Evolution and expression of LEAFY genes in ferns and lycophytes

Background The LEAFY (LFY) transcription factors are present in algae and across land plants. The available expression and functional data of these genes in embryophytes suggest that LFY genes control a plethora of processes including the first zygotic cell division in bryophytes, shoot cell divisions of the gametophyte and sporophyte in ferns, cone differentiation in gymnosperms and floral meristem identity in flowering plants. However, their putative plesiomorphic role in plant reproductive transition in vascular plants remains untested. Results We perform Maximum Likelihood (ML) phylogenetic analyses for the LFY gene lineage in embryophytes with expanded sampling in lycophytes and ferns. We recover the previously identified seed plant duplication that results in LEAFY and NEEDLY paralogs. In addition, we recover multiple species-specific duplications in ferns and lycophytes and large-scale duplications possibly correlated with the occurrence of whole genome duplication (WGD) events in Equisetales and Salviniales. To test putative roles in diverse ferns and lycophytes we perform LFY expression analyses in Adiantum raddianum, Equisetum giganteum and Selaginella moellendorffii. Our results show that LFY genes are active in vegetative and reproductive tissues, with higher expression in early fertile developmental stages and during sporangia differentiation. Conclusions Our data point to previously unrecognized roles of LFY genes in sporangia differentiation in lycophytes and ferns and suggests that functions linked to reproductive structure development are not exclusive to seed plant LFY homologs.

OsbZIP62/OsFD7, a functional ortholog of FLOWERING LOCUS D, regulates floral transition and panicle development in rice

We have characterized a rice bZIP protein-coding gene OsbZIP62/OsFD7 that is expressed preferentially in the shoot apical meristem and during early panicle developmental stages in comparison with other OsFD genes characterized to date. Surprisingly, unlike OsFD1, OsFD7 interacts directly and more efficiently with OsFTLs; the interaction is strongest with OsFTL1 followed by Hd3a and RFT1, as confirmed by fluorescence lifetime imaging-Förster resonant energy transfer (FLIM-FRET) analysis. In addition, OsFD7 is phosphorylated at its C-terminal end by OsCDPK41 and OsCDPK49 in vitro, and this phosphorylated moiety is recognized by OsGF14 proteins. OsFD7 RNAi transgenics were late flowering; the transcript levels of some floral meristem identity genes (e.g. OsMADS14, OsMADS15, and OsMADS18) were also down-regulated. RNAi lines also exhibited dense panicle morphology with an increase in the number of primary and secondary branches resulting in longer panicles and more seeds, probably due to down-regulation of SEPALLATA family genes. In comparison with other FD-like proteins previously characterized in rice, it appears that OsFD7 may have undergone diversification during evolution, resulting in the acquisition of newer functions and thus playing a dual role in floral transition and panicle development in rice.

LEAFY, a Pioneer Transcription Factor in Plants: A Mini-Review

A subset of eukaryotic transcription factors (TFs) possess the ability to reprogram one cell type into another. Genes important for cellular reprograming are typically located in closed chromatin, which is covered by nucleosomes. Pioneer factors are a special class of TFs that can initially engage their target sites in closed chromatin prior to the engagement with, opening of, or modification of the sites by other factors. Although many pioneer factors are known in animals, a few have been characterized in plants. The TF LEAFY (LFY) acts as a pioneer factor specifying floral fate in Arabidopsis. In response to endogenous and environmental cues, plants produce appropriate floral inducers (florigens). During the vegetative phase, LFY is repressed by the TERMINAL FLOWER 1 (TFL1)–FD complex, which functions as a floral inhibitor, or anti-florigen. The florigen FLOWERING LOCUS T (FT) competes with TFL1 to prevent the binding of the FD TF to the LFY locus. The resulting FT–FD complex functions as a transient stimulus to activate its targets. Once LFY has been transcribed in the appropriate spatiotemporal manner, LFY binds to nucleosomes in closed chromatin regions. Subsequently, LFY opens the chromatin by displacing H1 linker histones and recruiting the SWI/SNF chromatin-remodeling complex. Such local changes permit the binding of other TFs, leading to the expression of the floral meristem identity gene APETALA1. This mini-review describes the latest advances in our understanding of the pioneer TF LFY, providing insight into the establishment of gene expression competence through the shaping of the plant epigenetic landscape.

Auxin-induced AUXIN RESPONSE FACTOR4 activates APETALA1 and FRUITFULL to promote flowering in woodland strawberry

Flowering time is known to be regulated by numerous pathways, such as the autonomous, gibberellin, aging, photoperiod-mediated, and vernalization pathways. These regulatory mechanisms involve both environmental triggers and endogenous hormonal cues. Additional flowering control mechanisms mediated by other phytohormones, such as auxin, are less well understood. We found that in cultivated strawberry (Fragaria × ananassa), the expression of auxin response factor4 (FaARF4) was higher in the flowering stage than in the vegetative stage. Overexpression of FaARF4 in Arabidopsis thaliana and woodland strawberry (Fragaria vesca) resulted in transgenic plants flowering earlier than control plants. In addition, FveARF4-silenced strawberry plants showed delayed flowering compared to control plants, indicating that FaARF4 and FveARF4 function similarly in regulating flowering. Further studies showed that ARF4 can bind to the promoters of the floral meristem identity genes APETALA1 (AP1) and FRUITFULL (FUL), inducing their expression and, consequently, flowering in woodland strawberry. Our studies reveal an auxin-mediated flowering pathway in strawberry involving the induction of ARF4 expression.

OsbZIP62/OsFD7, a functional ortholog of Flowering Locus D (FD), regulates floral transition and panicle development in rice

We have characterized a rice bZIP protein coding gene OsbZIP62/OsFD7 that expresses preferentially in SAM and during early panicle developmental stages in comparison to other OsFDs characterised till date. Surprisingly, unlike OsFD1, OsFD7 interacts directly and more efficiently with OsFTLs; the interaction is strongest with OsFTL1 followed by Hd3a and RFT1, as confirmed by FLIM-FRET analysis. Also, OsFD7 is phosphorylated at its C-terminal end by OsCDPK41 and OsCDPK49 in vitro and this phosphorylated moiety is recognized by OsGF14 proteins. OsFD7 RNAi transgenics were late flowering; the transcript levels of some floral meristem identity genes (e.g. OsMADS14, OsMADS15 and OsMADS18) were also down-regulated. It was quite interesting to note that these RNAi lines exhibited dense panicle morphology with increase in the number of primary and secondary branches resulting in longer panicles and more seeds probably due to downregulation of Sepallata (SEP) family genes. In comparison to other FD-like proteins characterized thus far from rice, it appears that OsFD7 may have undergone diversification during evolution resulting in the acquisition of newer functions and thus playing dual role in floral transition and panicle development in rice.HighlightOsbZIP62/OsFD7 interacts with major flowering regulators participating in the processes of floral transition as well as panicle and floral organ development.

A new branch of understanding for barley inflorescence development

This article comments on: Shang Y, Yuan L, Di Y, Jia Y, Zhang Z, Li S, Xing L, Qi Z, Wang X, Zhu J, Hua W, Wu X, Zhu M, Li G, Li C. 2020. A CYC/TB1 type TCP transcription factor controls spikelet meristem identity in barley. Journal of Experimental Botany 71, 7118–7131.

The SINGLE FLOWER (SFL) gene encodes a MYB transcription factor that regulates the number of flowers produced by the inflorescence of chickpea

SUMMARYresearch conducted & rationaleLegume species usually have compound inflorescences, where flowers appear in secondary inflorescences (I2), at lateral positions of the primary inflorescence (I1), in contrast to simple inflorescences, as in Arabidopsis, where flowers are formed in the primary inflorescence stem. The number of flowers per I2, characteristic of each legume species, determines inflorescence diversity, and the number of pods produced, which can affect yield. Gene Regulatory Network that controls the activity of I2 meristems, and therefore the number of flowers per secondary inflorescence is mostly unknown, as well as how specific are factors controlling this trait and whether they share this function in other meristems.methodsChickpea produces one flower per I2 but single flower (sfl) mutants produce two (double-pod phenotype). By mapping the sfl-d mutation and identification and analysis of a second mutant allele we have isolated SFL. We used scanning electron microscopy to study the effect of sfl mutations on inflorescence ontogeny and in situ hybridization to study the expression of SFL and of meristem identity genes in the developing chickpea inflorescence.key resultWe show that the SFL gene corresponds to CaRAX1/2a, encoding a MYB transcription factor. Our results show that CaRAX1/2a / SFL is specifically expressed in the I2 meristem, possibly activated by CaVEGETATIVE1.main conclusion & key points for discussionOur findings reveal that SFL plays a central role in the control of chickpea inflorescence architecture, specifically acting in the I2 meristem to control the time length for which it is active, and therefore determining the number of floral meristems that it can produce.

OsMADS32 Regulates Rice Floral Patterning through Interactions with Multiple Floral Homeotic Genes

Floral patterning is regulated by intricate networks of floral identity genes. The peculiar MADS32 subfamily genes, absent in eudicots but prevalent in monocots, regulate floral organ identity. However, how the MADS32 family genes interact with other floral homeotic genes during flower development is mostly unknown. We show here that the rice homeotic transcription factor OsMADS32 regulates floral patterning by interacting synergistically with E class protein OsMADS6 in a dosage-dependent manner. Furthermore, our results indicate important roles of OsMADS32 in defining stamen, pistil and ovule development through physical and genetic interactions with OsMADS1, OsMADS58 and OsMADS13, and in specifying floral meristem identity with OsMADS6, OsMADS3 and OsMADS58 respectively. Our findings suggest that OsMADS32 is an important factor for floral meristem identity maintenance and that it integrates the action of other MADS-box homeotic proteins to sustain floral organ specification and development in rice. Given that OsMADS32 is an orphan gene and absent in eudicots, our data substantially expand our understanding of flower development in plants.

The movement of a leaf-derived mobile AGL24 mRNA specifies floral organ identity in Arabidopsis

Cell-to-cell and inter-organ communication play pivotal roles in synchronizing and coordinating plant development. In addition to serving as templates for protein translation within cells, many mRNAs can move and exert their function non-cell-autonomously. However, because the proteins encoded by some mobile mRNAs are also mobile, whether the systemic function of mobile mRNAs is attributed to proteins transported distally or translated locally remains controversial. Here, we show that Arabidopsis AGAMOUS-LIKE 24 (AGL24) mRNA acts as a leaf-derived signal to specify meristem identity. AGL24 is expressed in both apex and leaves. Upon floral meristem (FM) transition, apex-expressed AGL24 is transcriptionally inhibited by APETALA1 (AP1) to ensure FM differentiation. The leaf-expressed AGL24 can act as a mobile signal to bypass AP1 inhibition and revert FM differentiation. Although AGL24 mRNA is expressed in leaves, AGL24 protein is rapidly degraded in leaves. In contrast, AGL24 mRNA can move long distance from leaf to apex where the translocated AGL24 mRNAs can be used as templates to translate into proteins. Thus, the movement of AGL24 mRNA can provide the developmental plasticity to fit with environmental dynamics.

COMPOSITUM 1 contributes to the architectural simplification of barley inflorescence via meristem identity signals

Grasses have varying inflorescence shapes; however, little is known about the genetic mechanisms specifying such shapes among tribes. Here, we identify the grass-specific TCP transcription factor COMPOSITUM 1 (COM1) expressing in inflorescence meristematic boundaries of different grasses. COM1 specifies branch-inhibition in barley (Triticeae) versus branch-formation in non-Triticeae grasses. Analyses of cell size, cell walls and transcripts reveal barley COM1 regulates cell growth, thereby affecting cell wall properties and signaling specifically in meristematic boundaries to establish identity of adjacent meristems. COM1 acts upstream of the boundary gene Liguleless1 and confers meristem identity partially independent of the COM2 pathway. Furthermore, COM1 is subject to purifying natural selection, thereby contributing to specification of the spike inflorescence shape. This meristem identity pathway has conceptual implications for both inflorescence evolution and molecular breeding in Triticeae.