FON2 SPARE1 Redundantly Regulates Floral Meristem Maintenance with FLORAL ORGAN NUMBER2 in Rice

CLAVATA signaling restricts stem cell identity in the shoot apical meristem (SAM) in Arabidopsis thaliana. In rice (Oryza sativa), FLORAL ORGAN NUMBER2 (FON2), closely related to CLV3, is involved as a signaling molecule in a similar pathway to negatively regulate stem cell proliferation in the floral meristem (FM). Here we show that the FON2 SPARE1 (FOS1) gene encoding a CLE protein functions along with FON2 in maintenance of the FM. In addition, FOS1 appears to be involved in maintenance of the SAM in the vegetative phase, because constitutive expression of FOS1 caused termination of the vegetative SAM. Genetic analysis revealed that FOS1 does not need FON1, the putative receptor of FON2, for its action, suggesting that FOS1 and FON2 may function in meristem maintenance as signaling molecules in independent pathways. Initially, we identified FOS1 as a suppressor that originates from O. sativa indica and suppresses the fon2 mutation in O. sativa japonica. FOS1 function in japonica appears to be compromised by a functional nucleotide polymorphism (FNP) at the putative processing site of the signal peptide. Sequence comparison of FOS1 in about 150 domesticated rice and wild rice species indicates that this FNP is present only in japonica, suggesting that redundant regulation by FOS1 and FON2 is commonplace in species in the Oryza genus. Distribution of the FNP also suggests that this mutation may have occurred during the divergence of japonica from its wild ancestor. Stem cell maintenance may be regulated by at least three negative pathways in rice, and each pathway may contribute differently to this regulation depending on the type of the meristem. This situation contrasts with that in Arabidopsis, where CLV signaling is the major single pathway in all meristems.


Introduction
Intercellular communication plays a crucial role in the determination of cell fate in plant development.Cell fate is determined by positional information emanating from neighboring or distant cells.Recent molecular genetic studies have revealed that peptide signaling molecules are involved in intercellular communication to regulate various aspects of plant development, such as stem cell maintenance, vascular differentiation, stomata patterning, and leaf size control [1][2][3][4][5].
The CLE genes encode small secreted proteins with a plantspecific domain called the CLE domain [6].The CLAVATA3 (CLV3) gene of Arabidopsis thaliana, and the FLORAL ORGAN NUMBER2 (FON2) and FON2-LIKE CLE PROTEIN1 (FCP1) genes of rice (Oryza sativa) are involved in stem cell maintenance in the shoot apical meristem (SAM) and the floral meristem (FM) [1,7,8].Tracheary element differentiation inhibitory factor (TDIF) has a role in suppressing the differentiation of tracheary elements in Zinnia elegans [3].Recent biochemical studies have revealed that functional peptides of CLV3 and TDIF in vivo are dodeca peptides derived from the conserved CLE domains [3,4].
In Arabidopsis, stem cell identity in the SAM is maintained by a regulatory feedback loop comprising the CLV and WUSCHEL (WUS) genes [9,10].CLV3 acts as a negative regulator of stem cell maintenance by repressing WUS, which encodes a novel homeodomain transcription factor that is expressed in the organizing center and promotes the identity of the stem cells overlying its expression domain [9][10][11].Conversely, WUS positively regulates CLV3 expression in the stem cell region.CLV3 peptide secreted from the stem cell appears to act through putative receptor complexes, consisting of CLV1, CLV2 or CORYNE/SOL2 [1,[12][13][14][15].A recent biochemical study has revealed that CLV3 peptide binds directly to the extracellular domain of CLV1 [16].When negative regulation of CLV signaling is removed by severe mutations of the CLV1 and CLV3 genes, enlargement of the SAM and the FM occurs, resulting in a fasciated stem and an increase in the number of flowers and floral organs [17,18].
A similar genetic mechanism to regulate stem cell maintenance seems to be conserved in monocots.Mutations in the FON1 and FON2 genes in rice cause enlargement of the FM, resulting in an increase in the number of floral organs such as stamens and carpels [7,8,19,20].A double mutant of fon1 and fon2 shows no additive phenotype, suggesting that the two genes act in the same genetic pathway [8].FON1 encodes a receptor-like kinase with a leucine-rich repeat (LRR) structure in the extracellular domain that is closely related to Arabidopsis CLV1 [7].FON2 is a member of the CLE gene family, and the CLE domain of FON2 is similar to that of CLV3 [8,21].Likewise, in maize (Zea mays), the thick tassel dwarf1 (td1) gene encodes a CLV1-like receptor kinase, and the fasciated ear2 (fea2) gene, like Arabidopsis CLV2, encodes an LRR protein that lacks a cytoplasmic domain [22,23].Loss of function of these genes results in enlargement of the inflorescence meristem (IM) and the FM, causing fasciation of the inflorescences and an increase in floral organ number in maize.Constitutive expression of the FON2 gene results in a severe decrease in the number of flowers and floral organs, probably because of a reduction in the size of the IM and the FM in rice, resulting in a phenotype similar to the wus flower [8,11].The effect of FON2 overexpression is not observed in the fon1 mutant, suggesting that FON1 is a putative receptor of FON2.Thus, CLV-related genes negatively regulate stem cell proliferation in the reproductive meristems in both rice and maize, as they do in Arabidopsis.
Despite this conservation, meristems in the vegetative phase are not affected by mutations in these CLV-related genes in the grasses, unlike in Arabidopsis [7,8,22,23].In rice, constitutive expression of FON2 does not affect meristem maintenance in the vegetative phase [8,24].We previously showed that FCP1 is probably involved in stem cell maintenance in the vegetative SAM because constitutive expression of FCP1 causes consumption of the SAM, similar to overexpression of CLV3 in Arabidopsis [24].This action of FCP1 is also observed in fon1 mutants, suggesting that FCP1 requires a receptor other than FON1.Thus, it is likely that, depending on the type of meristem, two independent pathways negatively regulate stem cell maintenance in rice.In maize, expression of td1 is excluded from the vegetative SAM [23].Thus, meristem maintenance in the vegetative phase is regulated differently from that in the reproductive phase in the grasses.
During the positional cloning of FON2, we found that expressivity of the fon2 mutation is markedly reduced in F 2 plants from a cross between the fon2 mutant (O.sativa japonica) and Kasalath (O.sativa indica) [8].To explain this difference, we hypothesized that the indica genome might contain genes that suppress the fon2 mutation.In this paper, we describe the isolation and characterization of a gene, named FON2 SPARE1 (FOS1), that suppresses the fon2 mutation.FOS1 encodes a secreted protein with a CLE domain, and is expressed in the SAM, IM and FM.Genetic and molecular analyses indicate that FOS1, together with FON2, is likely to be involved in stem cell maintenance in the FM, in rice species in the Oryza genus including O. sativa indica; by contrast, FOS1 function seems to be severely compromised in O. sativa japonica.In addition, FOS1 is likely to be involved in maintenance of the SAM in the vegetative phase, because overexpression of FOS1 caused the formation of abnormal shoots with a terminated meristem.Analysis of the FOS1 sequence from a large number of domesticated and wild rice species reveals that a nucleotide substitution related to the function of FOS1 may have occurred during divergence of the domesticated rice O. sativa japonica from its wild ancestor.

Results
Expressivity of the fon2 mutation is reduced in F 2 plants of a cross between fon2-1 (japonica) and Kasalath (indica) In wild-type rice, a single pistil derived from congenitally fused carpels develops into a floret, and a single ovule is formed in the pistil.After fertilization, a single seed is formed within the husks, which are derived from the palea and lemma in a floret (Figure 1A).In fon1 and fon2 mutants, by contrast, the number of floral organs such as pistils increases due to an enlargement of the FM (Figure 2B) [8,19].Therefore, ''twin seeds'' are formed within the husks in these fon mutants (Figure 1B) when two or more pistils are produced in a floret (the third and fourth seeds cannot develop to maturity).Here we used the twin seed phenotype as an indication of fon2 mutation.
In a previous screen of the fon2 phenotype for positional cloning [8], we found that expressivity of the fon2 mutation was reduced in F 2 plants from a cross between the fon2-1 mutant (japonica) and Kasalath (indica).To estimate quantitatively the frequency of the appearance of the fon2 phenotype, we assessed the numbers of twin-seed phenotypes in this study.First, we counted the number of plants producing the twin-seed phenotype among F 2 plants from the fon2-1 and Kasalath cross.As a result, we found that the number of F 2 plants showing a fon2 phenotype was reduced markedly in the F 2 plants: only 4.5% of F 2 plants showed a fon2 phenotype (Table 1).Second, we found that the number of the twin-seed phenotypes per panicle was also reduced markedly (Figure 1C).The median frequency of the appearance of the twinseed phenotype per panicle was 71% in the fon2-1 mutant (japonica); by contrast, it was reduced to 17% in the F 2 plants showing a fon2 phenotype.These results suggest that the indica (Kasalath) genome causes a reduction in the expressivity of the fon2 mutation in the F 2 progenies.In other words, it is likely that the indica genome has one or more genes that suppress the phenotype caused by the fon2 mutation.
To address this possibility, we performed quantitative trait locus (QTL) analysis (see Materials and Methods).For QTL analysis, we checked the genotypes of the F 2 plants showing the fon2 phenotype to confirm that the fon2 locus was homozygous for the mutation.As a result, a major QTL that suppressed the fon2 mutation was detected in the region between 40 and 80 cM on chromosome 2.In a group of F 2 plants showing high suppressor activity, the frequency of genotypes homozygous for the indica genome was very high, whereas that of genotypes homozygous for the japonica genome was very low (Figure 1D).In a group of F 2 plants showing low suppressor activity, by contrast, the opposite result was obtained (Figure 1E).Thus, in this region of chromosome 2, high or low suppressor activity was closely associated with a genotype homozygous for indica or japonica, respectively.

Author Summary
The body plan of plants is regulated by the function of apical meristems that are generated in the embryo.Leaves and floral organs are derived from cells supplied by stem cells in the vegetative shoot apical meristem (SAM) and the floral meristem (FM), respectively.Thus, genetic regulation of stem cell maintenance is a central issue in plant development.In the model plant Arabidopsis thaliana, CLAVATA3 (CLV3) functions as a key signaling molecule to restrict the size of the stem cell population in both the SAM and the FM.In rice, however, we show here that two CLV3-like genes, FLORAL ORGAN NUMBER2 (FON2) and FON2 SPARE1 (FOS1), redundantly regulate maintenance of the FM.We also show that FOS1 is likely to be involved in maintenance of the vegetative SAM, whereas FON2 plays no role in regulation in this meristem.FOS1 appears to act via a putative receptor that differs from the FON2 receptor, suggesting that these two signaling molecules function in independent pathways to restrict stem cells in different ways depending on the type of meristem.In addition, we show that the FOS1 gene was compromised in the standard rice, Oryza sativa spp.japonica, during the evolution of rice.

Identification of a gene that suppresses the fon2 mutation in the indica genome
The above results indicated that a putative gene that suppresses the fon2 mutation is located in the 40-80 cM region of chromosome 2 in the indica genome.We assumed that if indica has a gene that is functionally redundant to FON2 in this region, this gene should behave as a suppressor-like gene function in genetic analyses.A strong candidate for such a gene would be a CLE gene, like FON2.A survey of rice genomic sequences identified a candidate CLE gene located at about 54 cM on chromosome 2.
Next, we examined whether the CLE gene on chromosome 2 in indica (tentatively named CLE-C2) could suppress the fon2 mutation by conducting the following two experiments.First, we introduced a 3.3-kb genomic fragment from Kasalath containing the CLE gene into the fon2-1 mutant by Agrobacterium-mediated transformation.We found that the defect in the fon2 flowers was completely rescued in the transgenic plants, suggesting that the CLE-C2 gene suppressed the fon2 mutation (Figure 2C, 2G, and 2H).Second, we applied a genetic approach using a Nipponbare/Kasalath chromosomal segment substitution line (N/K CSSL#9), in which the chromosomal segment of Nipponbare (japonica) encompassing the CLE-C2 gene was replaced by that of the Kasalath (indica) genome.We crossed fon2-1 (japonica) with N/K CSSL#9, and then screened for F 2 plants that were homozygous for both fon2-1 and the indica CLE-C2 allele by determining the genotype with molecular markers.The results indicated that the flower phenotype of the plants screened was identical to that of wild type, suggesting that the fon2 mutation was also suppressed (Figure 2D, 2G, and 2H).Taken together, these results clearly indicate that the CLE-C2 gene located at about 54 cM on chromosome 2 functions as a fon2 suppressor.Thus, we designated this CLE gene as FON2 SPARE1 (FOS1) because this gene can substitute for FON2.

Molecular characterization of FOS1
Sequence analysis revealed that FOS1 consists of one exon with a single open reading frame and encodes a putative small protein of 131 amino acids (Figure S1).FOS1 has a signal peptide that is rich in hydrophobic amino acids at its N-terminus and a CLE domain at its C-terminus (Figure 3A).Among the CLE proteins in rice and Arabidopsis, the CLE domain of FOS1 is more similar to those of CLE8 and CLE13 than to those of FON2, FCP1 and CLV3 (Figure 3B).
Notably, the nucleotide sequence of FOS1 in the fon2-1 mutant (background, Fukei71) was identical to that of standard japonica wild-type strains such as Nipponbare and Taichung65 (T65).By contrast, we found an amino acid difference at the putative cleavage site of the signal peptide between japonica (all three stains; AB455109) and indica (Kasalath; AB455108) (Figure 3A; Figure S1).It is possible that this amino acid substitution in japonica FOS1 causes a defect in the processing of FOS1 and a reduction in the amount of active CLE peptide in japonica.Except for this mutation, no nucleotide change causing indels of amino acids was detected in the FOS1 gene between indica and japonica.

FOS1 seems to be involved in meristem maintenance
We analyzed the spatial and temporal expression patterns of FOS1 by in situ hybridization.In indica, FOS1 was expressed in all aerial apical meristems, not only in the FM and the IM in the reproductive phase, but also in the SAM in the vegetative phase (Figure 4A-4C).In japonica, FOS1 transcripts were also detected in all apical meristems in a spatial distribution pattern similar to that observed in indica (Figure 4E-4G).These spatial expression patterns suggest that FOS1 may be involved in meristem maintenance in rice.In addition to the meristems, FOS1 transcripts were also detected in the primordia of lateral organs such as the leaf and the floral organs.No significant differences were observed at the transcriptional level in the expression patterns of FOS1 between indica and japonica, suggesting that the functional difference between indica FOS1 and japonica FOS1 is not due to differences at the transcriptional level.No signals were detected in the SAM and FM when sense probes were used (Figure 4D and 4H).
Next, we expressed constitutively indica FOS1 by using the rice Actin1 promoter.Unlike shoots transformed with a control vector, Actin1:indica-FOS1 shoots stopped growing at the seedling stage after a few abnormal and malformed leaves were produced (Figure 4I and 4P).A longitudinal section of the shoot apex revealed that a dome-shaped shoot apical meristem (SAM) was strongly compromised in Actin1:indica-FOS1 plants, as compared with transgenic seedlings carrying a control vector (Figure 4K and  4L).Next, we examined the expression pattern of rice OSH1, an ortholog of Arabidopsis SHOOT MERISTEMLESS (STM) and maize knotted1 (kn1), which marks undifferentiated cells in the meristem [25].OSH1 was expressed uniformly in the meristem except for the site of leaf initiation (P0) (Figure 4M).By contrast, OSH1 expression was not observed in the meristem of Actin1:indica-FOS1 shoots (Figure 4N).These results indicate that constitutive expression of indica-FOS1 terminated meristem function, suggesting that FOS1 is involved in the maintenance of stem cells in the vegetative SAM as well as in the FM.

FOS1 is likely to act independently of FON1
To address whether, FON1, a putative receptor of FON2, is required for FOS1 function, we introduced an indica genomic fragment containing FOS1 into the fon1-5 mutant, which has a severe mutation and is thought to be a null allele of fon1.The numbers of floral organs such as stamens and pistils in fon1-5 transformed with the indica FOS1 gene were identical to those in wild type, suggesting that FOS1 functions normally in this fon1 mutant (Figure 2F-2H).Next, we expressed indica-FOS1 constitutively in fon1-5.The resulting shoot showed a phenotype identical to that of wild type constitutively expressing indica FOS1 (Figure 4J).These results suggest that the FON1 receptor is not required for the function of FOS1 and that FOS1 is likely to function in an independent signaling pathway.

Origin of the japonica FOS1 allele
To elucidate when the mutation observed in japonica FOS1 occurred during rice evolution, we compared the FOS1 sequence of a number of varieties/species of domesticated rice and wild rice species such as O. rufipogon.To encompass genetic diversity, we examined a core collection of domesticated rice from around the world (WRC, 67 accessions) and from Japan (JRC, 50 accessions) (Table S1; Table S2) [26,27].As described above, the one-base change that causes an amino acid substitution at the putative cleavage site of the signal peptide in FOS1 and is associated with its function was found in three japonica strains (fon2-1, Nipponbare and T65).Hereafter, we call this mutation a functional nucleotide polymorphism (FNP) without reference to the japonica or indica type.Sequence analysis showed that 66 out of 68 accessions of japonica had the FNP (Haplotype B, see below), whereas 59 out of 60 accessions of indica did not (Haplotype A) (Table S1; Table S2; Figure S2).Thus, the FNP was closely associated with japonica except for three accessions (Calotoc, Pinulupot 1, Padi Perak).Although the accessions in the WRC have been designated indica or japonica by phenotypic analysis, it seemed likely that the genome of two subspecies might have been introgressed into each other during recent breeding programs.Thus, we examined the type of genome around the FOS1 locus in the three exceptional accessions by using molecular markers.The results clearly indicated that the FNP is consistent with the japonica genome, but not with the indica genome (Table 2).
Next, we compared the FOS1 sequence from five wild rice species (22 accessions) and the African domesticated rice O. glaberrima (2 accessions), all of which have an AA genome (Table S3).Nucleotide polymorphisms were found in FOS1 among the wild and domesticated rice accessions (Figure S2).We classified the FOS1 sequences into 13 haplotypes, and generated a network of these haplotypes (Figure 5).The network indicated that the prototype of FOS1 is haplotype C, which is shared by two wild rice

Discussion
In this paper, we identified a new CLE gene, FOS1, in rice by screening for a suppressor of the fon2 mutation.Like FON2, FOS1 is likely to regulate stem cell maintenance negatively in the FM, but the action of FOS1 is independent of FON1, the putative receptor of FON2.In addition, FOS1 appears to be associated with maintenance of the SAM in the vegetative phase.Genetic analysis suggests that the function of FOS1 in japonica appears to be reduced by an FNP occurring at the putative cleavage site of the signal peptide.Distribution of the FNP suggests that this mutation might have occurred during the divergence of japonica from its wild ancestor.

Identification of FOS1
The presence of a factor that suppresses fon mutations in indica was initially assumed from the low expressivity of the fon phenotype in F 2 plants from a cross between japonica and indica.Although there are two possible explanations for this low expressivity -namely, differences in the genetic background of japonica and indica, or the presence of a major gene in the genome of indica -QTL analysis provided evidence in support of the latter possibility.
Several lines of evidence suggest that the function of FOS1 is likely to be compromised in japonica.As a result, mutations at the FON2 locus result in enlargement of the FM and an increase in the floral organ number in japonica [8].In indica, by contrast, functional FOS1 probably masks fon2 mutations by substituting for FON2 function in regulating maintenance of the FM (Figure S3).Likewise, in F 2 plants from a cross between japonica and indica, FOS1 derived from indica is likely to mask the fon2 mutation.The frequency (4.5%) of the appearance of the fon2 phenotype, which is also confirmed by the genotype, in those F 2 plants is roughly consistent with that expected for the appearance of double mutants.Overexpression of japonica FOS1 produced an abnormal shoot, as did overexpression of indica FOS1, suggesting that japonica FOS1 is not a complete loss-of-function mutant.In wild-type japonica, however, FOS1 CLE peptide, even if produced in part, would be insufficient to restrict stem cells in the FM.
Because our rice research is principally based on japonica, indica FOS1 appears to behave as though it is a suppressor of the fon2 mutation.A more likely interpretation is, however, that FOS1 regulates maintenance of the FM redundantly with FON2 in a wide range of species in the genus Oryza (see below) and that japonica is a mutant for the FOS1 locus.
In plant development, it is well known that genes that encode closely related proteins have redundant functions.APETALA1 (AP1) and CAULIFLOWER (CAL), which that encode MADS-box transcription factors, regulate floral meristem identity together with LEAFY [31,32].The ap1 cal double mutant has a striking phenotype, showing excessive proliferation of the inflorescence meristem, which resembles a cauliflower.This phenotype differs from that of the ap1 single mutant.Because CAL has less effect on floral meristem identity, its single mutation shows no phenotype.CAL was identified as an enhancer of the ap1 phenotype in F 2 plants from a cross between the ap1 mutant on a Landsberg electa background and wild-type Wassilewskija [31].Thus, the identification of FOS1 in this study resembles the discovery of CAL in Arabidopsis, although FOS1 has the opposite effect; that is, it appears to be a suppressor of fon2.In the case of AP1 and CAL, functional redundancy is due to the factors themselves; by contrast, signaling pathways comprising a different signaling molecule and its receptor might be redundant in the case of meristem maintenance in rice, as discussed below.

FOS1 and FON2 function together in stem cell maintenance in the FM in rice
Our previous study demonstrated that FON2 is a negative regulator of stem cell maintenance in the FM [8].In this study, introduction of indica FOS1 into fon2-1 by genetic methods using a chromosomal segment substitution line or by Agrobacteriummediated transformation completely suppressed the fon2 mutation.This finding suggests that FOS1 can substitute for the function of FON2.Thus, FOS1 is likely to play an important role in maintenance of the FM in indica and either one of FOS1 and FON2 appears to be sufficient to restrict stem cell proliferation in the FM.
There are two possible explanations for the redundancy of FOS1 and FON2.Both CLE peptides may be involved in the same pathway and may share their receptors.Alternatively, there may exist two independent pathways: one involving FOS1 and one involving FON2 as signaling molecules.Two experiments in this study supported the latter possibility.First, a genomic fragment containing indica FOS1 was able to rescue a severe mutant of fon1, in which the putative receptor of FON2 is defective [7].Second, constitutive expression of indica FOS1 in fon1 mutant showed abnormal shoots, a phenotype that is similar to that of wild type overexpressing indica FOS1.These results suggest that FON1 is not required for FOS1 function and that the signaling pathways involving FON2 and FOS1 are independent of each other.Because wild species in the Oryza genus have no mutation in the functional region of FOS1, these two pathways may function in the FM in all Oryza species except for japonica (Figure 6).
We found that FOS1 is expressed in the vegetative phase, and constitutive expression of FOS1 generates abnormal shoots with malformed leaves.It is, therefore, likely that FOS1 may be involved in maintenance of the vegetative SAM.Constitutive expression of FON2, by contrast, does not cause abnormalities in the shoot [24].In this respect, FOS1 and FON2 may have diversified functionally (Figure 6).
In contrast to the FM, the vegetative SAM seems to be unaffected by loss of both FOS1 and FON2 because shoot morphology is normal in fon2 mutants in japonica [8].Therefore, stem cell maintenance in the vegetative SAM may be regulated by an as yet unidentified negative pathway.FCP1 is likely to be involved in this pathway because its constitutive expression consumes stem cells in the vegetative SAM [24].Thus, stem cell maintenance may be regulated by at least three negative pathways in rice, and each pathway may contribute differently to this regulation depending on the type of the meristem (Figure 6).This situation contrasts with that in Arabidopsis, where CLV signaling is the major single pathway in all meristems.

Distribution of the FNP in FOS1 in the Oryza genus
Recent genetic and phylogenetic analyses have revealed that indica and japonica arose independently from a genetically distinct population in a wild ancestor, O. rufipogon [28][29][30]33].Our haplotype network of FOS1 is also consistent with an independent origin of the two subspecies.In our network, haplotype C would have been the prototype of FOS1 for all domesticated and wild rice species.Haplotype A, associated with indica, and haplotype B, associated with japonica, would have been produced by the occurrence of a single nucleotide change in haplotype C during rice evolution.Indica may have been derived from an O. rufipogon species with haplotype A. The FNP at the cleavage site of the signal peptide is responsible for the generation of haplotype B. Although there is no O.rufipogon accession with haplotype B, it is possible that japonica might have been domesticated from an unidentified ancestor with this FNP.
Many types of mutation are found in FOS1 of wild rice species, including not only amino acid substitutions but also insertions or deletions (Figure S2).There are, however, no mutations that affect The line marked with X indicates a pathway with no function.See text and our two previous reports for details [8,24].doi:10.1371/journal.pgen.1000693.g006the function of FOS1 in the coding region, such as an amino acid change in the CLE domain or a frameshift mutation.This observation suggests that defects in FOS1 may not be neutral and that FOS1 may be essential for the growth and survival of wild rice species under natural conditions.In line with this hypothesis, it is unlikely that an O. rufipogon species that has the FNP in FOS1 will be found in the natural population at present.

Plant materials
Taichung 65 (T65) and Kasalath were used as representative strains of wild-type japonica and indica, respectively, in molecular genetic and histochemical analyses.Nipponbare/Kasalath chromosomal segment substitution line #9 (N/K CSSL#9) was obtained from the Rice Genome Resource Center, Japan.Core collections of O. sativa (World Rice Collection (WRC) and Japanese Rice Collection (JRC)) were obtained from the Genebank of National Institute of Agrobiological Sciences, Japan (Table S1; Table S2) [26,27].Wild rice species were obtained from the National Institute of Genetics, Japan (Table S3).

QTL analysis and identification of FOS1
F 2 plants from a cross between fon2-1 and Kasalath were used to search for a gene that suppresses the fon2 mutation.We obtained 154 F 2 plants showing a fon2 phenotype from about 2,000 F 2 plants and checked their genotypes to confirm that the fon2 locus has the mutant allele.For QTL analysis, the suppressor activity in each F 2 plant that had the fon2 mutation was estimated by calculating the frequency of the twin seeds, an indication of the fon2 mutation.Next, the genotypes of about 90 loci in the 89 F 2 plants were determined by using molecular markers [34].As a result, a major QTL was found at around 40-80 cM on chromosome 2 (LOD score: 6.3).A gene (FOS1) encoding a protein with a CLE domain was then identified at around 40 and 80 cM on chromosome 2 by searching the rice genomic sequence database using the amino acid sequence of the FON2 CLE domain as a query.
FOS1 cDNA was amplified with the appropriate primers (Table S4) from total RNA isolated from young panicles of T65 (japonica) and Kasalath (indica).After sequencing of the RT-PCR product, the open reading frame was predicted.

Transformation of rice
To introduce indica FOS1 into the fon2 mutant, a 3.3-kb FOS1 genomic fragment, including 2.6 kb of sequence directly upstream of the initiation codon of FOS1, from the Kasalath genome was used.For constitutive expression of FOS1, a FOS1 cDNA derived from T65 or Kasalath was placed under the rice Actin1 promoter [35].The resulting plasmids, designated Actin1:japonica-FOS1 (T65) and Actin1:indica-FOS1 (Kasalath), were introduced into Agrobacterium tumefaciens strain EHA101 and transformed into rice as described previously [36].

In situ hybridization
For the in situ hybridization probe for FOS1, a 646-bp fragment consisting of the entire coding region, the 59 UTR (137 bp) and the 39 UTR (113 bp) was amplified with the appropriate primers (Table S4).The fragment was cloned into a T-vector by TAcloning (Novagen, Madison).The OSH1 probe was prepared as described in the original paper [25].Probe synthesis, preparation of sections, in situ hybridization, and microscopic observation were performed as described previously [7,24].

Analysis of FOS1 haplotype
The genomic region of FOS1 was amplified with the appropriate primers (Table S4).The amplified fragments were purified with Montage PCR Filter Units (Millipore, Billerica) and sequenced with the same primers used for amplification.The haplotype network was constructed by using the program TCS1 [37].Table S1 Accessions in WRC and their FOS1 haplotypes.Found at: doi:10.1371/journal.pgen.1000693.s004(0.02 MB PDF)

Figure 6 .
Figure 6.Model of meristem maintenance in rice.Rice is likely to have three negative regulators that restrict stem cell population in the three types of aerial meristem.Each pathway contributes differently depending on the type of meristem.FM, floral meristem; IM inflorescence meristem; Vegetative SAM, shoot apical meristem in the vegetative phase.The pathway indicated by the red thick line has been demonstrated by both loss-of-function and gain-of-function analyses.The pathways indicated by red or blue thin lines have been demonstrated by loss-of-function or gain-of-function analysis, respectively.Dashed lines indicate pathways to be analyzed in future studies.The line marked with X indicates a pathway with no function.See text and our two previous reports for details[8,24].doi:10.1371/journal.pgen.1000693.g006

Figure S1
Figure S1 Sequences of the FOS1 gene and FOS1 protein.(A) Nucleotides sequence corresponding to the coding region of the indica FOS1 gene.The nucleotide substituted in japonica is indicated in red.(B) Amino acid sequence of the indica FOS1 protein.The amino acid substituted in japonica is indicated in red.Amino acids in the putative active CLE peptide are indicated in blue.Underline indicates the putative signal sequence predicted by signalP (http://www.cbs.dtu.dk/services/SignalP)[1].Found at: doi:10.1371/journal.pgen.1000693.s001(0.02 MB PDF) Figure S2 Nucleotide changes or indels in FOS1 haplotypes.The FNP is located at the 69th position.Haplotype C is used as a reference.Synonymous substitution is indicated with light blue and nonsynonymous substitution with pink.Twelve nucleotides are deleted at positions 85-96 without a frameshift in haplotype H. Positions 358-393 correspond to the CLE domain (12 aa).Found at: doi:10.1371/journal.pgen.1000693.s002(0.05 MB PDF) Figure S3 FON2 and FOS1 redundantly restrict stem cell proliferation in the FM in indica but not in japonica.See text for details.Found at: doi:10.1371/journal.pgen.1000693.s003(0.00 MB PDF)

Table 1 .
Segregation ratio of the fon2 phenotype in F 2 plants from a fon2-1 and Kasalath cross.

Table 2 .
Genotyping of the chromosomal regions around the FOS1 locus.
[28][29][30]journal.pgen.1000693.t002species,O.rufipogon and O. glumaepatula.The FOS1 sequence in wild rice species and domesticated rice may have been derived from this haplotype.None of the accessions of wild rice species showed the FNP at the processing site.Therefore, the FNP in FOS1 is specific to the genome of O. sativa japonica.Because Asian domesticated rice species, namely japonica and indica, are thought to have derived independently from O. rufipogon[28][29][30], this FNP may have occurred during the diversification of japonica from O. rufipogon.