Maternal auxin supply contributes to early embryo patterning in Arabidopsis

Bacteria existing in pre-pollinated styles (silks) can defend the exposed male gamete fertilization channel of maize against an environmental Fusarium pathogen

In flowering plants, fertilization requires exposing maternal style channels to the external environment to capture pollen and transmit its resident sperm nuclei to eggs. This results in progeny seed. However, environmental fungal pathogens invade developing seeds through the style. We hypothesized that prior to environmental exposure, style tissue already possesses bacteria that can protect styles and seed from such pathogens. We further hypothesized that farmers have been inadvertently selecting immature styles over many generations to have such bacteria. We tested these hypotheses in maize, a wind-pollinated crop, which has unusually long styles (silks) that are invaded by the economically-important fungal pathogen Fusarium graminearum (Fg). Here, unpollinated silk-associated bacteria were cultured from a wild teosinte ancestor of maize and diverse maize landraces selected by indigenous farmers across the Americas, grown in a common Canadian field for one season. The bacteria were taxonomically classified using 16S rRNA sequencing. In total, 201 bacteria were cultured, spanning 29 genera, 63 species, and 62 unique OTUs, dominated by Pseudomonas, Pantoea and Microbacterium. These bacteria were tested for their ability to suppress Fg in vitro which identified 10 strains belonging to 6 species: Rouxiella badensis, Pantoea ananatis, Pantoea dispersa, Pseudomonas koreensis, Rahnella aquatilis, and Ewingella americana. Two anti-Fg strains were sprayed onto silks before/after Fg inoculation, resulting in ≤90% reductions in disease (Gibberella ear rot) and 70-100% reductions in associated mycotoxins (deoxynivalenol and zearalenone) in progeny seeds. These strains also protected progeny seeds post-harvest. Confocal fluorescent imaging showed that one silk bacterium (Rouxiella AS112) colonized susceptible entry points of Fg on living silks including stigmatic trichomes, wounds, and epidermal surfaces where they formed thick biofilms. Post-infection, AS112 was associated with masses of dead Fg hyphae. These results suggest that the maize style (silk) is endowed with potent bacteria from the mother plant to protect itself and progeny from Fusarium. The evidence suggests this trait may have been selected by specific indigenous peoples, though this interpretation requires further study.

The shift to 3D growth during embryogenesis of kelp species, atlas of cell division and differentiation of Saccharina latissima

In most organisms, 3D growth takes place at the onset of embryogenesis. In some brown algae, 3D growth occurs later in development, when the organism consists of several hundred cells. We studied the cellular events that take place when 3D growth is established in the embryo of the brown alga Saccharina, a kelp species. Semi-thin sections, taken from where growth shifts from 2D to 3D, show that 3D growth first initiates from symmetrical cell division in the monolayered lamina, and then is enhanced through a series of asymmetrical cell divisions in a peripheral monolayer of cells called the meristoderm. Then, daughter cells rapidly differentiate into cortical and medullary cells, characterised by their position, size and shape. In essence, 3D growth in kelps is based on a series of differentiation steps that occur rapidly after the initiation of a bilayered lamina, followed by further growth of the established differentiated tissues. Our study depicts the cellular landscape necessary to study cell-fate programming in the context of a novel mode of 3D growth in an organism phylogenetically distant from plants and animals.

The orchid seed coat: a developmental and functional perspective

Orchid seeds are 'dust-like.' The seed coat is usually thin, with only one to a few cell layers. It originates from the integuments formed during ovule development. In orchids, the outer integument is primarily responsible for forming a mature seed coat. The inner integument usually fails to develop after fertilization, becomes compressed, and collapses over the expanding embryo. Hence, the seed coat is formed from the funiculus, chalaza, and outer integumentary cells. The outermost layer of the seed coat, the testa, is lignified, usually at the radial and inner tangential walls. The subepidermal thin-walled layer(s), the tegmen, subsequently cold, resulting in seeds having only a single layer of seed coat cells. In some species, cells of the inner integument remain alive with the ability to synthesize and accumulate lipidic and or phenolic compounds in their walls covering the embryo. This cover is called the 'carapace,' a protective shield contributing to the embryo's added protection. A developmental and functional perspective of the integuments and seed coat during seed development and germination is presented in this review.

RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize

Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.

AUX1, PIN3, and TAA1 collectively maintain fertility in Arabidopsis

MAIN CONCLUSION

We found that auxin synthesis gene TAA1 and auxin polar transport genes AUX1 and PIN3 collectively maintain fertility and seed size in Arabidopsis. Auxin plays a vital role in plant gametophyte development and embryogenesis. The auxin synthesis gene TAA1 and the auxin polar transport genes AUX1 and PIN3 are expressed during Arabidopsis gametophyte and seed development. However, aux1, pin3, and taa1 single mutants only exhibit mild reproductive defects. We, therefore, generated aux1-T pin3 taa1-k2 and aux1-T pin3-2 taa1-k1 triple mutants by crossing or CRISPR/Cas9 technique. These triple mutants displayed severe reproductive defects with approximately 70% and 77%, respectively, of the siliques failing to elongate after anthesis. Reciprocal crosses and microscopy analyses showed that the development of pollen and ovules in the aux1 pin3 taa1 mutants was normal, whereas the filaments were remarkably short, which might be the cause of the silique sterility. Further analyses indicated that the development and morphology of aux1 pin3 taa1 seeds were normal, but their size was smaller compared with that of the wild type. These results indicate that AUX1, PIN3, and TAA1 act in concert to maintain fertility and seed size in Arabidopsis.

Hormonal regulation of anthocyanin biosynthesis for improved stress tolerance in plants

Due to unprecedented climate change, rapid industrialization and increasing use of agrochemicals, abiotic stress, such as drought, low temperature, high salinity and heavy metal pollution, has become an increasingly serious problem in global agriculture. Anthocyanins, an important plant pigment, are synthesized through the phenylpropanoid pathway and have a variety of physiological and ecological functions, providing multifunctional and effective protection for plants under stress. Foliar anthocyanin accumulation often occurs under abiotic stress including high light, cold, drought, salinity, nutrient deficiency and heavy metal stress, causing leaf reddening or purpling in many plant species. Anthocyanins are used as sunscreens and antioxidants to scavenge reactive oxygen species (ROS), as metal(loid) chelators to mitigate heavy metal stress, and as crucial molecules with a role in delaying leaf senescence. In addition to environmental factors, anthocyanin synthesis is affected by various endogenous factors. Plant hormones such as abscisic acid, jasmonic acid, ethylene and gibberellin have been shown to be involved in regulating anthocyanin synthesis either positively or negatively. Particularly when plants are under abiotic stress, several plant hormones can induce foliar anthocyanin synthesis to enhance plant stress resistance. In this review, we revisit the role of plant hormones in anthocyanin biosynthesis and the mechanism of plant hormone-mediated anthocyanin accumulation and abiotic stress tolerance. We conclude that enhancing anthocyanin content with plant hormones could be a prospective management strategy for improving plant stress resistance, but extensive further research is essentially needed to provide future guidance for practical crop production.

Opposite Auxin Dynamics Determine the Gametophytic and Embryogenic Fates of the Microspore

The microspore can follow two different developmental pathways. In vivo microspores follow the gametophytic program to produce pollen grains. In vitro, isolated microspores can be reprogrammed by stress treatments and follow the embryogenic program, producing doubled-haploid embryos. In the present study, we analyzed the dynamics and role of endogenous auxin in microspore development during these two different scenarios, in Brassica napus. We analyzed auxin concentration, cellular accumulation, the expression of the TAA1 auxin biosynthesis gene, and the PIN1-like efflux carrier gene, as well as the effects of inhibiting auxin biosynthesis by kynurenine on microspore embryogenesis. During the gametophytic pathway, auxin levels and TAA1 and PIN1-like expression were high at early stages, in tetrads and tapetum, while they progressively decreased during gametogenesis in both pollen and tapetum cells. In contrast, in microspore embryogenesis, TAA1 and PIN1-like genes were upregulated, and auxin concentration increased from the first embryogenic divisions. Kynurenine treatment decreased both embryogenesis induction and embryo production, indicating that auxin biosynthesis is required for microspore embryogenesis initiation and progression. The findings indicate that auxin exhibits two opposite profiles during these two microspore developmental pathways, which determine the different cell fates of the microspore.

Transcriptome Landscape Analyses of the Regulatory Network for Zygotic Embryo Development in Paeonia ostii

Paeonia ostii is a worldwide ornamental flower and an emerging oil crop. Zyotic embryogenesis is a critical process during seed development, and it can provide a basis for improving the efficiency of somatic embryogenesis (SE). In this study, transcriptome sequencing of embryo development was performed to investigate gene expression profiling in P. ostii and identified Differentially expressed genes (DEGs) related to transcription factors, plant hormones, and antioxidant enzymes. The results indicated that IAA (Indole-3-acetic acid), GA (Gibberellin), BR (Brassinosteroid) and ETH (Ethylene) were beneficial to early embryonic morphogenesis, while CTK (Cytokinin) and ABA (Abscisic Acid) promoted embryo morphogenesis and maturation. The antioxidant enzymes' activity was the highest in early embryos and an important participant in embryo formation. The high expression of the genes encoding fatty acid desaturase was beneficial to fast oil accumulation. Representative DEGs were selected and validated using qRT-PCR. Protein-protein interaction network (PPI) was predicted, and six central node proteins, including AUX1, PIN1, ARF6, LAX3, ABCB19, PIF3, and PIF4, were screened. Our results provided new insights into the formation of embryo development and even somatic embryo development in tree peonies.

Transcriptome analysis of ovules offers early developmental clues after fertilization in Cicer arietinum L

Chickpea (Cicer arietinum L.) seeds are valued for their nutritional scores and limited information on the molecular mechanisms of chickpea fertilization and seed development is available. In the current work, comparative transcriptome analysis was performed on two different stages of chickpea ovules (pre- and post-fertilization) to identify key regulatory transcripts. Two-staged transcriptome sequencing was generated and over 208 million reads were mapped to quantify transcript abundance during fertilization events. Mapping to the reference genome showed that the majority (92.88%) of high-quality Illumina reads were aligned to the chickpea genome. Reference-guided genome and transcriptome assembly yielded a total of 28,783 genes. Of these, 3399 genes were differentially expressed after the fertilization event. These involve upregulated genes including a protease-like secreted in CO(2) response (LOC101500970), amino acid permease 4-like (LOC101506539), and downregulated genes MYB-related protein 305-like (LOC101493897), receptor like protein 29 (LOC101491695). WGCNA analysis and pairwise comparison of datasets, successfully constructed four co-expression modules. Transcription factor families including bHLH, MYB, MYB-related, C2H2 zinc finger, ERF, WRKY and NAC transcription factor were also found to be activated after fertilization. Activation of these genes and transcription factors results in the accumulation of carbohydrates and proteins by enhancing their trafficking and biosynthesis. Total 17 differentially expressed genes, were randomly selected for qRT-PCR for validation of transcriptome analysis and showed statistically significant correlations with the transcriptome data. Our findings provide insights into the regulatory mechanisms underlying changes in fertilized chickpea ovules. This work may come closer to a comprehensive understanding of the mechanisms that initiate developmental events in chickpea seeds after fertilization.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03599-8.

Transgenerational Paternal Inheritance of TaCKX GFMs Expression Patterns Indicate a Way to Select Wheat Lines with Better Parameters for Yield-Related Traits

Members of the TaCKX gene family (GFMs) encode the cytokinin oxygenase/dehydrogenase enzyme (CKX), which irreversibly degrades cytokinins in the organs of wheat plants; therefore, these genes perform a key role in the regulation of yield-related traits. The purpose of the investigation was to determine how expression patterns of these genes, together with the transcription factor-encoding gene TaNAC2-5A, and yield-related traits are inherited to apply this knowledge to speed up breeding processes. The traits were tested in 7 days after pollination (DAP) spikes and seedling roots of maternal and paternal parents and their F₂ progeny. The expression levels of most of them and the yield were inherited in F₂ from the paternal parent. Some pairs or groups of genes cooperated, and some showed opposite functions. Models of up- or down-regulation of TaCKX GFMs and TaNAC2-5A in low-yielding maternal plants crossed with higher-yielding paternal plants and their high-yielding F₂ progeny reproduced gene expression and yield of the paternal parent. The correlation coefficients between TaCKX GFMs, TaNAC2-5A, and yield-related traits in high-yielding F₂ progeny indicated which of these genes were specifically correlated with individual yield-related traits. The most common was expressed in 7 DAP spikes TaCKX2.1, which positively correlated with grain number, grain yield, spike number, and spike length, and seedling root mass. The expression levels of TaCKX1 or TaNAC2-5A in the seedling roots were negatively correlated with these traits. In contrast, the thousand grain weight (TGW) was negatively regulated by TaCKX2.2.2, TaCKX2.1, and TaCKX10 in 7 DAP spikes but positively correlated with TaCKX10 and TaNAC2-5A in seedling roots. Transmission of TaCKX GFMs and TaNAC2-5A expression patterns and yield-related traits from parents to the F₂ generation indicate their paternal imprinting. These newly shown data of nonmendelian epigenetic inheritance shed new light on crossing strategies to obtain a high-yielding F₂ generation.

Regulatory networks of hormone-involved transcription factors and their downstream pathways during somatic embryogenesis of Arabidopsis thaliana

Somatic embryogenesis (SE) depends on a variety of developmental pathways that are influenced by several environmental factors. Therefore, it is important to understand the relationship between environmental and genetic factors by identifying the gene networks involved in SE through gene set enrichment analysis (GSEA). For determination of SE effective transcription factors, upstream sequences of core-enriched genes were analyzed. The results indicated that response to hormones is one of the biological pathways activated by the enriched TFs at all stages of somatic embryogenesis and about half of the hormonal pathways were enriched. On the fifth day after 2,4-Dichlorophenoxyacetic acid (2,4-D) treatment, the activity of hormone-affecting genes reached its maximum. At this time, more transcription factors regulated the enriched genes compared to the other stages of somatic embryogenesis. MYBs, AT-HOOKs, and HSFs are the main families of transcription factors which affect core-enriched genes during SE. CCA1, PRR7, and TOC1 and their related genes at the center of protein-protein interaction of SE-key transcription factors, involved in the regulation of the circadian clock. Gene expression analysis of CCA1, PRR7, and TOC1 revealed that the genes involved in circadian clock reached their maximum activity when embryonic cells formed. Also, auxin response elements were identified at the upstream of SE-circadian clock transcription factors, indicating that they might mediate between auxin signaling and SE-related hormonal pathways as well as SE marker genes such as AGL15, BBM, and LECs. Based on these results, it is possible that the cellular circadian rhythm activates various developmental pathways under the influence of auxin signal transduction and their interactions determine the induction of somatic embryogenesis. According to the results of this study, modifying pathways affected by SE-related transcription factors such as circadian rhythm may result in cell reprogramming and increase somatic embryogenesis efficiency.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03546-7.

Carbon and nitrogen metabolism affects kentucky bluegrass rhizome expansion

BACKGROUND

Rhizome is vital for carbon and nitrogen metabolism of the whole plant. However, the effect of carbon and nitrogen in the rhizome on rhizome expansion remains unclear.

RESULTS

Three wild Kentucky bluegrass (Poa pratensis L.) germplasms with different rhizome expansion capacity (strong expansion capacity, 'YZ'; medium expansion capacity, 'WY'; and weak expansion capacity, 'AD') were planted in the field and the rhizomes number, tiller number, rhizome dry weight, physiological indicators and enzyme activity associated carbon and nitrogen metabolisms were measured. Liquid chromatography coupled to mass spectrometry (LC-MS) was utilized to analyze the metabolomic of the rhizomes. The results showed that the rhizome and tiller numbers of the YZ were 3.26 and 2.69-fold of that of the AD, respectively. The aboveground dry weight of the YZ was the greatest among all three germplasms. Contents of soluble sugar, starch, sucrose, NO₃^--N, and free amino acid were significantly higher in rhizomes of the YZ than those of the WY and AD (P < 0.05). The activities of glutamine synthetase (GS), glutamate dehydrogenase (GDH) and sucrose phosphate synthase (SPS) of the YZ were the highest among all three germplasm, with values of 17.73 A·g^- 1 h^- 1, 5.96 µmol·g^- 1 min^- 1, and 11.35 mg·g^- 1 h^- 1, respectively. Metabolomics analyses revealed that a total of 28 differentially expressed metabolites (DEMs) were up-regulated, and 25 DEMs were down-regulated in both comparison groups (AD vs. YZ group and WY vs. YZ group). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis demonstrated that metabolites related to histidine metabolism, tyrosine metabolism, tryptophan metabolism, and phenylalanine metabolism were associated with rhizomes carbon and nitrogen metabolism.

CONCLUSIONS

Overall, the results suggest that soluble sugar, starch, sucrose, NO₃^--N, and free amino acid in rhizome are important to and promote rhizome expansion in Kentucky bluegrass, while tryptamine, 3-methylhistidine, 3-indoleacetonitrile, indole, and histamine may be key metabolites in promoting carbon and nitrogen metabolism of rhizome.

Biosynthesis- and transport-mediated dynamic auxin distribution during seed development controls seed size in Arabidopsis

Auxin is indispensable to the fertilization-induced coordinated development of the embryo, endosperm, and seed coat. However, little attention has been given to the distribution pattern, maintenance mechanism, and function of auxin throughout the process of seed development. In the present study, we found that auxin response signals display a dynamic distribution pattern during Arabidopsis seed development. Shortly after fertilization, strong auxin response signals were observed at the funiculus, chalaza, and micropylar integument where the embryo attaches. Later, additional signals appeared at the middle layer of the inner integument (ii1') above the chalaza and the whole inner layer of the outer integument (oi1). These signals peaked when the seed was mature, then declined upon desiccation and disappeared in the dried seed. Auxin biosynthesis genes, including ASB1, TAA1, YUC1, YUC4, YUC8, and YUC9, contributed to the accumulation of auxin in the funiculus and seed coat. Auxin efflux carrier PIN3 and influx carrier AUX1 also contributed to the polar auxin distribution in the seed coat. PIN3 was expressed in the ii1 (innermost layer of the inner integument) and oi1 layers of the integument and showed polar localization. AUX1 was expressed in both layers of the outer integument and the endosperm and displayed a uniform localization. Further research demonstrated that the accumulation of auxin in the seed coat regulates seed size. Transgenic plants that specifically express the YUC8 gene in the oi2 or ii1 seed coat produced larger seeds. These results provide useful tools for cultivating high-yielding crops.

Asymmetric cell division in plant development

Asymmetric cell division (ACD) is a fundamental process that generates new cell types during development in eukaryotic species. In plant development, post-embryonic organogenesis driven by ACD is universal and more important than in animals, in which organ pattern is preset during embryogenesis. Thus, plant development provides a powerful system to study molecular mechanisms underlying ACD. During the past decade, tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants. Here, we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems. We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD. Finally, we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.

Maternal control of triploid seed development by the TRANSPARENT TESTA 8 (TT8) transcription factor in Arabidopsis thaliana

The balance between parental genome dosage is critical to offspring development in both animals and plants. In some angiosperm species, despite the imbalance between maternally and paternally inherited chromosome sets, crosses between parental lines of different ploidy may result in viable offspring. However, many plant species, like Arabidopsis thaliana, present a post-zygotic reproductive barrier, known as triploid block which results in the inability of crosses between individuals of different ploidy to generate viable seeds but also, in defective development of the seed. Several paternal regulators have been proposed as active players in establishing the triploid block. Maternal regulators known to be involved in this process are some flavonoid biosynthetic (FB) genes, expressed in the innermost layer of the seed coat. Here we explore the role of selected flavonoid pathway genes in triploid block, including TRANSPARENT TESTA 4 (TT4), TRANSPARENT TESTA 7 (TT7), SEEDSTICK (STK), TRANSPARENT TESTA 16 (TT16), TT8 and TRANSPARENT TESTA 13 (TT13). This approach allowed us to detect that TT8, a bHLH transcription factor, member of this FB pathway is required for the paternal genome dosage, as loss of function tt8, leads to complete rescue of the triploid block to seed development.

Endogenous auxin maintains embryonic cell identity and promotes somatic embryo development in Arabidopsis

Somatic embryogenesis (SE), or embryo development from in vitro cultured vegetative explants, can be induced in Arabidopsis by the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) or by overexpression of specific transcription factors, such as AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15). Here, we explored the role of endogenous auxin [indole-3-acetic acid (IAA)] during 2,4-D and AHL15-induced SE. Using the pWOX2:NLS-YFP reporter, we identified three distinct developmental stages for 2,4-D and AHL15-induced SE in Arabidopsis, with these being (i) acquisition of embryo identity; (ii) formation of pro-embryos; and (iii) somatic embryo patterning and development. The acquisition of embryo identity coincided with enhanced expression of the indole-3-pyruvic acid auxin biosynthesis YUCCA genes, resulting in an enhanced pDR5:GFP-reported auxin response in the embryo-forming tissues. Chemical inhibition of the indole-3-pyruvic acid pathway did not affect the acquisition of embryo identity, but significantly reduced or completely inhibited the formation of pro-embryos. Co-application of IAA with auxin biosynthesis inhibitors in the AHL15-induced SE system rescued differentiated somatic embryo formation, confirming that increased IAA levels are important during the last two stages of SE. Our analyses also showed that polar auxin transport, with AUXIN/LIKE-AUX influx and PIN-FORMED1 efflux carriers as important drivers, is required for the transition of embryonic cells to proembryos and, later, for correct cell fate specification and differentiation. Taken together, our results indicate that endogenous IAA biosynthesis and its polar transport are not required for the acquisition of embryo identity, but rather to maintain embryonic cell identity and for the formation of multicellular proembryos and their development into histodifferentiated embryos.

Live-cell imaging reveals the cellular dynamics in seed development

Seed development in flowering plants is highly complex and governed by three genetically distinct tissues: the fertilization products, the diploid embryo and triploid endosperm, as well as the seed coat that has maternal origin. There are diverse cellular dynamics such as nuclear movement in gamete cells for fertilization, cell polarity establishment for embryo development, and multinuclear endosperm formation. These tissues also coordinate and synchronize the developmental timing for proper seed formation through cell-to-cell communications. Live-cell imaging using advanced microscopy techniques enables us to decipher the dynamics of these events. Especially, the establishment of a less-invasive semi-in vivo live-cell imaging approach has allowed us to perform time-lapse analyses for long period observation of Arabidopsis thaliana intact seed development dynamics. Here we highlight the recent trends of live-cell imaging for seed development and discuss where we are heading.

Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice

The auxin efflux transporter proteins called PINs ferry auxin from its source to sinks in particular directions depending on their polar localizations in the plasma membrane, thus facilitating the development of the entire plant architecture. The rice genome has 12 PIN genes distributed over eight chromosomes. To study their roles in plant development, abiotic stress responsiveness, and shaping an auxin-dependent root architecture, a genome-wide analysis was carried out. Based on phylogeny, cellular localization, and hydrophilic loop domain size, the PINs were categorized into canonical and noncanonical PINs. PINs were found expressed in all of the organs of plants that emphasized their indispensable role throughout the plant's life cycle. We discovered that PIN5C and PIN9 were upregulated during salt and drought stress. We also found that regardless of its cellular level, auxin functioned as a molecular switch to turn on auxin biosynthesis genes. On the contrary, although PIN expression was upregulated upon initial treatment with auxin, prolonged auxin treatment not only led to their downregulation but also led to the development of auxin-dependent altered root formation in rice. Our study paves the way for developing stress-tolerant rice and plants with a desirable root architecture by genetic engineering.

Pivotal role of STIP in ovule pattern formation and female germline development in Arabidopsis thaliana

In spermatophytes the sporophytic (diploid) and the gametophytic (haploid) generations co-exist in ovules, and the coordination of their developmental programs is of pivotal importance for plant reproduction. To achieve efficient fertilization, the haploid female gametophyte and the diploid ovule structures must coordinate their development to form a functional and correctly shaped ovule. WUSCHEL-RELATED HOMEOBOX (WOX) genes encode a family of transcription factors that share important roles in a wide range of processes throughout plant development. Here, we show that STIP is required for the correct patterning and curvature of the ovule in Arabidopsis thaliana. The knockout mutant stip-2 is characterized by a radialized ovule phenotype due to severe defects in outer integument development. In addition, alteration of STIP expression affects the correct differentiation and progression of the female germline. Finally, our results reveal that STIP is required to tightly regulate the key ovule factors INNER NO OUTER, PHABULOSA and WUSCHEL, and they define a novel genetic interplay in the regulatory networks determining ovule development.

Mechanism of fertilization-induced auxin synthesis in the endosperm for seed and fruit development

The dominance of flowering plants on earth is owed largely to the evolution of maternal tissues such as fruit and seedcoat that protect and disseminate the seeds. The mechanism of how fertilization triggers the development of these specialized maternal tissues is not well understood. A key event is the induction of auxin synthesis in the endosperm, and the mobile auxin subsequently stimulates seedcoat and fruit development. However, the regulatory mechanism of auxin synthesis in the endosperm remains unknown. Here, we show that a type I MADS box gene AGL62 is required for the activation of auxin synthesis in the endosperm in both Fragaria vesca, a diploid strawberry, and in Arabidopsis. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis. In this work, we identify a key mechanism for auxin induction to mediate fertilization success, a finding broadly relevant to flowering plants.

In flowering plants, fertilization triggers auxin synthesis in the endosperm to promote seed and fruit development. Here the authors show that an MADS-box transcription factor AGL62 is required to activate auxin synthesis in the endosperms of Fragaria vesca, a diploid strawberry, and Arabidopsis.

A Small Gtp-Binding Protein GhROP3 Interacts with GhGGB Protein and Negatively Regulates Drought Tolerance in Cotton (Gossypium hirsutum L.)

As a plant-specific Rho-like small G protein, the ROP (Rho-related GTPase of plants) protein regulates the growth and development of plants and various stress responses in the form of molecular switches. Drought is a major abiotic stress that limits cotton yield and fiber quality. In this study, virus-induced gene silencing (VIGS) technology was used to analyze the biological function of GhROP3 in cotton drought stress tolerance. Meanwhile, we used yeast two-hybrid and bimolecular fluorescence complementation assays to examine the interaction between GhROP3 and GhGGB. GhROP3 has a high expression level in cotton true leaves and roots, and responds to drought, high salt, cold, heat stress, and exogenous abscisic acid (ABA) and auxin (IAA) treatments. Silencing GhROP3 improved the drought tolerance of cotton. The water loss rates (WLR) of detached leaves significantly reduced in silenced plants. Also, the relative water content (RWC) and total contents of chlorophyll (Chl) and proline (Pro) of leaves after drought stress and the activities of three antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) significantly increased, whereas the contents of hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) significantly reduced. In the leaves of silenced plants, the expression of genes related to ABA synthesis and its related pathway was significantly upregulated, and the expression of decomposition-related GhCYP707A gene and genes related to IAA synthesis and its related pathways was significantly downregulated. It indicated that GhROP3 was a negative regulator of cotton response to drought by participating in the negative regulation of the ABA signaling pathway and the positive regulation of the IAA signaling pathway. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhROP3 protein interacted with the GhGGB protein in vivo and in vitro. This study provided a theoretical basis for the in-depth investigation of the drought resistance–related molecular mechanism of the GhROP3 gene and the biological function of the GhGGB gene.

The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein

Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.

Spatially expressed WIP genes control Arabidopsis embryonic root development

Development of plant organs is a highly organized process. In Arabidopsis, proper root development requires that distinct cell types and tissue layers are specified and formed in a restricted manner in space and over time. Despite its importance, genetic controls underlying such regularity remain elusive. Here we found that WIP genes expressed in the embryo and suspensor functionally oppose those expressed in the surrounding maternal tissues to orchestrate cell division orientation and cell fate specification in the embryonic root, thereby promoting regular root formation. The maternal WIPs act non-cell autonomously to repress root cell fate specification through SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) family members. When losing all WIPs, root cells divide irregularly in the early embryo, but this barely alters their fate specification and the morphology of post-embryonic roots. Our results reveal cross-communication between the embryonic and maternal WIPs in controlling root development.

Fourteen Stations of Auxin

Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.

Embryo-Endosperm Interactions

In angiosperms, double fertilization triggers the concomitant development of two closely juxtaposed tissues, the embryo and the endosperm. Successful seed development and germination require constant interactions between these tissues, which occur across their common interface. The embryo-endosperm interface is a complex and poorly understood compound apoplast comprising components derived from both tissues, across which nutrients transit to fuel embryo development. Interface properties, which affect molecular diffusion and thus communication, are themselves dynamically regulated by molecular and physical dialogues between the embryo and endosperm. We review the current understanding of embryo-endosperm interactions, with a focus on the structure, properties, and function of their shared interface. Concentrating on Arabidopsis, but with reference to other species, we aim to situate recent findings within the broader context of seed physiology, developmental biology, and genetic factors such as parental conflicts over resource allocation.

Building an embryo: An auxin gene toolkit for zygotic and somatic embryogenesis in Brazilian pine

Many studies in the model species Arabidopsis thaliana characterized genes involved in embryo formation. However, much remains to be learned about the portfolio of genes that are involved in signal transduction and transcriptional regulation during plant embryo development in other species, particularly in an evolutionary context, especially considering that some genes involved in embryo patterning are not exclusive of land plants. This study, used a combination of domain architecture phylostratigraphy and phylogenetic reconstruction to investigate the evolutionary history of embryo patterning and auxin metabolism (EPAM) genes in Viridiplantae. This approach shed light on the co-optation of auxin metabolism and other molecular mechanisms that contributed to the radiation of land plants, and specifically to embryo formation. These results have potential to assist conservation programs, by directing the development of tools for obtaining somatic embryos. In this context, we employed this methodology with critically endangered and non-model species Araucaria angustifolia, the Brazilian pine, which is current focus of conservation efforts using somatic embryogenesis. So far, this approach had little success since somatic embryos fail to completely develop. By profiling the expression of genes that we identified as necessary for the emergence of land-plant embryos, we found striking differences between zygotic and somatic embryos that might explain the developmental arrest and be used to improve A. angustifolia somatic culture.

Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana

Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.

Screening of Differentially Expressed Genes and Localization Analysis of Female Gametophyte at the Free Nuclear Mitosis Stage in Pinus tabuliformis Carr

Female sterility is a common phenomenon in the plant world, and systematic research has not been carried out in gymnosperms. In this study, the ovules of No. 28 sterile line and No. 15 fertile line Pinus tabuliformis were used as materials, and a total of 18 cDNA libraries were sequenced by the HiSeqTM 4000 platform to analyze the differentially expressed genes (DEGs) and simple sequence repeats (SSRs) between the two lines. In addition, this study further analyzed the DEGs involved in the signal transduction of plant hormones, revealing that the signal pathways related to auxin, cytokinin, and gibberellin were blocked in the sterile ovule. Additionally, real-time fluorescent quantitative PCR verified that the expression trend of DEGs related to plant hormones was consistent with the results of high-throughput sequencing. Frozen sections and fluorescence in situ hybridization (FISH) were used to study the temporal and spatial expression patterns of PtRab in the ovules of P. tabuliformis. It was found that PtRab was significantly expressed in female gametophytes and rarely expressed in the surrounding diploid tissues. This study further explained the molecular regulation mechanism of female sterility in P. tabuliformis, preliminarily mining the key factors of ovule abortion in gymnosperms at the transcriptional level.

Molecular Aspects of Seed Development Controlled by Gibberellins and Abscisic Acids

Plants have evolved seeds to permit the survival and dispersion of their lineages by providing nutrition for embryo growth and resistance to unfavorable environmental conditions. Seed formation is a complicated process that can be roughly divided into embryogenesis and the maturation phase, characterized by accumulation of storage compound, acquisition of desiccation tolerance, arrest of growth, and acquisition of dormancy. Concerted regulation of several signaling pathways, including hormonal and metabolic signals and gene networks, is required to accomplish seed formation. Recent studies have identified the major network of genes and hormonal signals in seed development, mainly in maturation. Gibberellin (GA) and abscisic acids (ABA) are recognized as the main hormones that antagonistically regulate seed development and germination. Especially, knowledge of the molecular mechanism of ABA regulation of seed maturation, including regulation of dormancy, accumulation of storage compounds, and desiccation tolerance, has been accumulated. However, the function of ABA and GA during embryogenesis still remains elusive. In this review, we summarize the current understanding of the sophisticated molecular networks of genes and signaling of GA and ABA in the regulation of seed development from embryogenesis to maturation.

Auxin biosynthesis maintains embryo identity and growth during BABY BOOM-induced somatic embryogenesis

Somatic embryogenesis is a type of plant cell totipotency where embryos develop from nonreproductive (vegetative) cells without fertilization. Somatic embryogenesis can be induced in vitro by auxins, and by ectopic expression of embryo-expressed transcription factors like the BABY BOOM (BBM) AINTEGUMENTA-LIKE APETALA2/ETHYLENE RESPONSE FACTOR domain protein. These different pathways are thought to converge to promote auxin response and biosynthesis, but the specific roles of the endogenous auxin pathway in somatic embryogenesis induction have not been well-characterized. Here we show that BBM transcriptionally regulates the YUCCA3 (YUC3) and YUC8 auxin biosynthesis genes during BBM-mediated somatic embryogenesis in Arabidopsis (Arabidopsis thaliana) seedlings. BBM induced local and ectopic YUC3 and YUC8 expression in seedlings, which coincided with increased DR5 auxin response and indole-3-acetic acid (IAA) biosynthesis and with ectopic expression of the WOX2 embryo reporter. YUC-driven auxin biosynthesis was required for BBM-mediated somatic embryogenesis, as the number of embryogenic explants was reduced by ca. 50% in yuc3 yuc8 mutants and abolished after chemical inhibition of YUC enzyme activity. However, a detailed YUC inhibitor time-course study revealed that YUC-dependent IAA biosynthesis is not required for the re-initiation of totipotent cell identity in seedlings. Rather, YUC enzymes are required later in somatic embryo development for the maintenance of embryo identity and growth. This study resolves a long-standing question about the role of endogenous auxin biosynthesis in transcription factor-mediated somatic embryogenesis and also provides an experimental framework for understanding the role of endogenous auxin biosynthesis in other in planta and in vitro embryogenesis systems.

The parental contributions to early plant embryogenesis and the concept of maternal-to-zygotic transition in plants

The maternal-to-zygotic transition (MZT) is a major developmental transition in the life cycles of animals. It consists of two associated processes: maternal transcript clearance and zygotic genome activation (ZGA). The concept of MZT has been controversially discussed in plants. In this short review, we summarize recent advances in understanding the timing of ZGA and the similarities and differences between ZGA in eudicots and monocots. We discuss the parental contributions to the transcriptome of the proembryo and parental control of early embryogenesis, and we examine distinct differences in the ZGA between animals and plants, update relevant concepts on MZT, and highlight outstanding questions in this field.

New insights into cell-cell communications during seed development in flowering plants

The evolution of seeds is a major reason why flowering plants are a dominant life form on Earth. The developing seed is composed of two fertilization products, the embryo and endosperm, which are surrounded by a maternally derived seed coat. Accumulating evidence indicates that efficient communication among all three seed components is required to ensure coordinated seed development. Cell communication within plant seeds has drawn much attention in recent years. In this study, we review current knowledge of cross-talk among the endosperm, embryo, and seed coat during seed development, and highlight recent advances in this field.

Auxin canalization: From speculative models toward molecular players

Among the most fascinated properties of the plant hormone auxin is its ability to promote formation of its own directional transport routes. These gradually narrowing auxin channels form from the auxin source toward the sink and involve coordinated, collective polarization of individual cells. Once established, the channels provide positional information, along which new vascular strands form, for example, during organogenesis, regeneration, or leave venation. The main prerequisite of this still mysterious auxin canalization mechanism is a feedback between auxin signaling and its directional transport. This is manifested by auxin-induced re-arrangements of polar, subcellular localization of PIN-FORMED (PIN) auxin exporters. Immanent open questions relate to how position of auxin source and sink as well as tissue context are sensed and translated into tissue polarization and how cells communicate to polarize coordinately. Recently, identification of the first molecular players opens new avenues into molecular studies of this intriguing example of self-organizing plant development.

Pole position: How plant cells polarize along the axes

Having a sense of direction is a fundamental cellular trait that can determine cell shape, division orientation, or function, and ultimately the formation of a functional, multicellular body. Cells acquire and integrate directional information by establishing discrete subcellular domains along an axis with distinct molecular profiles, a process known as cell polarization. Insight into the principles and mechanisms underlying cell polarity has been propelled by decades of extensive research mostly in yeast and animal models. Our understanding of cell polarity establishment in plants, which lack most of the regulatory molecules identified in other eukaryotes, is more limited, but significant progress has been made in recent years. In this review, we explore how plant cells coordinately establish stable polarity axes aligned with the organ axes, highlighting similarities in the molecular logic used to polarize both plant and animal cells. We propose a classification system for plant cell polarity events and nomenclature guidelines. Finally, we provide a deep phylogenetic analysis of polar proteins and discuss the evolution of polarity machineries in plants.

Anatomical and hormonal factors determining the development of haploid and zygotic embryos of oat (Avena sativa L.)

A critical step in the production of doubled haploids is a conversion of the haploid embryos into plants. Our study aimed to recognize the reasons for the low germination rate of Avena sativa haploid embryos obtained by distant crossing with maize. Oat cultivars of ‘Krezus’ and ‘Akt’ were investigated regarding embryo anatomy, the endogenous phytohormone profiles, and antioxidant capacity. The zygotic embryos of oat were used as a reference. It was found that twenty-one days old haploid embryos were smaller and had a less advanced structure than zygotic ones. Morphology and anatomy modifications of haploid embryos were accompanied by extremely low levels of endogenous auxins. Higher levels of cytokinins, as well as tenfold higher cytokinin to auxin ratio in haploid than in zygotic embryos, may suggest an earlier stage of development of these former. Individual gibberellins reached higher values in ‘Akt’ haploid embryos than in the respective zygotic ones, while the differences in both types of ‘Krezus’ embryos were not noticed. Additionally to the hormonal regulation of haploid embryogenesis, the poor germination of oat haploid embryos can be a result of the overproduction of reactive oxygen species, and therefore higher levels of low molecular weight antioxidants and stress hormones.

Long-Term High-Temperature Stress Impacts on Embryo and Seed Development in Brassica napus

Brassica napus (rapeseed) is the second most important oilseed crop worldwide. Global rise in average ambient temperature and extreme weather severely impact rapeseed seed yield. However, fewer research explained the phenotype changes caused by moderate-to-high temperatures in rapeseed. To investigate these events, we determined the long-term response of three spring cultivars to different temperature regimes (21/18°C, 28/18°C, and 34/18°C) mimicking natural temperature variations. The analysis focused on the plant appearance, seed yield, quality and viability, and embryo development. Our microscopic observations suggest that embryonic development is accelerated and defective in high temperatures. Reduced viable seed yield at warm ambient temperature is due to a reduced fertilization rate, increased abortion rate, defective embryonic development, and pre-harvest sprouting. Reduced auxin levels in young seeds and low ABA and auxin levels in mature seeds may cause embryo pattern defects and reduced seed dormancy, respectively. Glucosinolates and oil composition measurements suggest reduced seed quality. These identified cues help understand seed thermomorphogenesis and pave the way to developing thermoresilient rapeseed.

Plant development: Suspensors as a battlefield for parental tug-of-war?

Parental contributions to zygotes can influence early embryogenesis and may regulate the distribution of maternal resources to progeny. A new study in Arabidopsis thaliana has demonstrated that signaling components from maternal sporophytic tissues and paternal gametes converge in zygotes to promote elongation of the extraembryonic suspensor, which supports the developing embryo proper.

Independent parental contributions initiate zygote polarization in Arabidopsis thaliana

Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. The daughter cells of the asymmetric zygote division form the pro-embryo and the mostly extra-embryonic suspensor.¹ The suspensor plays a pivotal role in nutrient and hormone transport and rapid growth of the embryo.^2,3 Zygote polarization is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase (MAP3K) YODA (YDA)⁴ and the upstream membrane-associated proteins BRASINOSTEROID SIGNALING KINASE 1 (BSK1) and BSK2.^5,6 Furthermore, suspensor development is controlled by cysteine-rich peptides of the EMBRYO SURROUNDING FACTOR 1 (ESF1) family.⁷ While they act genetically upstream of YDA, the corresponding receptor to perceive these potential ligands is unknown. In other developmental processes, such as stomata development, YDA activity is controlled by receptor kinases of the ERECTA family (ERf).^8-12 While the receptor kinases upstream of BSK1/2 in the embryo have so far not been identified,¹ YDA is in part activated by the sperm cell-derived BSK family member SHORT SUSPENSOR (SSP) that represents a naturally occurring, constitutively active variant of BSK1.^5,13 It has been speculated that SSP might be a paternal component of a parental tug-of-war controlling resource allocation toward the embryo.^2,13 Here, we show that in addition to SSP, the receptor kinase ERECTA plays a crucial role in zygote polarization as a maternally contributed part of the embryonic YDA pathway. We conclude that two independent parental contributions initiate zygote polarization and control embryo development.

Auxin and Target of Rapamycin Spatiotemporally Regulate Root Organogenesis

The programs associated with embryonic roots (ERs), primary roots (PRs), lateral roots (LRs), and adventitious roots (ARs) play crucial roles in the growth and development of roots in plants. The root functions are involved in diverse processes such as water and nutrient absorption and their utilization, the storage of photosynthetic products, and stress tolerance. Hormones and signaling pathways play regulatory roles during root development. Among these, auxin is the most important hormone regulating root development. The target of rapamycin (TOR) signaling pathway has also been shown to play a key role in root developmental programs. In this article, the milestones and influential progress of studying crosstalk between auxin and TOR during the development of ERs, PRs, LRs and ARs, as well as their functional implications in root morphogenesis, development, and architecture, are systematically summarized and discussed.

Conserved, divergent and heterochronic gene expression during Brachypodium and Arabidopsis embryo development

KEY MESSAGE

Developmental and transcriptomic analysis of Brachypodium embryogenesis and comparison with Arabidopsis identifies conserved and divergent phases of embryogenesis and reveals widespread heterochrony of developmental gene expression. Embryogenesis, transforming the zygote into the mature embryo, represents a fundamental process for all flowering plants. Current knowledge of cell specification and differentiation during plant embryogenesis is largely based on studies of the dicot model plant Arabidopsis thaliana. However, the major crops are monocots and the transcriptional programs associated with the differentiation processes during embryogenesis in this clade were largely unknown. Here, we combined analysis of cell division patterns with development of a temporal transcriptomic resource during embryogenesis of the monocot model plant Brachypodium distachyon. We found that early divisions of the Brachypodium embryo were highly regular, while later stages were marked by less stereotypic patterns. Comparative transcriptomic analysis between Brachypodium and Arabidopsis revealed that early and late embryogenesis shared a common transcriptional program, whereas mid-embryogenesis was divergent between species. Analysis of orthology groups revealed widespread heterochronic expression of potential developmental regulators between the species. Interestingly, Brachypodium genes tend to be expressed at earlier stages than Arabidopsis counterparts, which suggests that embryo patterning may occur early during Brachypodium embryogenesis. Detailed investigation of auxin-related genes shows that the capacity to synthesize, transport and respond to auxin is established early in the embryo. However, while early PIN1 polarity could be confirmed, it is unclear if an active response is mounted. This study presents a resource for studying Brachypodium and grass embryogenesis and shows that divergent angiosperms share a conserved genetic program that is marked by heterochronic gene expression.

Temporal Control of Seed Development in Dicots: Molecular Bases, Ecological Impact and Possible Evolutionary Ramifications

In flowering plants, seeds serve as organs of both propagation and dispersal. The developing seed passes through several consecutive stages, following a conserved general outline. The overall time needed for a seed to develop, however, may vary both within and between plant species, and these temporal developmental properties remain poorly understood. In the present paper, we summarize the existing data for seed development alterations in dicot plants. For genetic mutations, the reported cases were grouped in respect of the key processes distorted in the mutant specimens. Similar phenotypes arising from the environmental influence, either biotic or abiotic, were also considered. Based on these data, we suggest several general trends of timing alterations and how respective mechanisms might add to the ecological plasticity of the families considered. We also propose that the developmental timing alterations may be perceived as an evolutionary substrate for heterochronic events. Given the current lack of plausible models describing timing control in plant seeds, the presented suggestions might provide certain insights for future studies in this field.

Transcriptional control of local auxin distribution by the CsDFB1-CsPHB module regulates floral organogenesis in cucumber

Auxin is a key phytohormone influencing multiple aspects of plant development, including meristem maintenance, primordia initiation, floral organogenesis, and vascular differentiation. Local auxin biosynthesis and polar auxin transport are essential to establish and maintain auxin gradients that ensure proper plant development. Here, we demonstrate that CsDFB1, a member of the plant cystatin superfamily, which was previously implicated in defense responses, plays a critical role in regulating local auxin distribution and thus influences floral organogenesis in cucumber. Genetic and biochemical assays suggest that CsDFB1 affects local auxin distribution by acting as an attenuator that interacts with CsPHB and modulates CsPHB-mediated transcriptional control of CsYUC2 and CsPIN1. Our results shed light on the fine tuning of local auxin distribution in plants.

Plant cystatins are cysteine proteinase inhibitors that play key roles in defense responses. In this work, we describe an unexpected role for the cystatin-like protein DEFORMED FLORAL BUD1 (CsDFB1) as a transcriptional regulator of local auxin distribution in cucumber (Cucumis sativus L.). CsDFB1 was strongly expressed in the floral meristems, floral primordia, and vasculature. RNA interference (RNAi)-mediated silencing of CsDFB1 led to a significantly increased number of floral organs and vascular bundles, together with a pronounced accumulation of auxin. Conversely, accompanied by a decrease of auxin, overexpression of CsDFB1 resulted in a dramatic reduction in floral organ number and an obvious defect in vascular patterning, as well as organ fusion. CsDFB1 physically interacted with the cucumber ortholog of PHABULOSA (CsPHB), an HD-ZIP III transcription factor whose transcripts exhibit the same pattern as CsDFB1. Overexpression of CsPHB increased auxin accumulation in shoot tips and induced a floral phenotype similar to that of CsDFB1-RNAi lines. Furthermore, genetic and biochemical analyses revealed that CsDFB1 impairs CsPHB-mediated transcriptional regulation of the auxin biosynthetic gene YUCCA2 and the auxin efflux carrier PIN-FORMED1, and thus plays a pivotal role in auxin distribution. In summary, we propose that the CsDFB1-CsPHB module represents a regulatory pathway for local auxin distribution that governs floral organogenesis and vascular differentiation in cucumber.

The Rab Geranylgeranyl Transferase Beta Subunit Is Essential for Embryo and Seed Development in Arabidopsis thaliana

Auxin is a key regulator of plant development affecting the formation and maturation of reproductive structures. The apoplastic route of auxin transport engages influx and efflux facilitators from the PIN, AUX and ABCB families. The polar localization of these proteins and constant recycling from the plasma membrane to endosomes is dependent on Rab-mediated vesicular traffic. Rab proteins are anchored to membranes via posttranslational addition of two geranylgeranyl moieties by the Rab Geranylgeranyl Transferase enzyme (RGT), which consists of RGTA, RGTB and REP subunits. Here, we present data showing that seed development in the rgtb1 mutant, with decreased vesicular transport capacity, is disturbed. Both pre- and post-fertilization events are affected, leading to a decrease in seed yield. Pollen tube recognition at the stigma and its guidance to the micropyle is compromised and the seed coat forms incorrectly. Excess auxin in the sporophytic tissues of the ovule in the rgtb1 plants leads to an increased tendency of autonomous endosperm formation in unfertilized ovules and influences embryo development in a maternal sporophytic manner. The results show the importance of vesicular traffic for sexual reproduction in flowering plants, and highlight RGTB1 as a key component of sporophytic-filial signaling.

The Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 protein modulates maternal auxin biosynthesis and controls seed size by inducing AINTEGUMENTA

Seed size is a major factor determining crop yields that is controlled through the coordinated development of maternal and zygotic tissues. Here, we identified Arabidopsis MATERNAL EFFECT EMBRYO ARREST45 (MEE45) as a B3 transcription factor that controls cell proliferation and maternally regulates seed size through its transcriptional activation of AINTEGUMENTA (ANT) and its downstream control of auxin biosynthesis in the ovule integument. After characterizing reduced seed and organ size phenotypes in mee45 mutants and finding that overexpression of MEE45 causes oversized seeds, we discovered that the MEE45 protein can bind to the promoter region of the ANT locus and positively regulate its transcription. ANT in-turn activates the expression of auxin biosynthetic genes (e.g. YUCCA4) in the ovule integument. Our results thus illustrate mechanisms underlying maternal tissue-mediated regulation of seed size and suggest that MEE45 and its downstream components can be harnessed to develop higher-yielding crop varieties.

Gene expression variation in Arabidopsis embryos at single-nucleus resolution

Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.

Comparative Embryogenesis in Angiosperms: Activation and Patterning of Embryonic Cell Lineages

Following fertilization in flowering plants (angiosperms), egg and sperm cells unite to form the zygote, which generates an entire new organism through a process called embryogenesis. In this review, we provide a comparative perspective on early zygotic embryogenesis in flowering plants by using the Poaceae maize and rice as monocot grass and crop models as well as Arabidopsis as a eudicot model of the Brassicaceae family. Beginning with the activation of the egg cell, we summarize and discuss the process of maternal-to-zygotic transition in plants, also taking recent work on parthenogenesis and haploid induction into consideration. Aspects like imprinting, which is mainly associated with endosperm development and somatic embryogenesis, are not considered. Controversial findings about the timing of zygotic genome activation as well as maternal versus paternal contribution to zygote and early embryo development are highlighted. The establishment of zygotic polarity, asymmetric division, and apical and basal cell lineages represents another chapter in which we also examine and compare the role of major signaling pathways, cell fate genes, and hormones in early embryogenesis. Except for the model Arabidopsis, little is known about embryopatterning and the establishment of the basic body plan in angiosperms. Using available in situ hybridization, RNA-sequencing, and marker data, we try to compare how and when stem cell niches are established. Finally, evolutionary aspects of plant embryo development are discussed.

Systematic analysis of specific and nonspecific auxin effects on endocytosis and trafficking

The phytohormone auxin and its directional transport through tissues are intensively studied. However, a mechanistic understanding of auxin-mediated feedback on endocytosis and polar distribution of PIN auxin transporters remains limited due to contradictory observations and interpretations. Here, we used state-of-the-art methods to reexamine the auxin effects on PIN endocytic trafficking. We used high auxin concentrations or longer treatments versus lower concentrations and shorter treatments of natural indole-3-acetic acid (IAA) and synthetic naphthalene acetic acid (NAA) auxins to distinguish between specific and nonspecific effects. Longer treatments of both auxins interfere with Brefeldin A-mediated intracellular PIN2 accumulation and also with general aggregation of endomembrane compartments. NAA treatment decreased the internalization of the endocytic tracer dye, FM4-64; however, NAA treatment also affected the number, distribution, and compartment identity of the early endosome/trans-Golgi network, rendering the FM4-64 endocytic assays at high NAA concentrations unreliable. To circumvent these nonspecific effects of NAA and IAA affecting the endomembrane system, we opted for alternative approaches visualizing the endocytic events directly at the plasma membrane (PM). Using total internal reflection fluorescence microscopy, we saw no significant effects of IAA or NAA treatments on the incidence and dynamics of clathrin foci, implying that these treatments do not affect the overall endocytosis rate. However, both NAA and IAA at low concentrations rapidly and specifically promoted endocytosis of photo-converted PIN2 from the PM. These analyses identify a specific effect of NAA and IAA on PIN2 endocytosis, thus, contributing to its polarity maintenance and furthermore illustrate that high auxin levels have nonspecific effects on trafficking and endomembrane compartments.

Auxin efflux controls orderly nucellar degeneration and expansion of the female gametophyte in Arabidopsis

The nucellus tissue in flowering plants provides nutrition for the development of the female gametophyte (FG) and young embryo. The nucellus degenerates as the FG develops, but the mechanism controlling the coupled process of nucellar degeneration and FG expansion remains largely unknown. The degeneration process of the nucellus and spatiotemporal auxin distribution in the developing ovule before fertilization were investigated in Arabidopsis thaliana. Nucellar degeneration before fertilization occurs through vacuolar cell death and in an ordered degeneration fashion. This sequential nucellar degeneration is controlled by the signalling molecule auxin. Auxin efflux plays the core role in precisely controlling the spatiotemporal pattern of auxin distribution in the nucellus surrounding the FG. The auxin efflux carrier PIN1 transports maternal auxin into the nucellus while PIN3/PIN4/PIN7 further delivers auxin to degenerating nucellar cells and concurrently controls FG central vacuole expansion. Notably, auxin concentration and auxin efflux are controlled by the maternal tissues, acting as a key communication from maternal to filial tissue.

Endosperm development is an autonomously programmed process independent of embryogenesis

The seeds of flowering plants contain three genetically distinct structures: the embryo, endosperm, and seed coat. The embryo and endosperm need to interact and exchange signals to ensure coordinated growth. Accumulating evidence has confirmed that embryo growth is supported by the nourishing endosperm and regulated by signals originating from the endosperm. Available data also support that endosperm development requires communication with the embryo. Here, using single-fertilization mutants, Arabidopsis thaliana dmp8 dmp9 and gex2, we demonstrate that in the absence of a zygote and embryo, endosperm initiation, syncytium formation, free nuclear cellularization, and endosperm degeneration occur as in the wild type in terms of the cytological process and time course. Although rapid embryo expansion accelerates endosperm breakdown, our findings strongly suggest that endosperm development is an autonomously organized process, independent of egg cell fertilization and embryo-endosperm communication. This work confirms both the altruistic and self-directed nature of the endosperm during coordinated embryo-endosperm development. Our findings provide insights into the intricate interaction between the two fertilization products and will help to distinguish the physiological roles of the signaling between endosperm and embryo. These findings also open new avenues in agro-biotechnology for crop improvement.