Genome-wide analysis of genes targeted by PHYTOCHROME INTERACTING FACTOR 3-LIKE5 during seed germination in Arabidopsis

Stress induced factor 2 is a dual regulator for defense and seed germination in Arabidopsis

Receptor-like kinases (RLKs) constitute a diverse superfamily of proteins pivotal for various plant physiological processes, including responses to pathogens, hormone perception, growth, and development. Their ability to recognize conserved epitopes for general elicitors and specific pathogens marked significant advancements in plant pathology research. Emerging evidence suggests that RLKs and associated components also act as modulators in hormone signaling and cellular trafficking, showcasing their multifunctional roles in growth and development. Notably, STRESS INDUCED FACTOR 2 (SIF2) stands out as a representative with distinct expression patterns in different Arabidopsis organs. Our prior work highlighted the specific induction of SIF2 expression in guard cells, emphasizing its positive contribution to stomatal immunity. Expanding on these findings, our present study delves into the diverse functions of SIF2 expression in root tissues. Utilizing comprehensive physiology, molecular biology, protein biochemistry, and genetic analyses, we reveal that SIF2 modulates abscisic acid (ABA) signaling in Arabidopsis roots. SIF2 is epistatic with key regulators in the ABA signaling pathway, thereby governing the expression of genes crucial for dormancy release and, consequently, Arabidopsis seed germination. This study sheds light on the intricate roles of SIF2 as a multi-functional RLK, underscoring its organ-specific contributions to plant immunity, hormonal regulation, and seed germination.

The phytochrome-interacting factor genes PIF1 and PIF4 are functionally diversified due to divergence of promoters and proteins

Phytochrome-interacting factors (PIFs) are basic helix-loop-helix transcription factors that regulate light responses downstream of phytochromes. In Arabidopsis (Arabidopsis thaliana), 8 PIFs (PIF1-8) regulate light responses, either redundantly or distinctively. Distinctive roles of PIFs may be attributed to differences in mRNA expression patterns governed by promoters or variations in molecular activities of proteins. However, elements responsible for the functional diversification of PIFs have yet to be determined. Here, we investigated the role of promoters and proteins in the functional diversification of PIF1 and PIF4 by analyzing transgenic lines expressing promoter-swapped PIF1 and PIF4, as well as chimeric PIF1 and PIF4 proteins. For seed germination, PIF1 promoter played a major role, conferring dominance to PIF1 gene with a minor contribution from PIF1 protein. Conversely, for hypocotyl elongation under red light, PIF4 protein was the major element conferring dominance to PIF4 gene with the minor contribution from PIF4 promoter. In contrast, both PIF4 promoter and PIF4 protein were required for the dominant role of PIF4 in promoting hypocotyl elongation at high ambient temperatures. Together, our results support that the functional diversification of PIF1 and PIF4 genes resulted from contributions of both promoters and proteins, with their relative importance varying depending on specific light responses.

Promotion of seedling germination in Arabidopsis by B-box zinc-finger protein BBX32

Seed germination represents a determinant for plants to enter ecosystems and is thus regarded as a key ecological and agronomic trait. It is tightly regulated by a variety of environmental cues to ensure that seeds germinate under favorable conditions. Here, we characterize BBX32, a B-box zinc-finger protein, as an imbibition-stimulated positive regulator of seed germination. Belonging to subgroup V of the BBX family, BBX32 exhibits distinct characteristics compared with its close counterparts within the same subgroup. BBX32 is transiently induced at both the transcriptional and post-transcriptional levels in the embryo upon water absorption. Genetic evidence indicates that BBX32 acts upstream of the master transcription factor PHYTOCHROME-INTERACTING FACTOR 1 (PIF1) to facilitate light-induced seed germination. BBX32 directly interacts with PIF1, suppressing its protein-interacting and DNA-binding capabilities, thereby relieving PIF1's repression on seed germination. Furthermore, the imbibition-stimulated BBX32 functions in parallel with the light-induced transcription regulator HFR1 to collectively attenuate the transcriptional activities of PIF1. The BBX32-PIF1 de-repression module serves as a molecular connection that enables plants to integrate signals of water availability and light exposure, effectively coordinating the initiation of seed germination.

Regulation of seed germination: ROS, epigenetic, and hormonal aspects

BACKGROUND

The whole life of a plant is regulated by complex environmental or hormonal signaling networks that control genomic stability, environmental signal transduction, and gene expression affecting plant development and viability. Seed germination, responsible for the transformation from seed to seedling, is a key initiation step in plant growth and is controlled by unique physiological and biochemical processes. It is continuously modulated by various factors including epigenetic modifications, hormone transport, ROS signaling, and interaction among them. ROS showed versatile crucial functions in seed germination including various physiological oxidations to nucleic acid, protein, lipid, or chromatin in the cytoplasm, cell wall, and nucleus.

AIM

of review: This review intends to provide novel insights into underlying mechanisms of seed germination especially associated with the ROS, and considers how these versatile regulatory mechanisms can be developed as useful tools for crop improvement.

KEY SCIENTIFIC CONCEPTS OF REVIEW

We have summarized the generation and elimination of ROS during seed germination, with a specific focus on uncovering and understanding the mechanisms of seed germination at the level of phytohormones, ROS, and epigenetic switches, as well as the close connections between them. The findings exhibit that ROS plays multiple roles in regulating the ethylene, ABA, and GA homeostasis as well as the Ca2+ signaling, NO signaling, and MAPK cascade in seed germination via either the signal trigger or the oxidative modifier agent. Further, ROS shows the potential in the nuclear genome remodeling and some epigenetic modifiers function, although the detailed mechanisms are unclear in seed germination. We propose that ROS functions as a hub in the complex network regulating seed germination.

Complex control of seed germination timing by ERF50 involves RGL2 antagonism and negative feedback regulation of DOG1

Seed dormancy governs germination timing, with both evolutionary and applied consequences. Despite extensive studies on the hormonal and genetic control of these processes, molecular mechanisms directly linking dormancy and germination remain poorly understood. By screening a collection of lines overexpressing Arabidopsis transcription factors, we identified ERF50 as a key gene to control dormancy and germination. To study its regulation, we measured seed-related physiological parameters in loss-of-function mutants and carried out transactivation, protein interaction and ChIP-PCR analyses. We found direct ERF50-mediated repression of DOG1 and activation of EXPA2 transcription, which results in enhanced seed germination. Although ERF50 expression is increased by DOG1 in dormant seeds, ERF50 germination-promoting activity is blocked by RGL2. The physiological, genetic and molecular evidence gathered here supports that ERF50 controls germination timing by regulating DOG1 levels to leverage its role as enhancer of seed germination, via RGL2 antagonism on EXPA2 expression. Our results highlight the central role of ERF50 as a feedback regulator to couple and fine-tune seed dormancy and germination.

Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.)

Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.

SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists

Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.

Unveiling Molecular Signatures in Light-Induced Seed Germination: Insights from PIN3, PIN7, and AUX1 in Arabidopsis thaliana

Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.

Chromatin Immunoprecipitation Using Imbibed Seeds of Arabidopsis thaliana

Chromatin immunoprecipitation (ChIP) is used to analyze the targeting of a protein to a specific region of chromatin in vivo. Here, we present an instructive ChIP protocol for Arabidopsis imbibed seeds. The protocol covers all steps, from the sampling of imbibed seeds to the reverse crosslinking of immunoprecipitated protein-DNA complexes, and includes experimental tips and notes. The targeting of the protein to DNA is determined by quantitative PCR (qPCR) using reverse crosslinked DNA. The protocol can be further scaled up for ChIP-sequencing (ChIP-seq) analysis. As an example of the protocol, we include a ChIP-quantitative PCR (ChIP-qPCR) analysis demonstrating the targeting of PIF1 to the ABI5 promoter.

The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module

The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In Arabidopsis thaliana, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the ζ, ε, and γ whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in Marchantia polymorpha, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals.

Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review

Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.

Brassinosteroids regulate cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis

Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFA contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 overexpression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.

The Role of Blue and Red Light in the Orchestration of Secondary Metabolites, Nutrient Transport and Plant Quality

Light is a fundamental environmental parameter for plant growth and development because it provides an energy source for carbon fixation during photosynthesis and regulates many other physiological processes through its signaling. In indoor horticultural cultivation systems, sole-source light-emitting diodes (LEDs) have shown great potential for optimizing growth and producing high-quality products. Light is also a regulator of flowering, acting on phytochromes and inducing or inhibiting photoperiodic plants. Plants respond to light quality through several light receptors that can absorb light at different wavelengths. This review summarizes recent progress in our understanding of the role of blue and red light in the modulation of important plant quality traits, nutrient absorption and assimilation, as well as secondary metabolites, and includes the dynamic signaling networks that are orchestrated by blue and red wavelengths with a focus on transcriptional and metabolic reprogramming, plant productivity, and the nutritional quality of products. Moreover, it highlights future lines of research that should increase our knowledge to develop tailored light recipes to shape the plant characteristics and the nutritional and nutraceutical value of horticultural products.

Withdrawn as duplicate: Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1

This article has been withdrawn due to an error that caused the article to be duplicated. The definitive version of this article is published under DOI https://doi.org/10.1093/plphys/kiad029.

Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60

BACKGROUND

Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield.

RESULTS

Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation.

CONCLUSIONS

A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.

Shade represses photosynthetic genes by disrupting the DNA binding of GOLDEN2-LIKE1

PHYTOCHROME-INTERACTING FACTORs (PIFs) repress photosynthetic genes partly by upregulating REPRESSOR OF PHOTOSYNTHETIC GENES 1 (RPGE1) and RPGE2. However, it is unknown how RPGEs inhibit gene expression at the molecular level. Here, we show that Arabidopsis (Arabidopsis thaliana) RPGE overexpression lines display extensive similarities to the golden2-like 1 (glk1)/glk2 double mutant at the phenotypic and transcriptomic levels, prompting us to hypothesize that there is a close molecular relationship between RPGEs and chloroplast development-regulating GLK transcription factors. Indeed, we found that RPGE1 disrupts the homodimerization of GLK1 by interacting with its dimerization domain and debilitates the DNA-binding activity of GLK1. The interaction was not restricted to the Arabidopsis RPGE1-GLK1 pair, but rather extended to RPGE-GLK homolog pairs across species, providing a molecular basis for the pale green leaves of Arabidopsis transgenic lines expressing a rice (Oryza sativa) RPGE homolog. Our discovery of RPGE-GLK regulatory pairs suggests that any condition leading to an increase in RPGE levels would decrease the expression levels of GLK target genes. Consistently, we found that shade, which upregulates the RPGE mRNA by stabilizing PIFs, represses the expression of photosynthetic genes partly by inhibiting the DNA-binding activity of GLK1. Taken together, these results indicate that RPGE-GLK regulatory pairs regulate photosynthetic gene expression downstream of PIFs.

Genome-Wide Characterization and Expression Analysis of Transcription Factor Families in Desert Moss Syntrichia caninervis under Abiotic Stresses

Transcription factor (TF) families play important roles in plant stress responses. S. caninervis is a new model moss for plant desiccation tolerance studies. Here, we report a high-confidence identification and characterization of 591 TFs representing 52 families that covered all chromosomes in S. caninervis. GO term and KEGG pathway analysis showed that TFs were involved in the regulation of transcription, DNA-templated, gene expression, binding activities, plant hormone signal transduction, and circadian rhythm. A number of TF promoter regions have a mixture of various hormones-related cis-regulatory elements. AP2/ERF, bHLH, MYB, and C2H2-zinc finger TFs were the overrepresented TF families in S. caninervis, and the detailed classification of each family is performed based on structural features. Transcriptome analysis revealed the transcript abundances of some ScAP2/ERF, bHLH, MYB, and C2H2 genes were accumulated in the treated S. caninervis under cold, dehydration, and rehydration stresses. The RT-qPCR results strongly agreed with RNA-seq analysis, indicating these TFs might play a key role in S. caninervis response to abiotic stress. Our comparative TF characterization and classification provide the foundations for functional investigations of the dominant TF genes involved in S. caninervis stress response, as well as excellent stress tolerance gene resources for plant stress resistance breeding.

Shade avoidance in the context of climate change

When exposed to changes in the light environment caused by neighboring vegetation, shade-avoiding plants modify their growth and/or developmental patterns to access more sunlight. In Arabidopsis (Arabidopsis thaliana), neighbor cues reduce the activity of the photosensory receptors phytochrome B (phyB) and cryptochrome 1, releasing photoreceptor repression imposed on PHYTOCHROME INTERACTING FACTORs (PIFs) and leading to transcriptional reprogramming. The phyB-PIF hub is at the core of all shade-avoidance responses, whilst other photosensory receptors and transcription factors contribute in a context-specific manner. CONSTITUTIVELY PHOTOMORPHOGENIC1 is a master regulator of this hub, indirectly stabilizing PIFs and targeting negative regulators of shade avoidance for degradation. Warm temperatures reduce the activity of phyB, which operates as a temperature sensor and further increases the activities of PIF4 and PIF7 by independent temperature sensing mechanisms. The signaling network controlling shade avoidance is not buffered against climate change; rather, it integrates information about shade, temperature, salinity, drought, and likely flooding. We, therefore, predict that climate change will exacerbate shade-induced growth responses in some regions of the planet while limiting the growth potential in others.

Alternative splicing in ABA signaling during seed germination

Seed germination is an essential step in a plant's life cycle. It is controlled by complex physiological, biochemical, and molecular mechanisms and external factors. Alternative splicing (AS) is a co-transcriptional mechanism that regulates gene expression and produces multiple mRNA variants from a single gene to modulate transcriptome diversity. However, little is known about the effect of AS on the function of generated protein isoforms. The latest reports indicate that alternative splicing (AS), the relevant mechanism controlling gene expression, plays a significant role in abscisic acid (ABA) signaling. In this review, we present the current state of the art about the identified AS regulators and the ABA-related changes in AS during seed germination. We show how they are connected with the ABA signaling and the seed germination process. We also discuss changes in the structure of the generated AS isoforms and their impact on the functionality of the generated proteins. Also, we point out that the advances in sequencing technology allow for a better explanation of the role of AS in gene regulation by more accurate detection of AS events and identification of full-length splicing isoforms.

Influence of Light of Different Spectral Compositions on Growth Parameters, Photosynthetic Pigment Contents and Gene Expression in Scots Pine Plantlets

The photoreceptors of red light (phytochromes) and blue light (cryptochromes) impact plant growth and metabolism. However, their action has been barely studied, especially in coniferous plants. Therefore, the influence of blue (maximum 450 nm), red (maximum 660 nm), white light (maxima 450 nm + 575 nm), far-red light (maximum 730 nm), white fluorescent light and dark on seed germination, growth, chlorophyll and carotenoid contents, as well as the transcript levels of genes involved in reception, photosynthesis, light and hormonal signaling of Scots pine plantlets, was investigated. The highest values of dry weight, root length and photosynthetic pigment contents were characteristic of 9-day-old plantlets grown under red light, whereas in the dark plantlet length, seed vigor, seed germination, dry weight and pigment contents were decreased. Under blue and white lights, the main studied morphological parameters were decreased or close to red light. The cotyledons were undeveloped under dark conditions, likely due to the reduced content of photosynthetic pigments, which agrees with the low transcript levels of genes encoding protochlorophyllide oxidoreductase (PORA) and phytoene synthase (PSY). The transcript levels of a number of genes involved in phytohormone biosynthesis and signaling, such as GA3ox, RRa, KAO and JazA, were enhanced under red light, unlike under dark conditions. We suggest that the observed phenomena of red light are the most important for the germination of the plantlets and may be based on earlier and enhanced expression of auxin, cytokinin, gibberellin and jasmonate signaling genes activated by corresponding photoreceptors. The obtained results may help to improve reforestation technology; however, this problem needs further study.

Systematic analysis of photo/sko-regulated germination and post-germination development of shallow photodormant seeds in Nicotiana tabacum L

INTRODUCTION

Light is a major environmental factor in regulating germination and post-germination development of shallow photo-dormant seeds in Nicotiana tabacum L. (tobacco). However, its molecular mechanism remains largely unclear.

METHODS AND RESULTS

In this study, we compared the phenotypes of the seeds germinated under light and dark, and systematically investigated their regulatory networks by integrating transcriptomic and proteomic data. Under light, the germination increased ~25%, the length of the hypocotyl shortened ~3 cm, and the apical hook disappeared. 9, 161, 342 differentially expressed genes (DEGs) and 128, 185, 81 differentially expressed proteins (DEPs) were regulated by light in the development stage of seed imbibition, radicle protrusion and cotyledon expansion respectively. 0, 19 and 1 co-up-regulated and 1, 30 and 64 co-down-regulated DEGs (DEP) were observed in the three stages, respectively. Of them, 2S albumin large chain, was down-regulated by light in imbibed seed. Oleosin 18.5 kDa (OLEO1) and Glyceraldehyde-3-phosphate dehydrogenase (GAPA1), Oxygen-evolving enhancer protein 1-1 and anchloroplastic (PSBO1), hub genes (proteins) in protein-protein interaction network (PPI), were downregulated and up-regulated in germinated seeds by light, respectively. OLEO1, a hub gene (proteins), was down-regulated by light in post-germination seedling.

CONCLUSION

These results systematically revealed the molecular networks regulated by light during germination and post-germination development of shallow photo-dormant tobacco seeds.

Histone Deacetylase HDA15 Restrains PHYB-Dependent Seed Germination via Directly Repressing GA20ox1/2 Gene Expression

Seed germination is essential for the colonization of the land plants. Light is a major environmental factor affecting seed germination, which is predominantly regulated by photoreceptor phytochrome B (PHYB). PHYB is activated by red light (designated as PHYB-on) whereas it is inactivated by far-red light (referred as PHYB-off). We previously reported that Arabidopsis histone deacetylase HDA15 interacts with phytochrome-interacting factor1 (PIF1) to repress seed germination under PHYB-off conditions. Here, we show that HDA15 plays a negative role in regulating seed germination under PHYB-on conditions. Overexpression of HDA15 in Arabidopsis restrains PHYB-dependent seed germination, while gibberellin (GA) relieves the repressive role of HDA15 under PHYB-off conditions. We further show that HDA15 directly binds to GA20ox1 and GA20ox2, two key GA biosynthesis genes and represses their expression by removal of histone H3 and H4 acetylation. Moreover, the levels of HDA15 transcript and HDA15 protein are up-regulated in the phyB mutant. Collectively, our work proposes that HDA15 acts as a negative regulator of PHYB-dependent seed germination by directly repressing GA20ox1/2 gene expression.

Phytochrome interacting factor regulates stomatal aperture by coordinating red light and abscisic acid

Stomata are crucial valves coordinating the fixation of carbon dioxide by photosynthesis and water loss through leaf transpiration. Phytochrome interacting factors (PIFs) are negative regulators of red light responses that belong to the basic helix-loop-helix family of transcription factors. Here, we show that the rice (Oryza sativa) PIF family gene OsPIL15 acts as a negative regulator of stomatal aperture to control transpiration in rice. OsPIL15 reduces stomatal aperture by activating rice ABSCISIC ACID INSENSITIVE 5 (OsABI5), which encodes a critical positive regulator of ABSCISIC ACID (ABA) signaling in rice. Moreover, OsPIL15 interacts with the NIGT1/HRS1/HHO family transcription factor rice HRS1 HOMOLOG 3 (OsHHO3) to possibly enhance the regulation of stomatal aperture. Notably, we discovered that the maize (Zea mays) PIF family genes ZmPIF1 and ZmPIF3, which are homologous to OsPIL15, are also involved in the regulation of stomatal aperture in maize, indicating that PIF-mediated regulation of stomatal aperture may be conserved in the plant lineage. Our findings explain the molecular mechanism by which PIFs play a role in red-light-mediated stomatal opening, and demonstrate that PIFs regulate stomatal aperture by coordinating the red light and ABA signaling pathways.

Role of cytokinins in seed development in pulses and oilseed crops: Current status and future perspective

Cytokinins constitutes a vital group of plant hormones regulating several developmental processes, including growth and cell division, and have a strong influence on grain yield. Chemically, they are the derivatives of adenine and are the most complex and diverse group of hormones affecting plant physiology. In this review, we have provided a molecular understanding of the role of cytokinins in developing seeds, with special emphasis on pulses and oilseed crops. The importance of cytokinin-responsive genes including cytokinin oxidases and dehydrogenases (CKX), isopentenyl transferase (IPT), and cytokinin-mediated genetic regulation of seed size are described in detail. In addition, cytokinin expression in germinating seeds, its biosynthesis, source-sink dynamics, cytokinin signaling, and spatial expression of cytokinin family genes in oilseeds and pulses have been discussed in context to its impact on increasing economy yields. Recently, it has been shown that manipulation of the cytokinin-responsive genes by mutation, RNA interference, or genome editing has a significant effect on seed number and/or weight in several crops. Nevertheless, the usage of cytokinins in improving crop quality and yield remains significantly underutilized. This is primarily due to the multigene control of cytokinin expression. The information summarized in this review will help the researchers in innovating newer and more efficient ways of manipulating cytokinin expression including CKX genes with the aim to improve crop production, specifically of pulses and oilseed crops.

Emerging roles of the ubiquitin-proteasome pathway in enhancing crop yield by optimizing seed agronomic traits

Ubiquitin-proteasome pathway has the potential to modulate crop productivity by influencing agronomic traits. Being sessile, the plant often uses the ubiquitin-proteasome pathway to maintain the stability of different regulatory proteins to survive in an ever-changing environment. The ubiquitin system influences plant reproduction, growth, development, responses to the environment, and processes that control critical agronomic traits. E3 ligases are the major players in this pathway, and they are responsible for recognizing and tagging the targets/substrates. Plants have a variety of E3 ubiquitin ligases, whose functions have been studied extensively, ranging from plant growth to defense strategies. Here we summarize three agronomic traits influenced by ubiquitination: seed size and weight, seed germination, and accessory plant agronomic traits particularly panicle architecture, tillering in rice, and tassels branch number in maize. This review article highlights some recent progress on how the ubiquitin system influences the stability/modification of proteins that determine seed agronomic properties like size, weight, germination and filling, and ultimately agricultural productivity and quality. Further research into the molecular basis of the aforementioned processes might lead to the identification of genes that could be modified or selected for crop development. Likewise, we also propose advances and future perspectives in this regard.

Integration of ABA, GA, and light signaling in seed germination through the regulation of ABI5

Seed germination is precisely controlled by a variety of signals, among which light signals and the phytohormones abscisic acid (ABA) and gibberellin (GA) play crucial roles. New findings have greatly increased our understanding of the mechanisms by which these three signals regulate seed germination and the close connections between them. Although much work has been devoted to ABA, GA, and light signal interactions, there is still no systematic description of their combination, especially in seed germination. In this review, we integrate ABA, GA, and light signaling in seed germination through the direct and indirect regulation of ABSCISIC ACID INSENSITIVE5 (ABI5), the core transcription factor that represses seed germination in ABA signaling, into our current understanding of the regulatory mechanism of seed germination.

Overexpressing Phytochrome Interacting Factor 8 of Myrothamnus flabellifolia Enhanced Drought and Salt Tolerance in Arabidopsis

Myrothamnus flabellifolia is the only woody resurrection plant found in the world and can survive from long-term desiccation. Therefore, M. flabellifolia could be considered as a valuable resource for study of plant adaptation to abiotic stress. However, few genes related to its drought tolerance have been functionally characterized and the molecular mechanisms underlying the stress tolerance of M. flabellifolia are largely unknown. The phytochrome interacting factor (PIF) family is a group of basic helix–loop–helix (bHLH) transcription factors and functions as the core regulator in plant growth and development. However, less is known of its participation in abiotic stress response. In this study, we isolated and characterized a dehydration-inducible PIF gene MfPIF8 from M. flabellifolia. Heterologous expression of MfPIF8 in Arabidopsis enhanced tolerance to drought and salinity stresses at seedling and adult stages. It significantly increased primary root length and stomatal aperture (ration of length/width) under stress treatments and decreased water loss rate. Compared with WT, the transgenic lines overexpressing MfPIF8 exhibited higher chlorophyll content and lower malondialdehyde accumulation. The abilities of osmotic adjustment and reactive oxygen species scavenging were also enhanced in MfPIF8 transgenic lines. These results suggest that MfPIF8 may participate in the positive regulation of abiotic stress responses. Additional investigation of its mechanism is needed in the future.

CONSTITUTIVE PHOTOMORPHOGENIC 1 promotes seed germination by destabilizing RGA-LIKE 2 in Arabidopsis

Under favorable moisture, temperature, and light conditions, gibberellin (GA) biosynthesis is induced and triggers seed germination. A major mechanism by which GA promotes seed germination is by promoting the degradation of the DELLA protein RGA-LIKE 2 (RGL2), a major repressor of germination in Arabidopsis (Arabidopsis thaliana) seeds. Analysis of seed germination phenotypes of constitutive photomorphogenic 1 (cop1) mutants and complemented COP1-OX/cop1-4 lines in response to GA and paclobutrazol (PAC) suggested a positive role for COP1 in seed germination and a relation with GA signaling. cop1-4 mutant seeds showed PAC hypersensitivity, but transformation with a COP1 overexpression construct rendered them PAC insensitive, with a phenotype similar to that of rgl2 mutant (rgl2-SK54) seeds. Furthermore, cop1-4 rgl2-SK54 double mutants showed a PAC-insensitive germination phenotype like that of rgl2-SK54, identifying COP1 as an upstream negative regulator of RGL2. COP1 interacted directly with RGL2, and in vivo this interaction was strongly enhanced by SUPPRESSOR OF PHYA-105 1. COP1 directly ubiquitinated RGL2 to promote its degradation. Moreover, GA stabilized COP1 with consequent RGL2 destabilization. By uncovering this COP1-RGL2 regulatory module, we reveal a mechanism whereby COP1 positively regulates seed germination and controls the expression of germination-promoting genes.

ABI3- and PIF1-mediated regulation of GIG1 enhances seed germination by detoxification of methylglyoxal in Arabidopsis

Methylglyoxal (MG) is a toxic by-product of the glycolysis pathway in most living organisms and was previously shown to inhibit seed germination. MG is detoxified by glyoxalase I and II family proteins in plants. MG is abundantly produced during early embryogenesis in Arabidopsis seeds. However, the mechanism that alleviates the toxic effect of MG in maturing seeds is poorly understood. In this study, by T-DNA mutant population screening, we found that mutations in a glyoxalase I gene (named GERMINATION-IMPAIRED GLYOXALASE 1, GIG1) led to significantly impaired germination compared with wild-type seeds. Transformation of full-length GIG1 cDNA under the constitutively active cauliflower mosaic virus 35S promoter in the gig1 background completely recovered the seed germination phenotype. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses revealed that GIG1 is uniquely expressed in seeds and is upregulated by abscisic acid (ABA) and downregulated by gibberellic acid (GA) during seed germination. An ABA signaling component, ABI3, directly activated GIG1 in maturing seeds. In addition, PHYTOCHROME INTERACTING FACTOR 1 (PIF1) also plays cooperatively with ABI3 in the regulation of GIG1 expression in the early stage of imbibed seeds. Furthermore, GIG1 expression is stably silenced by epigenetic repressors such as polycomb repressor complexes. Altogether, our results indicate that light and ABA signaling cooperate to enhance seed germination by the upregulation of GIG1 to detoxify MG in maturing seeds.

Comparative proteomics analysis of Arabidopsis thaliana response to light-emitting diode of narrow wavelength 450 nm, 595 nm, and 650 nm

Incident light is a central modulator of plant growth and development. However, there are still open questions surrounding wavelength-specific plant proteomic responses. Here we applied tandem mass tag based quantitative proteomics technology to acquire an in-depth view of proteome changes in Arabidopsis thaliana response to narrow wavelength blue (B; 450 nm), amber (A; 595 nm), or red (R; 650 nm) light treatments. A total of 16,707 proteins were identified with 9120 proteins quantified across all three light treatments in three biological replicates. This enabled examination of changes in the abundance for proteins with low abundance and important regulatory roles including transcription factors and hormone signaling. Importantly, 18% (1631 proteins) of the A. thaliana proteome is differentially abundant in response to narrow wavelength lights, and changes in proteome correlate well with different morphologies exhibited by plants. To showcase the usefulness of this resource, data were placed in the context of more than thirty published datasets, providing orthogonal validation and further insights into light-specific biological pathways, including Systemic Acquired Resistance and Shade Avoidance Syndrome. This high-resolution resource for A. thaliana provides baseline data and a tool for defining molecular mechanisms that control fundamental aspects of plant response to changing light conditions, with implications in plant development and adaptation. SIGNIFICANCE: Understanding of molecular mechanisms involved in wavelength-specific response of plant is question of widespread interest both to basic researchers and to those interested in applying such knowledge to the engineering of novel proteins, as well as targeted lighting systems. Here we sought to generate a high-resolution labeling proteomic profile of plant leaves, based on exposure to specific narrow-wavelength lights. Although changes in plant physiology in response to light spectral composition is well documented, there is limited knowledge on the roles of specific light wavelengths and their impact. Most previous studies have utilized relatively broad wavebands in their experiments. These multi-wavelengths lights function in a complex signaling network, which provide major challenges in inference of wavelength-specific molecular processes that underly the plant response. Besides, most studies have compared the effect of blue and red wavelengths comparing with FL, as control. As FL light consists the mixed spectra composition of both red and blue as well as numerous other wavelengths, comparing undeniably results in inconsistent and overlapping responses that will hamper effects to elucidate the plant response to specific wavelengths [1, 2]. Monitoring plant proteome response to specific wavelengths and further compare the changes to one another, rather than comparing plants proteome to FL, is thus necessary to gain the clear insights to specific underlying biological pathways and their effect consequences in plant response. Here, we employed narrow wavelength LED lights in our design to eliminate the potential overlap in molecular responses by ensuring non-overlapping wavelengths in the light treatments. We further applied TMT-labeling technology to gain a high-resolution view on the associates of proteome changes. Our proteomics data provides an in-depth coverage suitable for system-wide analyses, providing deep insights on plant physiological processes particularly because of the tremendous increase in the amount of identified proteins which outreach the other biological data.

Endosperm weakening: The gateway to a seed's new life

Seed germination is a crucial stage in a plant's life cycle, during which the embryo, surrounded by several tissues, undergoes a transition from the quiescent to a highly active state. Endosperm weakening, a key step in this transition, plays an important role in radicle protrusion. Endosperm weakening is initiated upon water uptake, followed by multiple key molecular events occurring within and outside endosperm cells. Although available transcriptomes have provided information about pivotal genes involved in this process, a complete understanding of the signaling pathways are yet to be elucidated. Much remains to be learnt about the diverse intercellular signals, such as reactive oxygen species-mediated redox signals, phytohormone crosstalk, environmental cue-dependent oxidative phosphorylation, peroxisomal-mediated pectin degradation, and storage protein mobilization during endosperm cell wall loosening. This review discusses the evidences from recent researches into the mechanism of endosperm weakening. Further, given that the endosperm has great potential for manipulation by crop breeding and biotechnology, we offer several novel insights, which will be helpful in this research field and in its application to the improvement of crop production.

Jasmonate regulates seed dormancy in wheat via modulating the balance between gibberellin and abscisic acid

Jasmonate (JA) regulates seed dormancy and germination; however, the underlying mechanisms remain poorly understood. Furthermore, it is unclear if JA is an essential regulator of dormancy and germination. We investigated whether the role of JA in regulating seed dormancy in wheat (Triticum aestivum L.) is mediated by modulation of gibberellin (GA)/abscisic acid (ABA) balance and if the reciprocal modulation of JA level and sensitivity is required for GA-mediated dormancy loss using physiological, pharmacological, and targeted transcriptomic and metabolomic approaches. JA-induced dormancy release in wheat seeds was associated with no change in GA level but up-regulation of GA signaling and ABA catabolism genes, and reduction of the ABA level. Although JA did not affect the expression levels of ABA signaling genes, up-regulation of germination-associated genes indicates a contribution of reduced ABA sensitivity to dormancy release. After-ripening-mediated dormancy loss was also associated with JA-GA synergistic and JA-ABA antagonistic interplays. The prevalence of no effect of GA, which effectively broke dormancy, on the JA-Ile level and expression patterns of JA biosynthesis/signaling and responsive genes reflects that GA-mediated dormancy release occurs independently of JA. Our study concludes that JA induces seed dormancy release in wheat via modulating ABA/GA balance; however, JA is not an essential regulator of dormancy and germination.

The phytochrome interacting proteins ERF55 and ERF58 repress light-induced seed germination in Arabidopsis thaliana

Seed germination is a critical step in the life cycle of plants controlled by the phytohormones abscisic acid (ABA) and gibberellin (GA), and by phytochromes, an important class of photoreceptors in plants. Here we show that light-dependent germination is enhanced in mutants deficient in the AP2/ERF transcription factors ERF55 and ERF58. Light-activated phytochromes repress ERF55/ERF58 expression and directly bind ERF55/ERF58 to displace them from the promoter of PIF1 and SOM, genes encoding transcriptional regulators that prevent the completion of germination. The same mechanism controls the expression of genes that encode ABA or GA metabolic enzymes to decrease levels of ABA and possibly increase levels of GA. Interestingly, ERF55 and ERF58 are themselves under transcriptional control of ABA and GA, suggesting that they are part of a self-reinforcing signalling loop which controls the completion of germination. Overall, we identified a role of ERF55/ERF58 in phytochrome-mediated regulation of germination completion.

The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis

AGAMOUS-Like 18 (AGL18) is a MADS domain transcription factor (TF) that is structurally related to AGL15. Here we show that, like AGL15, AGL18 can promote somatic embryogenesis (SE) when ectopically expressed in Arabidopsis (Arabidopsis thaliana). Based on loss-of-function mutants, AGL15 and AGL18 have redundant functions in developmental processes such as SE. To understand the nature of this redundancy, we undertook a number of studies to look at the interaction between these factors. We studied the genome-wide direct targets of AGL18 to characterize its roles at the molecular level using chromatin immunoprecipitation (ChIP)-SEQ combined with RNA-SEQ. The results demonstrated that AGL18 binds to thousands of sites in the genome. Comparison of ChIP-SEQ data for AGL15 and AGL18 revealed substantial numbers of genes bound by both AGL15 and AGL18, but there were also differences. Gene ontology analysis revealed that target genes were enriched for seed, embryo, and reproductive development as well as hormone and stress responses. The results also demonstrated that AGL15 and AGL18 interact in a complex regulatory loop, where AGL15 inhibited transcript accumulation of AGL18, while AGL18 increased AGL15 transcript accumulation. Co-immunoprecipitation revealed an interaction between AGL18 and AGL15 in somatic embryo tissue. The binding and expression analyses revealed a complex crosstalk and interactions among embryo TFs and their target genes. In addition, our study also revealed that phosphorylation of AGL18 and AGL15 was crucial for the promotion of SE.

The Opposite Roles of White Light in Regulating Germination of Fresh and Aged Seed in Tobacco

Light is one of the important environmental factors for seeds to evaluate whether the natural environment is appropriate for germination and subsequent seedlings emergence. The mechanism of light-mediated germination is mainly concerned with fresh seeds (FS) of model plants but is poorly understood in aged seeds. Here, the effects of light on germination of FS and naturally aged seeds (NAS) in tobacco and their relationship with plant hormones gibberellins (GA) and abscisic acid (ABA) were investigated. The results demonstrated that light promoted and inhibited the germination of FS and NAS, respectively. GA and ABA were involved in the germination control of NAS, as well as in FS. However, light suppressed GA signal and stimulated ABA signal in NAS, whereas it stimulated GA signal and suppressed ABA signal in FS. In addition, light stimulated the GA accumulation and reduction in ABA in FS while inhibiting the increase in GA level in NAS. Together, the present study demonstrates that light has opposite effects on the germination of FS and NAS, which are closely related to the metabolism and/or signaling of plant hormones ABA and GA.

Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects

Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.

The circadian-controlled PIF8-BBX28 module regulates petal senescence in rose flowers by governing mitochondrial ROS homeostasis at night

Reactive oxygen species (ROS) are unstable reactive molecules that are toxic to cells. Regulation of ROS homeostasis is crucial to protect cells from dysfunction, senescence, and death. In plant leaves, ROS are mainly generated from chloroplasts and are tightly temporally restricted by the circadian clock. However, little is known about how ROS homeostasis is regulated in nonphotosynthetic organs, such as petals. Here, we showed that hydrogen peroxide (H2O2) levels exhibit typical circadian rhythmicity in rose (Rosa hybrida) petals, consistent with the measured respiratory rate. RNA-seq and functional screening identified a B-box gene, RhBBX28, whose expression was associated with H2O2 rhythms. Silencing RhBBX28 accelerated flower senescence and promoted H2O2 accumulation at night in petals, while overexpression of RhBBX28 had the opposite effects. RhBBX28 influenced the expression of various genes related to respiratory metabolism, including the TCA cycle and glycolysis, and directly repressed the expression of SUCCINATE DEHYDROGENASE 1, which plays a central role in mitochondrial ROS (mtROS) homeostasis. We also found that PHYTOCHROME-INTERACTING FACTOR8 (RhPIF8) could activate RhBBX28 expression to control H2O2 levels in petals and thus flower senescence. Our results indicate that the circadian-controlled RhPIF8-RhBBX28 module is a critical player that controls flower senescence by governing mtROS homeostasis in rose.

Post-transcriptional regulation of seed dormancy and germination: Current understanding and future directions

Seed dormancy is a developmental checkpoint that prevents mature seeds from germinating under conditions that are otherwise favorable for germination. Temperature and light are the most relevant environmental factors that regulate seed dormancy and germination. These environmental cues can trigger molecular and physiological responses including hormone signaling, particularly that of abscisic acid and gibberellin. The balance between the content and sensitivity of these hormones is the key to the regulation of seed dormancy. Temperature and light tightly regulate the transcription of thousands of genes, as well as other aspects of gene expression such as mRNA splicing, translation, and stability. Chromatin remodeling determines specific transcriptional outputs, and alternative splicing leads to different outcomes and produces transcripts that encode proteins with altered or lost functions. Proper regulation of chromatin remodeling and alternative splicing may be highly relevant to seed germination. Moreover, microRNAs are also critical for the control of gene expression in seeds. This review aims to discuss recent updates on post-transcriptional regulation during seed maturation, dormancy, germination, and post-germination events. We propose future prospects for understanding how different post-transcriptional processes in crop seeds can contribute to the design of genotypes with better performance and higher productivity.

The PIF1-miR408-PLANTACYANIN repression cascade regulates light-dependent seed germination

Light-dependent seed germination is a vital process for many seed plants. A decisive event in light-induced germination is degradation of the central repressor PHYTOCHROME INTERACTING FACTOR 1 (PIF1). The balance between gibberellic acid (GA) and abscisic acid (ABA) helps to control germination. However, the cellular mechanisms linking PIF1 turnover to hormonal balancing remain elusive. Here, employing far-red light-induced Arabidopsis thaliana seed germination as the experimental system, we identified PLANTACYANIN (PCY) as an inhibitor of germination. It is a blue copper protein associated with the vacuole that is both highly expressed in mature seeds and rapidly silenced during germination. Molecular analyses showed that PIF1 binds to the miR408 promoter and represses miR408 accumulation. This in turn posttranscriptionally modulates PCY abundance, forming the PIF1-miR408-PCY repression cascade for translating PIF1 turnover to PCY turnover during early germination. Genetic analysis, RNA-sequencing, and hormone quantification revealed that PCY is necessary and sufficient to maintain the PIF1-mediated seed transcriptome and the low-GA-high-ABA state. Furthermore, we found that PCY domain organization and regulation by miR408 are conserved features in seed plants. These results revealed a cellular mechanism whereby PIF1-relayed external light signals are converted through PCY turnover to internal hormonal profiles for controlling seed germination.

Regulatory mechanism of GA3 on tuber growth by DELLA-dependent pathway in yam (Dioscorea opposita)

Endogenous and exogenous GA₃ responses to DoEXP and DoXTH depend on the DoGA20ox1, DoGA3ox1, DoGA2ox3, DoGA2ox4, DoGID1a, and DoDELLA1 to regulate yam tuber growth. Yam tuber undergoes significant alteration in morphogenesis and functions during growth, and gibberellins (GA) are considered potentially important regulators of tuber growth. However, it is little known about the regulation of GA metabolism and GA signaling components genes in tuber growth of yam. In this study, the cloning and expressions of GA₃ level, GA metabolism and signaling genes, and cell wall genes in tuber growth in response to GA₃ and GA biosynthesis inhibitor paclobutrazol (PP₃₃₃) treatments were studied. The contents of GA₃ accumulated at the tuber growth, with the highest levels in the early expansion stage. DoGA20ox1, DoGA3ox1, and four DoGA2ox genes were significantly abundant in the early expansion stage of tuber and gradually declined along with tuber growth. Three DoGID1 and three DoDELLA genes were showed different expression patterns in the early expansion stage of tuber and gradually declined along with tuber growth. Five DoEXP and three DoXTH genes expression levels were higher in the early expansion stage than in other stages. Exogenous GA₃ increased endogenous GA₃ levels, whereas the expression levels of DoGA20ox1, DoGA3ox1, DoGID1a, and DoDELLA1 were down-regulated in the early expansion stage of tuber by GA₃ treatment, DoGA2ox3 and DoGA2ox4 were up-regulated. PP₃₃₃ application exhibited opposite consequences. Thus, a mechanism of GA₃ regulating yam tuber growth by DELLA-dependent pathway is established.

PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants

The interplay between light receptors and PHYTOCHROME-INTERACTING FACTORs (PIFs) serves as a regulatory hub that perceives and integrates environmental cues into transcriptional networks of plants^1,2. Although occupancy of the histone variant H2A.Z and acetylation of histone H3 have emerged as regulators of environmentally responsive gene networks, how these epigenomic features interface with PIF activity is poorly understood^3-7. By taking advantage of rapid and reversible light-mediated manipulation of PIF7 subnuclear localization and phosphorylation, we simultaneously assayed the DNA-binding properties of PIF7, as well as its impact on chromatin dynamics genome wide. We found that PIFs act rapidly to reshape the H2A.Z and H3K9ac epigenetic landscape in response to a change in light quality. Furthermore, we discovered that PIFs achieve H2A.Z removal through direct interaction with EIN6 ENHANCER (EEN), the Arabidopsis thaliana homolog of the chromatin remodeling complex subunit INO80 Subunit 6 (Ies6). Thus, we describe a PIF-INO80 regulatory module that is an intermediate step for allowing plants to change their growth trajectory in response to environmental changes.

ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds

The germination timing of seeds is of the utmost adaptive importance for plant populations. Light is one of the best characterized factors promoting seed germination in several species. The germination is also finely regulated by changes in hormones levels, mainly those of gibberellin (GA) and abscisic acid (ABA). Here, we performed physiological, pharmacological, and molecular analyses to uncover the role of ATHB2, an HD-ZIP II transcription factor, in germination of Arabidopsis seeds. Our study demonstrated that ATHB2 is a negative regulator and sustains the expression of transcription factors to block germination promoted by light. Besides, we found that ATHB2 increases ABA sensitivity. Moreover, ABA and auxin content in athb2-2 mutant is higher than wild-type in dry seeds, but the differences disappeared during the imbibition in darkness and the first hours of exposition to light, respectively. Some ABA and light transcription factors are up-regulated by ATHB2, such as ABI5, ABI3, XERICO, SOMNUS and PIL5/PIF1. In opposition, PIN7, an auxin transport, is down-regulated. The role of ATHB2 as a repressor of germination induced by light affecting the gemination timing, could have differential effects on the establishment of seedlings altering the competitiveness between crops and weeds in the field.

Gene co-expression network analysis of the heat-responsive core transcriptome identifies hub genes in Brassica rapa

Gene co-expression network analysis of the heat-responsive core transcriptome in two contrasting Brassica rapa accessions reveals the main metabolic pathways, key modules and hub genes, are involved in long-term heat stress. Brassica rapa is a widely cultivated and economically important vegetable in Asia. High temperature is a common stress that severely impacts leaf head formation in B. rapa, resulting in reduced quality and production. The purpose of this study was thus to identify candidate heat tolerance genes by comparative transcriptome analysis of two contrasting B. rapa accessions in response to long-term heat stress. Two B. rapa accessions, '268' and '334', which showed significant differences in heat tolerance, were used for RNA sequencing analysis. We identified a total of 11,055 and 8921 differentially expressed genes (DEGs) in '268' and '334', respectively. Functional enrichment analyses of all of the identified DEGs, together with the genes identified from weighted gene co-expression network analyses (WGCNA), revealed that the autophagy pathway, glutathione metabolism, and ribosome biogenesis in eukaryotes were significantly up-regulated, whereas photosynthesis was down-regulated, in the heat resistance of B. rapa '268'. Furthermore, when B. rapa '334' was subjected to long-term high-temperature stress, heat stress caused significant changes in the expression of certain functional genes linked to protein processing in the endoplasmic reticulum and plant hormone signal transduction pathways. Autophagy-related genes might have been induced by persistent heat stress and remained high during recovery. Several hub genes like HSP17.6, HSP17.6B, HSP70-8, CLPB1, PAP1, PYR1, ADC2, and GSTF11 were discussed in this study, which may be potential candidates for further analyses of the response to long-term heat stress. These results should help elucidate the molecular mechanisms of heat stress adaptation in B. rapa.

Aethionema arabicum genome annotation using PacBio full-length transcripts provides a valuable resource for seed dormancy and Brassicaceae evolution research

Aethionema arabicum is an important model plant for Brassicaceae trait evolution, particularly of seed (development, regulation, germination, dormancy) and fruit (development, dehiscence mechanisms) characters. Its genome assembly was recently improved but the gene annotation was not updated. Here, we improved the Ae. arabicum gene annotation using 294 RNA-seq libraries and 136 307 full-length PacBio Iso-seq transcripts, increasing BUSCO completeness by 11.6% and featuring 5606 additional genes. Analysis of orthologs showed a lower number of genes in Ae. arabicum than in other Brassicaceae, which could be partially explained by loss of homeologs derived from the At-α polyploidization event and by a lower occurrence of tandem duplications after divergence of Aethionema from the other Brassicaceae. Benchmarking of MADS-box genes identified orthologs of FUL and AGL79 not found in previous versions. Analysis of full-length transcripts related to ABA-mediated seed dormancy discovered a conserved isoform of PIF6-β and antisense transcripts in ABI3, ABI4 and DOG1, among other cases found of different alternative splicing between Turkey and Cyprus ecotypes. The presented data allow alternative splicing mining and proposition of numerous hypotheses to research evolution and functional genomics. Annotation data and sequences are available at the Ae. arabicum DB (https://plantcode.online.uni-marburg.de/aetar_db).

Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization

Phytochrome-interacting factors (PIFs) are members of basic helix-loop-helix (bHLH) transcription factors and the primary partners of phytochromes (PHY) in light signaling. PIFs interact with the P_fr forms of phytochrome to play an important role in the pathways of response to light and temperature in plants. In this study, 30, 12, and 16 potential PIF genes were identified in Brassica napus, Brassica rapa, Brassica oleracea, respectively, which could be divided into three subgroups. The Br/Bo/BnaPIF genes are intron-rich and similar to the PIF genes in Arabidopsis. However, unlike the AtPIFs that exist in multiple alternative-splicing forms, the majority of Br/Bo/BnaPIF genes have no alternative-splicing forms. A total of 52 Br/Bo/BnaPIF proteins have both the conserved active PHYB binding (APB) and bHLH domains. The Ka/Ks ratio revealed that most BnaPIFs underwent purifying selection. A promoter analysis found that light-related, abscisic acid-related and MYB-binding sites were the most abundant in the promoters of BnaPIFs. BnaPIF genes displayed different spatiotemporal patterns of expression and were regulated by light quality, circadian rhythms, cold, heat, and vernalization. Our results are useful for understanding the biological functions of PIF proteins in rapeseed.

The transcription factor WRKY75 positively regulates jasmonate-mediated plant defense to necrotrophic fungal pathogens

Necrotrophic fungi cause devastating diseases in both horticultural and agronomic crops, but our understanding of plant defense responses against these pathogens is still limited. In this study, we demonstrated that WRKY75 positively regulates jasmonate (JA)-mediated plant defense against necrotrophic fungal pathogens Botrytis cinerea and Alternaria brassicicola, and also affects the sensitivity of plants to JA-inhibited seed germination and root growth. Quantitative analysis indicated that several JA-associated genes, such as OCTADECANOID-RESPONSIVE ARABIDOPSIS (ORA59) and PLANT DEFENSIN 1.2A (PDF1.2), were significantly reduced in expression in wrky75 mutants, and enhanced in WRKY75 overexpressing transgenic plants. Immunoprecipitation assays revealed that WRKY75 directly binds to the promoter of ORA59 and represses itstranscription. In vivo and in vitro experiments suggested that WRKY75 interacts with several JASMONATE ZIM-domain proteins, repressors of the JA signaling pathway. We determined that JASMONATE-ZIM-DOMAIN PROTEIN 8 (JAZ8) represses the transcriptional function of WRKY75, thereby attenuating the expression of its regulation. Overexpression of JAZ8 repressed plant defense responses to B. cinerea. Our study provides evidence that WRKY75 functions as a critical component of the JA-mediated signaling pathway to positively regulate Arabidopsis defense responses to necrotrophic pathogens.

Red Light and the Dormancy-Germination Decision in Arabidopsis Seeds

The Arabidopsis dormancy-germination transition is known to be environmentally cued and controlled by the competing hormones abscisic acid (ABA) and gibberellin (GA) produced by the seed. Recently, new molecular details have emerged concerning the propagation of red light through a complex gene regulatory network involving PhyB, PIF1, and RVE1. This network influences the formation of the PIF1-RVE1 complex [1,2]. The PIF1-RVE1 complex is a transcription factor that regulates the production of ABA and GA and helps shift the balance to high concentration of ABA and low concentration of GA, which corresponds to a dormant seed state. This newly discovered gene regulatory network has not been analyzed mathematically. Our analysis shows that this gene regulatory network exhibits switch-like bistability as a function of the red light input and makes a suite of biologically testable predictions concerning seed dormancy and germination in response to the amplitude and periodicity of an oscillatory red light input.

Basic Protein Modules Combining Abscisic Acid and Light Signaling in Arabidopsis

It is generally accepted that plants use the complex signaling system regulated by light and abscisic acid (ABA) signaling components to optimize growth and development in different situations. The role of ABA-light interactions is evident in the coupling of stress defense reactions with seed germination and root development, maintaining of stem cell identity and stem cell specification, stem elongation and leaf development, flowering and fruit formation, senescence, and shade avoidance. All these processes are regulated jointly by the ABA-light signaling system. Although a lot of work has been devoted to ABA-light signal interactions, there is still no systematic description of central signaling components and protein modules, which jointly regulate plant development. New data have emerged to promote understanding of how ABA and light signals are integrated at the molecular level, representing an extensively growing area of research. This work is intended to fill existing gaps by using literature data combined with bioinformatics analysis.