Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation

Advance computational tools for multiomics data learning

The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial role in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.

ABSCISIC ACID INSENSITIVE 3 promotes auxin signalling by regulating SHY2 expression to control primary root growth in response to dehydration stress

Plants combat dehydration stress through different strategies including root architectural changes. Here we show that when exposed to varying levels of dehydration stress, primary root growth in Arabidopsis is modulated by regulating root meristem activity. Abscisic acid (ABA) in concert with auxin signalling adjust primary root growth according to stress levels. ABSCISIC ACID INSENSITIVE 3 (ABI3), an ABA-responsive transcription factor, stands at the intersection of ABA and auxin signalling and fine-tunes primary root growth in response to dehydration stress. Under low ABA or dehydration stress, induction of ABI3 expression promotes auxin signalling by decreasing expression of SHY2, a negative regulator of auxin response. This further enhances the expression of auxin transporter gene PIN1 and cell cycle gene CYCB1;1, resulting in an increase in primary root meristem size and root length. Higher levels of dehydration stress or ABA repress ABI3 expression and promote ABSCISIC ACID INSENSITIVE 5 (ABI5) expression. This elevates SHY2 expression, thereby impairing primary root meristem activity and retarding root growth. Notably, ABI5 can promote SHY2 expression only in the absence of ABI3. Such ABA concentration-dependent expression of ABI3 therefore functions as a regulatory sensor of dehydration stress levels and orchestrates primary root growth by coordinating its downstream regulation.

Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn.

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.

Dormancy heterogeneity among Arabidopsis thaliana seeds is linked to individual seed size

Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops produce visually homogenous seeds. Using automated phenotype analysis, we observed that small seeds in Arabidopsis tend to have higher primary and secondary dormancy levels than large seeds. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds have higher expression of translation-related genes implicated in germination competence. By contrast, small seeds have elevated expression of many positive regulators of dormancy, including a key regulator of this process, the DOG1 gene. Differences in DOG1 expression are associated with differential production of its alternative cleavage and polyadenylation isoforms; in small seeds, the proximal poly(A) site is selected, resulting in a short mRNA isoform. Furthermore, single-seed RNA sequencing analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single-seed level, expression of genes affected by seed size is correlated with expression of genes that position seeds on the path toward germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species that produces highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.

Melatonin as a key regulator in seed germination under abiotic stress

Seed germination (SG) is the first stage in a plant's life and has an immense importance in sustaining crop production. Abiotic stresses reduce SG by increasing the deterioration of seed quality, and reducing germination potential, and seed vigor. Thus, to achieve a sustainable level of crop yield, it is important to improve SG under abiotic stress conditions. Melatonin (MEL) is an important biomolecule that interplays in developmental processes and regulates many adaptive responses in plants, especially under abiotic stresses. Thus, this review specifically summarizes and discusses the mechanistic basis of MEL-mediated SG under abiotic stresses. MEL regulates SG by regulating some stress-specific responses and some common responses. For instance, MEL induced stress specific responses include the regulation of ionic homeostasis, and hydrolysis of storage proteins under salinity stress, regulation of C-repeat binding factors signaling under cold stress, starch metabolism under high temperature and heavy metal stress, and activation of aquaporins and accumulation of osmolytes under drought stress. On other hand, MEL mediated regulation of gibberellins biosynthesis and abscisic acid catabolism, redox homeostasis, and Ca2+ signaling are amongst the common responses. Nonetheless factors such as endogenous MEL contents, plant species, and growth conditions also influence above-mentioned responses. In conclusion, MEL regulates SG under abiotic stress conditions by interacting with different physiological mechanisms.

Carotenoid Cleavage Dioxygenase 1 and Its Application for the Production of C13-Apocarotenoids in Microbial Cell Factories: A Review

C13-apocarotenoids are naturally derived from the C9-C10 (C9'-C10') double-bond cleavage of carotenoids by carotenoid cleavage dioxygenases (CCDs). As high-value flavors and fragrances in the food and cosmetic industries, the sustainable production of C13-apocarotenoids is emerging in microbial cell factories by the carotenoid cleavage dioxygenase 1 (CCD1) subfamily. However, the commercialization of microbial-based C13-apocarotenoids is still limited by the poor performance of CCD1, which severely constrains its conversion efficiency from precursor carotenoids. This review focuses on the classification of CCDs and their cleavage modes for carotenoids to generate corresponding apocarotenoids. We then emphatically discuss the advances for C13-apocarotenoid biosynthesis in microbial cell factories with various strategies, including optimization of CCD1 expression, improvement of CCD1's catalytic activity and substrate specificity, strengthening of substrate channeling, and development of oleaginous microbial hosts, which have been verified to increase the conversion rate from carotenoids. Lastly, the current challenges and future directions will be discussed to enhance CCDs' application for C13-apocarotenoids biomanufacturing.

The Soybean Expression Atlas v2: A comprehensive database of over 5000 RNA-seq samples

Soybean is a crucial crop worldwide, used as a source of food, feed, and industrial products due to its high protein and oil content. Previously, the rapid accumulation of soybean RNA-seq data in public databases and the computational challenges of processing raw RNA-seq data motivated us to develop the Soybean Expression Atlas, a gene expression database of over a thousand RNA-seq samples. Over the past few years, our database has allowed researchers to explore the expression profiles of important gene families, discover genes associated with agronomic traits, and understand the transcriptional dynamics of cellular processes. Here, we present the Soybean Expression Atlas v2, an updated version of our database with a fourfold increase in the number of samples, featuring transcript- and gene-level transcript abundance matrices for 5481 publicly available RNA-seq samples. New features in our database include the availability of transcript-level abundance estimates and equivalence classes to explore differential transcript usage, abundance estimates in bias-corrected counts to increase the accuracy of differential gene expression analyses, a new web interface with improved data visualization and user experience, and a reproducible and scalable pipeline available as an R package. The Soybean Expression Atlas v2 is available at https://soyatlas.venanciogroup.uenf.br/, and it will accelerate soybean research, empowering researchers with high-quality and easily accessible gene expression data.

Cucumber abscisic acid 8'-hydroxylase Csyf2 regulates yellow flesh by modulating carotenoid biosynthesis

Cucumber (Cucumis sativus L.) flesh is typically colorless or pale green. Flesh with yellow or orange pigment, determined mainly by carotenoid content and composition, is mostly found in semi-wild Xishuangbanna cucumber, which has a very narrow genetic background. Here, we identified a spontaneous cucumber mutant with yellow flesh (yf-343), which accumulated more β-cryptoxanthin and less lutein than regular cultivated European glasshouse-type cucumbers. Genetic analysis revealed that the yellow flesh phenotype was controlled by a single recessive gene. Through fine mapping and gene sequencing, we identified the candidate gene C. sativus yellow flesh 2 (Csyf2), encoding an abscisic acid (ABA) 8'-hydroxylase. Overexpression and RNAi-silencing of Csyf2 in cucumber hairy roots produced lower and higher ABA contents than in non-transgenic controls, respectively. Further, RNA-seq analysis suggested that genes related to ABA signal transduction were differentially expressed in fruit flesh between yf-343 and its wild type, BY, with white flesh. The carotenoid biosynthesis pathway was specifically enriched in fruit flesh at 30 days after pollination when yf-343 fruit flesh turns yellow. Our findings highlight a promising target for gene editing to increase carotenoid content, expanding our genetic resources for pigmented cucumber flesh breeding for improving the nutritional quality of cucumber.

Effect of high salinity and of priming of non-germinated seeds by UV-C light on photosynthesis of lettuce plants grown in a controlled soilless system

High salinity results in a decrease in plant photosynthesis and crop productivity. The aim of the present study was to evaluate the effect of UV-C priming treatments of lettuce seeds on photosynthesis of plants grown at high salinity. Non-primed and primed seeds were grown in an hydroponic system, with a standard nutrient solution, either supplemented with 100 mM NaCl (high salinity), or not (control). Considering that leaf and root K⁺ concentrations remained constant and that chlorophyll fluorescence parameters and root growth were not affected negatively in the high salinity treatment, we conclude that the latter was at the origin of a moderate stress only. A substantial decrease in leaf net photosynthetic assimilation (A_net) was however observed as a consequence of stomatal and non-stomatal limitations in the high salinity treatment. This decrease in A_net translated into a decrease in growth parameters; it may be attributed partially to the high salinity-associated increase in leaf concentration in abscisic acid and decrease in stomatal conductance. Priming by UV-C light resulted in an increase in total photosynthetic electron transport rate and A_net in the leaves of plants grown at high salinity. The increase of the latter translated into a moderate increase in growth parameters. It is hypothesized that the positive effect of UV-C priming on A_net and growth of the aerial part of lettuce plants grown at high salinity, is mainly due to its stimulating effect on leaf concentration in salicylic acid. Even though leaf cytokinins' concentration was higher in plants from primed seeds, maintenance of the cytokinins-to-abscisic acid ratio also supports the idea that UV-C priming resulted in protection of plants exposed to high salinity.

Linking plant functional genes to rhizosphere microbes: a review

The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant-microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene-related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe-host gene interactions, which could potentially be used for managing plant health in agricultural systems.

The Arabidopsis pre-mRNA 3' end processing related protein FIP1 promotes seed dormancy via the DOG1 and ABA pathways

Seed dormancy is an important adaptive trait to prevent germination occurring at an inappropriate time. The mechanisms governing seed dormancy and germination are complex. Here, we report that FACTOR INTERACTING WITH POLY(A) POLYMERASE 1 (FIP1), a component of the pre-mRNA 3' end processing machinery, is involved in seed dormancy and germination processes in Arabidopsis thaliana. FIP1 is mainly expressed in seeds and the knockout of FIP1 causes reduced seed dormancy, indicating that FIP1 positively influences seed dormancy. Meanwhile, fip1 mutants are insensitive to exogenous ABA during seed germination and early seedling establishment. The terms 'seed maturation' and 'response to ABA stimulus' are significantly enriched in a gene ontology analysis based on genes differentially expressed between fip1-1 and the wild type. Several of these genes, including ABI5, DOG1 and PYL12, show significantly decreased transcript levels in fip1. Genetic analysis showed that either cyp707a2 or dog1-5 partially, but in combination completely, represses the reduced seed dormancy of fip1, indicating that the double mutant cyp707a2 dog1-5 is epistatic to fip1. Moreover, FIP1 is required for CFIM59, another component of pre-mRNA 3' end processing machinery, to govern seed dormancy and germination. Overall, we identified FIP1 as a regulator of seed dormancy and germination that plays a crucial role in governing these processes through the DOG1 and ABA pathways.

The RING-H2 gene LdXERICO plays a negative role in dormancy release regulated by low temperature in Lilium davidii var. unicolor

Dormancy regulation is the basis of the sustainable development of the lily industry. Therefore, basic research on lily dormancy is crucial for innovation in lily cultivation and breeding. Previous studies revealed that dormancy release largely depends on abscisic acid (ABA) degradation. However, the key genes and potential regulatory network remain unclear. We used exogenous ABA and ABA inhibitors to elucidate the effect of ABA on lily dormancy. Based on the results of weighted gene coexpression network analysis (WGCNA), the hub gene LdXERICO was identified in modules highly related to endogenous ABA, and a large number of coexpressed genes were identified. LdXERICO was induced by exogenous ABA and expressed at higher levels in tissues with vigorous physiological activity. Silencing LdXERICO increased the low-temperature sensitivity of bulblets and accelerated bulblet sprouting. LdXERICO rescued the ABA insensitivity of xerico mutants during seed germination in Arabidopsis, suggesting that it promotes seed dormancy and supporting overexpression studies on lily bulblets. The significant increase in ABA levels in transgenic Arabidopsis expressing LdXERICO indicated that LdXERICO played a role by promoting ABA synthesis. We generated three transgenic lines by overexpressing LdICE1 in Arabidopsis thaliana and showed that, in contrast to LdXERICO, LdICE1 positively regulated dormancy release. Finally, qRT-PCR confirmed that LdXERICO was epistatic to LdICE1 for dormancy release. We propose that LdXERICO, an essential gene in dormancy regulation through the ABA-related pathway, has a complex regulatory network involving temperature signals. This study provides a theoretical basis for further exploring the mechanism of bulb dormancy release.

Mass spectrometric exploration of phytohormone profiles and signaling networks

Phytohormones have crucial roles in plant growth, development, and acclimation to environmental stress; however, measuring phytohormone levels and unraveling their complex signaling networks and interactions remains challenging. Mass spectrometry (MS) has revolutionized the study of complex biological systems, enabling the comprehensive identification and quantification of phytohormones and their related targets. Here, we review recent advances in MS technologies and highlight studies that have used MS to discover and analyze phytohormone-mediated molecular events. In particular, we focus on the application of MS for profiling phytohormones, elucidating phosphorylation signaling, and mapping protein interactions in plants.

Genetic mapping and functional genomics of soybean seed protein

Soybean is an utterly important crop for high-quality meal protein and vegetative oil. Soybean seed protein content has become a key factor in nutrients for livestock feed as well as human dietary consumption. Genetic improvement of soybean seed protein is highly desired to meet the demands of rapidly growing world population. Molecular mapping and genomic analysis in soybean have identified many quantitative trait loci (QTL) underlying seed protein content control. Exploring the mechanisms of seed storage protein regulation will be helpful to achieve the improvement of protein content. However, the practice of breeding higher protein soybean is challenging because soybean seed protein is negatively correlated with seed oil content and yield. To overcome the limitation of such inverse relationship, deeper insights into the property and genetic control of seed protein are required. Recent advances of soybean genomics have strongly enhanced the understandings for molecular mechanisms of soybean with better seed quality. Here, we review the research progress in the genetic characteristics of soybean storage protein, and up-to-date advances of molecular mappings and genomics of soybean protein. The key factors underlying the mechanisms of the negative correlation between protein and oil in soybean seeds are elaborated. We also briefly discuss the future prospects of breaking the bottleneck of the negative correlation to develop high protein soybean without penalty of oil and yield.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01373-5.

Effects of seasonal temperature regimes on embryo growth and endogenous hormones of Taxus chinensis var. mairei seeds

Seed dormancy is a mechanism that prevents seeds from germinating at times of the year when conditions are unfavorable, that is, when the chance of seed survival is low. Determining the seasonal dynamics of seed dormancy is important for exploring how plant regeneration is adapted to the environment. We studied the seed dormancy status of Taxus chinensis var. mairei, an endangered species in China, under simulated seasonal temperature regimes. The embryo length, embryo-to-seed (E : S) ratio, and percentage of seeds with a split seed coat increased when seeds were stratified at spring and autumn temperature regimes. The abscisic acid (ABA) content decreased during stratification at simulated seasonal temperatures, but no obvious pattern in the content of gibberellic acid (GA) and indole acetic acid (IAA) was observed. The GA-ABA and IAA-ABA ratios increased during stratification. These results suggest that T. chinensis var. mairei seeds have morphophysiological dormancy, and that the seasonal dynamics of seed dormancy break are controlled by endogenous hormones and their balances, which was confirmed by the results of a field experiment. Our study provides useful information for understanding the natural population regeneration and propagation of this threatened species.

Endosperm cellularization failure induces a dehydration-stress response leading to embryo arrest

The endosperm is a nutritive tissue supporting embryo growth in flowering plants. Most commonly, the endosperm initially develops as a coenocyte (multinucleate cell) and then cellularizes. This process of cellularization is frequently disrupted in hybrid seeds generated by crosses between different flowering plant species or plants that differ in ploidy, resulting in embryo arrest and seed lethality. The reason for embryo arrest upon cellularization failure remains unclear. In this study, we show that triploid Arabidopsis thaliana embryos surrounded by uncellularized endosperm mount an osmotic stress response that is connected to increased levels of abscisic acid (ABA) and enhanced ABA responses. Impairing ABA biosynthesis and signaling aggravated triploid seed abortion, while increasing endogenous ABA levels as well as the exogenous application of ABA-induced endosperm cellularization and suppressed embryo growth arrest. Taking these results together, we propose that endosperm cellularization is required to establish dehydration tolerance in the developing embryo, ensuring its survival during seed maturation.

Recent progress in molecular genetics and omics-driven research in seed biology

Elucidating the mechanisms that control seed development, metabolism, and physiology is a fundamental issue in biology. Michel Caboche had long been a catalyst for seed biology research in France up until his untimely passing away last year. To honour his memory, we have updated a review written under his coordination in 2010 entitled "Arabidopsis seed secrets unravelled after a decade of genetic and omics-driven research". This review encompassed different molecular aspects of seed development, reserve accumulation, dormancy and germination, that are studied in the lab created by M. Caboche. We have extended the scope of this review to highlight original experimental approaches implemented in the field over the past decade such as omics approaches aimed at investigating the control of gene expression, protein modifications, primary and specialized metabolites at the tissue or even cellular level, as well as seed biodiversity and the impact of the environment on seed quality.

Abscisic acid inhibits primary root growth by impairing ABI4-mediated cell cycle and auxin biosynthesis

Cell cycle progression and the phytohormones auxin and abscisic acid (ABA) play key roles in primary root growth, but how ABA mediates the transcription of cell cycle-related genes and the mechanism of crosstalk between ABA and auxin requires further research. Here, we report that ABA inhibits primary root growth by regulating the ABA INSENSITIVE4 (ABI4)-CYCLIN-DEPENDENT KINASE B2;2 (CDKB2;2)/CYCLIN B1;1 (CYCB1;1) module-mediated cell cycle as well as auxin biosynthesis in Arabidopsis (Arabidopsis thaliana). ABA induced ABI4 transcription in the primary root tip, and the abi4 mutant showed an ABA-insensitive phenotype in primary root growth. Compared with the wild type (WT), the meristem size and cell number of the primary root in abi4 increased in response to ABA. Further, the transcription levels of several cell-cycle positive regulator genes, including CDKB2;2 and CYCB1;1, were upregulated in abi4 primary root tips. Subsequent chromatin immunoprecipitation (ChIP)-seq, ChIP-qPCR, and biochemical analysis revealed that ABI4 repressed the expression of CDKB2;2 and CYCB1;1 by physically interacting with their promoters. Genetic analysis demonstrated that overexpression of CDKB2;2 or CYCB1;1 fully rescued the shorter primary root phenotype of ABI4-overexpression lines, and consistently, abi4/cdkb2;2-cr or abi4/cycb1;1-cr double mutations largely rescued the ABA-insensitive phenotype of abi4 with regard to primary root growth. The expression levels of DR5promoter-GFP and PIN1promoter::PIN1-GFP in abi4 primary root tips were significantly higher than those in WT after ABA treatment, with these changes being consistent with changes in auxin concentration and expression patterns of auxin biosynthesis genes. Taken together, these findings indicated that ABA inhibits primary root growth through ABI4-mediated cell cycle and auxin-related regulatory pathways.

Integrated Metabolomic and Transcriptomic Analyses Reveal the Basis for Carotenoid Biosynthesis in Sweet Potato (Ipomoea batatas (L.) Lam.) Storage Roots

Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. β-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (β-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8’-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management.

Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean

Although mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, >10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and Arabidopsis thaliana, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as VrEmp24/25 for SL and VrKIX8 for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and VrKIX8, VrPAT14, VrEmp24/25, VrIAR1, VrBEE3, VrSUC4, and Vrflo2 were further verified by RT-qPCR. Among 65 genes around these QEIs, VrFATB, VrGSO1, VrLACS2, and VrPAT14 were homologous to known seed-development genes in A. thaliana, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which VrKIX8, VrABA2, VrABI5, VrSHB1, and VrIKU2 were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.

Mild and severe salt stress responses are age-dependently regulated by abscisic acid in tomato

Salt stress hampers plant growth and development through both osmotic and ionic imbalances. One of the key players in modulating physiological responses towards salinity is the plant hormone abscisic acid (ABA). How plants cope with salinity largely depends on the magnitude of the soil salt content (stress severity), but also on age-related developmental processes (ontogeny). Here we studied how ABA directs salt stress responses in tomato plants for both mild and severe salt stress in leaves of different ages. We used the ABA-deficient mutant notabilis, which contains a null-mutation in the gene of a rate-limiting ABA biosynthesis enzyme 9-cis-epoxycarotenoid dioxygenase (NCED1), leading to impaired stomatal closure. We showed that both old and young leaves of notabilis plants keep a steady-state transpiration and photosynthesis rate during salt stress, probably due to their dysfunctional stomatal closure. At the whole plant level, transpiration declined similar to the wild-type, impacting final growth. Notabilis leaves were able to produce osmolytes and accumulate ions in a similar way as wild-type plants, but accumulated more proline, indicating that osmotic responses were not impaired by the NCED1 mutation. Besides NCED1, also NCED2 and NCED6 are strongly upregulated under salt stress, which could explain why the notabilis mutant did not show a lower ABA content upon salt stress, except in young leaves. This might be indicative of a salt-mediated feedback mechanism on NCED2/6 in notabilis and might explain why notabilis plants seem to perform better under salt stress compared to wild-type plants with respect to biomass and water content accumulation.

Multi-omics analysis reveals the molecular changes accompanying heavy-grazing-induced dwarfing of Stipa grandis

Heavy grazing significantly reduces Stipa grandis growth. To enhance our understanding of plant responses to heavy grazing, we conducted transcriptomic, proteomic, and metabolic analyses of the leaves of non-grazed plants (NG) and heavy-grazing-induced dwarf plants (HG) of S. grandis. A total of 101 metabolites, 167 proteins, and 1,268 genes differed in abundance between the HG and NG groups. Analysis of Kyoto Encyclopedia of Genes and Genomes pathways among differentially accumulated metabolites (DAMs) revealed that the most enriched pathways were flavone and flavonol biosynthesis, tryptophan metabolism, and phenylpropanoid biosynthesis. An integrative analysis of differentially expressed genes (DEGs) and proteins, and DAMs in these three pathways was performed. Heavy-grazing-induced dwarfism decreased the accumulation of DAMs enriched in phenylpropanoid biosynthesis, among which four DAMs were associated with lignin biosynthesis. In contrast, all DAMs enriched in flavone and flavonol biosynthesis and tryptophan metabolism showed increased accumulation in HG compared with NG plants. Among the DAMs enriched in tryptophan metabolism, three were involved in tryptophan-dependent IAA biosynthesis. Some of the DEGs and proteins enriched in these pathways showed different expression trends. The results indicated that these pathways play important roles in the regulation of growth and grazing-associated stress adaptions of S. grandis. This study enriches the knowledge of the mechanism of heavy-grazing-induced growth inhibition of S. grandis and provides valuable information for restoration of the productivity in degraded grassland.

Transcriptome analysis and identification of abscisic acid and gibberellin-related genes during seed development of alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa) is a widely cultivated plant. Unlike many crops, the main goal of breeding alfalfa is to increase its aboveground biomass rather than the biomass of its seeds. However, the low yield of alfalfa seeds limits alfalfa production. Many studies have explored the factors affecting seed development, in which phytohormones, especially ABA and GAs, play an important role in seed development.

RESULTS

Here, we performed a transcriptome analysis of alfalfa seeds at five development stages. A total of 16,899 differentially expressed genes (DEGs) were identified and classified into 10 clusters, and the enriched Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were determined. The contents of ABA, GA₁, GA₃, GA₄ and GA₇ in alfalfa seeds at five development stages were determined. In addition, 14 ABA-related DEGs and 20 GA-related DEGs were identified and analysed. These DEGs are involved in plant hormone pathways and play an important role in seed development. Moreover, morphological and physiological analyses revealed the dynamic changes during the development of alfalfa seeds.

CONCLUSION

Overall, our study is the first to analyse the transcriptome across various stages of seed development in alfalfa. The results of our study could be used to improve alfalfa seed yield. The key ABA and GA related-genes are potential targets for improving alfalfa seed yield via genetic engineering in the future.

Single seeds exhibit transcriptional heterogeneity during secondary dormancy induction

Seeds are highly resilient to the external environment, which allows plants to persist in unpredictable and unfavorable conditions. Some plant species have adopted a bet-hedging strategy to germinate a variable fraction of seeds in any given condition, and this could be explained by population-based threshold models. Here, in the model plant Arabidopsis (Arabidopsis thaliana), we induced secondary dormancy (SD) to address the transcriptional heterogeneity among seeds that leads to binary germination/nongermination outcomes. We developed a single-seed RNA-seq strategy that allowed us to observe a reduction in seed transcriptional heterogeneity as seeds enter stress conditions, followed by an increase during recovery. We identified groups of genes whose expression showed a specific pattern through a time course and used these groups to position the individual seeds along the transcriptional gradient of germination competence. In agreement, transcriptomes of dormancy-deficient seeds (mutant of DELAY OF GERMINATION 1) showed a shift toward higher values of the germination competence index. Interestingly, a significant fraction of genes with variable expression encoded translation-related factors. In summary, interrogating hundreds of single-seed transcriptomes during SD-inducing treatment revealed variability among the transcriptomes that could result from the distribution of population-based sensitivity thresholds. Our results also showed that single-seed RNA-seq is the method of choice for analyzing seed bet-hedging-related phenomena.

Seed Dormancy and Longevity: A Mutual Dependence or a Trade-Off?

Seed dormancy is an important agronomic trait in cereals and leguminous crops as low levels of seed dormancy during harvest season, coupled with high humidity, can cause preharvest sprouting. Seed longevity is another critical trait for commercial crop propagation and production, directly influencing seed germination and early seedling establishment. Both traits are precisely regulated by the integration of genetic and environmental cues. Despite the significance of these two traits in crop production, the relationship between them at the molecular level is still elusive, even with contradictory conclusions being reported. Some studies have proposed a positive correlation between seed dormancy and longevity in association with differences in seed coat permeability or seed reserve accumulation, whereas an increasing number of studies have highlighted a negative relationship, largely with respect to phytohormone-dependent pathways. In this review paper, we try to provide some insights into the interactions between regulatory mechanisms of genetic and environmental cues, which result in positive or negative relationships between seed dormancy and longevity. Finally, we conclude that further dissection of the molecular mechanism responsible for this apparently contradictory relationship between them is needed.

Transcriptome and co-expression network analyses of key genes and pathways associated with differential abscisic acid accumulation during maize seed maturation

BACKGROUND

Currently, mechanical maize kernel harvesting has not been fully utilized in developing countries including China, partly due to the absence of suitable cultivars capable of rapid desiccation during seed maturation. The initiation of rapid desiccation during seed maturation is regulated by abscisic acid (ABA). For further characterization of ABA-regulated key genes and cellular events, it is necessary to perform transcriptome analysis of maize developing embryos. The ABA synthesis-deficient mutant (vp5) and normal maize (Vp5) seeds are suitable materials for such purpose.

RESULTS

In the present work, developing vp5 and Vp5 embryos were compared by ABA content and transcriptome analyses. Quantitative analysis revealed the significant difference in ABA synthesis between both genotypes. From 29 days after pollination (DAP), ABA content increased rapidly in Vp5 embryos, but decreased gradually in vp5 embryos. At 36 DAP, ABA level in vp5 decreased to 1/4 that of Vp5, suggesting that the differential ABA levels would affect seed maturation. Comparative transcriptomic analysis has found 1019 differentially expressed genes (DEGs) between both genotypes, with the most DEGs (818) at 36 DAP. Further, weighted correlation network analysis (WGCNA) revealed eight DEGs co-expression modules. Particularly, a module was negatively correlated with ABA content in vp5 embryos. The module was mainly involved in metabolic and cellular processes, and its hub genes encoded thiamine, NPF proteins, calmodulin, metallothionein etc. Moreover, the expression of a set of key genes regulated by ABA was further verified by RT-qPCR. The results of the present work suggested that because of ABA deficiency, the vp5 seeds maintained strong metabolic activities and lacked dormancy initiation during seed maturation.

CONCLUSION

Transcriptome and WGCNA analyses revealed significant ABA-related changes in metabolic pathways and DEGs between vp5 and Vp5 during seed maturation. The results would provide insights for elucidating the molecular mechanism of ABA signaling and developing high dehydration tolerance maize suitable for mechanical harvesting.

ABI5 binding protein2 inhibits ABA responses during germination without ABA-INSENSITIVE5 degradation

Overexpression of ABA-INSENSITIVE5 binding proteins (AFPs) results in extreme ABA resistance of seeds and failure to acquire desiccation tolerance, at least in part through effects on chromatin modification. We tested the hypothesis that AFPs promote germination in Arabidopsis (Arabidopsis thaliana) by also functioning as adapters for E3 ligases that ubiquitinate ABI5, leading to its degradation. Interactions between AFPs and two well-characterized classes of E3 ligases targeting ABI5, DWD HYPERSENSITIVE TO ABA (DWA)s and KEEP ON GOING, were analyzed by yeast two-hybrid, bimolecular fluorescence complementation, and genetic assays. Although weak direct interactions were detected between AFPs and E3 ligases, loss of function for these E3 ligases did not impair ABA-resistance conferred by overexpression of the YFP-AFP2 fusion. Comparison of ABI5 and AFP2 levels in these lines showed that AFP2 accumulation increased during germination, but that ABI5 degradation followed germination, demonstrating that AFP2 overexpression reduces ABA sensitivity, thereby permitting germination prior to ABI5 degradation. Surprisingly, AFP2 overexpression in the dwa1 dwa2 mutant background produced the unusual combination of extreme ABA resistance and desiccation tolerance, creating an opportunity to separate the underlying biochemical characteristics of ABA sensitivity and desiccation tolerance. Our quantitative proteomics analysis identified at least three-fold more differentially accumulated seed proteins than previous studies. Comparison of dry seed proteomes of wild-type or dwa1 dwa2 mutants with or without AFP2 overexpression allowed us to separate and refine the changes in protein accumulation patterns associated with desiccation tolerance independently of ABA sensitivity, or vice versa, to a subset of cold-induced and defense stress-responsive proteins and signaling regulators.

A proteomic analysis of Arabidopsis ribosomal phosphoprotein P1A mutant

Ribosomal proteins are involved in the regulation of plant growth and development. However, the regulatory processes of most ribosomal proteins remain unclear. In this study, Arabidopsis plants with the mutation in ribosomal phosphoprotein P1A (RPP1A) produce larger and heavier seeds than wild-type plants. A comparative quantitative label-free proteomic analysis revealed that a total of 215 proteins were differentially accumulated between the young siliques of the wild type and rpp1a mutant. Knockout of RPP1A significantly reduced the abundance of proteins involved in carboxylic acid metabolism and lipid biosynthesis. Consistent with this, a metabolic analysis showed that the organic acids in the tricarboxylic acid cycle and the carbohydrates in the pentose phosphate pathway were severely reduced in the mature rpp1a mutant seeds. In contrast, the abundance of proteins related to seed maturation, especially seed storage proteins, was markedly increased during seed development. Indeed, seed storage proteins were accumulated in the mature rpp1a mutant seeds, and the seed nitrogen and sulfur contents were also increased. These results indicate that more carbon intermediates probably enter the nitrogen flow for the enhanced synthesis of seed storage proteins, which might subsequently contribute to the enlarged seed size in the rpp1a mutant. SIGNIFICANCE: Ribosomes are responsible for protein synthesis and are generally perceived as the housekeeping components in the cells. In this study, the knockout of RPP1A leads to an increased seed size through repressing carbon metabolism and lipid biosynthesis, and increasing the synthesis of seed storage proteins. Meanwhile, the abundance of seed storage proteins and the nitrogen and sulfur concentrations were increased in the mature rpp1a mutant seeds. The results provide a novel insight into the genetic regulatory networks for the control of seed size and seed storage protein accumulation, and this knowledge may facilitate the improvement of crop seed size.

Team effort: Combinatorial control of seed maturation by transcription factors

Seed development is under tight spatiotemporal regulation. Here, we summarize how transcriptional regulation helps shape the major traits during seed maturation, which include storage reserve accumulation, dormancy, desiccation tolerance, and longevity. The regulation is rarely a solo task by an individual transcription factor (TF). Rather, it often involves coordinated recruitment or replacement of multiple TFs to achieve combinatorial regulation. We highlight recent progress on the transcriptional integration of activation and repression of seed maturation genes, and discuss potential research directions to further understand the TF networks of seed maturation.

A New Role for Plastid Thioredoxins in Seed Physiology in Relation to Hormone Regulation

In Arabidopsis seeds, ROS have been shown to be enabling actors of cellular signaling pathways promoting germination, but their accumulation under stress conditions or during aging leads to a decrease in the ability to germinate. Previous biochemical work revealed that a specific class of plastid thioredoxins (Trxs), the y-type Trxs, can fulfill antioxidant functions. Among the ten plastidial Trx isoforms identified in Arabidopsis, Trx y1 mRNA is the most abundant in dry seeds. We hypothesized that Trx y1 and Trx y2 would play an important role in seed physiology as antioxidants. Using reverse genetics, we found important changes in the corresponding Arabidopsis mutant seeds. They display remarkable traits such as increased longevity and higher and faster germination in conditions of reduced water availability or oxidative stress. These phenotypes suggest that Trxs y do not play an antioxidant role in seeds, as further evidenced by no changes in global ROS contents and protein redox status found in the corresponding mutant seeds. Instead, we provide evidence that marker genes of ABA and GAs pathways are perturbed in mutant seeds, together with their sensitivity to specific hormone inhibitors. Altogether, our results suggest that Trxs y function in Arabidopsis seeds is not linked to their previously identified antioxidant roles and reveal a new role for plastid Trxs linked to hormone regulation.

The Response of Grain Yield and Root Morphological and Physiological Traits to Nitrogen Levels in Paddy Rice

Rice (Oryza sativa L.) is an important crop in China. Although it is known that its yield is restricted by nitrogen (N) supply, the response of the root system to N supply specifically has not been systematically explored. This study aimed to investigate the effect of N uptake on grain yield to clarify the relationships between root morphophysiological traits and N uptake, and to understand relation between phytohormones and root morphophysiological traits. Two N-efficient absorption cultivars (NEAs) and two N-inefficient absorption cultivars (NIAs) were grown in the field, and three N conditions, deficient N (60 kg ha-1), intermediate N (180 kg ha-1), and sufficient N (240 kg ha-1), were applied during the growing season. The results showed higher dry matter and grain yield in NEAs than in NIAs, which was mainly attributed to increased N uptake in the mid- and late growth stages under all N conditions. And NEAs have different root regulation methods to obtain higher N accumulation and yield under different N supply conditions. Under lower N conditions, compared with NIAs, NEAs shown greater total root length, root oxidation activity, and root active absorbing surface area and smaller root diameter owing to higher indole-3-acetic acid and cytokinin content and lower 1-aminocyclopropane-1-carboxylic acid content in the early growth stages to respond to low N stress faster, laying a morphophysiological basis for its high N-uptake capacity in the mid- and late growth stages. Under higher N conditions, NEAs had higher root oxidation activity and root active absorbing surface area for N uptake and yield formation owing to higher abscisic acid and cytokinin content in the mid- and late growth stages, which improved the seed setting rate, thereby increasing the rice grain yield. These results suggest that NEAs can optimize the morphophysiological characteristics of roots through phytohormone regulation to adapt to different nutrient conditions, thereby promoting N accumulation and yield formation in rice.

Beyond the Usual Suspects: Physiological Roles of the Arabidopsis Amidase Signature (AS) Superfamily Members in Plant Growth Processes and Stress Responses

The diversification of land plants largely relies on their ability to cope with constant environmental fluctuations, which negatively impact their reproductive fitness and trigger adaptive responses to biotic and abiotic stresses. In this limiting landscape, cumulative research attention has centred on deepening the roles of major phytohormones, mostly auxins, together with brassinosteroids, jasmonates, and abscisic acid, despite the signaling networks orchestrating the crosstalk among them are so far only poorly understood. Accordingly, this review focuses on the Arabidopsis Amidase Signature (AS) superfamily members, with the aim of highlighting the hitherto relatively underappreciated functions of AMIDASE1 (AMI1) and FATTY ACID AMIDE HYDROLASE (FAAH), as comparable coordinators of the growth-defense trade-off, by balancing auxin and ABA homeostasis through the conversion of their likely bioactive substrates, indole-3-acetamide and N-acylethanolamine.

Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins

During seed germination, desiccation tolerance is lost in the radicle with progressing radicle protrusion and seedling establishment. This process is accompanied by comprehensive changes in the metabolome and proteome. Germination of Arabidopsis seeds was investigated over 72 h with special focus on the heat-stable proteome including late embryogenesis abundant (LEA) proteins together with changes in primary metabolites. Six metabolites in dry seeds known to be important for seed longevity decreased during germination and seedling establishment, while all other metabolites increased simultaneously with activation of growth and development. Thermo-stable proteins were associated with a multitude of biological processes. In the heat-stable proteome, a relatively similar proportion of fully ordered and fully intrinsically disordered proteins (IDP) was discovered. Highly disordered proteins were found to be associated with functional categories development, protein, RNA and stress. As expected, the majority of LEA proteins decreased during germination and seedling establishment. However, four germination-specific dehydrins were identified, not present in dry seeds. A network analysis of proteins, metabolites and amino acids generated during the course of germination revealed a highly connected LEA protein network.

Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination

Magnolia sieboldii K. Koch (M. sieboldii) is a deciduous Chinese tree species of the Magnoliaceae family with high ornamental, medicinal, and economic benefits. The germination of M. sieboldii seeds under natural conditions is extremely difficult, thereby hindering the cultivation and breeding of this important species. The molecular mechanisms underlying M. sieboldii seed germination remain unclear due to the lack of genomic and transcriptomic resources. Here, we integrated both mRNA and miRNA sequencing to identify the genes and pathways related to M. sieboldii germination. A comprehensive full-length transcriptome containing 158,083 high-quality unigenes was obtained by single-molecule real-time (SMRT) sequencing technology. We identified a total of 13,877 genes that were differentially expressed between non-germinated and germinated seeds. These genes were mainly involved in plant hormone signal transduction and diverse metabolic pathways such as those involving lipids, sugars, and amino acids. Our results also identified a complex regulatory network between miRNAs and their target genes. Taken together, we present the first transcriptome of M. sieboldii and provide key genes and pathways associated with seed germination for further characterization. Future studies of the molecular basis of seed germination will facilitate the genetic improvement M. sieboldii.

ABA Metabolism and Homeostasis in Seed Dormancy and Germination

Abscisic acid (ABA) is a key hormone that promotes dormancy during seed development on the mother plant and after seed dispersal participates in the control of dormancy release and germination in response to environmental signals. The modulation of ABA endogenous levels is largely achieved by fine-tuning, in the different seed tissues, hormone synthesis by cleavage of carotenoid precursors and inactivation by 8'-hydroxylation. In this review, we provide an overview of the current knowledge on ABA metabolism in developing and germinating seeds; notably, how environmental signals such as light, temperature and nitrate control seed dormancy through the adjustment of hormone levels. A number of regulatory factors have been recently identified which functional relationships with major transcription factors, such as ABA INSENSITIVE3 (ABI3), ABI4 and ABI5, have an essential role in the control of seed ABA levels. The increasing importance of epigenetic mechanisms in the regulation of ABA metabolism gene expression is also described. In the last section, we give an overview of natural variations of ABA metabolism genes and their effects on seed germination, which could be useful both in future studies to better understand the regulation of ABA metabolism and to identify candidates as breeding materials for improving germination properties.

Transcriptome analysis reveals the mechanism of improving erect-plant-type peanut yield by single-seeding precision sowing

Background

In China, double-seed (DS) sowing (i.e., sowing two seeds per hole) has been conventionally performed towards the erect-plant-type peanuts to increase the low germination rate due to poor seed preservation conditions. However, the corresponding within-hole plant competition usually limits the subsequent plant growth and the final yield. We developed a high-yield cultivation system of single-seed (SS) precision sowing to solve this paradox, saving 20% of seeds and increasing yields by more than 10% relative to the conventional DS sowing.

Methods

To explore the mechanisms of these two different cropping patterns in peanut yields, we conducted transcriptomic and physiological comparisons in the seeding plant leaf and root tissues between SS precision sowing and standard DS sowing treatments.

Results

After assembly, each library contained an average of 43 million reads and generated a total of 523,800, 338 clean reads. After GO and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found the key genes for biotic and abiotic stress showed higher expression in roots of plants grown under the SS precision sowing treatment, including genes encoding disease resistance, oxidation-reduction, hormone related, and stress response transcription factors and signaling regulation proteins. In particular, the resveratrol synthesis genes related to stress and disease resistance appeared induced in roots under the SS sowing treatment.

Conclusion

These data indicated that Aspergillus flavus resistance and stress tolerance in roots under SS precision sowing were enhanced compared with roots under the DS sowing treatment. This work benefits the development of underground pods and thus increasing peanut yields.

Endogenous indole-3-acetamide levels contribute to the crosstalk between auxin and abscisic acid, and trigger plant stress responses in Arabidopsis

The evolutionary success of plants relies to a large extent on their extraordinary ability to adapt to changes in their environment. These adaptations require that plants balance their growth with their stress responses. Plant hormones are crucial mediators orchestrating the underlying adaptive processes. However, whether and how the growth-related hormone auxin and the stress-related hormones jasmonic acid, salicylic acid, and abscisic acid (ABA) are coordinated remains largely elusive. Here, we analyse the physiological role of AMIDASE 1 (AMI1) in Arabidopsis plant growth and its possible connection to plant adaptations to abiotic stresses. AMI1 contributes to cellular auxin homeostasis by catalysing the conversion of indole-acetamide into the major plant auxin indole-3-acetic acid. Functional impairment of AMI1 increases the plant's stress status rendering mutant plants more susceptible to abiotic stresses. Transcriptomic analysis of ami1 mutants disclosed the reprogramming of a considerable number of stress-related genes, including jasmonic acid and ABA biosynthesis genes. The ami1 mutants exhibit only moderately repressed growth but an enhanced ABA accumulation, which suggests a role for AMI1 in the crosstalk between auxin and ABA. Altogether, our results suggest that AMI1 is involved in coordinating the trade-off between plant growth and stress responses, balancing auxin and ABA homeostasis.

ABSCISIC ACID-DEFICIENT4 Has an Essential Function in Both cis-Violaxanthin and cis-Neoxanthin Synthesis

Abscisic acid (ABA), a plant hormone synthesized from carotenoids, functions in seed germination and abiotic stress responses. ABA is derived from the cleavage of 9-cis-isomers of violaxanthin and neoxanthin, which are oxygenated carotenoids, also called xanthophylls. Although genes encoding enzymes responsible for most steps of the ABA biosynthesis pathway have been identified, enzymatic reactions leading to the production of these cis-isomers from trans-violaxanthin remain poorly understood. Two mutants that lack trans- and cis-neoxanthin, tomato (Solanum lycopersicum) neoxanthin-deficient1 (nxd1) and Arabidopsis (Arabidopsis thaliana) ABA-deficient4 (aba4), were identified previously, but only aba4 exhibited ABA-deficient phenotypes. No enzymatic activity was detected for ABA4 and NXD1 proteins, and their exact function remained unknown. To further investigate ABA4 and NXD1 function in Arabidopsis, we compared phenotypes of single and double mutants, and analyzed the effect of ABA4 overexpression on ABA and carotenoid accumulation in wild-type and mutant backgrounds. We provide convergent evidence that ABA4 is not only required for the formation of trans- and 9'-cis-neoxanthin from trans-violaxanthin, but also controls 9-cis-violaxanthin accumulation. While nxd1 produces high amounts of 9-cis-violaxanthin and ABA, aba4 nxd1 exhibits reduced levels in both leaves and seeds. Furthermore, ABA4 constitutive expression in nxd1 increases both 9-cis-violaxanthin and ABA accumulation. Subcellular localization of NXD1 protein in transient expression assays suggests that production of the NXD1-derived factor required for neoxanthin synthesis takes place in the cytosol. Finally, we postulate that ABA4, with additional unknown cofactor(s), is required for, or contributes to, trans-to-cis violaxanthin isomerase activity, producing both cis-xanthophyll precursors of ABA.

OsDOG1L-3 regulates seed dormancy through the abscisic acid pathway in rice

Seed dormancy is closely related to pre-harvest sprouting resistance. Both plant hormone abscisic acid (ABA) and DELAY OF GERMINATION 1 (DOG1) protein are key regulators of seed dormancy. Their relationship is well reported in Arabidopsis, but little is known in rice. Here, we show that a quantitative trait locus, qSd-1-1 contributes significantly to seed dormancy differences between the strongly dormant indica variety N22 and non-dormant japonica variety Nanjing35. It encodes a DOG1-like protein named OsDOG1L-3 with homology to Arabidopsis DOG1. There were evident promoter and expression differences in OsDOG1L-3 between N22 and Nanjing35, and overexpression or introduction of the N22 OsDOG1L-3 allele in Nanjing35 enhanced its seed dormancy. OsDOG1L-3 expression was positively correlated with seed dormancy and induced by ABA. OsbZIP75 and OsbZIP78 bound directly with the promoter of OsDOG1L-3 to induce its expression. Overexpression of OsbZIP75 increased OsDOG1L-3 protein abundance and promoted seed dormancy. OsDOG1L-3 upregulated expression of ABA-related genes and increased ABA content. We propose that the N22 OsDOG1L-3 allele is a candidate gene for the seed dormancy in QTL qSd-1-1, and that it participates in the ABA pathway to establish seed dormancy in rice.

Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides

Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.

Molecular and environmental factors regulating seed longevity

Seed longevity is a central pivot of the preservation of biodiversity, being of main importance to face the challenges linked to global climate change and population growth. This complex, quantitative seed quality trait is acquired on the mother plant during the second part of seed development. Understanding what factors contribute to lifespan is one of the oldest and most challenging questions in plant biology. One of these challenges is to recognize that longevity depends on the storage conditions that are experimentally used because they determine the type and rate of deleterious conditions that lead to cell death and loss of viability. In this review, we will briefly review the different storage methods that accelerate the deteriorative reactions during storage and argue that a minimum amount of information is necessary to interpret the longevity data. Next, we will give an update on recent discoveries on the hormonal factors regulating longevity, both from the ABA signaling pathway but also other hormonal pathways. In addition, we will review the effect of both maternal and abiotic factors that influence longevity. In the last section of this review, we discuss the problems in unraveling cause-effect relationship between the time of death during storage and deteriorative reactions leading to seed ageing. We focus on the three major types of cellular damage, namely membrane permeability, lipid peroxidation and RNA integrity for which germination data on seed stored in dedicated seed banks for long period times are now available.

Research Advances on Biosynthesis, Regulation, and Biological Activities of Apocarotenoid Aroma in Horticultural Plants

Apocarotenoids, which play important roles in the growth and development of horticultural plants, are produced by the action of carotenoid cleavage oxygenase (CCO) family members or nonenzymatic cleavage actions. Apocarotenoids are commonly found in leaves, flowers, and fruits of many horticultural plants and participate in the formation of pigments, flavors, hormones, and signaling compounds. Some of them are recognized as important aroma components of fruit and flower with aromatic odor, such as βß-ionone, β-damascenone, and 6-methyl-5-hepten-2-one in tomato fruit, and have low odor thresholds with β-ionone having odor threshold of only 0.007 ppb. In this review, the main apocarotenoid aroma components in horticultural plants were listed, and factors influencing their production were discussed at first. Then, the biosynthetic pathway of apocarotenoid aromas was briefly introduced, and the CCDs gene family was highlighted, and the nonenzymatic production of apocarotenoid aromas was also mentioned. Next, chemical and molecular regulations of apocarotenoid aromas and their biological activities were summarized. Finally, further exploration aspects needed were suggested. We anticipate that this review can afford some crucial information for comprehensive application of apocarotenoid volatile compounds in horticultural plants.

Deciphering aquaporin regulation and roles in seed biology

Seeds are the typical dispersal and propagation units of angiosperms and gymnosperms. Water movement into and out of seeds plays a crucial role from the point of fertilization through to imbibition and seed germination. A class of membrane intrinsic proteins called aquaporins (AQPs) assist with the movement of water and other solutes within seeds. These highly diverse and abundant proteins are associated with different processes in the development, longevity, imbibition, and germination of seed. However, there are many AQPs encoded in a plant's genome and it is not yet clear how, when, or which AQPs are involved in critical stages of seed biology. Here we review the literature to examine the evidence for AQP involvement in seeds and analyse Arabidopsis seed-related transcriptomic data to assess which AQPs are likely to be important in seed water relations and explore additional roles for AQPs in seed biology.

The Long-Standing Paradox of Seed Dormancy Unfolded?

There has been a long-standing question in seed research, why cyanide, a respiration inhibitor, breaks seed dormancy. While the alternative respiratory pathway and reactive oxygen species have been suggested to be part of the mechanism, the cell biological and mechanistic significance of this paradox remains unclear. The outcomes of recent research on mitochondrial RNA processing for the subunits of the electron transport chain complexes seem to offer a logical explanation. This opinion article attempts to integrate the accumulating evidence of mitochondrial involvement in ABA signaling with the frontier of seed research on DELAY OF GERMINATION1, a master regulator of dormancy, to present a coherent model for ABA signaling in seeds, which could also address the old paradox in seed research.