Divergent roles of FT-like 9 in flowering transition under different day lengths in Brachypodium distachyon

The H3K4 demethylase JMJ1 is required for proper timing of flowering in Brachypodium distachyon

Flowering is a key developmental transition in the plant life cycle. In temperate climates, flowering often occurs in response to the perception of seasonal cues such as changes in day-length and temperature. However, the mechanisms that have evolved to control the timing of flowering in temperate grasses are not fully understood. We identified a Brachypodium distachyon mutant whose flowering is delayed under inductive long-day conditions due to a mutation in the JMJ1 gene, which encodes a Jumonji domain-containing protein. JMJ1 is a histone demethylase that mainly demethylates H3K4me2 and H3K4me3 in vitro and in vivo. Analysis of the genome-wide distribution of H3K4me1, H3K4me2, and H3K4me3 in wild-type plants by chromatin immunoprecipitation and sequencing combined with RNA sequencing revealed that H3K4m1 and H3K4me3 are positively associated with gene transcript levels, whereas H3K4me2 is negatively correlated with transcript levels. Furthermore, JMJ1 directly binds to the chromatin of the flowering regulator genes VRN1 and ID1 and affects their transcription by modifying their H3K4me2 and H3K4me3 levels. Genetic analyses indicated that JMJ1 promotes flowering by activating VRN1 expression. Our study reveals a role for JMJ1-mediated chromatin modification in the proper timing of flowering in B. distachyon.

GHCU, a Molecular Chaperone, Regulates Leaf Curling by Modulating the Distribution of KNGH1 in Cotton

Leaf shape is considered to be one of the most significant agronomic traits in crop breeding. However, the molecular basis underlying leaf morphogenesis in cotton is still largely unknown. In this study, through genetic mapping and molecular investigation using a natural cotton mutant cu with leaves curling upward, the causal gene GHCU is successfully identified as the key regulator of leaf flattening. Knockout of GHCU or its homolog in cotton and tobacco using CRISPR results in abnormal leaf shape. It is further discovered that GHCU facilitates the transport of the HD protein KNOTTED1-like (KNGH1) from the adaxial to the abaxial domain. Loss of GHCU function restricts KNGH1 to the adaxial epidermal region, leading to lower auxin response levels in the adaxial boundary compared to the abaxial. This spatial asymmetry in auxin distribution produces the upward-curled leaf phenotype of the cu mutant. By analysis of single-cell RNA sequencing and spatiotemporal transcriptomic data, auxin biosynthesis genes are confirmed to be expressed asymmetrically in the adaxial-abaxial epidermal cells. Overall, these findings suggest that GHCU plays a crucial role in the regulation of leaf flattening through facilitating cell-to-cell trafficking of KNGH1 and hence influencing the auxin response level.

Functional divergence of FTL9 and FTL10 in flowering control in rice

BACKGROUND

Floral transition in cereals is a critical phenomenon influenced by exogenous and endogenous signals, determining crop yield and reproduction. Flowering Locus T-like (FT-like) genes encode a mobile florigen, the main signaling molecule for flowering.

RESULTS

In this study, we characterized two FT-like genes, FTL9 and FTL10, to study their functional diversity in flowering control in rice. We compared independent mutant lines of ftl10 with WT and observed negligible differences in the flowering phenotype, or agronomic traits implying potentially redundant roles of FTL10 loss-of-function in flowering control in rice. Nevertheless, we found that overexpression of FTL10, but not FTL9, substantially accelerated flowering, indicating the flowering-promoting role of FTL10 and the divergent functions between FTL9 and FTL10 in flowering. Besides flowering, additive agronomic roles were observed for FTL10-OE regulating the number of effective panicles per plant, the number of primary branches per panicle, and spikelets per panicle without regulating seed size. Mechanistically, our Y2H and BiFC analyses demonstrate that FTL10, in contrast to FTL9, can interact with FD1 and GF14c, forming a flowering activation complex and thereby regulating flowering.

CONCLUSION

Altogether, our results elucidate the regulatory roles of FTL9 and FTL10 in flowering control, unveiling the molecular basis of functional divergence between FTL10 and FTL9, which provides mechanistic insights into shaping the dynamics of flowering time regulation in rice.

Comparative and functional analysis unveils the contribution of photoperiod to DNA methylation, sRNA accumulation, and gene expression variations in short-day and long-day grasses

Photoperiod employs complicated networks to regulate various developmental processes in plants, including flowering transition. However, the specific mechanisms by which photoperiod affects epigenetic modifications and gene expression variations in plants remain elusive. In this study, we conducted a comprehensive analysis of DNA methylation, small RNA (sRNA) accumulation, and gene expressions under different daylengths in facultative long-day (LD) grass Brachypodium distachyon and short-day (SD) grass rice. Our results showed that while overall DNA methylation levels were minimally affected by different photoperiods, CHH methylation levels were repressed under their favorable light conditions, particularly in rice. We identified numerous differentially methylated regions (DMRs) that were influenced by photoperiod in both plant species. Apart from differential sRNA clusters, we observed alterations in the expression of key components of the RNA-directed DNA methylation pathway, DNA methyltransferases, and demethylases, which may contribute to the identified photoperiod-influenced CHH DMRs. Furthermore, we identified many differentially expressed genes in response to different daylengths, some of which were associated with the DMRs. Notably, we discovered a photoperiod-responsive gene MYB11 in the transcriptome of B. distachyon, and further demonstrated its role as a flowering inhibitor by repressing FT1 transcription. Together, our comparative and functional analysis sheds light on the effects of daylength on DNA methylation, sRNA accumulation, and gene expression variations in LD and SD plants, thereby facilitating better designing breeding programs aimed at developing high-yield crops that can adapt to local growing seasons.

Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time

KEY MESSAGE

111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.

Polygenic architecture of flowering time and its relationship with local environments in the grass Brachypodium distachyon

Synchronizing the timing of reproduction with the environment is crucial in the wild. Among the multiple mechanisms, annual plants evolved to sense their environment, the requirement of cold-mediated vernalization is a major process that prevents individuals from flowering during winter. In many annual plants including crops, both a long and short vernalization requirement can be observed within species, resulting in so-called early-(spring) and late-(winter) flowering genotypes. Here, using the grass model Brachypodium distachyon, we explored the link between flowering-time-related traits (vernalization requirement and flowering time), environmental variation, and diversity at flowering-time genes by combining measurements under greenhouse and outdoor conditions. These experiments confirmed that B. distachyon natural accessions display large differences regarding vernalization requirements and ultimately flowering time. We underline significant, albeit quantitative effects of current environmental conditions on flowering-time-related traits. While disentangling the confounding effects of population structure on flowering-time-related traits remains challenging, population genomics analyses indicate that well-characterized flowering-time genes may contribute significantly to flowering-time variation and display signs of polygenic selection. Flowering-time genes, however, do not colocalize with genome-wide association peaks obtained with outdoor measurements, suggesting that additional genetic factors contribute to flowering-time variation in the wild. Altogether, our study fosters our understanding of the polygenic architecture of flowering time in a natural grass system and opens new avenues of research to investigate the gene-by-environment interaction at play for this trait.

The evolution and functional divergence of FT-related genes in controlling flowering time in Brassica rapa ssp. rapa

KEY MESSAGE

The BrrFT paralogues exhibit distinct expression patterns and play different roles in regulating flowering time, and BrrFT4 competes with BrrFT1 and BrrFT2 to interact with BrrFD proteins. Flowering time is an important agricultural trait for Brassica crops, and early bolting strongly affects the yield and quality of Brassica rapa ssp. rapa. Flowering Locus T paralogues play an important role in regulating flowering time. In this study, we identified FT-related genes in turnip by phylogenetic classification, and four BrrFT homoeologs that shared with high identities with BraFT genes were isolated. The different gene structures, promoter binding sites, and expression patterns observed indicated that these genes may play different roles in flowering time regulation. Further genetic and biochemical experiments showed that as for FT-like paralogues, BrrFT2 acted as the key floral inducer, and BrrFT1 seems to act as a mild 'florigen' protein. However, BrrFT4 acts as a floral repressor and antagonistically regulates flowering time by competing with BrrFT1 and BrrFT2 to bind BrrFD proteins. BrrFT3 may have experienced loss of function via base shift mutation. Our results revealed the potential roles of FT-related genes in flowering time regulation in turnip.

Interactive mode of biochar-based silicon and iron nanoparticles mitigated Cd-toxicity in maize

Cadmium contamination poses severe environmental and health threats, necessitating effective mitigation strategies. Rice husk biochar (BC) and nanoparticle (NP) treatments are emerging strategies with limited research on their synergistic benefits. This study assesses BC, silicon NPs (nSi), and iron NPs (nFe) modifications (B-nSi, B-nFe, and B-nSi-nFe) to reduce Cd-bioavailability in soil and its toxicity in maize, not reported before. Characterization of amendments validated, nSi and nFe attachment to BC, forming new mineral crystals to adsorb Cd. We found that B-nSi-nFe induced Cd-immobilization in soil by the formation of Cd-ligand complexes with the effective retention of NPs within microporous structure of BC. B-nSi-nFe increased soil pH by 0.76 units while reducing bioavailable Cd by 49 %, than Ck-Cd. Resultantly, B-nSi-nFe reduced Cd concentrations in roots and shoots by 51 % and 75 %, respectively. Moreover, the application of B-nSi-nFe significantly enhanced plant biomass, antioxidant activities, and upregulated the expression of antioxidant genes [ZmAPX (3.28 FC), ZmCAT (3.20 FC), ZmPOD (2.58 FC), ZmSOD (3.08 FC), ZmGSH (3.17 FC), and ZmMDHAR (3.80 FC)] while downregulating Cd transporter genes [ZmNramp5 (3.65 FC), ZmHMA2 (2.92 FC), and ZmHMA3 (3.40 FC)] compared to Ck-Cd. Additionally, confocal microscopy confirmed the efficacy of B-nSi-nFe in maintaining cell integrity due to reduced oxidative stress. SEM and TEM observations revealed alleviation of Cd toxicity to stomata, guard cells, and ultracellular structures with B-nSi-nFe treatment. Overall, this study demonstrated the potential of B-nSi-nFe for reducing Cd mobility in soil-plant system, mitigating Cd-toxicity in plants and improving enzymatic activities in soil.

INDETERMINATE1-mediated expression of FT family genes is required for proper timing of flowering in Brachypodium distachyon

The transition to flowering is a major developmental switch in plants. In many temperate grasses, perception of indicators of seasonal change, such as changing day-length and temperature, leads to expression of FLOWERING LOCUS T1 (FT1) and FT-Like (FTL) genes that are essential for promoting the transition to flowering. However, little is known about the upstream regulators of FT1 and FTL genes in temperate grasses. Here, we characterize the monocot-specific gene INDETERMINATE1 (BdID1) in Brachypodium distachyon and demonstrate that BdID1 is a regulator of FT family genes. Mutations in ID1 impact the ability of the short-day (SD) vernalization, cold vernalization, and long-day (LD) photoperiod pathways to induce certain FTL genes. BdID1 is required for upregulation of FTL9 (FT-LIKE9) expression by the SD vernalization pathway, and overexpression of FTL9 in an id1 background can partially restore the delayed flowering phenotype of id1. We show that BdID1 binds in vitro to the promoter region of FTL genes suggesting that ID1 directly activates FTL expression. Transcriptome analysis shows that BdID1 is required for FT1, FT2, FTL12, and FTL13 expression under inductive LD photoperiods, indicating that BdID1 is a regulator of the FT gene family. Moreover, overexpression of FT1 in the id1 background results in rapid flowering similar to overexpressing FT1 in the wild type, demonstrating that BdID1 is upstream of FT family genes. Interestingly, ID1 negatively regulates a previously uncharacterized FTL gene, FTL4, and we show that FTL4 is a repressor of flowering. Thus, BdID1 is critical for proper timing of flowering in temperate grasses.

VERNALIZATION1 represses FLOWERING PROMOTING FACTOR1-LIKE1 in leaves for timely flowering in Brachypodium distachyon

FLOWERING PROMOTING FACTOR1 (FPF1), a small protein without any known domains, promotes flowering in several plants; however, its functional mechanism remains unknown. Here, we characterized 2 FPF1-like proteins, FPL1 and FPL7, which, in contrast, function as flowering repressors in Brachypodium distachyon. FPL1 and FPL7 interact with the components of the florigen activation complex (FAC) and inhibit FAC activity to restrict expression of its critical target, VERNALIZATION1 (VRN1), in leaves, thereby preventing overaccumulation of FLOWERING LOCUS T1 (FT1) at the juvenile stage. Further, VRN1 can directly bind to the FPL1 promoter and repress FPL1 expression; hence, as VRN1 gradually accumulates during the late vegetative stage, FAC is released. This accurate feedback regulation of FPL1 by VRN1 allows proper FT1 expression in leaves and ensures sufficient FAC formation in shoot apical meristems to trigger timely flowering. Overall, we define a sophisticated modulatory loop for flowering initiation in a temperate grass, providing insights toward resolving the molecular basis underlying fine-tuning flowering time in plants.

OsFTL12, a member of FT-like family, modulates the heading date and plant architecture by florigen repression complex in rice

FLOWERING LOCUS T (FT), a florigen in Arabidopsis, plays critical roles in floral transition. Among 13 FT-like members in rice, OsFTL2 (Hd3a) and OsFTL3 (RFT1), two rice homologues of FT, have been well characterized to act as florigens to induce flowering under short-day (SD) and long-day (LD) conditions, respectively, but the functions of other rice FT-like members remain largely unclear. Here, we show that OsFTL12 plays an antagonistic function against Hd3a and RFT1 to modulate the heading date and plant architecture in rice. Unlike Hd3a and RFT1, OsFTL12 is not regulated by daylength and highly expressed in both SD and LD conditions, and delays the heading date under either SD or LD conditions. We further demonstrate that OsFTL12 interacts with GF14b and OsFD1, two key components of the florigen activation complex (FAC), to form the florigen repression complex (FRC) by competing with Hd3a for binding GF14b. Notably, OsFTL12-FRC can bind to the promoters of the floral identity genes OsMADS14 and OsMADS15 and suppress their expression. The osmads14 osmads15 double mutants could not develop panicles and showed erect leaves. Taken together, our results reveal that different FT-like members can fine-tune heading date and plant architecture by regulating the balance of FAC and FRC in rice.

The Molecular Mechanism of GhbHLH121 in Response to Iron Deficiency in Cotton Seedlings

Iron deficiency caused by high pH of saline-alkali soil is a major source of abiotic stress affecting plant growth. However, the molecular mechanism underlying the iron deficiency response in cotton (Gossypium hirsutum) is poorly understood. In this study, we investigated the impacts of iron deficiency at the cotton seedling stage and elucidated the corresponding molecular regulation network, which centered on a hub gene GhbHLH121. Iron deficiency induced the expression of genes with roles in the response to iron deficiency, especially GhbHLH121. The suppression of GhbHLH121 with virus-induced gene silence technology reduced seedlings' tolerance to iron deficiency, with low photosynthetic efficiency and severe damage to the structure of the chloroplast. Contrarily, ectopic expression of GhbHLH121 in Arabidopsis enhanced tolerance to iron deficiency. Further analysis of protein/protein interactions revealed that GhbHLH121 can interact with GhbHLH IVc and GhPYE. In addition, GhbHLH121 can directly activate the expression of GhbHLH38, GhFIT, and GhPYE independent of GhbHLH IVc. All told, GhbHLH121 is a positive regulator of the response to iron deficiency in cotton, directly regulating iron uptake as the upstream gene of GhFIT. Our results provide insight into the complex network of the iron deficiency response in cotton.

EARLY FLOWERING 3 interactions with PHYTOCHROME B and PHOTOPERIOD1 are critical for the photoperiodic regulation of wheat heading time

The photoperiodic response is critical for plants to adjust their reproductive phase to the most favorable season. Wheat heads earlier under long days (LD) than under short days (SD) and this difference is mainly regulated by the PHOTOPERIOD1 (PPD1) gene. Tetraploid wheat plants carrying the Ppd-A1a allele with a large deletion in the promoter head earlier under SD than plants carrying the wildtype Ppd-A1b allele with an intact promoter. Phytochromes PHYB and PHYC are necessary for the light activation of PPD1, and mutations in either of these genes result in the downregulation of PPD1 and very late heading time. We show here that both effects are reverted when the phyB mutant is combined with loss-of-function mutations in EARLY FLOWERING 3 (ELF3), a component of the Evening Complex (EC) in the circadian clock. We also show that the wheat ELF3 protein interacts with PHYB and PHYC, is rapidly modified by light, and binds to the PPD1 promoter in planta (likely as part of the EC). Deletion of the ELF3 binding region in the Ppd-A1a promoter results in PPD1 upregulation at dawn, similar to PPD1 alleles with intact promoters in the elf3 mutant background. The upregulation of PPD1 is correlated with the upregulation of the florigen gene FLOWERING LOCUS T1 (FT1) and early heading time. Loss-of-function mutations in PPD1 result in the downregulation of FT1 and delayed heading, even when combined with the elf3 mutation. Taken together, these results indicate that ELF3 operates downstream of PHYB as a direct transcriptional repressor of PPD1, and that this repression is relaxed both by light and by the deletion of the ELF3 binding region in the Ppd-A1a promoter. In summary, the regulation of the light mediated activation of PPD1 by ELF3 is critical for the photoperiodic regulation of wheat heading time.

A leaf-emanated signal orchestrates grain size and number in response to maternal resources

In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT-like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long-range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss-of-function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication.

A stress-inducible protein regulates drought tolerance and flowering time in Brachypodium and Arabidopsis

To cope with environmental stresses and ensure maximal reproductive success, plants have developed strategies to adjust the timing of their transition to reproductive growth. This has a substantial impact on the stress resilience of crops and ultimately on agricultural productivity. Here, we report a previously uncharacterized, plant-specific gene family designated as Regulator of Flowering and Stress (RFS). Overexpression of the BdRFS gene in Brachypodium distachyon delayed flowering, increased biomass accumulation, and promoted drought tolerance, whereas clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated knockout mutants exhibited opposite phenotypes. A double T-DNA insertional mutant in the two Arabidopsis (Arabidopsis thaliana) homologs replicated the effects on flowering and water deprivation seen in the B. distachyon CRISPR knockout lines, highlighting the functional conservation of the family between monocots and dicots. Lipid analysis of B. distachyon and Arabidopsis revealed that digalactosyldiacylglycerol (DGDG) and phosphatidylcholine (PC) contents were significantly, and reciprocally, altered in overexpressor and knockout mutants. Importantly, alteration of C16:0-containing PC, a Flowering Locus T-interacting lipid, associated with flowering phenotype, with elevated levels corresponding to earlier flowering. Co-immunoprecipitation analysis suggested that BdRFS interacts with phospholipase Dα1 as well as several other abscisic acid-related proteins. Furthermore, reduction of C18:3 fatty acids in DGDG corresponded with reduced jasmonic acid metabolites in CRISPR mutants. Collectively, we suggest that stress-inducible RFS proteins represent a regulatory component of lipid metabolism that impacts several agronomic traits of biotechnological importance.

Brachypodium: 20 years as a grass biology model system; the way forward?

It has been 20 years since Brachypodium distachyon was suggested as a model grass species, but ongoing research now encompasses the entire genus. Extensive Brachypodium genome sequencing programmes have provided resources to explore the determinants and drivers of population diversity. This has been accompanied by cytomolecular studies to make Brachypodium a platform to investigate speciation, polyploidisation, perenniality, and various aspects of chromosome and interphase nucleus organisation. The value of Brachypodium as a functional genomic platform has been underscored by the identification of key genes for development, biotic and abiotic stress, and cell wall structure and function. While Brachypodium is relevant to the biofuel industry, its impact goes far beyond that as an intriguing model to study climate change and combinatorial stress.

A Pleiotropic Flowering Time QTL Exhibits Gene-by-Environment Interaction for Fitness in a Perennial Grass

Appropriate flowering time is a crucial adaptation impacting fitness in natural plant populations. Although the genetic basis of flowering variation has been extensively studied, its mechanisms in nonmodel organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. Genetic mapping in populations derived from inland and coastal ecotypes identified flowering time quantitative trait loci (QTL) and many exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments. Fine-mapping and expression studies identified a gene with orthology to a rice FLOWERING LOCUS T-like 9 (PhFTL9) as the candidate underlying q-FT5. We used a reciprocal transplant experiment to test for local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analyses identified an excess of low-frequency polymorphisms at the PhFTL9 promoter in the inland lineage, suggesting a role for either selection or population expansion on promoter evolution. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering time divergence.

Circadian-period variation underlies the local adaptation of photoperiodism in the short-day plant Lemna aequinoctialis

Phenotypic variation is the basis for trait adaptation via evolutionary selection. However, the driving forces behind quantitative trait variations remain unclear owing to their complexity at the molecular level. This study focused on the natural variation of the free-running period (FRP) of the circadian clock because FRP is a determining factor of the phase phenotype of clock-dependent physiology. Lemna aequinoctialis in Japan is a paddy field duckweed that exhibits a latitudinal cline of critical day length (CDL) for short-day flowering. We collected 72 strains of L. aequinoctialis and found a significant correlation between FRPs and locally adaptive CDLs, confirming that variation in the FRP-dependent phase phenotype underlies photoperiodic adaptation. Diel transcriptome analysis revealed that the induction timing of an FT gene is key to connecting the clock phase to photoperiodism at the molecular level. This study highlights the importance of FRP as a variation resource for evolutionary adaptation.

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Natural variation of flowering/circadian traits in a paddy-field duckweed is studied.

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Critical day length for flowering of the duckweed in Japan shows a latitudinal cline.

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A negative correlation between critical day length and circadian period was found.

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An FT gene responding to lengthening of the dark period was isolated.

The wild grass Brachypodium distachyon as a developmental model system

The arrival of cheap and high-throughput sequencing paired with efficient gene editing technologies allows us to use non-traditional model systems and mechanistically approach biological phenomena beyond what was conceivable just a decade ago. Venturing into different model systems enables us to explore for example clade-specific environmental responses to changing climates or the genetics and development of clade-specific organs, tissues and cell types. We-both early career researchers working with the wild grass model Brachypodium distachyon-want to use this review to (1) highlight why we think B. distachyon is a fantastic grass developmental model system, (2) summarize the tools and resources that have enabled discoveries made in B. distachyon, and (3) discuss a handful of developmental biology vignettes made possible by using B. distachyon as a model system. Finally, we want to conclude by (4) relating our personal stories with this emerging model system and (5) share what we think is important to consider before starting work with an emerging model system.

Comparative Transcriptomic Analysis Provides Insight into the Key Regulatory Pathways and Differentially Expressed Genes in Blueberry Flower Bud Endo- and Ecodormancy Release

Endodormancy is the stage that perennial plants must go through to prepare for the next seasonal cycle, and it is also an adaptation that allows plants to survive harsh winters. Blueberries (Vaccinium spp.) are known to have high nutritional and commercial value. To better understand the molecular mechanisms of bud dormancy release, the transcriptomes of flower buds from the southern highbush blueberry variety “O’Neal” were analyzed at seven time points of the endo- and ecodormancy release processes. Pairwise comparisons were conducted between adjacent time points; five kinds of phytohormone were identified via these processes. A total of 12,350 differentially expressed genes (DEGs) were obtained from six comparisons. Gene Ontology analysis indicated that these DEGs were significantly involved in metabolic processes and catalytic activity. KEGG pathway analysis showed that these DEGs were predominantly mapped to metabolic pathways and the biosynthesis of secondary metabolites in endodormancy release, but these DEGs were significantly enriched in RNA transport, plant hormone signal transduction, and circadian rhythm pathways in the process of ecodormancy release. The contents of abscisic acid (ABA), salicylic acid (SA), and 1-aminocyclopropane-1-carboxylate (ACC) decreased in endo- and ecodormancy release, and the jasmonic acid (JA) level first decreased in endodormancy release and then increased in ecodormancy release. Weighted correlation network analysis (WGCNA) of transcriptomic data associated with hormone contents generated 25 modules, 9 of which were significantly related to the change in hormone content. The results of this study have important reference value for elucidating the molecular mechanism of flower bud dormancy release.

EARLY FLOWERING 3 and Photoperiod Sensing in Brachypodium distachyon

The proper timing of flowering, which is key to maximize reproductive success and yield, relies in many plant species on the coordination between environmental cues and endogenous developmental programs. The perception of changes in day length is one of the most reliable cues of seasonal change, and this involves the interplay between the sensing of light signals and the circadian clock. Here, we describe a Brachypodium distachyon mutant allele of the evening complex protein EARLY FLOWERING 3 (ELF3). We show that the elf3 mutant flowers more rapidly than wild type plants in short days as well as under longer photoperiods but, in very long (20 h) days, flowering is equally rapid in elf3 and wild type. Furthermore, flowering in the elf3 mutant is still sensitive to vernalization, but not to ambient temperature changes. Molecular analyses revealed that the expression of a short-day marker gene is suppressed in elf3 grown in short days, and the expression patterns of clock genes and flowering time regulators are altered. We also explored the mechanisms of photoperiodic perception in temperate grasses by exposing B. distachyon plants grown under a 12 h photoperiod to a daily night break consisting of a mixture of red and far-red light. We showed that 2 h breaks are sufficient to accelerate flowering in B. distachyon under non-inductive photoperiods and that this acceleration of flowering is mediated by red light. Finally, we discuss advances and perspectives for research on the perception of photoperiod in temperate grasses.

Asymmetric expansions of FT and TFL1 lineages characterize differential evolution of the EuPEBP family in the major angiosperm lineages

Background

In flowering plants, precise timing of the floral transition is crucial to maximize chances of reproductive success, and as such, this process has been intensively studied. FLOWERING LOCUS T (FT) and TERMINAL FLOWER1 (TFL1) have been identified as closely related eukaryotic phosphatidylethanolamine-binding proteins (‘EuPEBPs’) that integrate multiple environmental stimuli, and act antagonistically to determine the optimal timing of the floral transition. Extensive research has demonstrated that FT acts similar to hormonal signals, being transported in the phloem from its primary site of expression in leaves to its primary site of action in the shoot meristem; TFL1 also appears to act as a mobile signal. Recent work implicates FT, TFL1, and the other members of the EuPEBP family, in the control of other important processes, suggesting that the EuPEBP family may be key general regulators of developmental transitions in flowering plants. In eudicots, there are a small number of EuPEBP proteins, but in monocots, and particularly grasses, there has been a large, but uncharacterized expansion of EuPEBP copy number, with unknown consequences for the EuPEBP function.

Results

To systematically characterize the evolution of EuPEBP proteins in flowering plants, and in land plants more generally, we performed a high-resolution phylogenetic analysis of 701 PEBP sequences from 208 species. We refine previous models of EuPEBP evolution in early land plants, demonstrating the algal origin of the family, and pin-pointing the origin of the FT/TFL1 clade at the base of monilophytes. We demonstrate how a core set of genes (MFT1, MFT2, FT, and TCB) at the base of flowering plants has undergone differential evolution in the major angiosperm lineages. This includes the radical expansion of the FT family in monocots into 5 core lineages, further re-duplicated in the grass family to 12 conserved clades.

Conclusions

We show that many grass FT proteins are strongly divergent from other FTs and are likely neo-functional regulators of development. Our analysis shows that monocots and eudicots have strongly divergent patterns of EuPEBP evolution.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-021-01128-8.

GhUBX controlling helical growth results in production of stronger cotton fiber

Cotton fiber is an excellent model for studying plant cell elongation and cell wall biogenesis as well because they are highly polarized and use conserved polarized diffuse growth mechanism. Fiber strength is an important trait among cotton fiber qualities due to ongoing changes in spinning technology. However, the molecular mechanism of fiber strength forming is obscure. Through map-based cloning, we identified the fiber strength gene GhUBX. Increasing its expression, the fiber strength of the transgenic cotton was significantly enhanced compared to the receptor W0 and the helices number of the transgenic fiber was remarkably increased. Additionally, we proved that GhUBX regulates the fiber helical growth by degrading the GhSPL1 via the ubiquitin 26S–proteasome pathway. Taken together, we revealed the internal relationship between fiber helices and fiber stronger. It will be useful for improving the fiber quality in cotton breeding and illustrating the molecular mechanism for plant twisted growth.

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Isolation of the first fiber strength gene GhUBX using map-based cloning strategy

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Verification of the function of GhUBX experimentally in transgenic cotton

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Link helices to the cotton fiber strength, that more helices make fiber stronger

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An ubiquitin–proteasome system regulating the development of cotton fiber

BdFAR4, a root-specific fatty acyl-coenzyme A reductase, is involved in fatty alcohol synthesis of root suberin polyester in Brachypodium distachyon

Suberin is a complex hydrophobic polymer of aliphatic and phenolic compounds which controls the movement of gases, water, and solutes and protects plants from environmental stresses and pathogenic infection. The synthesis and regulatory pathways of suberin remain unknown in Brachypodium distachyon. Here we describe the identification of a B. distachyon gene, BdFAR4, encoding a fatty acyl-coenzyme A reductase (FAR) by a reverse genetic approach, and investigate the molecular relevance of BdFAR4 in the root suberin synthesis of B. distachyon. BdFAR4 is specifically expressed throughout root development. Heterologous expression of BdFAR4 in yeast (Saccharomyces cerevisiae) afforded the production of C20:0 and C22:0 fatty alcohols. The loss-of-function knockout of BdFAR4 by CRISPR/Cas9-mediated gene editing significantly reduced the content of C20:0 and C22:0 fatty alcohols associated with root suberin. In contrast, overexpression of BdFAR4 in B. distachyon and tomato (Solanum lycopersicum) resulted in the accumulation of root suberin-associated C20:0 and C22:0 fatty alcohols, suggesting that BdFAR4 preferentially accepts C20:0 and C22:0 fatty acyl-CoAs as substrates. The BdFAR4 protein was localized to the endoplasmic reticulum in Arabidopsis thaliana protoplasts and Nicotiana benthamiana leaf epidermal cells. BdFAR4 transcript levels can be increased by abiotic stresses and abscisic acid treatment. Furthermore, yeast one-hybrid, dual-luciferase activity, and electrophoretic mobility shift assays indicated that the R2R3-MYB transcription factor BdMYB41 directly binds to the promoter of BdFAR4. Taken together, these results imply that BdFAR4 is essential for the production of root suberin-associated fatty alcohols, especially under stress conditions, and that its activity is transcriptionally regulated by the BdMYB41 transcription factor.

Identification of transcription factors controlling cell wall invertase gene expression for reproductive development via bioinformatic and transgenic analyses

Cell wall invertase (CWIN) hydrolyses sucrose into glucose and fructose in the extracellular matrix and plays crucial roles in assimilate partitioning and sugar signalling. However, the molecular regulators controlling CWIN gene transcription remain unknown. As the first step to address this issue, we performed bioinformatic and transgenic studies, which identified a cohort of transcription factors (TFs) modulating CWIN gene expression in Arabidopsis thaliana. Comprehensive bioinformatic analyses identified 18 TFs as putative regulators of the expression of AtCWIN2 and AtCWIN4 that are predominantly expressed in Arabidopsis reproductive organs. Among them, MYB21, ARF6, ARF8, AP3 and CRC were subsequently shown to be the most likely regulators of CWIN gene expression based on molecular characterization of the respective mutant of each candidate TF. More specifically, the obtained data indicate that ARF6, ARF8 and MYB21 regulate CWIN2 expression in the anthers and CWIN4 in nectaries, anthers and petals, whereas AP3 and CRC were determined primarily to regulate the transcriptional activity of CWIN4. TF-promoter interaction assays demonstrated that ARF6 and ARF8 directly control CWIN2 and CWIN4 transcription with AP3 activating CWIN4. The involvement of ARF8 in regulating CWIN4 expression was further supported by the finding that enhanced CWIN4 expression partially recovered the short silique phenotype displayed by the arf8-3 mutant. The identification of the five TFs regulating CWIN expression serves as a launching pad for future studies to dissect the upstream molecular network underpinning the transcription of CWINs and provides a new avenue, potentially, to engineer assimilate allocation and reproductive development for improving seed yield.

Identification and Characterization of Perennial Ryegrass (Lolium perenne) Vernalization Genes

Perennial ryegrass (Lolium perenne) is a temperate grass species commonly used as pasture for livestock. Flowering (heading) of ryegrass impacts metabolizable energy content and seed yield, therefore this trait is important for both farmers and seed producers. In related grass species, the VRN genes (VRN1-3) have been largely implicated in the determination of vernalization response and are responsible for much of the intra-species variation in this trait. Many other important flowering-time regulators have been cataloged in the model grass Brachypodium distachyon; however, in several cases, such as VRN2, their ryegrass homologs have not been well-characterized. Here, ryegrass homologs of important flowering time genes from B. distachyon were identified through available synteny data and sequence similarity. Phylogenetic analysis of VRN3/FT-like and VRN2-like genes was performed to elucidate these families further. The expression patterns of these genes were assessed during vernalization. This confirmed the key roles played by LpVRN1 and LpFT3 in the promotion of flowering. Furthermore, two orthologs of VRN2 identified here, as well as an ortholog of CO9, were expressed prior to vernalization, and were repressed in flowering plants, suggesting a role in floral repression. Significant variability in expression of these flowering pathway genes in diverse genotypes was detected and may underlie variation in flowering time and vernalization response.

FLOWERING LOCUS T4 delays flowering and decreases floret fertility in barley

FLOWERING LOCUS T-like (FT-like) genes control the photoperiodic regulation of flowering in many angiosperm plants. The family of FT-like genes is characterized by extensive gene duplication and subsequent diversification of FT functions which occurred independently in modern angiosperm lineages. In barley, there are 12 known FT-like genes (HvFT), but the function of most of them remains uncharacterized. This study aimed to characterize the role of HvFT4 in flowering time control and development in barley. The overexpression of HvFT4 in the spring cultivar Golden Promise delayed flowering time under long-day conditions. Microscopic dissection of the shoot apical meristem revealed that overexpression of HvFT4 specifically delayed spikelet initiation and reduced the number of spikelet primordia and grains per spike. Furthermore, ectopic overexpression of HvFT4 was associated with floret abortion and with the down-regulation of the barley MADS-box genes VRN-H1, HvBM3, and HvBM8 which promote floral development. This suggests that HvFT4 functions as a repressor of reproductive development in barley. Unraveling the genetic basis of FT-like genes can contribute to the identification of novel breeding targets to modify reproductive development and thereby spike morphology and grain yield.

The lotus NnFTIP1 and NnFT1 regulate flowering time in Arabidopsis

In higher plants, floral signals are mainly collected and transduced to FLOWERING LOCUS T (FT) in Arabidopsis and its orthologues. The movement of FT from leaves to the shoot apical meristem (SAM) is partially mediated by FT-INTERACTING PROTEIN1 (FTIP1). Although the functions of OsFTIP1 in rice and DOFTIP1 in orchid in FT transport have also been investigated, the FTIP1 homologue in lotus (Nelumbo nucifera Gaertn.), a type of horticultural plant with high economic and cultural value, has not been isolated, and the mechanism of NnFT1 transport has not been explored. Here, we revealed that NnFTIP1 mediates the transport of NnFT1 in ectopic transgenic lines in Arabidopsis. Overexpression of NnFTIP1 in the ftip1-1 background rescued the late flowering phenotype of ftip1-1, indicating that NnFTIP1 has a conserved function as FTIP1. NnFTIP1 and NnFT1 share similar tissue expression patterns and subcellular localization. NnFTIP1 and NnFT1 interact both in vitro and in vivo. In addition, NnFTIP1 affects NnFT1 transport from leaves to the SAM. Furthermore, we found that NnUOF8, a MYB-like transcription factor, directly regulates the expression of NnFTIP1. Our results suggest that the functions of FTIP1 and FT are conserved during evolution in flowering plants.

Suppression of Phytochrome-Interacting Factors Enhances Photoresponses of Seedlings and Delays Flowering With Increased Plant Height in Brachypodium distachyon

Phytochromes are red and far-red photoreceptors that regulate plant growth and development under ambient light conditions. During phytochrome-mediated photomorphogenesis, phytochrome-interacting factors (PIFs) are the most important signaling partners that regulate the expression of light-responsive genes. However, the function of PIFs in monocots has not been studied well. In this study, using RNA interference (RNAi), we investigated the functions of BdPIL1 and BdPIL3, two PIF-like genes identified in Brachypodium distachyon, which are closely related to Arabidopsis PIF1 and PIF3. The expression of their genes is light-inducible, and both BdPIL1 and BdPIL3 proteins interact with phytochromes in an active form-specific manner. Transgenic Brachypodium seedlings with the RNAi constructs of BdPIL1 and BdPIL3 showed decreased coleoptile lengths and increased leaf growth when exposed to both red and far-red light. In addition, the transgenic plants were taller with elongated internodes than wild-type Bd21-3 plant, exhibiting late flowering. Moreover, RNA-seq analysis revealed downregulation of many genes in the transgenic plants, especially those related to the regulation of cell number, floral induction, and chlorophyll biosynthesis, which were consistent with the phenotypes of increased plant height, delayed flowering, and pale green leaves. Furthermore, we demonstrated the DNA-binding ability of BdPIL1 and BdPIL3 to the putative target promoters and that the DNA-binding was inhibited in the presence of phytochromes. Therefore, this study determines a molecular mechanism underlying phytochrome-mediated PIF regulation in Brachypodium, i.e., sequestration, and also elucidates the functions of BdPIL1 and BdPIL3 in the growth and development of the monocot plant.

Global analysis of SBP gene family in Brachypodium distachyon reveals its association with spike development

SQUAMOSA-promoter binding like proteins (SBPs/SPLs) are plant specific transcription factors targeted by miR156 and involved in various biological pathways, playing multi-faceted developmental roles. This gene family is not well characterized in Brachypodium. We identified a total of 18 SBP genes in B. distachyon genome. Phylogenetic analysis revealed that SBP gene family in Brachypodium expanded through large scale duplication. A total of 10 BdSBP genes were identified as targets of miR156. Transcript cleavage analysis of selected BdSBPs by miR156 confirmed their antagonistic connection. Alternative splicing was observed playing an important role in BdSBPs and miR156 interaction. Characterization of T-DNA Bdsbp9 mutant showed reduced plant growth and spike length, reflecting its involvement in the spike development. Expression of a majority of BdSBPs elevated during spikelet initiation. Specifically, BdSBP1 and BdSBP3 differentially expressed in response to vernalization. Differential transcript abundance of BdSBP1, BdSBP3, BdSBP8, BdSBP9, BdSBP14, BdSBP18 and BdSBP23 genes was observed during the spike development under high temperature. Co-expression network, protein-protein interaction and biological pathway analysis indicate that BdSBP genes mainly regulate transcription, hormone, RNA and transport pathways. Our work reveals the multi-layered control of SBP genes and demonstrates their association with spike development and temperature sensitivity in Brachypodium.

Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat

In Arabidopsis, CONSTANS (CO) integrates light and circadian clock signals to promote flowering under long days (LD). In the grasses, a duplication generated two paralogs designated as CONSTANS1 (CO1) and CONSTANS2 (CO2). Here we show that in tetraploid wheat plants grown under LD, combined loss-of-function mutations in the A and B-genome homeologs of CO1 and CO2 (co1 co2) result in a small (3 d) but significant (P<0.0001) acceleration of heading time both in PHOTOPERIOD1 (PPD1) sensitive (Ppd-A1b, functional ancestral allele) and insensitive (Ppd-A1a, functional dominant allele) backgrounds. Under short days (SD), co1 co2 mutants headed 13 d earlier than the wild type (P<0.0001) in the presence of Ppd-A1a. However, in the presence of Ppd-A1b, spikes from both genotypes failed to emerge by 180 d. These results indicate that CO1 and CO2 operate mainly as weak heading time repressors in both LD and SD. By contrast, in ppd1 mutants with loss-of-function mutations in both PPD1 homeologs, the wild type Co1 allele accelerated heading time >60 d relative to the co1 mutant allele under LD. We detected significant genetic interactions among CO1, CO2 and PPD1 genes on heading time, which were reflected in complex interactions at the transcriptional and protein levels. Loss-of-function mutations in PPD1 delayed heading more than combined co1 co2 mutations and, more importantly, PPD1 was able to perceive and respond to differences in photoperiod in the absence of functional CO1 and CO2 genes. Similarly, CO1 was able to accelerate heading time in response to LD in the absence of a functional PPD1. Taken together, these results indicate that PPD1 and CO1 are able to respond to photoperiod in the absence of each other, and that interactions between these two photoperiod pathways at the transcriptional and protein levels are important to fine-tune the flowering response in wheat.

Understanding Past, and Predicting Future, Niche Transitions based on Grass Flowering Time Variation

Since their origin in the early Cretaceous, grasses have diversified across every continent on Earth, with a handful of species (rice [Oryza sativa], maize [Zea mays], and wheat [Triticum aestivum]) providing most of the caloric intake of contemporary humans and their livestock. The ecological dominance of grasses can be attributed to a number of physiological innovations, many of which contributed to shifts from closed to open habitats that incur daily (e.g. tropical mountains) and/or seasonal extremes in temperature (e.g. temperate/continental regions) and precipitation (e.g. tropical savannas). In addition to strategies that allow them to tolerate or resist periodically stressful environments, plants can adopt escape behaviors by modifying the relative timing of distinct development phases. Flowering time is one of these behaviors that can also act as a postzygotic barrier to reproduction and allow temporal partitioning of resources to promote coexistence. In this review, we explore what is known about the phylogenetic pattern of flowering control in grasses, and how this relates to broad- and fine-scale niche transitions within the family. We then synthesize recent findings on the genetic basis of flowering time evolution as a way to begin deciphering why certain aspects of flowering are seemingly so conserved, and what the implications of this are for future adaptation under climate change.

Effect of phyB and phyC loss-of-function mutations on the wheat transcriptome under short and long day photoperiods

BACKGROUND

Photoperiod signals provide important cues by which plants regulate their growth and development in response to predictable seasonal changes. Phytochromes, a family of red and far-red light receptors, play critical roles in regulating flowering time in response to changing photoperiods. A previous study showed that loss-of-function mutations in either PHYB or PHYC result in large delays in heading time and in the differential regulation of a large number of genes in wheat plants grown in an inductive long day (LD) photoperiod.

RESULTS

We found that under non-inductive short-day (SD) photoperiods, phyB-null and phyC-null mutants were taller, had a reduced number of tillers, longer and wider leaves, and headed later than wild-type (WT) plants. The delay in heading between WT and phy mutants was greater in LD than in SD, confirming the importance of PHYB and PHYC in accelerating heading date in LDs. Both mutants flowered earlier in SD than LD, the inverse response to that of WT plants. In both SD and LD photoperiods, PHYB regulated more genes than PHYC. We identified subsets of differentially expressed and alternatively spliced genes that were specifically regulated by PHYB and PHYC in either SD or LD photoperiods, and a smaller set of genes that were regulated in both photoperiods. We found that photoperiod had a contrasting effect on transcript levels of the flowering promoting genes VRN-A1 and PPD-B1 in phyB and phyC mutants compared to the WT.

CONCLUSIONS

Our study confirms the major role of both PHYB and PHYC in flowering promotion in LD conditions. Transcriptome characterization revealed an unexpected reversion of the wheat LD plants into SD plants in the phyB-null and phyC-null mutants and identified flowering genes showing significant interactions between phytochromes and photoperiod that may be involved in this phenomenon. Our RNA-seq data provides insight into light signaling pathways in inductive and non-inductive photoperiods and a set of candidate genes to dissect the underlying developmental regulatory networks in wheat.

A CRISPR/Cas9-Based Mutagenesis Protocol for Brachypodium distachyon and Its Allopolyploid Relative, Brachypodium hybridum

The CRISPR/Cas9 system enables precise genome editing and is a useful tool for functional genomic studies. Here we report a detailed protocol for targeted genome editing in the model grass Brachypodium distachyon and its allotetraploid relative B. hybridum, describing gRNA design, a transient protoplast assay to test gRNA efficiency, Agrobacterium-mediated transformation and the selection and analysis of regenerated plants. In B. distachyon, we targeted the gene encoding phytoene desaturase (PDS), which is a crucial enzyme in the chlorophyll biosynthesis pathway. The albino phenotype of mutants obtained confirmed the effectiveness of the protocol for functional gene analysis. Additionally, we targeted two genes related to cell wall maintenance, encoding a fasciclin-like arabinogalactan protein (FLA) and a pectin methylesterase (PME), also in B. distachyon. Two genes encoding cyclin-dependent kinases (CDKG1 and CDKG2), which may be involved in DNA recombination were targeted in both B. distachyon and B. hybridum. Cas9 activity induces mainly insertions or deletions, resulting in frameshift mutations that, may lead to premature stop codons. Because of the close phylogenetic relationship between Brachypodium species and key temperate cereals and forage grasses, this protocol should be easily adapted to target genes underpinning agronomically important traits.

An Insertion Mutation in Bra032169 Encoding a Histone Methyltransferase Is Responsible for Early Bolting in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Bolting is an important agronomic character of the Chinese cabbage, but premature bolting can greatly reduce its commercial value, yield, and quality. Here, early-bolting mutant 1 (ebm1) was obtained from a Chinese cabbage doubled haploid (DH) line "FT," by using an isolated microspore culture and ethyl methanesulfonate (EMS) mutagenesis. The ebm1 was found to bolt extremely earlier than the wild type "FT." Genetic analysis indicated that the phenotype of the ebm1 was controlled by a single recessive nuclear gene. Using a mapping population of 1,502 recessive homozygous F2 individuals with the ebm1 phenotype, the ebm1 gene was mapped to between the markers SSRhl-53 and SSRhl-61 on chromosome A04 by using SSR markers, and its physical distance was 73.4 kb. Seven genes were predicted in the target region and then cloned and sequenced; the only difference in the sequences of the ebm1 and "FT" genes was with Bra032169. Unlike that in "FT," the Bra032169 in ebm1 had a novel 53 bp insertion that caused the termination of amino acid coding. The mutation was not consistent with EMS mutagenesis, and thus, may have been caused by spontaneous mutations during the microspore culture. Based on the gene annotation information, Bra032169 was found to encode the histone methyltransferase CURLY LEAF (CLF) in Arabidopsis thaliana. CLF regulates the expression of flowering-related genes. Further genotyping revealed that the early-bolting phenotype was fully co-segregated with the insertion mutation, suggesting that Bra032169 was the most likely candidate gene for ebm1. No significant differences were noted in the Bra032169 expression levels between the ebm1 and "FT." However, the expression levels of the flowering-related genes FLC, FT, AG, and SEP3 were significantly higher in the ebm1 than in the "FT." Thus, the mutation of Bra032169 is responsible for the early-bolting trait in Chinese cabbage. These results provide foundation information to help understand the molecular mechanisms of bolting in the Chinese cabbage.

In Vitro Tissue Culture in Brachypodium: Applications and Challenges

Brachypodium distachyon has become an excellent model for plant breeding and bioenergy grasses that permits many fundamental questions in grass biology to be addressed. One of the constraints to performing research in many grasses has been the difficulty with which they can be genetically transformed and the generally low frequency of such transformations. In this review, we discuss the contribution that transformation techniques have made in Brachypodium biology as well as how Brachypodium could be used to determine the factors that might contribute to transformation efficiency. In particular, we highlight the latest research on the mechanisms that govern the gradual loss of embryogenic potential in a tissue culture and propose using B. distachyon as a model for other recalcitrant monocots.

Pesticide application has little influence on coding and non-coding gene expressions in rice

Background

Agricultural insects are one of the major threats to crop yield. It is a known fact that pesticide application is an extensive approach to eliminate insect pests, and has severe adverse effects on environment and ecosystem; however, there is lack of knowledge whether it could influence the physiology and metabolic processes in plants.

Results

Here, we systemically analyzed the transcriptomic changes in rice after a spray of two commercial pesticides, Abamectin (ABM) and Thiamethoxam (TXM). We found only a limited number of genes (0.91%) and (1.24%) were altered by ABM and TXM respectively, indicating that these pesticides cannot dramatically affect the performance of rice. Nevertheless, we characterized 1140 Differentially Expressed Genes (DEGs) interacting with 105 long non-coding RNAs (lncRNAs) that can be impacted by the two pesticides, suggesting their certain involvement in response to farm chemicals. Moreover, we detected 274 alternative splicing (AS) alterations accompanied by host genes expressions, elucidating a potential role of AS in control of gene transcription during insecticide spraying. Finally, we identified 488 transposons that were significantly changed with pesticides treatment, leading to a variation in adjacent coding or non-coding transcripts.

Conclusion

Altogether, our results provide valuable insights into pest management through appropriate timing and balanced mixture, these pesticides have no harmful effects on crop physiology over sustainable application of field drugs.

Expression Pattern of FT/TFL1 and miR156-Targeted SPL Genes Associated with Developmental Stages in Dendrobium catenatum

Time to flower, a process either referring to juvenile-adult phase change or vegetative-reproductive transition, is strictly controlled by an intricate regulatory network involving at least both FT/TFL1 and the micro RNA (miR)156-regulated SPL family members. Despite substantial progresses recently achieved in Arabidopsis and other plant species, information regarding the involvement of these genes during orchid development and flowering competence is still limited. Dendrobium catenatum, a popular orchid species, exhibits a juvenile phase of at least three years. Here, through whole-genome mining and whole-family expression profiling, we analyzed the homologous genes of FT/TFL1, miR156, and SPL with special reference to the developmental stages. The FT/TFL1 family contains nine members; among them, DcHd3b transcribes abundantly in young and juvenile tissues but not in adult, contrasting with the low levels of others. We also found that mature miR156, encoded by a single locus, accumulated in large quantity in protocorms and declined by seedling development, coincident with an increase in transcripts of three of its targeted SPL members, namely DcSPL14, DcSPL7, and DcSPL18. Moreover, among the seven predicted miR156-targeted SPLs, only DcSPL3 was significantly expressed in adult plants and was associated with plant maturation. Our results might suggest that the juvenile phase change or maturation in this orchid plant likely involves both the repressive action of a TFL1-like pathway and the promotive effect from an SPL3-mediated mechanism.