ARABIDOPSIS NITRATE REGULATED 1 acts as a negative modulator of seed germination by activating ABI3 expression

Integration of nitrate and abscisic acid signaling in plants

To meet the demands of the new Green Revolution and sustainable agriculture, it is important to develop crop varieties with improved yield, nitrogen use efficiency, and stress resistance. Nitrate is the major form of inorganic nitrogen available for plant growth in many well-aerated agricultural soils, and acts as a signaling molecule regulating plant development, growth, and stress responses. Abscisic acid (ABA), an important phytohormone, plays vital roles in integrating extrinsic and intrinsic responses and mediating plant growth and development in response to biotic and abiotic stresses. Therefore, elucidating the interplay between nitrate and ABA can contribute to crop breeding and sustainable agriculture. Here, we review studies that have investigated the interplay between nitrate and ABA in root growth modulation, nitrate and ABA transport processes, seed germination regulation, and drought responses. We also focus on nitrate and ABA interplay in several reported omics analyses with some important nodes in the crosstalk between nitrate and ABA. Through these insights, we proposed some research perspectives that could help to develop crop varieties adapted to a changing environment and to improve crop yield with high nitrogen use efficiency and strong stress resistance.

Linum usitatissimum AccD Enhances Seed Fatty Acid Accumulation and Tolerance to Environmental Stresses during Seed Germination in Arabidopsis thaliana

Flax (Linum usitatissimum L.), as an important oil-producing crop, is widely distributed throughout the world, and its seeds are rich in polyunsaturated fatty acids (FAs). Previous studies have revealed that Arabidopsis thaliana ACETYL-CoA CARBOXYLASE (AtACCase) is vital for FA biosynthesis. However, the functions of L. usitatissimum AccD (LuAccD) on FA accumulation and seed germination remain unclear. In the present study, we cloned the LuAccD coding sequence from the flax cultivar 'Longya 10', identified conserved protein domains, and performed a phylogenetic analysis to elucidate its relationship with homologs from a range of plant species. Ectopic expression of LuAccD in A. thaliana wild-type background enhanced seed FA accumulation without altering seed morphological characteristics, including seed size, 1000-seed weight, and seed coat color. Consistently, the expression of key genes involved in FA biosynthesis was greatly up-regulated in the developing seeds of LuAccD overexpression lines. Additionally, we demonstrated that LuAccD acts as a positive regulator of salt and mannitol tolerance during seed germination in A. thaliana. These results provide important insights into the functions of LuAccD, which facilitates the oil quantity and abiotic stress tolerance of oil-producing crops through genetic manipulation.

Nitric Oxide Regulates Seed Germination by Integrating Multiple Signalling Pathways

Seed germination is of great significance for plant development and crop yield. Recently, nitric oxide (NO) has been shown to not only serve as an important nitrogen source during seed development but also to participate in a variety of stress responses in plants to high salt, drought, and high temperature. In addition, NO can affect the process of seed germination by integrating multiple signaling pathways. However, due to the instability of NO gas activity, the network mechanism for its fine regulation of seed germination remains unclear. Therefore, this review aims to summarize the complex anabolic processes of NO in plants, to analyze the interaction mechanisms between NO-triggered signaling pathways and different plant hormones such as abscisic acid (ABA) and gibberellic acid (GA), ethylene (ET) and reactive oxygen species (ROS) signaling molecules, and to discuss the physiological responses and molecular mechanisms of seeds during the involvement of NO in abiotic stress, so as to provide a reference for solving the problems of seed dormancy release and improving plant stress tolerance.

Linum usitatissimum ABI3 enhances the accumulation of seed storage reserves and tolerance to environmental stresses during seed germination and seedling establishment in Arabidopsis thaliana

Flax (Linum usitatissimum) is an important oil crop in arid and semi-arid regions of North and Northwest China, and its seeds are rich in nutritious storage reserves, such as polyunsaturated fatty acids (FAs) and proteins. However, the regulatory networks that control the accumulation of seed storage reserves in flax are still largely unknown. In this study, we found that LuABI3-1 and LuABI3-2 homologs from the flax cultivar 'Longya 10' play important roles in regulating the accumulation of seed storage reserves in Arabidopsis thaliana. The results of subcellular localization and transcriptional activity assays showed that both LuABI3-1 and LuABI3-2 function as transcription factors. Overexpression of either LuABI3-1 or LuABI3-2 resulted in the significant increase in the contents of total seed FAs and storage proteins, but did not alter other key agronomic traits in A. thaliana. Accordingly, the expression of key genes involved in the biosynthesis of FAs and storage proteins was also greatly up-regulated in the developing seeds of LuABI3-1-overexpression lines. Additionally, both LuABI3-1 and LuABI3-2 enhanced the tolerance to the high salt and mannitol stresses during seed germination and seedling establishment in A. thaliana. These results increase our understanding of the LuABI3 regulatory functions and provide promising targets for genetic manipulation of L. usitatissimum to innovate the germplasm resources and cultivate high yield and quality varieties.

ALKBH9C, a potential RNA m6 A demethylase, regulates the response of Arabidopsis to abiotic stresses and abscisic acid

Although several studies have shown that AlkB homolog (ALKBH) proteins are potential RNA demethylases (referred to as 'erasers'), biological functions of only a few ALKBH proteins have been characterized to date. In this study, we determined the function of ALKBH9C (At4g36090) in seed germination and seedling growth of Arabidopsis thaliana in response to abiotic stress and abscisic acid (ABA). Seed germination of the alkbh9c mutant was delayed in response to salt, drought, cold and ABA. Moreover, seedling growth of the mutant was repressed under salt stress or ABA but enhanced under drought conditions. Notably, the stress-responsive phenotypes were associated with the altered expression of several m⁶ A-modified transcripts related to salt, drought or ABA response. Global m⁶ A levels were increased in the alkbh9c mutant, and ALKBH9C bound to m⁶ A-modified RNAs and had in vitro m⁶ A demethylase activity, suggesting its potential role as an m⁶ A eraser. The m⁶ A levels in several stress-responsive genes were increased in the alkbh9c mutant, and the stability of m⁶ A-modified transcripts was altered in the mutant. Collectively, our results suggest that m⁶ A eraser ALKBH9C is crucial for seed germination and seedling growth of Arabidopsis in response to abiotic stresses or ABA via affecting the stability of stress-responsive transcripts.

SALT AND ABA RESPONSE ERF1 improves seed germination and salt tolerance by repressing ABA signaling in rice

Rice (Oryza sativa) germination and seedling establishment, particularly in increasingly saline soils, are critical to ensure successful crop yields. Seed vigor, which determines germination and seedling growth, is a complex trait affected by exogenous (environmental) and endogenous (hormonal) factors. Here, we used genetic and biochemical analyses to uncover the role of an APETALA2-type transcription factor, SALT AND ABA RESPONSE ERF1 (OsSAE1), as a positive regulator of seed germination and salt tolerance in rice by repressing the expression of ABSCISIC ACID-INSENSITIVE5 (OsABI5). ossae1 knockout lines exhibited delayed seed germination, enhanced sensitivity to abscisic acid (ABA) during germination and in early seedling growth, and reduced seedling salt tolerance. OsSAE1 overexpression lines exhibited the converse phenotype, with increased seed germination and salt tolerance. In vivo and in vitro assays indicated that OsSAE1 binds directly to the promoter of OsABI5, a major downstream component of the ABA signaling pathway and acts as a major regulator of seed germination and stress response. Genetic analyses revealed that OsABI5-mediated ABA signaling functions downstream of OsSAE1. This study provides important insights into OsSAE1 regulation of seed vigor and salt tolerance and facilitates the practical use of OsSAE1 in breeding salt-tolerant varieties suitable for direct seeding cultivation.

The ABI3 Transcription Factor Interaction and Antagonism with Ubiquitin E3 Ligase ScPRT1 in Syntrichia caninervis

The ubiquitination pathway has been found to regulate plant responses to environmental stress. However, the role of E3 ubiquitin ligase in desiccation tolerant moss has not yet been elucidated. Previous research has shown that the abscisic acid (ABA) signaling factor ScABI3 can significantly increase desiccation tolerance and reduce ABA sensitivity in the desert moss Syntrichia caninervis. In this study, we identified a RING-type E3 ubiquitin ligase, ScPRT1, and showed that ScABI3 can directly interact with ScPRT1 in vitro and in vivo. Furthermore, we found that the high expression of ScPRT1 can interfere with the transcription of ScABI3 under ABA treatment. Therefore, we speculate that ScPRT1 may degrade ScABI3 through the ubiquitin-26S proteasome system and participate in ABA-dependent signaling in response to ABA-insensitivity or desiccation tolerance in S. caninervis. The findings from our study may enrich our knowledge of the role of E3 ubiquitin ligase in desiccation tolerance and lay a theoretical foundation for an in-depth study of the relationship between ubiquitination modification and ABA signal transduction under environmental stress.

Arabidopsis MADS-box factor AGL16 is a negative regulator of plant response to salt stress by downregulating salt-responsive genes

Sessile plants constantly experience environmental stresses in nature. They must have evolved effective mechanisms to balance growth with stress response. Here we report the MADS-box transcription factor AGL16 acting as a negative regulator in stress response in Arabidopsis. Loss-of-AGL16 confers resistance to salt stress in seed germination, root elongation and soil-grown plants, while elevated AGL16 expression confers the opposite phenotypes compared with wild-type. However, the sensitivity to abscisic acid (ABA) in seed germination is inversely correlated with AGL16 expression levels. Transcriptomic comparison revealed that the improved salt resistance of agl16 mutants was largely attributed to enhanced expression of stress-responsive transcriptional factors and the genes involved in ABA signalling and ion homeostasis. We further demonstrated that AGL16 directly binds to the CArG motifs in the promoter of HKT1;1, HsfA6a and MYB102 and represses their expression. Genetic analyses with double mutants also support that HsfA6a and MYB102 are target genes of AGL16. Taken together, our results show that AGL16 acts as a negative regulator transcriptionally suppressing key components in the stress response and may play a role in balancing stress response with growth.

MYB70 modulates seed germination and root system development in Arabidopsis

Crosstalk among ABA, auxin, and ROS plays critical roles in modulating seed germination, root growth, and suberization. However, the underlying molecular mechanisms remain largely elusive. Here, MYB70, a R2R3-MYB transcription factor was shown to be a key component of these processes in Arabidopsis thaliana. myb70 seeds displayed decreased sensitivity, while MYB70-overexpressing OX70 seeds showed increased sensitivity in germination in response to exogenous ABA through MYB70 physical interaction with ABI5 protein, leading to enhanced stabilization of ABI5. Furthermore, MYB70 modulates root system development (RSA) which is associated with increased conjugated IAA content and H₂O₂/O₂^⋅− ratio but reduced root suberin deposition, consequently affecting nutrient uptake. In support of these data, MYB70 positively regulates the expression of auxin conjugation-related GH3, while negatively peroxidase-encoding and suberin biosynthesis-related genes. Our findings collectively revealed a previously uncharacterized component that modulates ABA and auxin signaling pathways, H₂O₂/O₂^⋅− balance, and suberization, consequently regulating RSA and seed germination.

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MYB70 regulates seed germination by enhancing ABA signaling via interaction with ABI5

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MYB70 activates the IAA conjugation process by upregulating GH3 genes expression

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MYB70 mediates root growth via repression of PER genes

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MYB70 negatively regulates suberin biosynthesis in roots

OsABF1 Represses Gibberellin Biosynthesis to Regulate Plant Height and Seed Germination in Rice (Oryza sativa L.)

Gibberellins (GAs) are diterpenoid phytohormones regulating various aspects of plant growth and development, such as internode elongation and seed germination. Although the GA biosynthesis pathways have been identified, the transcriptional regulatory network of GA homeostasis still remains elusive. Here, we report the functional characterization of a GA-inducible OsABF1 in GA biosynthesis underpinning plant height and seed germination. Overexpression of OsABF1 produced a typical GA-deficient phenotype with semi-dwarf and retarded seed germination. Meanwhile, the phenotypes could be rescued by exogenous GA₃, suggesting that OsABF1 is a key regulator of GA homeostasis. OsABF1 could directly suppress the transcription of green revolution gene SD1, thus reducing the endogenous GA level in rice. Moreover, OsABF1 interacts with and transcriptionally antagonizes to the polycomb repression complex component OsEMF2b, whose mutant showed as similar but more severe phenotype to OsABF1 overexpression lines. It is suggested that OsABF1 recruits RRC2-mediated H3K27me3 deposition on the SD1 promoter, thus epigenetically silencing SD1 to maintain the GA homeostasis for growth and seed germination. These findings shed new insight into the functions of OsABF1 and regulatory mechanism underlying GA homeostasis in rice.

Comparative transcriptome analysis reveals function of TERF1 in promoting seed germination

Seed germination marks a new life cycle of a plant. Although ethylene promotes seed germination, the underlying molecular mechanism is poorly understood. Ethylene Responsive Factors (ERFs) play an essential role in ethylene signaling. Here we show that overexpression of Tomato Ethylene Responsive Factor 1 (TERF1), an ERF transcription factor isolated from tomato, can promote tobacco seed germination at 23 °C in darkness. Hormones analysis showed that salicylic acid (SA), 3-indoleacetic acid (IAA), abscisic acid (ABA) and gibberellic acids (GAs) were significantly increased by TERF1, while jasmonic acid (JA) was significantly reduced in TERF1 seeds. Transcriptome analysis identified 7,961 differentially expressed genes (DEGs), including 6,213 mRNAs, 25 miRNAs, 1,581 lncRNAs and 141 circRNAs. Gene Ontology (GO) enrichment analysis showed that cell cycles, sugar metabolism, microtubule-based processes were activated by TERF1, while DNA repair, lipid metabolism were repressed by TERF1. We also identified differentially expressed regulatory genes for ABA and GA biosynthesis or signaling in TERF1 seed, including transcription factors, kinases, phosphatases and ubiquitin protein ligases, non-coding RNAs (ncRNAs). At posttranscriptional level TERF1 also regulates gene expression through alternative splicing (AS). Protein-protein interaction (PPI) network analysis revealed three key biological processes regulated by TERF1, including nitrogen metabolism, light related processes and mitosis. Pheynotype and gene expression analysis showed that TERF1 significantly reduced seed sensitivity to ABA and auxin during germination through repressing key components of ABA signaling pathway. Our results unraveled the function of TERF1 in promoting seed germination.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01049-4.

The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice

Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, "conditionally neutral" alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.

Pre-harvest sprouting in cereals: genetic and biochemical mechanisms

With the growth of the global population and the increasing frequency of natural disasters, crop yields must be steadily increased to enhance human adaptability to risks. Pre-harvest sprouting (PHS), a term mainly used to describe the phenomenon in which grains germinate on the mother plant directly before harvest, is a serious global problem for agricultural production. After domestication, the dormancy level of cultivated crops was generally lower than that of their wild ancestors. Although the shortened dormancy period likely improved the industrial performance of cereals such as wheat, barley, rice, and maize, the excessive germination rate has caused frequent PHS in areas with higher rainfall, resulting in great economic losses. Here, we systematically review the causes of PHS and its consequences, the major indicators and methods for PHS assessment, and emphasize the biological significance of PHS in crop production. Wheat quantitative trait loci functioning in the control of PHS are also comprehensively summarized in a meta-analysis. Finally, we use Arabidopsis as a model plant to develop more complete PHS regulatory networks for wheat. The integration of this information is conducive to the development of custom-made cultivated lines suitable for different demands and regions, and is of great significance for improving crop yields and economic benefits.

Maize transcription factor ZmEREB20 enhanced salt tolerance in transgenic Arabidopsis

Soil salinity severely limits agricultural crop production worldwide. As one of the biggest plant specific transcription factor families, AP2/ERF members have been extensively studied to regulate plant growth, development and stress responses. However, the role of AP2/ERF family in maize salt tolerance remains largely unknown. In this study, we identified a maize AP2-ERF family member ZmEREB20 as a positive salinity responsive gene. Overexpression of ZmEREB20in Arabidopsis enhanced ABA sensitivity and resulted in delayed seed germination under salt stress through regulating ABA and GA related genes. ZmEREB20 overexpression lines also showed higher survival rates with elevated ROS scavenging toward high salinity. Furthermore, root hair growth inhibition by salt stress was markedly rescued in ZmEREB20 overexpression lines. Auxin transport inhibitor TIBA drastically enhanced root hair growth in ZmEREB20 overexpression Arabidopsis under salt stress, together with the increased expression of auxin-related genes, ion transporter genes and root hair growth genes by RNA-seq analysis. ZmEREB20 positively regulated salt tolerance through the molecular mechanism associated with hormone signaling, ROS scavenging and root hair plasticity, proving the potential target for crop breeding to improve salt resistance.