined is well conserved, consistent with the idea that duplication occurred in an ancestral grass genome and assumed much of the modern structure before the divergence of the rice, Brachypodium and temperate grass lineages. Segmental duplication accounts for the presence of two grass genes resembling Arabidopsis PRR7 (Figure 3), the presence of two CO-like genes (CO1, CO2) compared to one in rice (Hd1) (Figure 5) and the presence of two FUL/AP1 like genes (VRN1 and FUL2, Figure 10). Segmental duplication also shows the relationship between the grass VRN2 (ZCCT) genes and CO9 (Figure 11). Tandem duplications explain other differences such as the presence of one FT like gene in Brachypodium, barley and wheat (FT1) compared to two in rice (Hd3a and RFT1).

A significant feature of the segmental duplications is that multiple alleles conferring natural variation in flowering time in cereals are associated with only one of the genes in each pair. Variation in photoperiod response is provided by the PRR37 gene in barley (Ppd-H1) and wheat (Ppd-A1, -B1 and –D1, chromosomes 2A, 2B and 2D) but no such effect is known for the PRR73 gene. Variation in vernalization requirement is provided by the VRN-1 gene in barley and diploid, tetraploid and hexaploid wheat but no such effect is known for the FUL2 gene. Variation in vernalization requirement is also provided by the ZCCT gene in barley (Vrn-H2) and diploid and tetraploid wheat (Vrn-A2 and Vrn-B2) but no such effect is known for its counterpart CO9. This suggests that the gene pairs are diverged in function and that only one member can be mutated to provide useful variation, at least in an agricultural context. It would be interesting to explore this in wild grasses and to assess the function of the second member of each pair experimentally. Brachypodium would provide an excellent vehicle for this.

Clear versus fuzzy homology

Some genes such as CO and GI had convincing orthologues in all species, but other genes were harder to interpret. For example, the relationship between monocot and dicot members of the PRR, CDF1, TOE1, TEM and HAP genes is complex and is likely to reflect different patterns of expansion and contraction in these families since the divergence of Arabidopsis, rice and Brachypodium. However, even within these families, rice and Brachypodium genes were generally associated in pairs in the phylogenetic trees, suggesting that it will be possible to integrate knowledge of gene function between grasses if not between grasses and Arabidopsis.

The evolution of novel pathways

There are clear examples of distinct genetic controls in different lineages. The vernalization pathways are a prominent example, with FLC encoding the main repressor of flowering in Arabidopsis and VRN2 in cereals. The absence of VRN2 from Brachypodium was an unexpected finding but this may reflect the choice of accession used for sequencing. Analysis of additional Brachypodium accessions for the presence of VRN2 would be of great interest.

Other examples are Vgt1 from maize and Ehd1 and Ghd7 from rice which were not found in Brachypodium, and MADS51 and ID1 which were found in rice and Brachypodium but not in Arabidopsis. These genes are members of families and there is therefore the risk that “fuzzy” homology may be missed. This problem would be exacerbated by incorrect gene prediction. We therefore checked these examples carefully, especially as homologues of positive and negative regulators of Ehd7 and Ghd7 were found. We reanalyzed relevant regions using reciprocal TBLASTN searches of nucleotide sequence but were unable to find homologous sequences and we conclude that these genes are genuinely absent. As with VRN2, it would be interesting to explore further accessions to see if these genes are consistently absent from particular species or if gain or loss reflects local adaptation.

Our analysis used known flowering-time genes from species other than Brachypodium. As Brachypodium transformation is now established [126] it will be possible to experimentally test conservation of gene function. Novel flowering-time genes may be identified in Brachypodium itself from mutation screens or from the analysis of different ecotypes. The latter also provide an excellent system to test if flowering time variation between wild ecotypes involves the same genes that have been selected in cereals during domestication.

Materials and Methods

Sources of sequences

The following datasets were used for profile Hidden Markov Models (HMMs) analysis and BLAST searches: Arabidopsis TAIR9 (http://www.arabidopsis.org, TAIR9_pep_20090619), Rice MSU Osa1 Release 6.1 (http://rice.plantbiology.msu.edu, all.pep – June 2009) and Brachypodium v1 (http://www.modelcrop.org, Bd21_v1_Protein[1].fa – May 2009). Updated annotations for Brachypodium are available in Brachypodium v1.2. The representative gene model was used; for most genes this is the ‘.1’ version. If the alternative gene model version (‘.2’, ‘.3’) is used this is indicated in the phylogenetic trees (supplement) or in Table S1.

Protein sequences for wheat, barley and maize flowering-time genes were obtained from UNIPROT (http://www.uniprot.org) or NCBI (http://www.ncbi.nlm.nih.gov) and Sorghum sequences were obtained from (http://genome.jgi-psf.org/Sorbi1).

Homologue identification in rice and Brachypodium

Starting with Arabidopsis flowering-time genes (Table 1), BLASTP searches were carried out against rice protein sequences with an E-value threshold of 1e−20. The top ranked rice hit was used for BLASTP searches back into the Arabidopsis protein to confirm homology (reciprocal BLAST searching). Starting with both Arabidopsis and rice homologues, BLASTP and TBLASTN searches were carried out against the Brachypodium v1 protein predictions and genomic sequence, respectively. Putative orthologues were confirmed by reciprocal BLASTP searches of the Arabidopsis and rice protein sequence datasets and are summarized in Table S1. Genes that have been shown experimentally to have a role in flowering time in grasses were also included in the BLAST analyses. A ClustalW alignment (http://www.ebi.ac.uk/Tools/clustalw2) was performed for each gene set and the clustal score recorded as a measure of protein sequence identity (Table 1). For flowering-time genes that belong to large gene families where duplication and gene loss complicated the identification of homologues the following methods were used: 1) profile HMMs searches to identify all members of each family or subfamily followed by phylogenetic analysis, 2) genomic location. Specific strategies for finding homologues are discussed in the result section for the individual gene families.

Database searches using profile HMMs

For the larger transcription factor (TF) families (AP2 (TOE), ERF-B3 (TEM), bZIP (FD), NF-YB-like (HAP), Dof zinc finger (CDF), C2H2 zinc finger (ID), MADS-box) TCP (CHE), bHLH (CIB1), genes for particular subgroups were identified from Arabidopsis, rice and Brachypodium protein sequences by searches with profile HMMs using the HMMER suite of programs [24]. The profile HMM for each family was made from an alignment of the conserved region (centred around the DNA binding domain), seeded by protein sequences that were already known to play a role in the flowering time response and other close homologues (see main text for references). For the MADS-box family, the profile HMM was made from an alignment of all members of this family present in Arabidopsis, excluding sequences that did not align correctly. The full alignment was used in the case of the ERF-B3, CDF and ID families.

For some TF families, there was a cut off in the list of hits from the HMMSEARCH program below which it was clear that sequences belonged to different subgroups of the gene family (ERF-B3, Dof). For other families (AP2, C2H2 zinc finger, bZIP, TCP and bHLH), the boundary of the relevant subgroup was found by adding the sequence hits as queries to an online interrogatory tree for each family [98]. It was necessary to identify and perform phylogenetic analysis on all members of the MADS box family to identify the members of each subgroup of interest in the MIKC-type MADS-box proteins. In the case of the NF-YB-like (HAP) family, an E-value cut off of 1.0 was applied to the HMMSEARCH results.

The above approach was also adopted to search for all members of the 14-3-3, FRIGIDA-like and SPL gene families. In these cases, an existing profile HMM from the pFAM website was used, PF00244, PF07899 and PF03110 respectively.

All sequence matches selected from the HMMSEARCH output were aligned using PRANK [25], except for the HAP family whose matches were aligned back to the HMM using the HMMALIGN program. The resulting alignments were used for phylogenetic analysis.

Phylogenetic Analysis

The alignment for each gene family data set (see supplementary data) was used for distance-based phylogenetic analysis with the PHYLIP [127] or MEGA4.0 [128] software packages. With both packages, identical methods were used to calculate distance estimates (the Jones Taylor Thornton matrix (JTT) model of evolution) and to construct phylogenetic trees (Neighbor-Joining method). Each tree was rooted using the midpoint rooting method. To provide statistical support for each node, a consensus tree was generated from 100 (supplement) or 1000 bootstrap data sets.

From the larger trees shown as supplementary data, genes from particular subclades were taken and a second smaller tree generated for the main manuscript to illustrate the relationship of genes of interest and to include additional closely related genes from barley, wheat, maize or sorghum where relevant. Where appropriate, a longer alignment was used for the phylogenetic analysis (see supplementary data).

Protein domains

Protein domains and secondary structure were analysed using PROSITE at the ExPASY facility (http://us.expasy.org/).

Genome Duplication Data

Gene duplication data was obtained from three sources, the Plant Genome Duplication Database (PGDD - http://chibba.agtec.uga.edu/duplication/ [26], the Rice Genome MSU release 6.1 segmental duplications (http://rice.plantbiology.msu.edu/segmental_dup) and duplicated blocks in Arabidopsis [129]. Segmental duplications events were indicated in the phylogenetic tree diagrams for Arabidopsis and the grasses (rice and Brachypodium).

Supporting Information

Table S1

Complete list of Arabidopsis, Rice, Brachypodium and Cereal flowering time related proteins. Extended version of Table 1 showing details of accession numbers, reciprocal blast hits and EST evidence.

(0.08 MB XLS)

Figure S1

The relationship between Arabidopsis CHE and closely related TCP proteins. The region of the alignment used to estimate the tree spanned the TCP domain. Although there was no significant bootstrap value leading to the clade that contained CHE, there was sequence conservation outside the DNA binding domain for all six proteins in the clade. The sequence in the C-terminal end showed that the Bradi3g60350 protein was mostly closely related to CHE and At5g23280 relative to the other proteins in the clade. This indicates that Brachypodium contains an orthologue of CHE that rice has lost.

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Figure S2

The relationship between Arabidopsis TOE1 and other closely related proteins in the AP2 family. An alignment of both repeats that comprised the AP2 domain was used to estimate the tree.

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Figure S3

The relationship between the monocot ID1 proteins and other ID domain proteins. The alignment for estimating the tree contained only the region of the four tandemly arranged zinc finger domains, excluding a small number of columns containing non-homologous amino acids. A neighbouring subgroup within a full C2H2 zinc finger family tree is also shown at the base of the tree, illustrating that the main subgroup shown is distinct from other proteins of this family. The monocot ID1 proteins within this subgroup form another distinct, internal subgroup.

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Figure S4

The relationship between Arabidopsis CIB1 and other proteins in subgroup 12 of the bHLH family. The region of the alignment used to estimate the tree spanned the bHLH domain and adjacent regions that were also conserved in proteins belonging to this subgroup. Neither bootstrap analysis nor studying regions outside this region provided evidence for an orthologue of Arabidopsis CIB1 in Brachypodium.

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Figure S5

The relationship between members of the NF-YB-like (HAP) family. A conserved region of eighty four amino acids was identified in an alignment of these proteins and used to estimate the tree. For this family, the alignment was created by aligning the sequences to a profile HMM of the conserved region.

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Figure S6

The relationship between the rice GF14c protein and the rest of the 14-3-3 protein family. The full alignment was used to estimate the tree, except that the alignment ends were trimmed.

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Figure S7

The relationship between flowering time genes that belong to the MADS-box family. The alignment was created by aligning all the sequences corresponding to this family to a profile HMM of the MADS-box domain. Nineteen poorly aligned proteins were removed from the data set before estimating the tree.

(0.17 MB PPT)

Figure S8

The relationship between SPL proteins. The region of the alignment used to estimate the tree corresponded to the pFAM profile HMM (PF03110) but excluded columns containing non-homologous amino acids.

(0.08 MB PPT)

Figure S9

The relationship between the FRIGIDA protein and related proteins. The region of the alignment used to estimate the tree corresponded to the pFAM profile HMM (PF07899) but excluded columns containing non-homologous amino acids.

(0.07 MB PPT)

Dataset S1

Fasta formatted protein sequences for HvPRR genes (Figure 3).

(0.00 MB TXT)

Dataset S2

Fasta formatted alignment of CKIIa proteins used for tree in Figure 2A.

(0.01 MB TXT)

Dataset S3

Fasta formatted alignment of ZTL proteins used for tree in Figure 2B.

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Dataset S4

Fasta formatted alignment of ELF3 proteins used for tree in Figure 2C.

(0.01 MB TXT)

Dataset S5

Fasta formatted alignment of ELF4 proteins used for tree in Figure 2D.

(0.00 MB TXT)

Dataset S6

Fasta formatted alignment of PRR proteins used for tree in Figure 3A.

(0.00 MB TXT)

Dataset S7

Fasta formatted alignment of CDF proteins used for tree in Figure 4.

(0.04 MB TXT)

Dataset S8

Fasta formatted alignment of CO proteins used for tree in Figure 5A.

(0.03 MB TXT)

Dataset S9

Fasta formatted alignment of TOE proteins used for tree in Figure 6A.

(0.03 MB TXT)

Dataset S10

Fasta formatted alignment of TEM proteins used for tree in Figure 7A.

(0.01 MB TXT)

Dataset S11

Fasta formatted alignment of ID domain proteins used for tree in Figure 7C.

(0.00 MB TXT)

Dataset S12

Fasta formatted alignment of FT proteins used for tree in Figure 8A.

(0.01 MB TXT)

Dataset S13

Fasta formatted alignment of HAP3 proteins used for tree in Figure 8B.

(0.01 MB TXT)

Dataset S14

Fasta formatted alignment of HAP5 proteins used for tree in Figure 8C.

(0.01 MB TXT)

Dataset S15

Fasta formatted alignment of 14-3-3 proteins used for tree in Figure 9A.

(0.01 MB TXT)

Dataset S16

Fasta formatted alignment of SOC1 and MADS51 proteins used for tree in Figure 9B.

(0.02 MB TXT)

Dataset S17

Fasta formatted alignment of VRN1 proteins used for tree in Figure 10A.

(0.01 MB TXT)

Dataset S18

Fasta formatted alignment of VRN2/ZCCT proteins used for tree in Figure 11B.

(0.00 MB TXT)

Dataset S19

Fasta formatted alignment of FD proteins used for tree in Figure 12.

(0.01 MB TXT)

Dataset S20

Fasta formatted alignment of FLC proteins used for tree in Figure 13A.

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Dataset S21

Fasta formatted alignment of SVP proteins used for tree in Figure 13B.

(0.00 MB TXT)

Dataset S22

Fasta formatted alignment of FRI proteins used for tree in Figure 13C.

(0.00 MB TXT)

Dataset S23

Fasta formatted alignment of VRN5 proteins used for tree in Figure 13D.

(0.02 MB TXT)

Dataset S24

Fasta formatted alignment of VRN2 proteins used for tree in Figure 13E.

(0.01 MB TXT)

Acknowledgments

We would like to thank Jonathan Wright (John Innes Centre) for his assistance with Brachypodium genome resources.

Footnotes

Competing Interests: The authors have declared that no competing interests exist.

Funding: Funding was provided by a core grant from the United Kingdom Biotechnology and Biological Research Council, 6th European Integrated Projects AGRON-OMICS (LSHG-CT-2006-037704), and a Daphne Jackson Fellowship funded by The Gatsby Charitable Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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