Pure-breeding, early-flowering lines of flax, derived from treatment of germinating seeds with 5-azacytdine in 1990, flower 7-13 days before controls, have fewer leaves, are shorter, and have hypomethylated total DNA, relative to control lines. This thesis examines the changes in DNA methylation levels in the cotyledons and shoot tips of early-flowering Royal flax lines (i.e. RE1 and RE2) and their control (RC) to determine the changes from 24 days to the onset of flowering (approximately 34 days in RE1 and RE2, and 52 days in RC). It also examines the question of whether DNA is methylated in the chloroplast genome of flax. Finally, the thesis looks at the differences in transcript abundance of the flowering genes LEAFY and TERMINAL FLOWER1 in RC and RE2. Methylation levels in RE1 and RE2 were found to be lower than in RC from 24 days of age to the onset of flowering and the levels of all three lines increase with tissue age and/or differentiation. In addition, buds of RE2 were hypomethylated relative to RC. If plants were placed in the dark prior to DNA extraction, hypomethylation was not seen in the total DNA of RE2. The chloroplast DNA of flax was found to be methylated, and RE2 chloroplast DNA was hypomethylated relative to RC. Differences in transcript levels of LFY were seen in RC and RE2 shoot tips, where a higher accumulation of transcript seen in RE2 compared to RC may be related to its earlier flowering time. In leaves, there was no significant difference in the transcript abundance of LFY between RC and RE2. TFL1 was detected in genomic DNA of RC and RE2; it was not detected in the cDNA of the two lines. In summary, compared to RC, hypomethylation was seen in the total DNA of RE2 plants grown under regular light conditions and the methylation levels in the all lines increased with age in shoot tips, cotyledons, and leaves. The chloroplast DNA of RE2 was also hypomethylated relative to that of RC. RE2 accumulated LFY transcript in shoot tips at flowering, which was not the case in RC. Although these ideas cannot be linked at this time, they are all likely related to the early-flowering phenotype.

Pure-breeding, early-flowering lines of flax, derived from treatment of germinating seeds with 5-azacytdine in 1990, flower 7-13 days before controls, have fewer leaves, are shorter, and have hypomethylated total DNA, relative to control lines. This thesis examines the changes in DNA methylation levels in the cotyledons and shoot tips of early-flowering Royal flax lines (i.e. RE1 and RE2) and their control (RC) to determine the changes from 24 days to the onset of flowering (approximately 34 days in RE1 and RE2, and 52 days in RC). It also examines the question of whether DNA is methylated in the chloroplast genome of flax. Finally, the thesis looks at the differences in transcript abundance of the flowering genes LEAFY and TERMINAL FLOWER1 in RC and RE2. Methylation levels in RE1 and RE2 were found to be lower than in RC from 24 days of age to the onset of flowering and the levels of all three lines increase with tissue age and/or differentiation. In addition, buds of RE2 were hypomethylated relative to RC. If plants were placed in the dark prior to DNA extraction, hypomethylation was not seen in the total DNA of RE2. The chloroplast DNA of flax was found to be methylated, and RE2 chloroplast DNA was hypomethylated relative to RC. Differences in transcript levels of LFY were seen in RC and RE2 shoot tips, where a higher accumulation of transcript seen in RE2 compared to RC may be related to its earlier flowering time. In leaves, there was no significant difference in the transcript abundance of LFY between RC and RE2. TFL1 was detected in genomic DNA of RC and RE2; it was not detected in the cDNA of the two lines. In summary, compared to RC, hypomethylation was seen in the total DNA of RE2 plants grown under regular light conditions and the methylation levels in the all lines increased with age in shoot tips, cotyledons, and leaves. The chloroplast DNA of RE2 was also hypomethylated relative to that of RC. RE2 accumulated LFY transcript in shoot tips at flowering, which was not the case in RC. Although these ideas cannot be linked at this time, they are all likely related to the early-flowering phenotype.

No description available.

LFY of Arabidopsis is a member of a unique plant specific transcription factor family. It is involved in giving meristem a determinate floral fate by the activation of floral organ identity genes and preventing inflorescence meristem identity. RFL is a homolog of FLO/LFY in rice. Studies from our lab on rice RFL, based on the effects of knockdown or overexpression, showed its major functions are in timing the conversion of SAM to IM and to prevent the premature conversion of branch meristem to spikelets. Additionally roles in vegetative axillary meristem specification have been also been identified in laboratory. Here, we attempt to delineate molecular pathways directly regulated by RFL as a transcription factor controlling inflorescence and floral development in rice. Part I: Identification of global target genes bound by RFL in developing rice inflorescences We carried out ChIP sequencing of the DNA bound by RFL in panicles (01.-0.3cm stage) using anti-RFL antibody. DNA sequences in one library pool were analyses by the MACS algorithm (FDR<0.01), to find 8000 binding sites while the SPP algorithm identified 5000 enriched peaks. These mapped to 2500 or 2800 gene-associated loci respectively, 617 of which were common loci to both pipelines. Several RFL bound gene loci were homologs of Arabidopsis thaliana LFY gene targets. Such gene targets underscore conserved downstream targets for LFY-proteins in evolutionarily very distinct species. AtLFY is known to bind variants of CCANT/G cis element classified as primary, inflorescence or seedling type. We scanned for these three types of cis elements at 123 RFL bound genes with likely functions in flowering. For a few of these 123 rice loci we find one of these cis motifs (p-value<0.001) in RFL bound ChIP-seq data. To validate these targets of RFL, we adopted in vitro DNA-protein binding assays with bacterially purified RFL protein. We confirm RFL target interactions with some genes implicated in flowering time, others in photoperiod triggered flowering, circadian rhythm, gibberellin hormone pathway, inflorescence development and branching. The in vitro experiments hint different RFL-DNA binding properties as compared to Arabidopsis LFY. We report binding to sequences at rice gene loci that are unique targets. Part II: Pathways regulated by RFL for reproductive transition and panicle development To co-relate DNA binding of RFL to target loci with changes in their gene expression, expression studies were taken up for selected set of genes implicated in rice flowering transition and panicle architecture. To study in planta and tissue specific gene regulation by RFL we raised RFL dsRNAi transgenics. Comparative transcript analysis in these RFL partial knockdown lines and matched wild type tissues reveal that RFL is an activator for some genes and repressor for other gene targets. We also examined if the gene expression effects of RFL knockdown can be reversed by induced complementation with an RFL-GR protein. We raised transgenics plants with a T-DNA ubi:RFL-GR, 35S CaMV:amiR RFL for these experiments. In planta target gene transcript levels were assessed in various conditions conditions. These studies validate rice RFL as an activator of some panicle architecture genes. Part III: Analysis of endogenous RFL protein in WT rice tissues Studies in Arabidopsis and in petunia with LFY and AFL, respectively, implicate these some abnormal mobility as compared to their predicted molecular weight when overexpressed. We studied endogenous RFL protein abundance in planta, adopting western analysis with anti-RFL antibody. We consistently identify two prominent cross reacting bands in different tissues which can be also be pulled-down from whole nuclear extracts of panicle and axillary meristem tissues. We speculate on likely modifications and possible functions for the same.

[ES] En los cítricos, la baja temperatura promueve la inducción floral en otoño-invierno aumentando la expresión del gen promotor CiFT3 (homólogo en los cítricos del gen FLOWERING LOCUS T). La presencia de un gran número de frutos en el árbol durante ese momento inhibe la expresión de CiFT3 y la floración, pero se desconoce la señal inhibitoria que genera el fruto. Las hipótesis mayormente aceptadas proponen que la señal puede ser hormonal o nutricional. En el primer caso, el efecto inhibidor se atribuye a las hormonas que el fruto produce y exporta durante su desarrollo. En el segundo caso, el efecto inhibidor se atribuye a la alta demanda y consumo de carbohidratos por los frutos en desarrollo. Ambas hipótesis son complementarias y no excluyentes entre sí. Además, se ha demostrado que el fruto promueve la activación epigenética del represor de la floración CcMADS19 (homólogo en los cítricos del gen FLOWERING LOCUS C), que inhibe la expresión del gen CiFT3. Con el objetivo de determinar qué señal produce el fruto para inhibir la floración, en esta Tesis se propone la siguiente hipótesis: El fruto inhibe la floración a través de la síntesis y exportación de auxinas que activa la síntesis de giberelinas y, a su vez, la expresión de CcMADS19. Mediante experimentos con tratamientos exógenos de auxinas, giberelinas, y sus antagonistas, aclareo de frutos, y la interrupción del transporte por el floema entre el fruto y las yemas, los resultados indican que ni las giberelinas ni las auxinas se relacionan de forma consistente con la activación de la expresión de CcMADS19 en las hojas. En las yemas, las giberelinas se relacionan con la activación del gen inhibidor CENTRORRADIALIS (CEN), cuando hay fruto por aumento de la síntesis de GA4, y cuando no hay fruto por su aplicación exógena. La presencia del fruto aumenta la concentración de auxinas en el tallo y la yema en el momento de la inducción, y reprime su síntesis y trasporte. Pero esto no impide que, en la yema, el gen CcMADS19 esté epigenéticamente silenciado y que el silenciamiento se transmita a los nuevos brotes vegetativos. Estos brotes florecen en el siguiente ciclo, y, en sus yemas, la diferenciación floral se relaciona con un aumento de la síntesis y trasporte de auxinas y una reducción de la síntesis de giberelinas. / [CA] Als cítrics, les baixes temperatures promouen la inducció floral a la tardor i l'hivern augmentant l'expressió del gen promotor CiFT3 (homòleg en els cítrics del gen FLOWERING LOCUS T). La presència d'un gran nombre de fruita a l'arbre en aquest moment inhibeix l'expressió de CiFT3 i la floració, però es desconeix la senyal inhibidora que genera la fruita. Les hipòtesis majoritàriament acceptades proposen que la senyal pot ser hormonal o nutricional. En el primer cas, l'efecte inhibidor s'atribueix a les hormones que la fruita produeix i exporta durant el seu desenvolupament. En el segon cas, l'efecte inhibidor s'atribueix a la alta demanda i consum de carbohidrats per part de la fruita en desenvolupament. Ambdues hipòtesis són complementàries i no es descarten mútuament. A més, s'ha demostrat que la fruita promou l'activació epigenètica del repressor de la floració CcMADS19 (homòleg en els cítrics del gen FLOWERING LOCUS C), que inhibeix l'expressió del gen CiFT3. Amb l'objectiu de determinar quina senyal produeix la fruita per inhibir la floració, en aquesta Tesi es proposa la següent hipòtesi: La fruita inhibeix la floració mitjançant la síntesi i exportació d'auxines que activa la síntesi de giberelines i, al seu torn, l'expressió de CcMADS19. Mitjançant experiments amb tractaments exògens d'auxines, giberelines i els seus antagonistes, aclarida de fruita i la interrupció del transport pel floema entre la fruita i les brots, els resultats indiquen que ni les giberelines ni les auxines es relacionen de manera consistent amb l'activació de l'expressió de CcMADS19 a les fulles. A les gemmes, les giberelines es relacionen amb l'activació del gen inhibidor CENTRORRADIALIS (CEN) quan hi ha fruita per l'augment de la síntesi de GA4 i quan no hi ha fruita per la seua aplicació exògena. La presència de la fruita augmenta la concentració d'auxines a la tija i la gemma en el moment de la inducció i reprimeix la seua síntesi i transport. Però això no impedeix que, a la gemma, el gen CcMADS19 estigui epigenèticament silenciat i que el silenciament es transmeti als nous brots vegetatius. Aquests brots floreixen al següent cicle i, a les seues gemmes, la diferenciació floral es relaciona amb un augment de la síntesi i transport d'auxines i una reducció de la síntesi de giberelines. / [EN] In citrus, low temperature promotes flower induction in autumn-winter by increasing the expression of the CiFT3 promoter gene (citrus homologue of the FLOWERING LOCUS T gene). The presence of large numbers of fruits on the tree at this time inhibits CiFT3 expression and flowering, but the inhibitory signal produced by the fruits is unknown. The most widely accepted hypotheses are that the signal is hormonal or nutritional. In the first case, the inhibitory effect is attributed to hormones produced and exported by the fruit during development. In the second case, the inhibitory effect is attributed to the high demand and consumption of carbohydrates by the developing fruit. The two hypotheses are complementary and not mutually exclusive. In addition, it has been shown that the fruit promotes the epigenetic activation of the flowering repressor CcMADS19 (citrus homolog of the FLOWERING LOCUS C gene), which inhibits the expression of the CiFT3 gene. To determine which signal is produced by the fruit to inhibit flowering, the following hypothesis is proposed in this thesis: The fruit inhibits flowering through the synthesis and export of auxins, which activates the synthesis of gibberellins and, in turn, the expression of CcMADS19. Experiments with exogenous treatments of auxins, gibberellins and their antagonists, fruit thinning, and disruption of phloem transport between fruit and buds indicate that neither gibberellins nor auxins are consistently associated with the activation of CcMADS19 expression in leaves. In buds, gibberellins are associated with the activation of the flowering inhibitor CENTRORADIALIS (CEN), in the presence of fruit by increasing GA4 synthesis, and in the absence of fruit by its exogenous application. The presence of fruit increases the concentration of auxin in the stem and bud at the time of induction and suppresses its synthesis and transport. However, this does not prevent the epigenetic silencing of the CcMADS19 gene in the bud, which is transmitted to the leaves of the new vegetative shoots. These shoots flower in the following cycle, where floral differentiation is associated with an increase in auxin synthesis and transport and a decrease in gibberellin synthesis in the bud. / Marzal Blay, A. (2024). Study of the Fruit Inhibitory Mechanism on Citrus flowering. Nutritional, Hormonal and Genetic Factors [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/203155

Poaceae (or Gramineae) belong to the grass family and is one of the largest families among flowering plants on land. They include some of the most important cereal crops such as rice (Oryza sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), maize (Zea mays), and sorghum (Sorghum bicolor). The characteristic bushy appearance of grass plants, including cereal crops, is formed by the activities of axillary meristems (AMs) generated in the leaf axil. These give rise to tillers from the basal nodes which recapitulate secondary growth axis and AMs are formed during vegetative development. On transition to flowering the apical meristem transforming to an inflorescence meristem (IM) which produces branches from axillary meristem. These IM gives rise to branches that ultimately bear florets. Vegetative branching/tillering determines plant biomass and influences the number of inflorescences per plant. While inflorescence branching determines the number of florets and hence seeds. Thus the overall activity of axillary meristems plays a key role in determining plant architecture during both vegetative and reproductive stages. In Arabidopsis, research on the plant specific transcription factor LEAFY (LFY) has pioneered our understanding of its regulatory functions during transition from vegetative to reproductive development and its role in specifying a floral meristem (FM) identity to the newly arising lateral meristems. In the FM LFY activates other FM genes and genes for floral organ patterning transcription factors. LFY is strongly expressed throughout the young floral meristems from the earliest stages of specification but is completely absent from the IM (Weigel et al., 1992). LFY expression can also be detected at low levels in the newly emerging leaf primordia during the vegetative phase, and these levels gradually increase until the floral transition (Blazquez et al., 1997; Hempel et al., 1997). In rice, the LFY ortholog-RFL/APO2 is expressed predominantly in very young branching panicles/ inflorescence meristems (Kyozuka et al., 1998; Prasad et al., 2003) while in the vegetative phase RFL is expressed at axils of leaves (Rao et al., 2008). In rice FMs expression is restricted to primordia of lodicules, stamens, carpels and ovules (Ikeda-Kawakatsu et al., 2012). Knockdown of RFL activity or loss of function mutants show delayed flowering and poor panicle branching with reduced number of florets and lower fertility (Rao et al., 2008, Ikeda-Kawakatsu et al., 2012). In some genotypes reduced vegetative axillary branching is also compromised (Rao et al., 2008). On the other hand RFL overexpression leads to the early flowering, attributing a role as an activator for the transition of vegetative meristems to inflorescence meristems (Rao et al., 2008). Thus, RFL shows a distinct developmental expression profile, has unique mutant phenotypes as compared to Arabidopsis LFY thus indicating a divergence in functions. We have used various functional genomics approaches to investigate regulatory networks controlledby RFL in the vegetative axillary meristems and in branching panicles with florets. These regulatory effects influence tillering and panicle branching, thus contributing to rice plant architecture. RFL functions in axillary meristem Vegetative AMs are secondary shoot meristems whose outgrowth determines plant architecture. In rice, AMs form tillers from basal nodes and mutants with altered tillering reveal that an interplay between transcription factors and the phytohormones - auxin, strigolactone underpins this process. We probed the relationship between RFL and other factors that control AM development. Our findings indicate that the derangements in AM development that occur on RFL knockdown arise from its early effects during specification of these meristems and also later effects during their outgrowth of AM as a tiller. Overall, the derailments of both steps of AM development lead to reduced tillering in plants with reduced RFL activity. Our studies on the gene expression status for key transcription factor genes, genes for strigolactone pathway and for auxin transporters gave an insight on the interplay between RFL, LAX1 and strigolactone signalling. Expression levels of LAX1 and CUC genes, that encode transcription factors with AM specification functions, were modulated upon RFL knockdown and on induction of RFL:ΔGR fusion protein. Thus our findings imply a likely, direct activating role for RFL in AM development that acts in part, through attaining appropriate LAX1 expression levels. Our data place meristem specification transcription factors LAX1 and CUC downstream to RFL. Arabidopsis LFY has a predominant role in conferring floral meristem (FM) identity (Weigel et al., 1992; Wagner, 2009; Irish, 2010; Moyroud et al., 2010). Its functions in axillary meristems were not known until recently. The latter functions were uncovered with the new LFYHARA allele with only partial defects in floral meristem identity (Chahtane et al., 2013). This mutant allele showed LFY can promote growth of vegetative AMs through its direct target REGULATOR OF AXILLARY MERISTEMS1 (RAX1), a R2R3 myb domain factor (Chahtane et al., 2013). These functions for Arabidopsis LFY and RAX1 in AMs development are parallel to and redundant with the pathway regulated by LATERAL SUPPRESSOR (LAS) and REGULATOR OF AXILLARY MERISTEM FORMATION1 (ROX1) (Yang et al., 2012; Greb et al., 2003). Interestingly, ROX1 is orthologous to rice LAX1 and our data show LAX1 expression levels in rice panicles and in culms with vegetative AMs is dependent on the expression status of RFL. Thus, we speculate that as compared to Arabidopsis AM development, in rice the LFY-dependent and LFY-independent regulatory pathways for AMs development are closely linked. In Arabidopsis, CUC2 and CUC3 genes in addition to their role in shoot meristem formation and organ separation play a role in AM development possibly by defining a boundary for the emerging AM. These functions for the Arabidopsis CUC genes are routed through their effects on LAS and also by mechanisms independent of LAS (Hibara et al., 2006; Raman et al., 2008). These data show modulation in RFL activity using the inducible RFL:∆GR protein leads to corresponding expression changes in CUC1/CUC2 and CUC3 genes expression in culm tissues. Thus, during rice AM development the meristem functions of RFL and CUC genes are related. Consequent to specification of AM the buds are kept dormant. Bud outgrowth is influenced by auxin and strigolactone signalling pathways. We investigated the transcript levels, in rice culms of genes involved in strigolactone biosynthesis and perception and found the strigolactone biosynthesis gene D10 and hormone perception gene are significantly upregulated in RFL knockdown plants. Further, bioassays were done for strigolactone levels, where we used arbuscular mycorrhiza colonization assay as an indicator for strigolactone levels in wild type plants and in RFL knockdown plants. These data validate higher strigolactone signalling in RFL knockdown plants. To probe the relationship between RFL and the strigolactone pathway we created plants knocked down for both RFL and D3. For comparison of the tillering phenotype of these double knockdown plants we created plants with D3 knockdown alone. We observed reduced tillering in plants with knockdown of both RFL and D3 as compared to the tiller number in plants with knockdown of D3 alone. These data suggest that RFL acts upstream to D3 of control bud outgrowth. As effects of strigolactones are influenced by auxin transport we studied expression of OsPIN1 and OsPIN3 in RFL knockdown plants. Their reduced expression was correlated with auxin deficiency phenotypes of the roots in RFL knockdown plants. These data in conjunction with observations on OsPIN3 the gene expression modulation by the induction of RFL:∆GR allow us to speculate on a relationship between RFL, auxin transport and strigolactones with regard to bud outgrowth. We propose that the low tillering phenotype of RFL knockdown plants arises from weakened PATS, consequent to low levels of PIN1 and PIN3, coupled with moderate increase in strigolactones. Taken together, our findings suggest functions for RFL during AM specification and tiller bud outgrowth. RFL functions in panicle branching Prior studies on phenotypes of RFL knockdown or loss of function mutants suggested roles for RFL in transition to flowering, inflorescence meristem development, emergence of lateral organs and floral organ development (Rao et al., 2008; Ikeda-Kawakatsu et al., 2012). It has been speculated that RFL acts to suppress the transition from inflorescence meristem to floral meristem through its interaction with APO1 (Ikeda-Kawakatsu et al., 2012). The downstream genes regulated by RFL in these processes have not yet been elucidated. To identify direct targets of RFL in developing panicles we adopted ChIP-seq coupled with studies on gene expression modulation on induction of RFL. For the former we raised polyclonal anti-sera and chromatin from branching panicles with few florets. For gene expression modulation studies, we created transgenics with a T-DNA construct where an artificial miRNA against 3’UTR specifically knocked endogenous RFL and the same T-DNA had a second expression cassette for generation of a chemically inducible RFL-ΔGR protein that is not targeted by amiR RFL. Our preliminary ChIP-seq data in the wild type panicle tissues hints that RFL binds to hundreds of loci across the genome thus providing first glimpse of direct targets of RFL in these tissues. These data, while preliminary, were manually curated to identify likely targets that function in flowering, we summarize here some key findings. Our study indicates a role of RFL in flowering transition by activating genes like OsSPL14 and OsPRMT6a. Recent studies indicate that OsSPL14 directly binds to the promoter of OsMADS56 or FTL1, the rice homologs of SOC1 and FT to promote flowering (Lu et al., 2013). As RFL knockdown plants show highly reduced expression of OsMADS50/SOC1 and for RFT1 (Rao et al., 2008), and we show here RFL can bind and induce OsSPL14 expression we suggest the RFL¬OsSPL14 module can contribute to the transition of the SAM to flowering. Further, OsSPL14 in the young panicles directly activates DENSE AND ERECT PANICLE1 (DEP1) to control panicle length (Lu et al., 2013). Thus RFL-OsSPL14-DEP1 module could explain the role of RFL in controlling panicle architecture (Rao et al., 2008; Ikeda-Kawakatsu et al., 2012). Thus RFL plays a role in floral transition and this function is conserved across several LFY homologs. Our data ChIP-seq in the wild type tissue and gene expression modulation studies in transgenics also give molecular evidences for the role of RFL in suppression of floral fate. The direct binding of RFL to OsMADS17, OsYABBY3, OsMADS58 and HD-ZIP-IV loci and the changes in their transcript levels on induction of RFL support this hypothesis. Once the transition from SAM to FM takes place, we speculate RFL represses the conversion of inflorescence branch meristems to floral fate by negatively regulating OsYABBY3, HD-ZIP class IV and OsMADS17 that can promote differentiation. These hypotheses indicate a diverged function for RFL in floral fate repression. Arabidopsis LFY is known to activate the expression of AGAMOUS (AG), whose orthologs in rice are OsMADS3 and OsMADS58. Our studies confirm conservation with regard to RFL binding to cis elements at OsMADS58 locus that is homologous to Arabidopsis AG. But importantly we show altered consequences of this binding on gene expression. We find RFL can suppress the expression of OsMADS58 which we speculate can promote a meristematic fate. Further, we also present the abnormal upregulation of floral organ fate genes on RFL downregulation. These data too indicate functions of RFL, are in part, distinct from the role of Arabidopsis LFY where it works in promoting floral meristem specification and development. These inferences are supported by our data that rice gene homologs for AP1, AP3 and SEP3 are not directly regulated by RFL, unlike their direct regulation by Arabidopsis LFY during flower development. We also report the expression levels of LAX1, FZP, OsIDS1 and OsMADS34 genes involved in meristem phase change and IM branching are RFL dependent. This is consistent with its role in the suppression of determinacy, thereby extending the IM activity for branch formation. But as yet we do not know if these effects are direct. Together, our data report direct targets of RFL that contribute to its functions in meristem regulation, flowering transition, and suppression of floral organ development. Overall, our preliminary data on RFL chromatin occupancy combined with our detailed studies on the modulation of gene expression provides evidence for targets and pathways unique to the rice RFL during inflorescence development. Comparative analysis of genes downstream to RFL in vegetative tillers Vs panicles Tillers and panicle branches arise from the axillary meristems at vegetative and reproductive stages, respectively, of a rice plant and overall contribute to the plant architecture. Some regulatory factors control branching in both these tissues - for example, MOC1 and LAX1. Mutants at these loci affect tillers and panicle branch development thus indicating common mechanisms control lateral branch primordia development (Li et al., 2003; Komatsu et al., 2003; Oikawa and Kyozuka, 2009). Knockdown of RFL activity or loss-of-function mutants cause significantly reduced panicle branching and in few instances, reduction in vegetative axillary branching (Rao et al., 2008; Ikeda- Kawakatsu et al., 2012). We took up the global expression profiling of RFL knockdown plants compared to wild type plants in the axillary meristem and branching panicle tissue. These data provide a useful list of potential targets of RFL in axillary meristem and branching panicle tissue. The comparative analysis of the genes affected in the two tissues indicates only a subset of genes is affected by RFL in both the vegetative axillary meristems and branching panicle. These genes include transcription factors (OsSPL14, Zn finger domain protein, and bHLH domain protein), hormone signalling molecules (GA2 ox9) and cell signalling (LRR protein) as a set of genes activated by RFL in both tissues. On the other hand, these comparative expression profiling studies also show distinct set of genes deregulated by RFL knockdown in these two tissues therefore implicating RFL functions have a tissue-specific context. The genes deregulated only in axillary meristem tissue only include D3- involved in the perception of strigolactone, OsMADS34 speculated to have a role in floral transition and RCN1 involved in transition to flowering. On the other hand, the genes – CUC1, OsMADS3, OsMADS58 involved in organ development and floral meristem determination were found to be deregulated only in panicle tissues of RFL knockdown plants. These data point towards presence of distinct mechanisms for the development of AMs as tillers versus the development of panicle axillary as rachis branches. Overall, these data implicate genes involved in transition to flowering, axillary meristem development and floral meristem development are controlled by RFL in different meristems to thereby control plant architecture and transition to flowering.