Auxin and carbohydrate control flower bud development in Anthurium andraeanum during early stage of sexual reproduction

BACKGROUND

Flower buds of Anthurium andraeanum frequently cease to grow and abort during the early flowering stage, resulting in prolonged planting times and increased commercialization costs. Nevertheless, limited knowledge exists of the mechanism of flower development after initiation in A. andraeanum.

RESULTS

In this study, the measurement of carbohydrate flow and intensity between leaves and flowers during different growth stages showed that tender leaves are strong sinks and their concomitant flowers are weak ones. This suggested that the tender leaves compete with their concomitant flower buds for carbohydrates during the early growth stages, potentially causing the abortion of the flower buds. The analysis of transcriptomic differentially expressed genes suggested that genes related to sucrose metabolism and auxin response play an important role during flower bud development. Particularly, co-expression network analysis found that AaSPL12 is a hub gene engaged in flower development by collaborating carbohydrate and auxin signals. Yeast Two Hybrid assays revealed that AaSPL12 can interact with AaARP, a protein that serves as an indicator of dormancy. Additionally, the application of exogenous IAA and sucrose can suppress the expression of AaARP, augment the transcriptional abundance of AaSPL12, and consequently expedite flower development in Anthurium andraeanum.

CONCLUSIONS

Collectively, our findings indicated that the combination of auxin and sugar signals could potentially suppress the repression of AaARP protein to AaSPL12, thus advancing the development of flower buds in Anthurium andraeanum.

Life under the snow: A year-round transcriptome analysis of Antarctic mosses in natural habitats provides insight into the molecular adaptation of plants under extreme environment

Mosses are vital components of ecosystems, exhibiting remarkable adaptability across diverse habitats from deserts to polar ice caps. Sanionia uncinata (Hedw.) Loeske, a dominant Antarctic moss survives extreme environmental condition through perennial lifecycles involving growth and dormancy alternation. This study explores genetic controls and molecular mechanisms enabling S. uncinata to cope with seasonality of the Antarctic environment. We analysed the seasonal transcriptome dynamics of S. uncinata collected monthly from February 2015 to January 2016 in King George Island, Antarctica. Findings indicate that genes involved in plant growth were predominantly upregulated in Antarctic summer, while those associated with protein synthesis and cell cycle showed marked expression during the winter-to-summer transition. Genes implicated in cellular stress and abscisic acid signalling were highly expressed in winter. Further, validation included a comparison of the Antarctic field transcriptome data with controlled environment simulation of Antarctic summer and winter temperatures, which revealed consistent gene expression patterns in both datasets. This proposes a seasonal gene regulatory model of S. uncinate to understand moss adaptation to extreme environments. Additionally, this data set is a valuable resource for predicting genetic responses to climatic fluctuations, enhancing our knowledge of Antarctic flora's resilience to global climate change.

Dormancy-Associated Gene 1 (OsDRM1) as an axillary bud dormancy marker: Retarding Plant Development, and Modulating Auxin Response in Rice (Oryza sativa L.)

Dormancy-Associated Genes 1/Auxin-Repressed Proteins (DRM1/ARP) are associated with bud dormancy, repression of plant growth, and responsiveness to hormones. To further explore the function of DRM1 proteins in rice, we isolated a dormancy-associated gene1 (OsDRM1) through microarray analysis. In situ hybridization analyses revealed that OsDRM1 is predominantly expressed in dormant axillary buds, while it is weakly expressed in growing buds, indicating that OsDRM1 gene can be used as a molecular marker for bud dormancy in rice. Overexpression of OsDRM1 in transgenic plants delayed axillary bud outgrowth by suppressing cell division within the buds. Further studies in OsDRM1-overexpressing transgenic plants showed a reduction in plant height, inhibition of root and hypocotyl elongation, and delayed heading time. Under auxin treatment, overexpression of OsDRM1 in transgenic lines partially rescued the shortened length of the primary and crown root. Taken together, these results indicated that OsDRM1 delayed bud growth by arresting the cell cycle and act as a growth repressor affect rice development by modulated auxin signaling.

Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence

Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.

Molecular Cues for Phenological Events in the Flowering Cycle in Avocado

Reproductively mature horticultural trees undergo an annual flowering cycle that repeats each year of their reproductive life. This annual flowering cycle is critical for horticultural tree productivity. However, the molecular events underlying the regulation of flowering in tropical tree crops such as avocado are not fully understood or documented. In this study, we investigated the potential molecular cues regulating the yearly flowering cycle in avocado for two consecutive crop cycles. Homologues of flowering-related genes were identified and assessed for their expression profiles in various tissues throughout the year. Avocado homologues of known floral genes FT, AP1, LFY, FUL, SPL9, CO and SEP2/AGL4 were upregulated at the typical time of floral induction for avocado trees growing in Queensland, Australia. We suggest these are potential candidate markers for floral initiation in these crops. In addition, DAM and DRM1, which are associated with endodormancy, were downregulated at the time of floral bud break. In this study, a positive correlation between CO activation and FT in avocado leaves to regulate flowering was not seen. Furthermore, the SOC1-SPL4 model described in annual plants appears to be conserved in avocado. Lastly, no correlation of juvenility-related miRNAs miR156, miR172 with any phenological event was observed.

Amomum tsaoko DRM1 regulate seed germination and improve heat tolerance in Arabidopsis

Seed dormancy and germination are critical to medicinal plant reproduction. Dormancy-associated gene (DRM1) has been involved in the regulation of dormancy in Arabidopsis meristematic tissues or organs. However, research on molecular functions and regulations of DRM1 in Amomum tsaoko, an important medicinal plant, is rare. In this study, the DRM1 was isolated from embryos of A. tsaoko, and the results of protein subcellular localization in Arabidopsis protoplast indicated that DRM1 was mainly nucleus and cytoplasm. Expression analysis showed that DRM1 especially exhibited the highest transcript level in dormant seed and short-time stratification while displaying a high response of hormone and abiotic stress. Further investigation showed that ectopic expression of DRM1 in Arabidopsis exhibited delayed seed germination and germination capability to high temperatures. Additionally, DRM1 transgenic Arabidopsis exhibited increased tolerance to heat stress by enhancing antioxidative capacities and regulating stress-associated genes (AtHsp25.3-P, AtHsp18.2-CI, AtHsp70B, AtHsp101, AtGolS1, AtMBF1c, AtHsfA2, AtHsfB1 and AtHsfB2). Overall, our results reveal the role of DRM1 in seed germination and abiotic stress response.

Combined Transcriptomic and Metabolomic Analysis Reveals Insights into Resistance of Arabidopsis bam3 Mutant against the Phytopathogenic Fungus Fusarium oxysporum

The wilt-inducing strains of Fusarium oxysporum are responsible for severe damage to many economically important plant species. The most cost-effective and environmentally safe method for the management of Fusarium wilt is the use of resistant cultivars when they are available. In the present study, the Arabidopsis genotype with disruptions in the β-amylase 3 (BAM3) gene, which encodes the major hydrolytic enzyme that degrades starch to maltose, had significantly lower susceptibility to Fusarium oxysporum f. sp. raphani (For) compared to wild-type (wt) plants. It showed the lowest disease severity and contained reduced quantities of fungal DNA in the plant vascular tissues when analyzed with real-time PCR. Through metabolomic analysis using gas chromatography (GC)-mass spectrometry (MS) and gene-expression analysis by reverse-transcription quantitative PCR (RT-qPCR), we observed that defense responses of Arabidopsis bam3 mutants are associated with starch-degradation enzymes, the corresponding modification of the carbohydrate balance, and alterations in sugar (glucose, sucrose, trehalose, and myo-inositol) and auxin metabolism.

Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects

A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.

Comparative Transcriptome Analysis of Grafted Tomato with Drought Tolerance

Grafting is a method used in agriculture to improve crop production and tolerance to biotic and abiotic stress. This technique is widely used in tomato, Solanum lycopersicum L.; however, the effects of grafting on changes in gene expression associated with stress tolerance in shoot apical meristem cells are still under-discovered. To clarify the effect of grafting, we performed a transcriptomic analysis between non-grafted and grafted tomatoes using the tomato variety Momotaro-scion and rootstock varieties, TD1, GS, and GF. Drought tolerance was significantly improved not only by a combination of compatible resistant rootstock TD1 but also by self-grafted compared to non-grafted lines. Next, we found the differences in gene expression between grafted and non-grafted plants before and during drought stress treatment. These altered genes are involved in the regulation of plant hormones, stress response, and cell proliferation. Furthermore, when comparing compatible (Momo/TD1 and Momo/Momo) and incompatible (Momo/GF) grafted lines, the incompatible line reduced gene expression associated with phytohormones but increased in wounding and starvation stress-response genes. These results conclude that grafting generates drought stress tolerance through several gene expression changes in the apical meristem.

Biocontrol Methods in Avoidance and Downsizing of Mycotoxin Contamination of Food Crops

By increasing the resistance of seeds against abiotic and biotic stress, the possibility of cereal mold contamination and hence the occurrence of secondary mold metabolites mycotoxins decreases. The use of biological methods of seed treatment represents a complementary strategy, which can be implemented as an environmental-friendlier approach to increase the agricultural sustainability. Whereas the use of resistant cultivars helps to reduce mold growth and mycotoxin contamination at the very beginning of the production chain, biological detoxification of cereals provides additional weapons against fungal pathogens in the later stage. Most efficient techniques can be selected and combined on an industrial scale to reduce losses and boost crop yields and agriculture sustainability, increasing at the same time food and feed safety. This paper strives to emphasize the possibility of implementation of biocontrol methods in the production of resistant seeds and the prevention and reduction in cereal mycotoxin contamination.

Morphological, phenological, and transcriptional analyses provide insight into the diverse flowering traits of a mutant of the relic woody plant Liriodendron chinense

Flowering is crucial to plant reproduction and controlled by multiple factors. However, the mechanisms underlying the regulation of flowering in perennial plants are still largely unknown. Here, we first report a super long blooming 1 (slb1) mutant of the relict tree Liriodendron chinense possessing a prolonged blooming period of more than 5 months, in contrast to the 1 month blooming period in the wild type (WT). Phenotypic characterization showed that earlier maturation of lateral shoots was caused by accelerated axillary bud fate, leading to the phenotype of continuous flowering in slb1 mutants. The transcriptional activity of genes related to hormone signaling (auxin, cytokinin, and strigolactone), nutrient availability, and oxidative stress relief further indicated active outgrowth of lateral buds in slb1 mutants. Interestingly, we discovered a unique FT splicing variant with intron retention specific to slb1 mutants, representing a potential causal mutation in the slb1 mutants. Surprisingly, most slb1 inbred offspring flowered precociously with shorter juvenility (~4 months) than that (usually 8-10 years) required in WT plants, indicating heritable variation underlying continuous flowering in slb1 mutants. This study reports an example of a perennial tree mutant that flowers continuously, providing a rare resource for both breeding and genetic research.

Integrated Signals of Jasmonates, Sugars, Cytokinins and Auxin Influence the Initial Growth of the Second Buds of Chrysanthemum after Decapitation

Decapitation is common in horticulture for altering plant architecture. The decapitation of chrysanthemum plants breaks apical dominance and leads to more flowers on lateral branches, resulting in landscape flowers with good coverage. We performed both third- and second-generation transcriptome sequencing of the second buds of chrysanthemum. This third-generation transcriptome is the first sequenced third-generation transcriptome of chrysanthemum, revealing alternative splicing events, lncRNAs, and transcription factors. Aside from the classic hormones, the expression of jasmonate-related genes changed because of this process. Sugars also played an important role in this process, with upregulated expression of sucrose transport-related and TPS genes. We constructed a model of the initial growth of the second buds after decapitation. Auxin export and sugar influx activated the growth of these buds, while the JA-Ile caused by wounding inhibited the expression of CycD genes from 0 h to 6 h. After wound recovery, cytokinins accumulated in the second buds and might have induced ARR12 expression to upregulate CycD gene expression from 6 h to 48 h, together with sugars. Therefore, jasmonates, cytokinins, sugars, and auxin work together to determine the fate of the buds of plants with short internodes, such as chrysanthemum.

Gene co-expression analysis of tomato seed maturation reveals tissue-specific regulatory networks and hubs associated with the acquisition of desiccation tolerance and seed vigour

BACKGROUND

During maturation seeds acquire several physiological traits to enable them to survive drying and disseminate the species. Few studies have addressed the regulatory networks controlling acquisition of these traits at the tissue level particularly in endospermic seeds such as tomato, which matures in a fully hydrated environment and does not undergo maturation drying. Using temporal RNA-seq analyses of the different seed tissues during maturation, gene network and trait-based correlations were used to explore the transcriptome signatures associated with desiccation tolerance, longevity, germination under water stress and dormancy.

RESULTS

During maturation, 15,173 differentially expressed genes were detected, forming a gene network representing 21 expression modules, with 3 being specific to seed coat and embryo and 5 to the endosperm. A gene-trait significance measure identified a common gene module between endosperm and embryo associated with desiccation tolerance and conserved with non-endospermic seeds. In addition to genes involved in protection such LEA and HSP and ABA response, the module included antioxidant and repair genes. Dormancy was released concomitantly with the increase in longevity throughout fruit ripening until 14 days after the red fruit stage. This was paralleled by an increase in SlDOG1-2 and PROCERA transcripts. The progressive increase in seed vigour was captured by three gene modules, one in common between embryo and endosperm and two tissue-specific. The common module was enriched with genes associated with mRNA processing in chloroplast and mitochondria (including penta- and tetratricopeptide repeat-containing proteins) and post-transcriptional regulation, as well several flowering genes. The embryo-specific module contained homologues of ABI4 and CHOTTO1 as hub genes associated with seed vigour, whereas the endosperm-specific module revealed a diverse set of processes that were related to genome stability, defence against pathogens and ABA/GA response genes.

CONCLUSION

The spatio-temporal co-expression atlas of tomato seed maturation will serve as a valuable resource for the in-depth understanding of the dynamics of gene expression associated with the acquisition of seed vigour at the tissue level.

Plant stem-cell organization and differentiation at single-cell resolution

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.

Plant stem-cell organization and differentiation at single-cell resolution

Plants possess the remarkable ability to grow and produce new organs throughout their lifespan, owing to the activities of persistent populations of pluripotent stem cells within their meristematic tips. Here we isolated individual cells from the microscopic shoot apical meristem (SAM) of maize and provide single-cell transcriptomic analysis of a plant shoot meristem. This study enabled an unbiased analysis of the developmental genetic organization of the maize shoot apex and uncovered evolutionarily divergent and conserved signatures of SAM homeostasis. The fine-scale resolution of single-cell analysis was used to reconstruct the process of shoot cell differentiation, whereby stem cells acquire diverse and distinct cell fates over developmental time in wild-type and mutant maize seedlings.

Plants maintain populations of pluripotent stem cells in shoot apical meristems (SAMs), which continuously produce new aboveground organs. We used single-cell RNA sequencing (scRNA-seq) to achieve an unbiased characterization of the transcriptional landscape of the maize shoot stem-cell niche and its differentiating cellular descendants. Stem cells housed in the SAM tip are engaged in genome integrity maintenance and exhibit a low rate of cell division, consistent with their contributions to germline and somatic cell fates. Surprisingly, we find no evidence for a canonical stem-cell organizing center subtending these cells. In addition, trajectory inference was used to trace the gene expression changes that accompany cell differentiation, revealing that ectopic expression of KNOTTED1 (KN1) accelerates cell differentiation and promotes development of the sheathing maize leaf base. These single-cell transcriptomic analyses of the shoot apex yield insight into the processes of stem-cell function and cell-fate acquisition in the maize seedling and provide a valuable scaffold on which to better dissect the genetic control of plant shoot morphogenesis at the cellular level.

The Evening Complex and the Chromatin-Remodeling Factor PICKLE Coordinately Control Seed Dormancy by Directly Repressing DOG1 in Arabidopsis

Primary seed dormancy is acquired during seed development and maturation, which is important for plant fitness and survival. DELAY OF GERMINATION1 (DOG1) plays a critical role in inducing seed dormancy. DOG1 expression increases rapidly during seed development, but the precise mechanism underlying this process remains elusive. In this study, we showed that mutants with a loss or reduced function of the chromatin-remodeling factor PICKLE (PKL) exhibit increased seed dormancy. PKL associates with DOG1 chromatin and inhibits its transcription. We found that PKL physically interacts with LUX ARRHYTHMO (LUX), a member of the evening complex (EC) of the circadian clock. Furthermore, LUX directly binds to a specific coding sequence of DOG1, and DOG1 acts genetically downstream of PKL and LUX. Mutations in either LUX or EARLY FLOWERING3 (ELF3) encoding another member of the EC led to increased DOG1 expression and enhanced seed dormancy. Surprisingly, these phenotypes were abolished when the parent plants were grown under continuous light. In addition, we observed that loss of function of either PKL or LUX decreased H3K27me3 levels at the DOG1 locus. Taken together, our study reveals a regulatory mechanism in which EC proteins coordinate with PKL to transmit circadian signals for directly regulating DOG1 expression and seed dormancy during seed development.

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.

Regulation of Aegilops tauschii Coss Tiller Bud Growth by Plant Density: Transcriptomic, Physiological and Phytohormonal Responses

Aegilops tauschii Coss is one of the most hazardous weeds that severely infests wheat fields in China. The tillering ability of Ae. tauschii strongly affects the occurrence and spread by influencing its seed output. In this study, Ae. tauschii was sown at low plant density (LPD) and high plant density (HPD) to investigate the effect of plant density on tiller bud outgrowth and its potential regulators using RNA-Seq. Additionally, the chlorophyll content and photosynthesis, soluble sugar and phytohormone levels were also determined at different plant densities. The results showed that an increased plant density significantly inhibited the elongation of tiller buds in the axil of the first leaf at 15 days after planting, with 7.69 mm at LPD and 1.69 mm at HPD. A total of seven putative tiller-related genes were selected and validated using quantitative real-time PCR. Furthermore, chlorophyll levels, photosynthetic efficiency, and soluble sugar contents were distinctly inhibited by HPD in Ae. tauschii, which may be responsible for the restriction of tiller bud growth. In addition, differentially expressed genes (DEGs) were markedly enriched in indole-3-acetic acid (IAA), abscisic acid (ABA), and gibberellin metabolism and signaling. Accordingly, the levels of ABA and gibberellin A3 in Ae. tauschii were strikingly higher at HPD compared with those at LPD, yet the reverse tendency was observed for IAA. Undoubtedly, such results will be highly beneficial for illuminating the underlying regulators of the Ae. tauschii tillering response to plant density and may provide new ideas for the control of this weed in the future.

The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

BACKGROUND

The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth.

RESULTS

In this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH[Formula: see text] treated samples, ACLA-3 gene is up-regulated in samples treated with NO[Formula: see text] and with both NH[Formula: see text] and NO[Formula: see text], which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO[Formula: see text]. These potentially enhance the integrity and recover the growth of Panax notoginseng roots.

CONCLUSION

These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.

Developmental analysis of the early steps in strigolactone-mediated axillary bud dormancy in rice

By contrast with rapid progress in understanding the mechanisms of biosynthesis and signaling of strigolactone (SL), mechanisms by which SL inhibits axillary bud outgrowth are less well understood. We established a rice (Oryza sativa L.) hydroponic culture system to observe axillary buds at the critical point when the buds enter the dormant state. In situ hybridization analysis indicated that cell division stops in the leaf primordia of the buds entering dormancy. We compared transcriptomes in the axillary buds isolated by laser capture microdissection before and after entering the dormant state and identified genes that are specifically upregulated or downregulated in dormant buds respectively, in SL-mediated axillary bud dormancy. Typically, cell cycle genes and ribosomal genes are included among the active genes while abscisic acid (ABA)-inducible genes are among the dormant genes. Application of ABA to the hydroponic culture suppressed the growth of axillary buds of SL mutants to the same level as wild-type (WT) buds. Tiller number was decreased in the transgenic lines overexpressing OsNCED1, the gene that encodes ABA biosynthesis enzyme. These results indicated that the main site of SL function is the leaf primordia in the axillary bud and that ABA is involved in SL-mediated axillary bud dormancy.

Protein interference for regulation of gene expression in plants

Transcription factors (TFs) play a central role in the gene regulation associated with a plant's development and its response to the environmental factors. The work of TFs is well regulated at each stage of their activities. TFs usually consist of three protein domains required for DNA binding, dimerization, and transcriptional regulation. Alternative splicing (AS) produces multiple proteins with varying composition of domains. Recent studies have shown that AS of some TF genes form small proteins (small interfering peptide/small interfering protein, siPEP/siPRoT), which lack one or more domains and negatively regulate target TFs by the mechanism of protein interference (peptide interference/protein interference, PEPi/PROTi). The presence of an alternative form for the transcription factor CCA1 of Arabidopsis thaliana, has been shown to be involved in the regulation of the response to cold stress. For the PtFLC protein, one of the isoforms was found, which is formed as a result of alternative splicing and acts as a negative repressor, binding to the full-length TF PtFLC and therefore regulating the development of the Poncirus trifoliata. For A. thaliana, a FLM gene was found forming the FLM-б isoform, which acts as a dominant negative regulator and stimulates the development of the flower formation process due to the formation of a heterodimer with SVP TF. Small interfering peptides and proteins can actively participate in the regulation of gene expression, for example, in situations of stress or at different stages of plant development. Moreover, small interfering peptides and proteins can be used as a tool for fundamental research on the function of genes as well as for applied research for permanent or temporary knockout of genes. In this review, we have demonstrated recent studies related to siPEP/siPROT and their involvement in the response to various stresses, as well as possible ways to obtain small proteins.

Comparative transcriptomics provides novel insights into the mechanisms of selenium tolerance in the hyperaccumulator plant Cardamine hupingshanensis

Selenium (Se) is an essential mineral element for animals and humans. Cardamine hupingshanensis (Brassicaceae), found in the Wuling mountain area of China, has been identified as a novel Se hyperaccumulator plant. However, the mechanism for selenium tolerance in Cardamine plants remains unknown. In this study, two cDNA libraries were constructed from seedlings of C. hupingshanensis treated with selenite. Approximately 100 million clean sequencing reads were de novo assembled into 48,989 unigenes, of which 39,579 and 33,510 were expressed in the roots and leaves, respectively. Biological pathways and candidate genes involved in selenium tolerance mechanisms were identified. Differential expression analysis identified 25 genes located in four pathways that were significantly responsive to selenite in C. hupingshanensis seedlings. The results of RNA sequencing (RNA-Seq) and quantitative real-time PCR (RT-qPCR) confirmed that storage function, oxidation, transamination and selenation play very important roles in the selenium tolerance in C. hupingshanensis. Furthermore, a different degradation pathway synthesizing malformed or deformed selenoproteins increased selenium tolerance at different selenite concentrations. This study provides novel insights into the mechanisms of selenium tolerance in a hyperaccumulator plant, and should serve as a rich gene resource for C. hupingshanensis.

Comparative transcriptome analysis of the floral transition in Rosa chinensis 'Old Blush' and R. odorata var. gigantea

The floral transition is a crucial developmental event, but little is known about the underlying regulatory networks in seasonally and continuously flowering roses. In this study, we compared the genetic basis of flowering in two rose species, Rosa chinensis ‘Old Blush’, which flowers continuously, and R. odorata var. gigantea, which blooms in early spring. Gene ontology (GO) terms related to methylation, light reaction, and starch metabolism were enriched in R. odorata var. gigantea and terms associated with sugar metabolism were enriched in R. chinensis ‘Old Blush’ during the floral transition. A MapMan analysis revealed that genes involved in hormone signaling mediate the floral transition in both taxa. Furthermore, differentially expressed genes (DEGs) involved in vernalization, photoperiod, gibberellin (GA), and starch metabolism pathways converged on integrators, e.g., LFY, AGL24, SOC1, CAL, and COLs, to regulate the floral transition in R. odorata var. gigantea, while DEGs related to photoperiod, sugar metabolism, and GA pathways, including COL16, LFY, AGL11, 6PGDH, GASA4, and BAM, modulated the floral transition in R. chinensis ‘Old Blush.’ Our analysis of the genes underlying the floral transition in roses with different patterns of flowering provides a basis for further functional studies.

RWP-RK domain-containing transcription factors control cell differentiation during female gametophyte development in Arabidopsis

The formation of gametes is a prerequisite for any sexually reproducing organism in order to complete its life cycle. In plants, female gametes are formed in a multicellular tissue, the female gametophyte or embryo sac. Although the events leading to the formation of the female gametophyte have been morphologically characterized, the molecular control of embryo sac development remains elusive. We used single and double mutants as well as cell-specific marker lines to characterize a novel class of gene regulators in Arabidopsis thaliana, the RWP-RK domain-containing (RKD) transcription factors. Morphological and histological analyses were conducted using confocal laser scanning and differential interference contrast microscopy. Gene expression and transcriptome analyses were performed using quantitative reverse transcription-PCR and RNA sequencing, respectively. Our results showed that RKD genes are expressed during distinct stages of embryo sac development. Morphological analysis of the mutants revealed severe distortions in gametophyte polarity and cell differentiation. Transcriptome analysis revealed changes in the expression of several gametophyte-specific gene families (RKD2 and RKD3) and ovule development-specific genes (RKD3), and identified pleiotropic effects on phytohormone pathways (RKD5). Our data provide novel insight into the regulatory control of female gametophyte development. RKDs are involved in the control of cell differentiation and are required for normal gametophytic development.

Photosynthetic leaf area modulates tiller bud outgrowth in sorghum

Shoot branches or tillers develop from axillary buds. The dormancy versus outgrowth fates of buds depends on genetic, environmental and hormonal signals. Defoliation inhibits bud outgrowth indicating the role of leaf-derived metabolic factors such as sucrose in bud outgrowth. In this study, the sensitivity of bud outgrowth to selective defoliation was investigated. At 6 d after planting (6 DAP), the first two leaves of sorghum were fully expanded and the third was partially emerged. Therefore, the leaves were selectively defoliated at 6 DAP and the length of the bud in the first leaf axil was measured at 8 DAP. Bud outgrowth was inhibited by defoliation of only 2 cm from the tip of the second leaf blade. The expression of dormancy and sucrose-starvation marker genes was up-regulated and cell cycle and sucrose-inducible genes was down-regulated during the first 24 h post-defoliation of the second leaf. At 48 h, the expression of these genes was similar to controls as the defoliated plant recovers. Our results demonstrate that small changes in photosynthetic leaf area affect the propensity of tiller buds for outgrowth. Therefore, variation in leaf area and photosynthetic activity should be included when integrating sucrose into models of shoot branching.

DRM1 and DRM2 expression regulation: potential role of splice variants in response to stress and environmental factors in Arabidopsis

The DRM1/ARP gene family is increasingly exhibiting associations with stress conditions at the transcript level. Traditionally correlated with dormancy, increases in transcript levels in response to various treatments have also been reported in various species. As alternative transcript splicing is common in stress conditions, the splice variants of AtDRM1 and AtDRM2 were assessed further in this study. A previously undescribed splice variant of AtDRM1 (AtDRM1.6) is introduced in this work. In silico analyses of predicted protein sequence of all splice variants showed that all variants retain the predicted intrinsically disordered nature. Transcriptional studies of AtDRM1 and AtDRM2 in response to a wide range of abiotic, physical and hormonal treatments showed that AtDRM1.6 is differentially regulated at the transcriptional level compared with other splice variants. Promoter analyses demonstrated AtDRM1 light regulation via the upstream promoter sequence.