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Plant Cell. 2007 Feb; 19(2): 458–472.
PMCID: PMC1867329

Arabidopsis BRANCHED1 Acts as an Integrator of Branching Signals within Axillary Buds[W]


Shoot branching patterns depend on a key developmental decision: whether axillary buds grow out to give a branch or whether they remain dormant in the axils of leaves. This decision is controlled by endogenous and environmental stimuli mediated by hormonal signals. Although genes involved in the long-distance signaling of this process have been identified, the genes responding inside the buds to cause growth arrest remained unknown in Arabidopsis thaliana. Here, we describe an Arabidopsis gene encoding a TCP transcription factor closely related to teosinte branched1 (tb1) from maize (Zea mays), BRANCHED1 (BRC1), which represents a key point at which signals controlling branching are integrated within axillary buds. BRC1 is expressed in developing buds, where it arrests bud development. BRC1 downregulation leads to branch outgrowth. BRC1 responds to developmental and environmental stimuli controlling branching and mediates the response to these stimuli. Mutant and expression analyses suggest that BRC1 is downstream of the MORE AXILLARY GROWTH pathway and that it is required for auxin-induced apical dominance. Therefore, BRC1 acts inside the buds as an integrator of signals controlling bud outgrowth and translates them into a response of cell growth arrest. The conservation of BRC1/tb1 function among distantly related angiosperm species suggests that a single ancestral mechanism of branching control integration evolved before the radiation of flowering plants.


The vast diversity of plant architectures found in plants today depends largely on the control of branching. Branching patterns determine many aspects of plant form, light interception efficiency, and adaptation to resource availability. Shoot branching patterns are generated during postembryonic development. After germination, the shoot apical meristem (SAM) generates the main shoot, leaf primordia, and new meristems. New shoot meristems formed in the axils of leaves, axillary meristems (AMs), are established at the time of leaf primordia initiation or later in development from groups of cells that retain meristematic potential (Greb et al., 2003; Schmitz and Theres, 2005). After initiation, AMs develop into axillary buds. Branching patterns depend on a key developmental decision: whether axillary buds grow out to give a branch or whether they remain small and dormant in the axils of leaves. This decision is reversibly controlled by developmental and environmental stimuli perceived in different regions of the plant and transduced into the axillary buds to be translated into a local response of growth arrest (Lang et al., 1987; Horvath et al., 2003). This allows the plant to adapt to changing conditions.

In Arabidopsis thaliana, axillary bud development is well characterized morphologically (Hempel and Feldman, 1994; Grbic and Bleecker, 2000; Long and Barton, 2000), and some of the genes involved in AM initiation and long-distance signaling have been identified. However, the genes responding to these genetic pathways, acting inside the buds to directly cause cell proliferation arrest, remained unknown.

During prolonged vegetative development, AMs are initiated in an acropetal order, first in the axils of mature leaves distant from the shoot apex and later in younger leaves. After flowering, AMs are initiated in a basipetal order, first in leaf axils closest to the shoot apex (Hempel and Feldman, 1994; Grbic and Bleecker, 2000; Long and Barton, 2000). Genes such as LATERAL SUPPRESSOR (LAS), encoding a GRAS protein (Greb et al., 2003), and the REGULATOR OF AXILLARY MERISTEMS (RAX) genes, encoding a group of R2R3 MYB proteins (Keller et al., 2006; Muller et al., 2006), are necessary during AM initiation to maintain the meristematic potential of cells at the base of leaves and to allow the organization of a stem cell niche. REVOLUTA/INTERFASCICULAR FIBERLESS1 (REV/IFL1) (Talbert et al., 1995; Ratcliffe et al., 2000; Otsuga et al., 2001; Zhong and Ye, 2001), encoding a Homeobox-Leucine-Zipper protein, is also involved in early stages of AM initiation.

Once initiated, AMs go on to form a bud: first, leaf primordia are formed on the periphery of the AM (vegetative phase), and later, flower meristems are initiated (reproductive phase). Axillary buds bearing flowers may then elongate to give a branch, as in the case of cauline leaf buds, or they may become arrested for most of the plant life, as in the case of many rosette leaf buds. Long-range signaling promoting bud arrest is controlled both by auxin produced in the shoot apex and transported basipetally and by a novel carotenoid derivative synthesized in the root and transported acropetally (Cline, 1991; Shimizu-Sato and Mori, 2001; Leyser, 2003; Dun et al., 2006). Arabidopsis mutants with reduced auxin sensitivity (i.e., auxin-resistant1 [axr1]; Chatfield et al., 2000) have weaker apical dominance, and auxin overproducers (i.e., yucca1 [ycc1]; Zhao et al., 2001) have stronger apical dominance than wild-type plants. Also, mutations in the MORE AXILLARY GROWTH (MAX) genes, which control the synthesis and activity of the carotenoid-derived hormone (MAX-dependent signal) in Arabidopsis, cause an excess of branch outgrowth (Stirnberg et al., 2002; Sorefan et al., 2003; Booker et al., 2004, 2005). These two hormones, auxin and the MAX-dependent signal, act outside the axillary buds. Additional mechanisms affecting chromatin structure also seem to be involved (Peng et al., 2006). To date, the genes responding to these signals within the buds to directly cause growth arrest have remained uncharacterized in Arabidopsis.

Genes promoting bud arrest locally within the bud have been described in monocots. They are teosinte branched1 (tb1) from maize (Zea mays) (Doebley et al., 1997) and its homologs from rice (Oryza sativa), Os tb1 (Hu et al., 2003; Takeda et al., 2003), and sorghum (Sorghum bicolor), Sb tb1 (Kebrom et al., 2006). tb1-like genes encode transcription factors containing a TCP domain, a 59–amino acid domain that allows nuclear targeting, DNA binding, and protein–protein interactions (Kosugi and Ohashi, 1997; Cubas et al., 1999a; Kosugi and Ohashi, 2002). tb1 and Os tb1 are expressed in AMs and buds, where they suppress growth (Hubbard et al., 2002; Takeda et al., 2003). Their mutants, tb1 and fine culm1, respectively, have enhanced shoot branching (Doebley et al., 1997; Wang et al., 1999; Hu et al., 2003; Takeda et al., 2003). However, the general role of tb1 in the control of shoot branching in angiosperms remained to be established. First, tb1-like genes had not been analyzed in wild species, and second, they had not been studied in dicots; therefore, it was unclear whether this function was conserved in this group.

In this study, we have characterized BRANCHED1 (BRC1) and BRANCHED2 (BRC2), two of the three genes most closely related to tb1 in the wild dicot Arabidopsis. We show that both genes, but mainly BRC1, play a central role in the control of axillary bud development. BRC1 expression patterns are restricted mostly to axillary buds, its activity inversely correlates with bud outgrowth, and brc1 mutant phenotypes are nonpleiotropic and affect exclusively axillary bud development. Moreover, BRC1 responds to environmental and endogenous signals controlling bud outgrowth, and our genetic analyses indicate that auxin and the MAX pathway act through BRC1 to promote bud arrest. These results indicate that BRC1 acts as a local integrator of the genetic pathways controlling branch outgrowth.


The Arabidopsis TCP Gene Family

To identify the Arabidopsis genes closest to tb1, the complete Arabidopsis TCP gene family was analyzed (Figure 1A). This family comprised 24 genes encoding predicted proteins with a TCP domain (see Supplemental Table 1 and Supplemental Figure 1 online). Phylogenetic analysis of this domain revealed two subfamilies (Cubas et al., 1999a; Cubas, 2002; Kosugi and Ohashi, 2002; Palatnik et al., 2003): class I, formed by 13 predicted proteins related to the PCF rice factors (Kosugi and Ohashi, 1997), and class II, formed by 11 predicted proteins related to the Antirrhinum CYC and CIN genes and to tb1 (Luo et al., 1996; Doebley et al., 1997; Nath et al., 2003; Palatnik et al., 2003). Class II could be further subdivided into two groups: the CIN group formed by eight members, some of which are involved in the control of leaf primordia growth (Palatnik et al., 2003), and the tb1/CYC group (called the ECE group by Howarth and Donoghue [2006]), on which we have focused. Genes from this group have an R domain (see Supplemental Figure 1 online) (Cubas et al., 1999a) that is also present in TCP2 and TCP24 from the CIN group. Although in monocots only one type of tb1/CYC/ECE gene has been identified (e.g., tb1, Os tb1, and Sb tb1), in eudicots several tb1/CYC/ECE genes are found, and phylogenetic analyses have suggested that duplications within this clade occurred at the base of eudicots (Howarth and Donoghue, 2006). Therefore, no Arabidopsis TCP gene is a direct ortholog of tb1. TCP1, the gene most closely related to CYC, has been proposed to be the CYC ortholog (Cubas et al., 2001). Therefore, TCP12 and TCP18 were the only Arabidopsis TCP genes that remained as candidates for having retained a role in branching. Based on their similarity to tb1 in protein sequence, expression patterns, and mutant phenotypes (see below), they were renamed BRC1 and BRC2, respectively.

Figure 1.
The BRC1 and BRC2 Gene Family, Structure, Transcripts, and Proteins.

Full-length cDNAs of BRC1 and BRC2 were isolated. None of them corresponded to the predicted transcripts annotated in the Arabidopsis genome databases. The cDNA of BRC1 (1609 bp, three spliced introns; Figure 1B) contained an open reading frame of 1290 bp encoding a protein of 429 amino acids. The BRC2 cDNA (1380 bp, one spliced intron; Figure 1C) contained an open reading frame of 1071 bp encoding a protein of 356 amino acids. Both predicted proteins had a TCP domain and an R domain.

It has been proposed that the TCP domain is necessary for nuclear localization (Kosugi and Ohashi, 1997; Cubas et al., 1999a), and some TCP proteins have been shown to be targeted to the nuclei in heterologous systems (Suzuki et al., 2001; Qin et al., 2004). To investigate whether BRC1 and BRC2 encode nuclear proteins, the cDNAs of BRC1 and BRC2 were fused to green fluorescent protein (GFP), and transgenic Arabidopsis lines expressing these proteins under the control of the cauliflower mosaic virus (CaMV) 35S promoter were obtained. GFP:BRC1 and GFP:BRC2 were targeted to the nuclei in all tissues analyzed (Figure 1D for GFP:BRC1; GFP:BRC2 not shown). These data support their proposed role as transcriptional regulators. Plants expressing GFP:BRC1 showed pleiotropic developmental defects and retarded growth (see Supplemental Figure 3 online). Plants expressing GFP:BRC2 did not show any obvious phenotypic effect.

BRC1 and BRC2 Are Expressed in Axillary Buds

To explore the potential roles of BRC1 and BRC2 in the control of plant development, their mRNA levels were analyzed by real-time PCR in different tissues (Figure 1E). Both genes were transcribed at high levels in tissue that mainly contained axillary buds, supporting their putative role in the control of bud development. They were also expressed at lower levels (mainly BRC2) in other axillary structures such as flowers and siliques.

To define the spatial and temporal patterns of expression of these genes during bud development in more detail, BRC mRNAs were detected by in situ hybridization. BRC1 and BRC2 expression patterns were dynamic and similar, although BRC1 expression was much stronger than BRC2 expression, which was barely detectable in our experiments. Before flowering, when AMs were not yet initiated, BRC1 and BRC2 transcripts were not detectable (data not shown). After flowering, AMs became visible in the axils of leaves (Figure 2A) and BRC1 transcripts accumulated in all cell layers of these meristems (Figure 2D). During bud vegetative development (Figure 2B), BRC1 was downregulated in the outer layers of the meristem (Figure 2E) and transcripts accumulated in young leaf primordia (Figure 2F). Older expanding leaves did not express BRC1 (Figure 2G). In buds bearing flowers (Figure 2C), BRC1 transcripts were detectable in the provascular tissue underlying the bud (Figure 2G). BRC1 expression was downregulated at the time of bud outgrowth, so mRNA was not detectable in buds showing the first signs of shoot elongation (stem < 0.1 mm; data not shown). BRC1 expression appeared to be highest in rosette leaf buds that remained arrested for long periods of time and lowest in cauline leaf buds that grew out immediately (Figure 2I). Therefore, BRC1 is expressed locally in axillary buds in an evolving pattern during bud development and is downregulated at the time of branch elongation. BRC2 expression levels were much lower and were only clearly detectable in the provascular tissue of buds that had undergone flowering (Figure 2H). Neither gene was expressed in the SAM or in floral or leaf primordia derived from the SAM.

Figure 2.
BRC Gene Expression during Bud Development.

BRC1 and BRC2 Prevent Axillary Bud Outgrowth

To investigate the function of BRC1 and BRC2 in buds, the phenotype of plants with reduced function of these genes was analyzed. RNA interference (RNAi) lines were generated, and mutant collections were screened for insertions and point mutations affecting transcribed regions of BRC1 and BRC2 (Figures 1B and 1C; see Supplemental Table 2 online). For BRC1, 12 independent RNAi lines, 3 insertional lines, and 2 point mutant lines were analyzed (Figure 1B). brc1-1, brc1-2, and brc1-5 carried T-DNA insertions (Alonso et al., 2003; Rosso et al., 2003) located 218 bp downstream of the ATG (predicting a truncated protein of 72 amino acids), within the R domain (giving a protein of 208 residues lacking the R domain), and at the 5′ untranslated regions of the gene, respectively. brc1-3 and brc1-4 carried ethyl methanesulfonate–generated point mutations (Till et al., 2003) causing amino acid changes in conserved residues of the TCP domain. For BRC2, eight independent RNAi lines and one insertional line (Alonso et al., 2003) were studied (Figure 1C). brc2-1 predicted a truncated protein of 208 residues lacking the R domain. The double mutant brc1-2 brc2-1 was also analyzed.

Three weeks after flowering, brc1 mutants had a significantly higher number of rosette branches (RI and RII) than wild-type plants (Figures 3A, 3C, and 3D; see Supplemental Table 3 online). The phenotype of brc2 mutants was weaker but consistently affected RI and RII (Figures 3C and 3D; see Supplemental Table 3 online). Double mutants brc1-2 brc2-1 had a phenotype similar to that of strong brc1 mutants (Figure 3C; see Supplemental Table 3 online). The increase in rosette branches of brc mutants was not attributable to an increased number of vegetative nodes (see Supplemental Table 3 online) but to an increased frequency of bud outgrowth: for instance, in wild-type individuals, <40% of the RI buds grew out, whereas in brc1 mutants, almost every RI bud grew. On the other hand, brc1, brc2, and brc1 brc2 plants had a similar number of primary and secondary cauline leaf branches (CI and CII) as the wild type (Figures 3A and 3B; see Supplemental Table 3 online). These results indicate that BRC genes prevent rosette branch outgrowth.

Figure 3.
Shoot Branching Phenotype of brc Mutants.

BRC1 Delays Early Axillary Bud Development

As BRC1 was expressed at higher levels and had a stronger mutant phenotype than BRC2, we focused mainly on this gene for further studies. The phenotype of brc1 mutants was investigated during early bud development. Axillary buds formed at identical leaf positions (L1 = first-formed leaf; L2 = second-formed leaf, etc.) were compared in brc1-2 and wild-type plants just before flowering of the main shoot at 14 d after germination (Figure 4) and soon before bolting at 25 d after germination (Figure 5). To visualize AM initiation, these lines were studied in a ProCLV3:GUS background (Brand et al., 2002) that allows the identification of shoot and flower meristems by GUS staining (Figures 4A and 4C). Under long days, AMs are initiated only after flowering, in a basipetal order (Hempel and Feldman, 1994). Consistently, in wild-type plants, vegetative rosettes did not reveal any sign of AM initiation (data not shown). By contrast, 14-d-old vegetative rosettes of brc1-2 ProCLV3:GUS plants had AMs formed in the axils of cotyledons (c1 and c2) and L2 to L5 (Figures 4B and 4D). This finding indicates that BRC1 prevents AM initiation.

Figure 4.
AM Initiation in brc1 Mutants.
Figure 5.
Early Bud Development in brc Mutants.

At 25 d after germination, the SAM of wild-type and mutant plants had undergone flowering. In the wild type, buds nearest to the apex (i.e., L12 buds) were more advanced in development than buds farther from the apex (i.e., L1 buds), so that a gradient of developmental stages was found along the nodes: c1 and c2 never had axillary buds, newly formed meristems or empty axils were found in leaves L1 and L2, leaves L3 to L9 had buds in the early mid vegetative stage, buds in L10 were mostly in late vegetative stages, and a few flowering buds were found in leaves L11 and L12 (Figures 4E, 5A, 5B, and 5D). In brc1-2 mutants, the gradient of developmental stages was not so obvious: some c1 and c2 had vegetative or flowering buds, most L1 to L6 had buds in the late vegetative stage, and a large fraction of L7 to L12 had flowering buds (Figures 4F, 5A, 5C, and 5D). Mutant buds were not early flowering (they had a wild-type number of vegetative nodes); therefore, this effect should be attributable to rapid vegetative development. Moreover, leaves of the axillary buds grew faster and were larger than wild-type leaves (Figures 5B and 5C). This effect was more dramatic in plants grown under short days, in which wild-type and mutant AMs were initiated before flowering and bud development was prolonged for many weeks (Figure 5D).

Together, these results indicate that BRC1 retards all stages of bud development: first, it prevents vegetative AM initiation under long days and AM initiation in cotyledons; second, it delays the progression of bud vegetative development and prevents leaf bud growth and/or expansion; and third, it suppresses lateral shoot elongation. brc mutants were not affected in any other developmental trait, indicating that BRC genes acted exclusively in axillary buds or that their function was redundant in other developmental pathways.

BRC1 Is Strongly Downregulated in max Mutants

The relation of BRC1 to the genetic pathways controlling axillary bud development was studied. BRC1 (and BRC2) mRNA levels were analyzed in lines with altered AM initiation (las and rev/ifl1), bud outgrowth (ycc1, axr1, and max1 to max4), or both (amp1). Moreover, double mutants were obtained between brc1 mutants and these lines, and their phenotypes were studied. In the mutants las (Greb et al., 2003) and ifl1 (Talbert et al., 1995; Otsuga et al., 2001; Zhong and Ye, 2001), both affected in AM initiation, BRC1 and BRC2 levels were reduced, as would be expected if fewer buds were formed compared with the wild type (Figures 6A and 6B). Moreover, las and ifl1 mutations were epistatic to brc1 (Figures 6C and 6D; see Supplemental Table 4 online), suggesting that LAS and REV/IFL1 are necessary during AM initiation before BRC1.

Figure 6.
BRC Genes and Genetic Pathways of AM Development.

The auxin:cytokinin ratio is a strong determinant of the degree of lateral shoot outgrowth (Sachs and Thimann, 1967; Chatfield et al., 2000). Auxin promotes bud arrest, and cytokinin promotes AM development and shoot outgrowth (Sachs and Thimann, 1964; Turnbull et al., 1997). The amp1 mutant, for instance, with increased cytokinin levels (Helliwell et al., 2001), has more AMs initiated and more buds that grow out to give a branch than wild-type plants (Figure 6E; see Supplemental Table 4 online). In amp1 mutants, BRC1 levels were reduced slightly (Figure 6A), which could reflect a negative regulation of BRC1 by cytokinins or simply an effect of more buds elongating at this stage compared with the wild type. amp1 brc1 double mutants had a higher number of RI branches than the parental lines (Figure 6E), possibly reflecting an additive effect of the extra AMs formed in the amp1 mutants and the increased outgrowth caused by brc1.

The auxin-overproducer ycc1 mutants (Zhao et al., 2001) had most rosette leaf buds arrested (Figure 6F; see Supplemental Figure 2 and Supplemental Table 4 online), but BRC1 and BRC2 mRNA levels were not altered significantly (Figures 6A and 6B). However, brc1 mutations mostly suppressed the strong apical dominance phenotype of ycc1 (Figure 6F; see Supplemental Figure 2 online). This finding indicates that loss of brc1 function can to a great extent overcome the bud arrest caused by an excess of auxin activity. Therefore, although auxin does not seem to control BRC1 transcriptionally, BRC1 activity is necessary for the auxin-induced control of apical dominance.

MAX genes promote the synthesis and activity of a carotenoid derivative (Booker et al., 2005) that has been proposed to reduce auxin transport capacity in the stem, thus preventing auxin export from the buds and blocking bud outgrowth (Bennett et al., 2006). The four max mutants have an excess of branch outgrowth (Stirnberg et al., 2002; Sorefan et al., 2003; Booker et al., 2004). In these mutants, BRC1 was downregulated much more strongly than in other branching mutants, such as amp1 and axr1 (Figure 6A). In addition, the phenotype of max brc1 double mutants is similar to those of the single max and brc1 mutant parents (Figures 6G to 6I; see Supplemental Table 4 online), indicating that MAX and BRC1 may act in the same pathway and that the MAX effect on branching could be attributable mostly to transcriptional control of BRC1.

Finally, an upregulation of BRC2 was observed in brc1 mutants, which may reflect a negative feedback mechanism to compensate for the loss of BRC1 function (Figure 6B). The reverse (BRC1 upregulation in brc2 mutants) was not observed.

Together, these results suggest that during AM initiation, BRC1 acts after LAS and IFL1. During bud development, auxin-induced apical dominance requires the activity of BRC1, and the MAX-mediated pathway controls BRC1 expression. Cytokinins act in an antagonistic pathway independent of BRC1.

BRC1 Responds to Signals Controlling Bud Dormancy

The central role of BRC1 in the control of bud outgrowth raised the possibility that this gene acts as a local switch of axillary bud growth, integrating the responses to different stimuli that control bud dormancy. If that is the case, changes in those stimuli should affect BRC mRNA levels or protein activity. To test this hypothesis, BRC1 and BRC2 transcript levels were analyzed in plants grown under different environmental and developmental conditions that affected bud arrest.

Planting density is an environmental factor that affects branch outgrowth in many plant species. Plants grown at low density, for example, have more branches than plants grown in crowded conditions as a result of a neighbor-sensing response (Casal et al., 1986). To test whether this is true in Arabidopsis, wild-type and brc1 plants were sown at increasingly higher densities (1, 4, 9, and 16 plants per pot of 36 cm2) and RI branches were counted at maturity (Figure 7A). Wild-type plants responded to increased planting density with reduced branching such that, at a density of nine plants per pot, branch suppression was almost complete (86% reduction in branch number with respect to plants grown at one plant per pot). By contrast, brc1 mutants were partly insensitive to this condition (28% reduction with respect to plants at one plant per pot). brc2 mutants behaved like wild-type plants, and brc1 brc2 double mutants behaved like brc1 mutants (data not shown). The levels of BRC1 and BRC2 mRNA were then compared in wild-type plants grown at low (one plant per pot) and high (nine plants per pot) density. At high density, BRC1 mRNA levels were more than double those at low density, whereas BRC2 levels were similar in both conditions (Figure 7B). These results indicate that the environmentally induced bud dormancy observed in plants grown at high density was partly mediated through transcriptional regulation of BRC1 but not of BRC2.

Figure 7.
Response of BRC Genes to Branch-Suppressing or Branch-Promoting Stimuli.

Apical dominance is the inhibitory effect caused by an actively growing primary shoot apex on lateral shoot outgrowth (Cline, 1991, 1997). Decapitation is a classical assay to study bud reactivation after release from apical dominance (Sachs and Thimann, 1964; Hall and Hillman, 1975; Napoli et al., 1999; Beveridge et al., 2000; Cline, 2000; Tatematsu et al., 2005). In Arabidopsis, when the main shoot was removed, one axillary bud elongated prematurely. By contrast, no significant effect of decapitation was detected in brc1 mutants (Figure 7C). To analyze whether this response correlated with a downregulation of BRC genes, BRC mRNA levels were analyzed soon after decapitation, before any visible sign of bud outgrowth (Figure 7D). BRC1 was downregulated significantly in decapitated plants at 1 h after decapitation, reached a minimum at 6 h, and only approached predecapitation levels at 48 h. Downregulation of DRM1, an early marker for bud dormancy (Stafstrom et al., 1998; Tatematsu et al., 2005), was delayed with respect to BRC1 and reached its minimum levels at 24 h after decapitation. BRC2 was downregulated at 1 h after decapitation but recovered quickly, and at 24 h it was upregulated, possibly as a result of the reduced BRC1 function (see above). These results suggest that BRC1 downregulation is an early response to the bud release from apical dominance and is necessary for bud activation.

Together, these results indicate that BRC1 is transcriptionally regulated by environmental (planting density) and endogenous (apical dominance) stimuli controlling bud dormancy and that this regulation is necessary for the bud response to these signals.


We have shown that BRC1 acts inside developing buds to promote growth arrest. BRC1 upregulation (i.e., at high planting density) leads to an increase in branch suppression, and BRC1 negative regulation causes bud outgrowth. Moreover, environmental and developmental stimuli can modulate BRC1 transcription, and BRC1 function is necessary for the proper response to these stimuli. This indicates that BRC1 represents a key point at which signals controlling branching are integrated within axillary buds (Figure 8), allowing plants to tailor their degree of shoot outgrowth to changing conditions. BRC2, a closely related gene, seems to play a minor role in this process.

Figure 8.
Scheme of BRC1 Function in the Control of Bud Outgrowth.

BRC1 Promotes Bud Development Arrest

BRC1 is expressed throughout axillary bud development in different regions of the bud, where it seems to promote growth arrest. Downregulation of BRC1 leads to a relief of repression that allows the buds to continue their development and generate a branch. BRC1 may act (downstream of LAS and IFL1) to antagonize meristem organization or activity (i.e., maintenance of the stem cell niche, cell division, and lateral organ initiation) as the loss of brc1 function accelerates AM initiation and leads to ectopic AM formation. This would be consistent with the observed downregulation of BRC1 at the meristem dome before leaf initiation. BRC1 also controls early stages of bud leaf development, a function reminiscent of that of CIN-like genes closely related to BRC1 (Nath et al., 2003; Palatnik et al., 2003; Crawford et al., 2004). The late expression of BRC genes in the provascular tissue underlying mature buds may be necessary to prevent rosette branch outgrowth. This expression may arrest vascular tissue development, isolate buds from shoot growth-promoting signals, or prevent auxin export from the bud. BRC1 downregulation leads to a relief of growth repression and to lateral shoot outgrowth.

BRC1 Function and Hormone Signaling

Shoot branching is inhibited by hormonal signals that move through the plant. Auxin, moving down the plant in the main stem, and a MAX-dependent carotenoid hormone, moving up the plant, prevent bud outgrowth. Auxin is thought to prevent branching by reducing cytokinin synthesis and import into the bud through an AXR1-dependent pathway (Sachs and Thimann, 1967; Li et al., 1995; Chatfield et al., 2000; Leyser, 2003; Nordstrom et al., 2004; Tanaka et al., 2006). Our results suggest that BRC1 is independent of this pathway, as high auxin levels (ycc1 mutations), axr1 mutations, or high cytokinin levels (amp1 mutations) do not affect BRC1 transcription. Still, we cannot rule out the possibility that this pathway affects BRC1 protein stability. On the other hand, BRC1 is strongly downregulated in max mutants, suggesting that BRC1 may be downstream of the MAX signaling pathway. It has been proposed that the MAX-dependent hormone controls shoot branching through a mechanism independent of AXR1-mediated auxin signaling, by limiting auxin transport in the main stem (Bennett et al., 2006). As this carotenoid-derived compound acts (is required and sufficient) outside the buds (Turnbull et al., 2002), its control of BRC1 transcription must be indirect. The direct transcriptional regulators of BRC1 remain to be identified.

BRC1 Is an Integrator of Signals Controlling Bud Growth Arrest

BRC1 (and to a lesser extent BRC2) is, to date, the only gene described in Arabidopsis that functions locally within the bud to prevent bud outgrowth and whose downregulation is necessary to allow branches to develop. The central role of BRC1 in this process raised the possibility that this gene could integrate different pathways controlling branching. Our results confirm that BRC1 is transcriptionally controlled by both endogenous (apical dominance) and environmental (planting density) stimuli affecting bud dormancy and that BRC1 function is necessary for proper bud response to both stimuli. Moreover, in the case of decapitation, we have shown that those changes occur very fast (<1 h after decapitation), earlier than changes in markers of bud dormancy such as DRM1. This indicates that BRC1 is an integrator of signaling pathways controlling bud dormancy.

This mechanism of branching control, in which external and internal inputs perceived in different regions of the plant are transduced into the axils of leaves and are translated into local changes of BRC1 activity, is reminiscent of another key developmental process, the flowering transition (Ausin et al., 2005). During the control of flowering, several genetic pathways, mediated by signals transported through the plant, converge in the activation (transcriptional or posttranslational, respectively) of the integrator genes SOC1 and FT at the shoot apex (Blazquez, 2005; Parcy, 2005), which in turn set off the developmental program of flower initiation. In the case of branching, the integrating response, the promotion/relief of cell proliferation arrest, would depend on the activity of BRC1, controlled by the MAX signaling pathway.

Conservation of tb1/BRC Function among Angiosperms

BRC1 is closely related to the maize gene tb1 in sequence (Howarth and Donoghue, 2006), expression patterns, and mutant phenotypes. However, similarities between tb1 and BRC1 are not limited to their shared role in preventing branch outgrowth. tb1, like BRC1, is expressed in axillary buds as early as AM initiation. It is also expressed in developing husk leaves (the structures homologous with axillary bud leaves), where it suppresses husk leaf blade growth (tb1 mutants have very long husk leaves) (Hubbard et al., 2002). This function resembles that of CIN-like genes that control leaf shape and leaf growth patterns (Nath et al., 2003; Palatnik et al., 2003; Crawford et al., 2004). This similarity may reflect the common evolutionary origin of class II genes and a conservation of regulatory elements and functions. On the other hand, neither tb1 nor BRC1 affects branch node number, and neither is transcribed in the main SAM. However, some differences are also evident. Unlike BRC1, tb1 controls branch internode elongation and seems to have a role during maize inflorescence and flower development, functions for which we have not found equivalents in BRC1.

Conservation among species has already been described for other genes involved in branching. AM initiation is controlled by Ls/LAS/MONOCULM1 (Schumacher et al., 1999; Greb et al., 2003; Li et al., 2003) and Blind/RAX1 (Schmitz et al., 2002; Keller et al., 2006; Muller et al., 2006) in tomato (Solanum lycopersicum), Arabidopsis, and rice. Bud outgrowth is controlled by MAX2/RMS4/D3 (Stirnberg et al., 2002; Ishikawa et al., 2005; Johnson et al., 2006), MAX3/RMS5/HTD1 (Booker et al., 2004; Beveridge, 2006; Johnson et al., 2006; Zou et al., 2006), and MAX4/RMS1/DAD1 (Sorefan et al., 2003; Snowden et al., 2005) in Arabidopsis, pea (Pisum sativum), petunia (Petunia hybrida), and rice. The newly found functional conservation of tb1/BRC function between monocots and dicots suggests that the control of axillary bud development, from long-distance signaling to local responses during AM initiation, bud development, bud dormancy, and branch outgrowth, may be controlled by a conserved set of genetic functions throughout angiosperms that may correspond to an ancestral developmental pathway evolved before the radiation of flowering plants. Modulation of the process may be divergent in different species, as revealed by the differential regulation of MAX-like genes in pea, Arabidopsis, and rice (Beveridge, 2006; Johnson et al., 2006). It remains to be studied whether this conservation extends to more distantly related plant groups.


Plant Material

Mutant lines of Arabidopsis thaliana, in the Columbia background, were backcrossed twice to wild-type Columbia (brc1-1, brc1-2, brc1-5, and brc2-1) or three times (brc1-3 and brc1-4). To confirm the site of T-DNA insertion, genomic DNA of brc1-1, brc1-2, brc1-5, and brc2-1 was PCR-amplified with primers AB, CD, EF, and GH, respectively (see Supplemental Table 5 online), and the PCR products were sequenced.

Phenotypic Analysis

Arabidopsis seeds were sown on commercial soil and cold-treated (4°C) for 3 d. Then, they were transferred to a growth room at 20°C with a 16-h photoperiod (long days) or an 8-h photoperiod (short days). Branches (shoots > 0.5 cm) were counted 3 weeks after the time when the main inflorescence was visible, except for in the decapitation assay, in which branches were counted at 10 d after decapitation. For the early phenotype analysis, ProCLV3:GUS and brc1-2 ProCLV3:GUS plants were grown for 14 or 25 d. Fourteen days after germination, 10 plants for each genotype were GUS-stained according to Sessions et al. (1999). Twenty-five days after germination, 10 individuals of each genotype were dissected and the developmental stage of each axillary bud was determined with a stereoscopic microscope. Stages were defined as empty axil: no visible meristem; meristem: meristem with no visible leaf primordia, ∼100 μm (Figure 2A); leaf primordium: incipient first two leaf primordia, bud of ∼100 μm; vegetative 1: buds with two or more leaf primordia formed, no trichomes, 150 to 250 μm (Figure 2B); vegetative 2: mid vegetative stage, buds with differentiating trichome-bearing leaf primordia, <400 μm (Figure 5B); vegetative 3: late vegetative stage, buds with expanding trichome-bearing leaf primordia, >400 μm (Figure 5C); and reproductive: flower meristems visible within the bud (Figure 2C).

Phylogenetic Analysis and Sequence Alignment

The predicted amino acid sequences of the TCP and R domains were aligned with ClustalW (Chenna et al., 2003) using the default parameters (Protein Gap Open Penalty = 10.0, Protein Gap Extension Penalty = 0.2, Protein Matrix = Gonnet Protein/DNA, ENDGAP = −1, Protein/DNA GAPDIST = 4) and represented with Genedoc (Nicholas et al., 1997). One thousand bootstrapped data sets were obtained with SEQBOOT, distance matrices were calculated with PROTDIST (Dayhoff PAM matrix algorithm), trees were constructed with NEIGHBOR, and a consensus tree was obtained with CONSENSE. SEQBOOT, PROTDIST, NEIGHBOR, and CONSENSE are from the PHYLIP package (Felsenstein, 1988). Branches with support of ≥70% are indicated.

cDNA Isolation

RNA from dissected flowering rosettes comprising axillary buds but not rosette leaves was obtained with TRIzol (Invitrogen). cDNAs of BRC1 and BRC2 were isolated using the BD SMART RACE cDNA amplification kit (Clontech) according to the manufacturer's instructions. For 5′ rapid amplification of cDNA ends (RACE), PCR was performed with a primer anchored to the modified 5′ end and the nested gene-specific primers BRC1-A and BRC1-B for BRC1 and BRC2-A and BRC2-B for BRC2 (see Supplemental Table 5 online). For 3′ RACE, the PCR was performed with a primer anchored to the 3′ end and the gene-specific primers BRC1-C and BRC1-D and BRC2-C and BRC2-D, respectively (see Supplemental Table 5 online). Products from two independent experiments were cloned in pGEM-T Easy vector (Promega) and sequenced.

Real-Time PCR

Plant tissue was harvested and RNA was isolated with TRIzol (Invitrogen). Traces of DNA were eliminated with TURBO DNA-free (Ambion). Five micrograms of RNA was used to make cDNA with the High-Capacity cDNA Archive Kit (Applied Biosystems). Quantitative PCR was performed with FastStart TaqMan Probe Master-Rox (Roche) probes of the Universal ProbeLibrary Set-Arabidopsis (Roche) and the Applied Biosystems 7300 real-time PCR system, according to the manufacturer's instructions. The following pairs of primers were used (see Supplemental Table 5 online): for BRC1, RT-PCR-BRC1-A/RT-PCR-BRC1-B; for BRC2, RT-PCR-BRC2-A/RT-PCR-BRC2-B; for ACTIN8, RT-PCR-actin-A/RT-PCR-actin-B; for DRM1 (At1g28330), DRM1-L/DRM1-R. Three biological replicates were analyzed in each case. CT values were obtained with the 7300 Systems SDS software version 1.3 (Applied Biosystems). Relative fold expression changes were calculated by the comparative CT method: fold change is calculated as 2−ΔΔCT. The ΔCT values were calculated as the difference between the CT value and the CT value of ACTIN8. ΔΔCT was the difference between ΔCT and the CT value of the calibrator. In Figure 1E, the calibrator is the leaf sample; in Figures 6A and 6B, the calibrator is wild-type levels; in Figure 7B, density = 1; and in Figure 7D, time = 0.

Planting Density Test

Wild-type Columbia and brc1-2 plants were grown under long days at low density (one plant per pot) or high density (nine plants per pot). Five rosettes of each genotype were dissected when bolts were 1 cm long. RNA was extracted, and real-time PCR was performed as described. The experiment was repeated three times.

Apical Dominance Test

Wild-type Columbia and brc1-2 plants were grown under long days. When the main inflorescence began to bolt (<0.5 cm), plants were labeled. Four days later, in half of them, the main shoot, including the cauline nodes, was removed. Seven to 10 decapitated and nondecapitated rosettes were collected at T0 = 0 h, T1 = 1 h, T2 = 6 h, T3 = 24 h, and T5 = 48 h. RNA was extracted as described, and real-time PCR was performed. The experiment was repeated four times.

ProCaMV35S:RNAi Constructs

BRC1- and BRC2-specific PCR products (645 and 499 bp, respectively) were cloned into the binary vector pFGC1008 (http://www.chromdb.org) using restriction sites AscI/SwaI and BamHI/SpeI for the first and second cloning, respectively. Primers TCP18S5′/TCP18S3′ were used for BRC1 and TCP12S5′/TCP12S3′ were used for BRC2 (see Supplemental Table 5 online).

ProCaMV35S:GFP:BRC Constructs

The cDNAs of BRC1 and BRC2, cloned in pGEM, were amplified using Pwo polymerase (Roche) with primers 18B1/18B2 (see Supplemental Table 5 online). The PCR fragment was BP cloned into the entry vector pDONR207 (Gateway, Invitrogen) and then LR cloned into the destination vector pGWB6 (from Tsuyoshi Nakagawa, Shimane University).

Arabidopsis Transgenic Plants

Transgenic plants (Columbia ecotype) were generated by agroinfiltration using the floral dip method (Clough and Bent, 1998). T3 homozygous lines generated from T1 individuals carrying a single insertion of the transgene were analyzed.

In Situ Hybridization

Digoxigenin labeling of RNA probes, tissue preparation, and hybridization were performed as described by Calonje et al. (2004). The templates for BRC1 and BRC2 digoxigenin-labeled probes were 1.2- and 1-kb linearized fragments containing the complete coding regions. The hybridized sections were visualized with Nomarski optics in a DMR microscope (Leica).

Scanning Electron Microscopy

Rosettes were dissected and prepared for scanning electron microscopy analysis as described by Carmona et al. (2002).

Accession Numbers

The GenBank accession numbers for BRC1 cDNA and BRC2 cDNA are AM408560 and AM408561, respectively. Accession numbers for the complete Arabidopsis TCP gene family are given in Supplemental Table 1 online.

Supplemental Data

The following materials are available in the online version of this article.

  • Supplemental Table 1. Arabidopsis Genome Initiative Numbers for the Complete Arabidopsis TCP Gene Family.
  • Supplemental Table 2. Mutant Alleles and RNAi Lines Used in This Work.
  • Supplemental Table 3. Shoot Branching Phenotypes of brc Mutants.
  • Supplemental Table 4. Shoot Branching Phenotypes of Double Mutants with brc1.
  • Supplemental Table 5. Oligonucleotides Cited in Methods.
  • Supplemental Figure 1. Alignment of the TCP Domain for the Predicted Arabidopsis TCP Proteins.
  • Supplemental Figure 2. Shoot Branching Phenotypes of ycc1, ycc1 brc1-1, and brc1-1 Mutants.
  • Supplemental Figure 3. Phenotype of ProCaMV35S:GFP:BRC1 Plants.

Supplementary Material

[Supplemental Data]


We thank E. Coen, O. Leyser, D. Bradley, J.M. Martínez-Zapater, S. Prat, M. Martín, and M. Rodríguez for helpful comments on the manuscript; R. Piqueras and M. Peinado for technical assistance; M. Rodriguez, E. Jiménez, and C. Manzano for help with the phenotypic analysis; J.M. Martínez-Zapater for support during early stages of this work; R. Simon, A. Caño, Z.H. Ye, K. Theres, O. Leyser, and J.M. Franco-Zorrilla for seed stocks; and T. Nakagawa for Gateway vectors. This work was supported by the Ministerio de Ciencia y Tecnología (Grant BIO2002-00384) and the Ministerio de Educación y Ciencia (Grant BIO2005-00570). J.A.A.-M. is a predoctoral fellow of the Ministerio de Ciencia y Tecnología. C.P.-C. was supported in part by the Comunidad de Madrid (Grant GR/SAL/0658/2004) and in part by the Ministerio de Educación y Ciencia (Grant BIO2005-00570).


The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is: Pilar Cubas (se.mau.bnc@sabucp).

[W]Online version contains Web-only data.



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