Regulation of Seed Vigor by Manipulation of Raffinose Family Oligosaccharides in Maize and Arabidopsis thaliana

ZmDREB1A Regulates myo-Inositol-1-phosphate Synthase 2 Controlling Maize Germination at Low Temperatures

Transcription factor DREB1A positively regulates plant chilling stress tolerance. However, its role in regulating seed germination at low temperatures has remained a mystery. Our research has unveiled that maize zmdreb1a mutant seeds exhibit decreased ZmMIPS2 expression and a lower germination percentage than the control under low temperatures. The overexpression of ZmDREB1A upregulated ZmMIPS2 expression, while the mutation of DRE motifs in the ZmMIPS2 promoter nullified the influence of ZmDREB1A on the target gene expression. In addition, we demonstrated that ZmDREB1A directly binds to the three DRE motifs in the promoter of ZmMIPS2 both in vitro and in vivo. Further investigation has shown that maize zmmips2 mutant seeds are more sensitive, while ZmMIPS2 overexpressing seeds are more tolerant of low temperatures during seed germination. These findings could be applied to develop new crop varieties that are more resilient to low temperatures during the vulnerable germination phase.

Unraveling the Mechanistic Basis for Control of Seed Longevity

Seed longevity, which holds paramount importance for agriculture and biodiversity conservation, continues to represent a formidable frontier in plant biology research. While advances have been made in identifying regulatory elements, the precise mechanisms behind seed lifespan determination remain intricate and context-specific. This comprehensive review compiles extensive findings on seed longevity across plant species, focusing on the genetic and environmental underpinnings. Inter-species differences in seed lifespan are tied to genetic traits, with numerous Seed Longevity-Associated Genes (SLAGs) uncovered. These SLAGs encompass transcription factors and enzymes involved in stress responses, repair pathways, and hormone signaling. Environmental factors, particularly seed developmental conditions, significantly modulate seed longevity. Moreover, this review deliberates on the prospects of genetically engineering seed varieties with augmented longevity by precise manipulation of crucial genetic components, exemplifying the promising trajectory of seed science and its practical applications within agriculture and biodiversity preservation contexts. Collectively, our manuscript offers insights for improving seed performance and resilience in agriculture's evolving landscape.

ZmGolS1 underlies natural variation of raffinose content and salt tolerance in maize

Salt stress significantly inhibits crop growth and development, and mitigating this can enhance salt tolerance in various crops. Previous studies have shown that regulating saccharide biosynthesis is a key aspect of plant salt tolerance; however, the underlying molecular mechanisms remain largely unexplored. In this study, we demonstrate that overexpression of a salt-inducible galactinol synthase gene, ZmGolS1, alleviates salt-induced growth inhibition, likely by promoting raffinose synthesis. Additionally, we show that natural variation in ZmGolS1 transcript levels contributes to the diversity of raffinose content and salt tolerance in maize. We further reveal that ZmRR18, a type-B response regulator transcription factor, binds to the AATC element in the promoter of ZmGolS1, with this binding increases the transcript levels of ZmGolS1 under salt conditions. Moreover, a single nucleotide polymorphism (termed SNP-302T) within the ZmGolS1 promoter significantly reduces its binding affinity for ZmRR18, resulting in decreased ZmGolS1 expression and diminished raffinose content, ultimately leading to a salt-hypersensitive phenotype. Collectively, our findings reveal the molecular mechanisms by which the ZmRR18-ZmGolS1 module enhances raffinose biosynthesis, thereby promoting maize growth under salt conditions. This research provides important insights into salt tolerance mechanisms associated with saccharide biosynthesis and identifies valuable genetic loci for breeding salt-tolerant maize varieties.

ZmDREB1A controls plant immunity via regulating salicylic acid metabolism in maize

DREB1A, a pivotal transcription factor, has long been known to regulate plant abiotic stress tolerance. However, its role in plant biotic stress tolerance and the underlying mechanisms have remained a mystery. Our research reveals that the maize ZmDREB1A gene is up-regulated in maize seedlings when the plants are infected by Rhizoctonia solani (R. solani). The maize ZmDREB1A knock-out mutant exhibits increased disease resistance against the pathogen R. solani. Further investigation showed that ZmDREB1A regulates salicylic acid (SA) metabolism by inhibiting ZmSARD1 gene and activating ZmSAGT gene expression. Additionally, the SA level was increased while the SAG level was decreased in zmdreb1a mutant seedlings when the plants were infected with the pathogen R. solani. Furthermore, overexpression of ZmSAGT in Arabidopsis reduced plant resistance to Pst DC3000 by decreasing SA levels and increasing SAG levels. These data demonstrate that ZmDREB1A regulates the metabolism of SA and controls plant immune response in maize.

Effects of storage on volatile organic components and physiological properties of different storage-tolerant rice varieties

The effects of storage on rice flavor among different rice varieties have not been well studied. To address this gap, we analyzed volatile organic components (VOCs) identified by gas chromatography-ion mobility spectrometry (GC-IMS) and related physicochemical properties of different storage-tolerant rice varieties during storage. The results showed that VOCs of four rice varieties significantly changed after 6 months of storage; OPLS-DA analysis classified the four rice varieties into two groups. There were fewer (N81 and JH1) and more significant changes (N84 and ZJ96) after storage, and the hexanal and 2-pentylfuran were considered the key VOCs for flavor changes during storage. Lipoxygenase (LOX) activity first increased and then decreased, while antioxidant activities decreased during storage. Under these conditions, oleic and linoleic acids were hydrolyzed. These results provide a better understanding of rice flavor changes after storage between different storable rice varieties.

The BRAHMA-associated SWI/SNF chromatin remodeling complex controls Arabidopsis seed quality and physiology

The SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling complex is involved in various aspects of plant development and stress responses. Here, we investigated the role of BRM (BRAHMA), a core catalytic subunit of the SWI/SNF complex, in Arabidopsis thaliana seed biology. brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but did not show changes in primary dormancy or salt tolerance. Some of these phenotypes depended on the expression of DOG1, a key regulator of seed dormancy, as they were restored in the brm-3 dog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergistically modulate the expression of numerous genes. Some of the changes observed in the brm-3 mutant, including increased glutathione levels, depended on a functional DOG1. We demonstrated that the BRM-containing chromatin remodeling complex directly controls secondary dormancy through DOG1 by binding and remodeling its 3' region, where the promoter of the long noncoding RNA asDOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological properties and that BRM regulates DOG1 expression through asDOG1. This study reveals chromatin remodeling at the DOG1 locus as a molecular mechanism controlling the interplay between seed viability and dormancy.

A seed-specific DNA-binding with One Finger transcription factor, RPBF, positively regulates galactinol synthase to maintain seed vigour in rice

Seed vigour and longevity are intricate yet indispensable physiological traits for agricultural crops, as they play a crucial role in facilitating the successful emergence of seedlings and exert a substantial influence on crop productivity. Transcriptional regulation plays an important role in seed development, maturation, and desiccation tolerance, which are important attributes for seed vigour and longevity. Here, we have investigated the regulatory role of the seed-specific DNA-binding with One Finger (DOF) transcription factor and the rice prolamin box binding factor (RPBF) in seed vigour. RPBF modulates the transcription of galactinol synthase (GolS) and improves seed vigour. The promoter region of GolS-encoding genes from different species was enriched with DOF-binding sites, and the expression levels of both RPBF; OsGolS were found to enhance during seed development. Furthermore, direct interaction of RPBF with the OsGolS promoter has been demonstrated through multiple approaches: yeast one-hybrid assays, in planta promoter-GUS assays, dual luciferase assay, and in silico molecular docking. To assess functionality, Agrobacterium-mediated genetic transformation of rice was performed to generate the RNAi lines with reduced RPBF expression. In these RNAi lines, a reduction in both galactinol and raffinose content was observed. Since galactinol and raffinose are known contributors to seed vigour, the T2-transgenic lines were assessed for vigour and viability. For this, RNAi seeds were subjected to accelerated ageing by exposing them to high relative humidity and temperature, followed by scoring the germination and viability potential. Tetrazolium and seed germination assay revealed that the RNAi seeds were more sensitive to ageing compared to their wild-type and vector control counterparts. Collectively, this is the first report demonstrating that the DOF transcription factor RPBF controls the seed vigour through transcriptional regulation of GolS.

Raffinose catabolism enhances maize waterlogging tolerance by stimulating adventitious root growth and development

Raffinose mitigates plant heat, drought, and cold stresses; however, whether raffinose contributes to plant waterlogging tolerance is unknown. The maize raffinose synthase mutant zmrafs-1 had seedlings that lack raffinose, generated fewer and shorter adventitious roots, and were more sensitive to waterlogging stress, while overexpression of the raffinose synthase gene, ZmRAFS, increased raffinose content, stimulated adventitious root formation, and enhanced waterlogging tolerance of maize seedlings. Transcriptome analysis of null segregant seedlings compared with zmrafs-1, particularly when waterlogged, revealed that the expression of genes related to galactose metabolism and the auxin biosynthetic pathway were up-regulated by raffinose. Additionally, indole-3-acetic acid content was significantly decreased in zmrafs-1 seedlings and increased in ZmRAFS-overexpressing seedlings. Inhibition of the hydrolysis of raffinose by 1-deoxygalactonojirimycin decreased the waterlogging tolerance of maize seedlings, the expression of genes encoding proteins related to auxin transport-related genes, and the indole-3-acetic acid level in the seedlings, indicating that the hydrolysis of raffinose is necessary for maize waterlogging tolerance. These data demonstrate that raffinose catabolism stimulates adventitious root formation via the auxin signaling pathway to enhance maize waterlogging tolerance.

Genome‑wide analysis of the GT8 gene family in apple and functional identification of MhGolS2 in saline-alkali tolerance

Members of the glycosyltransferase 8 (GT8) family play an important role in regulating gene expression in response to many kinds of biotic and abiotic stress. In this study, 56 members of the apple GT8 family were identified, and their gene structure, phylogenetic relationships, chromosomal localization, and promoter cis-acting elements were comprehensively analyzed. Subsequently, 20 genes were randomly selected from the evolutionary tree for qRT-PCR detection, and it was found that MhGolS2 was significantly overexpressed under stress conditions. MhGolS2 was isolated from M.halliana and transgenic Arabidopsis thaliana, tobacco and apple callus tissues were successfully obtained. The transgenic plants grew better under stress conditions with higher polysaccharide, chlorophyll and proline content, lower conductivity and MDA content, significant increase in antioxidant enzyme activities (SOD, POD, CAT) and maintenance of low Na+/K+ as compared to the wild type. Meanwhile, the expression levels of reactive oxygen species-related genes (AtSOD, AtPOD, and AtCAT), Na+ transporter genes (AtCAX5, AtSOS1, and AtHKT1), H+-ATPase genes (AtAHA2 and AtAHA8), and raffinose synthesis-related genes (AtSTS, AtRFS1, and AtMIPS) were significantly up-regulated, while the expression levels of K+ transporter genes (AtSKOR, AtHAK5) were reduced. Finally, the Y2H experiment confirmed the interaction between MhGolS2 and MhbZIP23, MhMYB1R1, MhbHLH60, and MhNAC1 proteins. The above results indicate that MhGolS2 can improve plant saline-alkali tolerance by promoting polysaccharide synthesis, scavenging reactive oxygen species, and increasing the activity of antioxidant enzymes. This provides excellent stress resistance genes for the stress response regulatory network in apple.

A genome-wide association study uncovers a ZmRap2.7-ZCN9/ZCN10 module to regulate ABA signalling and seed vigour in maize

Seed vigour, including rapid, uniform germination and robust seedling establishment under various field conditions, is becoming an increasingly essential agronomic trait for achieving high yield in crops. However, little is known about this important seed quality trait. In this study, we performed a genome-wide association study to identify a key transcription factor ZmRap2.7, which regulates seed vigour through transcriptionally repressing expressions of three ABA signalling genes ZmPYL3, ZmPP2C and ZmABI5 and two phosphatidylethanolamine-binding genes ZCN9 and ZCN10. In addition, ZCN9 and ZCN10 proteins could interact with ZmPYL3, ZmPP2C and ZmABI5 proteins, and loss-of-function of ZmRap2.7 and overexpression of ZCN9 and ZCN10 reduced ABA sensitivity and seed vigour, suggesting a complex regulatory network for regulation of ABA signalling mediated seed vigour. Finally, we showed that four SNPs in ZmRap2.7 coding region influenced its transcriptionally binding activity to the downstream gene promoters. Together with previously identified functional variants within and surrounding ZmRap2.7, we concluded that the distinct allelic variations of ZmRap2.7 were obtained independently during maize domestication and improvement, and responded separately for the diversities of seed vigour, flowering time and brace root development. These results provide novel genes, a new regulatory network and an evolutional mechanism for understanding the molecular mechanism of seed vigour.

Comparative transcriptomic profiles of Paulownia catalpifolia under different degrees of chilling stress during the seedling stage

BACKGROUND

Paulownia, an ecologically and economically valuable plant species native to China, is notable for its excellent timber quality and strong adaptability. Among them, Paulownia catalpifolia displays the ability to survive in cold climate, a trait associated with northern China. Yet, the molecular information for its cold-tolerance has not been explored. This study was to investigate the changes in physiological indices and transcript levels of P. catalpifolia following cold exposure, which could provide evidence for revealing whether there were differences in the genetic basis of inducing physiological perturbations between moderate low temperature (MLT) and extreme low temperature (ELT).

RESULTS

The detection of physiological indices under diverse degrees of chilling stress showed similar patterns of alteration. Enhanced accumulation of osmoregulatory substances, such as soluble sugar and soluble protein, were more conducive under ELT compared to MLT in P. catalpifolia. Moreover, we observed leaf wilting symptoms distinctly after exposure to ELT for 48 h, while this effect was not obvious after MLT exposure for 48 h. Comparative transcriptomic analysis between MLT and ELT demonstrated 13,688 differentially expressed genes (DEGs), most of them appeared after 12 h and 48 h of treatment. GO and KEGG analyses elucidated prominent enrichment in aromatic-L-amino-acid decarboxylase activity term and carbohydrate metabolism pathways. Therefore, it was speculated that the DEGs involved in the above processes might be related to the difference in the contents of soluble protein and soluble sugar between MLT and ELT. Time series clustering analyses further highlighted several key genes engaged in the 'Glycosyltransferases', 'Galactose metabolism' and 'Starch and sucrose metabolism' pathways as well as the 'tyrosine decarboxylase activity' term. For instance, cellulose synthase-like A (CLSA2/9), raffinose synthase (RafS2), β-amylase (BAM1) and tyrosine/DOPA decarboxylase (TYDC1/2/5) genes, diverging in their expression trends between MLT and ELT, might significantly affect the soluble sugar and soluble protein abundance within P. catalpifolia.

CONCLUSION

Between MLT and ELT treatments, partial overlaps in response pathways of P. catalpifolia were identified, while several genes regulating the accumulation of osmotic adjustment substances had disparate expression patterns. These findings could provide a novel physiological and molecular perspective for P. catalpifolia to adapt to complex low temperature habitats.

ZmWRKY30 modulates drought tolerance in maize by influencing myo-inositol and reactive oxygen species homeostasis

Maize (Zea mays L.) is an important food crop with a wide range of uses in both industry and agriculture. Drought stress during its growth cycle can greatly reduce maize crop yield and quality. However, the molecular mechanisms underlying maize responses to drought stress remain unclear. In this work, a WRKY transcription factor-encoding gene, ZmWRKY30, from drought-treated maize leaves was screened out and characterized. ZmWRKY30 gene expression was induced by dehydration treatments. The ZmWRKY30 protein localized to the nucleus and displayed transactivation activity in yeast. Compared with wild-type (WT) plants, Arabidopsis lines overexpressing ZmWRKY30 exhibited a significantly enhanced drought stress tolerance, as evidenced by the improved survival rate, increased antioxidant enzyme activity by superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), elevated proline content, and reduced lipid peroxidation recorded after drought stress treatment. In contrast, the mutator (Mu)-interrupted ZmWRKY30 homozygous mutant (zmwrky30) was more sensitive to drought stress than its null segregant (NS), characterized by the decreased survival rate, reduced antioxidant enzyme activity (SOD, POD, and CAT) and proline content, as well as increased malondialdehyde accumulation. RNA-Seq analysis further revealed that, under drought conditions, the knockout of the ZmWRKY30 gene in maize affected the expression of genes involved in reactive oxygen species (ROS), proline, and myo-inositol metabolism. Meanwhile, the zmwrky30 mutant exhibited significant downregulation of myo-inositol content in leaves under drought stress. Combined, our results suggest that ZmWRKY30 positively regulates maize responses to water scarcity. This work provides potential target genes for the breeding of drought-tolerant maize.

Galactinol synthase 2 influences the metabolism of chlorophyll, carotenoids, and ethylene in tomato fruits

Galactinol synthase (GolS), which catalyses the synthesis of galactinol, is the first critical enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs) and contributes to plant growth and development, and resistance mechanisms. However, its role in fruit development remains largely unknown. In this study, we used CRISPR/Cas9 gene-editing technology in tomato (Solanum lycopersicum) to create the gols2 mutant showing uniformly green fruits without dark-green shoulders, and promoting fruit ripening. Analysis indicated that galactinol was undetectable in the ovaries and fruits of the mutant, and the accumulation of chlorophyll and chloroplast development was suppressed in the fruits. RNA-sequencing analysis showed that genes related to chlorophyll accumulation and chloroplast development were down-regulated, including PROTOCHLOROPHYLLIDE OXIDOREDUCTASE, GOLDEN 2-LIKE 2, and CHLOROPHYLL A/B-BINDING PROTEINS. In addition, early color transformation and ethylene release was prompted in the gols2 lines by regulation of the expression of genes involved in carotenoid and ethylene metabolism (e.g. PHYTOENE SYNTHASE 1, CAROTENE CIS-TRANS ISOMERASE, and 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE2/4) and fruit ripening (e.g. RIPENING INHIBITOR, NON-RIPENING, and APETALA2a). Our results provide evidence for the involvement of GolS2 in pigment and ethylene metabolism of tomato fruits.

Genetic dissection of Brassica napus seed vigor after aging

KEY MESSAGE

Stable and novel QTLs that affect seed vigor under different storage durations were discovered, and BnaOLE4, located in the interval of cqSW-C2-3, increased seed vigor after aging. Seed vigor is an important trait in crop breeding; however, the underlying molecular regulatory mechanisms governing this trait in rapeseed remain largely unknown. In the present study, vigor-related traits were analyzed in seeds from a doubled haploid (DH) rapeseed (Brassica napus) population grown in 2 different environments using seeds stored for 7, 5, and 3 years under natural storage conditions. A total of 229 quantitative trait loci (QTLs) were identified and were found to explain 3.78%-17.22% of the phenotypic variance for seed vigor-related traits after aging. We further demonstrated that seed vigor-related traits were positively correlated with oil content (OC) but negatively correlated with unsaturated fatty acids (FAs). Some pleiotropic QTLs that collectively regulate OC, FAs, and seed vigor, such as uq.A8, uq.A3-2, uq.A9-2, and uq.C3-1, were identified. The transcriptomic results from extreme pools of DH lines with distinct seed vigor phenotypes during accelerated aging revealed that various biological pathways and metabolic processes (such as glutathione metabolism and reactive oxygen species) were involved in seed vigor. Through integration of QTL analysis and RNA-Seq, a regulatory network for the control of seed vigor was constructed. Importantly, a candidate (BnaOLE4) from cqSW-C2-3 was selected for functional analysis, and transgenic lines overexpressing BnaOLE4 showed increased seed vigor after artificial aging. Collectively, these results provide novel information on QTL and potential candidate genes for molecular breeding for improved seed storability.

Metabolite-mediated adaptation of crops to drought and the acquisition of tolerance

Drought is one of the major and growing threats to agriculture productivity and food security. Metabolites are involved in the regulation of plant responses to various environmental stresses, including drought stress. The complex drought tolerance can be ascribed to several simple metabolic traits. These traits could then be used for detecting the genetic architecture of drought tolerance. Plant metabolomes show dynamic differences when drought occurs during different developmental stages or upon different levels of drought stress. Here, we reviewed the major and most recent findings regarding the metabolite-mediated plant drought response. Recent progress in the development of drought-tolerant agents is also discussed. We provide an updated schematic overview of metabolome-driven solutions for increasing crop drought tolerance and thereby addressing an impending agricultural challenge.

Significance of Raffinose Family Oligosaccharides (RFOs) metabolism in plants

Raffinose Family Oligosaccharides (RFOs) are a kind of polysaccharide containing D-galactose, and they widely exist in higher plants. Synthesis of RFOs begins with galactinol synthase (GolS; EC 2.4.1.123) to convert myo-inositol into galactinol. The subsequent formation of raffinose and stachyose are catalyzed by raffinose synthase (RS; EC 2.4.1.82) and stachyose synthase (STS; EC 2.4.1.67) using sucrose and galactinol as substrate, respectively. The hydrolysis of RFOs is finished by α-galactosidase (α-Gal; EC 3.2.1.22) to produce sucrose and galactose. Importance of RFOs metabolism have been summarized, e.g. In RFOs translocating plants, the phloem loading and unloading of RFOs are widely reported in mediating the plant development process. Interference function of RFOs synthesis or hydrolysis enzymes caused growth defect. In addition, the metabolism of RFOs involved in the biotic or abiotic stresses was discussed in this review. Overall, this literature summarizes our current understanding of RFOs metabolism and points out knowledge gaps that need to be filled in future.

Transcription factor OsMYB30 increases trehalose content to inhibit α-amylase and seed germination at low temperature

Low-temperature germination (LTG) is an important agronomic trait for direct-seeding cultivation of rice (Oryza sativa). Both OsMYB30 and OsTPP1 regulate the cold stress response in rice, but the function of OsMYB30 and OsTPP1 in regulating LTG and the underlying molecular mechanism remains unknown. Employing transcriptomics and functional studies revealed a sugar signaling pathway that regulates seed germination in response to low temperature (LT). Expression of OsMYB30 and OsTPP1 was induced by LT during seed germination, and overexpressing either OsMYB30 or OsTPP1 delayed seed germination and increased sensitivity to LT during seed germination. Transcriptomics and qPCR revealed that expression of OsTPP1 was upregulated in OsMYB30-overexpressing lines but downregulated in OsMYB30-knockout lines. In vitro and in vivo experiments revealed that OsMYB30 bound to the promoter of OsTPP1 and regulated the abundance of OsTPP1 transcripts. Overaccumulation of trehalose (Tre) was found in both OsMYB30- and OsTPP1-overexpressing lines, resulting in inhibition of α-amylase 1a (OsAMY1a) gene during seed germination. Both LT and exogenous Tre treatments suppressed the expression of OsAMY1a, and the osamy1a mutant was not sensitive to exogenous Tre during seed germination. Overall, we concluded that OsMYB30 expression was induced by LT to activate the expression of OsTPP1 and increase Tre content, which thus inhibited α-amylase activity and seed germination. This study identified a phytohormone-independent pathway that integrates environmental cues with internal factors to control seed germination.

Integration of transcriptome and metabolome reveals the accumulation of related metabolites and gene regulation networks during quinoa seed development

Quinoa seeds are gluten- and cholesterol-free, contain all amino acids required by the human body, have a high protein content, provide endocrine regulation, protein supplementation, and cardiovascular protection effects. However, metabolite accumulation and transcriptional regulatory networks in quinoa seed development are not well understood. Four key stages of seed development in Dianli-3260 and Dianli-557 were thus analyzed and 849 metabolites were identified, among which sugars, amino acids, and lipids were key for developmental processes, and their accumulation showed a gradual decrease. Transcriptome analysis identified 40,345 genes, of which 20,917 were differential between the M and F phases, including 8279 and 12,638 up- and down-regulated genes, respectively. Grain development processes were mainly enriched in galactose metabolism, pentose and glucuronate interconversions, the biosynthesis of amino acids, and carbon metabolism pathways, in which raffinose, phosphoenolpyruvate, series and other metabolites are significantly enriched, gene-LOC110689372, Gene-LOC110710556 and gene-LOC110714584 are significantly expressed, and these metabolites and genes play an important role in carbohydrate metabolism, lipid and Amino acid synthesis of quinoa. This study provides a theoretical basis to expand our understanding of the molecular and metabolic development of quinoa grains.

Reveal the kernel dehydration mechanisms in maize based on proteomic and metabolomic analysis

BACKGROUND

Kernel dehydration is an important factor for the mechanized harvest in maize. Kernel moisture content (KMC) and kernel dehydration rate (KDR) are important indicators for kernel dehydration. Although quantitative trait loci and genes related to KMC have been identified, where most of them only focus on the KMC at harvest, these are still far from sufficient to explain all genetic variations, and the relevant regulatory mechanisms are still unclear. In this study, we tried to reveal the key proteins and metabolites related to kernel dehydration in proteome and metabolome levels. Moreover, we preliminarily explored the relevant metabolic pathways that affect kernel dehydration combined proteome and metabolome. These results could accelerate the development of further mechanized maize technologies.

RESULTS

In this study, three maize inbred lines (KB182, KB207, and KB020) with different KMC and KDR were subjected to proteomic analysis 35, 42, and 49 days after pollination (DAP). In total, 8,358 proteins were quantified, and 2,779 of them were differentially expressed proteins in different inbred lines or at different stages. By comparative analysis, K-means cluster, and weighted gene co-expression network analysis based on the proteome data, some important proteins were identified, which are involved in carbohydrate metabolism, stress and defense response, lipid metabolism, and seed development. Through metabolomics analysis of KB182 and KB020 kernels at 42 DAP, 18 significantly different metabolites, including glucose, fructose, proline, and glycerol, were identified.

CONCLUSIONS

In sum, we inferred that kernel dehydration could be regulated through carbohydrate metabolism, antioxidant systems, and late embryogenesis abundant protein and heat shock protein expression, all of which were considered as important regulatory factors during kernel dehydration process. These results shed light on kernel dehydration and provide new insights into developing cultivars with low moisture content.

Analysis of Raffinose Metabolism-Related Sugar Components in Seeds

Raffinose family oligosaccharides (RFOs) are synthesized from sucrose and subsequent addition of galactose moieties which was provided by galactinol. Galactinol is synthesized from UDP-galactose and myo-inositol. RFOs accumulate at late stage of seed development and play important roles in seed longevity. RFOs are major components in seeds of many plant species. Here, we document a methodology for extraction and quantitative analysis of raffinose metabolism-related soluble sugars or the derivative alcohols in plant seeds. This protocol, based on high-performance liquid chromatography (HPLC), achieves the efficient separation and accurate quantification of sucrose, myo-inositol, galactinol, and raffinose within 25 min of retention time.

Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle

Background

Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.

Results

The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.

Conclusion

Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.

Analysis of Raffinose Synthase Gene Family in Bread Wheat and Identification of Drought Resistance and Salt Tolerance Function of TaRS15-3B

Raffinose synthase (RS) plays a crucial role in plant growth and development, as well as in responses to biotic stresses and abiotic stresses, yet few studies have been conducted on its role in bread wheat. Therefore, in this study we screened and identified a family of bread wheat raffinose synthase genes based on bread wheat genome information and analyzed their physicochemical properties, phylogenetic evolutionary relationships, conserved structural domains, promoter cis-acting elements, and expression patterns. The BSMV-induced silencing of TaRS15-3B resulted in the bread wheat seedlings being susceptible to drought and salt stress and reduced the expression levels of stress-related and ROS-scavenging genes in bread wheat plants. This further affected the ability of bread wheat to cope with drought and salt stress. In conclusion, this study revealed that the RS gene family in bread wheat plays an important role in plant response to abiotic stresses and that the TaRS15-3B gene can improve the tolerance of transgenic bread wheat to drought and salt stresses, provide directions for the study of other RS gene families in bread wheat, and supply candidate genes for use in molecular breeding of bread wheat for stress resistance.

Molecular dynamics of seed priming at the crossroads between basic and applied research

The potential of seed priming is still not fully exploited. Our limited knowledge of the molecular dynamics of seed pre-germinative metabolism is the main hindrance to more effective new-generation techniques. Climate change and other recent global crises are disrupting food security. To cope with the current demand for increased food, feed, and biofuel production, while preserving sustainability, continuous technological innovation should be provided to the agri-food sector. Seed priming, a pre-sowing technique used to increase seed vigor, has become a valuable tool due to its potential to enhance germination and stress resilience under changing environments. Successful priming protocols result from the ability to properly act on the seed pre-germinative metabolism and stimulate events that are crucial for seed quality. However, the technique still requires constant optimization, and researchers are committed to addressing some key open questions to overcome such drawbacks. In this review, an update of the current scientific and technical knowledge related to seed priming is provided. The rehydration-dehydration cycle associated with priming treatments can be described in terms of metabolic pathways that are triggered, modulated, or turned off, depending on the seed physiological stage. Understanding the ways seed priming affects, either positively or negatively, such metabolic pathways and impacts gene expression and protein/metabolite accumulation/depletion represents an essential step toward the identification of novel seed quality hallmarks. The need to expand the basic knowledge on the molecular mechanisms ruling the seed response to priming is underlined along with the strong potential of applied research on primed seeds as a source of seed quality hallmarks. This route will hasten the implementation of seed priming techniques needed to support sustainable agriculture systems.

Raffinose positively regulates maize drought tolerance by reducing leaf transpiration

Drought stress is one of the major constraints of global crop production. Raffinose, a non-reducing trisaccharide, has been considered to regulate positively the plant drought stress tolerance; however, evidence that augmenting raffinose production in leaves results in enhanced plant drought stress tolerance is lacking. The biochemical mechanism through which raffinose might act to mitigate plant drought stress remains unidentified. ZmRAFS encodes Zea mays RAFFINOSE SYNTHASE, a key enzyme that transfers galactose from the galactoside galactinol to sucrose for raffinose production. Overexpression of ZmRAFS in maize increased the RAFS protein and the raffinose content and decreased the water loss of leaves and enhanced plant drought stress tolerance. The biomass of the ZmRAFS overexpressing plants was similar to that of non-transgenic control plants when grown under optimal conditions, but was significantly greater than that of non-transgenic plants when grown under drought stress conditions. In contrast, the percentage of water loss of the detached leaves from two independent zmrafs mutant lines, incapable of synthesizing raffinose, was greater than that from null segregant controls and this phenomenon was partially rescued by supplementation of raffinose to detached zmrafs leaves. In addition, while there were differences in water loss among different maize lines, there was no difference in stomata density or aperture. Taken together, our work demonstrated that overexpression of the ZmRAFS gene in maize, in contrast to Arabidopsis, increased the raffinose content in leaves, assisted the leaf to retain water, and enhanced the plant drought stress tolerance without causing a detectable growth penalty.

Maize PIMT2 repairs damaged 3-METHYLCROTONYL COA CARBOXYLASE in mitochondria, affecting seed vigor

PROTEIN l-ISOASPARTYL O-METHYLTRANSFERASE (PIMT) affects seed vigor by repairing damaged proteins. While PIMT is capable of isoaspartyl (isoAsp) repair in all proteins, those proteins most susceptible to isoAsp formation have not been well characterized, and the mechanisms by which PIMT affects seed vigor remain largely unknown. Using co-immunoprecipitation and LC-MS/MS, we found that maize (Zea mays) PIMT2 (ZmPIMT2) interacted predominantly with both subunits of maize 3-METHYLCROTONYL COA CARBOXYLASE (ZmMCC). ZmPIMT2 is specifically expressed in the maize embryo. Both mRNA and protein levels of ZmPIMT2 increased during seed maturation and declined during imbibition. Maize seed vigor was decreased in the zmpimt2 mutant line, while overexpression of ZmPIMT2 in maize and Arabidopsis thaliana increased seed vigor upon artificial aging. ZmPIMT2 was localized in the mitochondria, as determined by subcellular localization assays using maize protoplasts. ZmPIMT2 binding to ZmMCCα was confirmed by luciferase complementation tests in both tobacco (Nicotiana benthamiana) leaves and maize protoplasts. Knockdown of ZmMCCα decreased maize seed aging tolerance. Furthermore, overexpression of ZmPIMT2 decreased the accumulation of isoAsp of ZmMCCα protein in seed embryos that underwent accelerated aging treatment. Taken together, our results demonstrate that ZmPIMT2 binds ZmMCCα in mitochondria, repairs isoAsp damage, and positively affects maize seed vigor.

Optimizing raffinose family oligosaccharides content in plants: A tightrope walk

Plants synthesize various compounds for their growth, metabolism, and stress mitigation, and one such group of compounds is the raffinose family of oligosaccharides (RFOs). RFOs are non-reducing oligosaccharides having galactose residues attached to a sucrose moiety. They act as carbohydrate reserves in plants, assisting in seed germination, desiccation tolerance, and biotic/abiotic stress tolerance. Although legumes are among the richest sources of dietary proteins, the direct consumption of legumes is hindered by an excess of RFOs in the edible parts of the plant, which causes flatulence in humans and monogastric animals. These opposing characteristics make RFOs manipulation a complicated tradeoff. An in-depth knowledge of the chemical composition, distribution pattern, tissue mobilization, and metabolism is required to optimize the levels of RFOs. The most recent developments in our understanding of RFOs distribution, physiological function, genetic regulation of their biosynthesis, transport, and degradation in food crops have been covered in this review. Additionally, we have suggested a few strategies that can sustainably reduce RFOs in order to solve the flatulence issue in animals. The comprehensive information in this review can be a tool for researchers to precisely control the level of RFOs in crops and create low antinutrient, nutritious food with wider consumer acceptability.

Effect of storage time on chemical compositions, physiological and cooking quality characteristics of different rice types

BACKGROUND

Storage affects rice quality significantly. The aim of this study was to investigate the changes in the chemical composition and in the physiological and cooking quality characteristics of three rice types after 1 year storage at 25 °C.

RESULTS

Two japonica, two indica, and two indica-japonica hybrid rice varieties were selected. After storage, the total starch content decreased. The amylose content of japonica, indica, and indica-japonica hybrid rice increased by 9.63%-11.65%, 2.99%-4.67%, and 8.07%-8.97%, respectively, and the fat content decreased by 60.00%-65.00%, 37.21%-46.51%, and 41.67%-42.42%, respectively. The abscisic acid (ABA) and raffinose content decreased after 1 year's storage; the former decreased gradually during the storage and the latter increased by 19.35%-45.45%, 7.02%-10.77%, and 16.13%-28.13%, respectively, after 4 months' storage and then decreased to the lowest level after 1 year's storage. The activity of antioxidant enzymes deceased, which resulted in the increases in fatty acid value and malondialdehyde (MDA). The changes in chemical composition after 1 year storage led to the deterioration of rice cooking quality, which was reflected in the decrease in viscosity and increases in gelatinization temperature and cooked rice hardness.

CONCLUSION

After 1 year's storage, the rice chemical composition changed and physiological and cooking quality characteristics decreased. Compared with japonica and indica-japonica hybrid rice, indica rice was more stable during 1 year storage. This may be due to the higher content of ABA and raffinose in fresh rice. Our findings will provide information for the identification and breeding of storable rice cultivars. © 2022 Society of Chemical Industry.

Rice lipid transfer protein, OsLTPL23, controls seed germination by regulating starch-sugar conversion and ABA homeostasis

Seed germination is vital for ensuring the continuity of life in spermatophyte. High-quality seed germination usually represents good seedling establishment and plant production. Here, we identified OsLTPL23, a putative rice non-specific lipid transport protein, as an important regulator responsible for seed germination. Subcellular localization analysis confirmed that OsLTPL23 is present in the plasma membrane and nucleus. The knockout mutants of OsLTPL23 were generated by CRISPR/Cas9-mediated genome editing, and osltpl23 lines significantly germinated slower and lower than the Nipponbare (NIP). Starch and soluble sugar contents measurement showed that OsLTPL23 may have alpha-amylase inhibitor activity, and high soluble sugar content may be a causal agent for the delayed seed germination of osltpl23 mutants. Transcript profiles in the germinating seeds exhibited that the abscisic acid (ABA)-responsive genes, OsABI3 and OsABI5, and biosynthesis genes, OsNCED1, OsNCED2, OsNCED3 and OsNCED4, are obviously upregulated in the osltpl23 mutants compared to NIP plants, conversely, ABA metabolism genes OsABA8ox1, OsABA8ox2 and OsABA8ox3 are stepwise decreased. Further investigations found that osltpl23 mutants displays weakened early seedling growth, with elevated gene expresssion of ABA catabolism genes and repressive transcription response of defence-related genes OsWRKY45, OsEiN3, OsPR1a, OsPR1b and OsNPR1. Integrated analysis indicated that OsLTPL23 may exert an favorable effect on rice seed germination and early seedling growth via modulating endogenous ABA homeostasis. Collectively, our study provides important insights into the roles of OsLTPL23-mediated carbohydrate conversion and endogenous ABA pathway on seed germination and early seedling growth, which contributes to high-vigor seed production in rice breeding.

Spatio-temporal expression pattern of Raffinose Synthase genes determine the levels of Raffinose Family Oligosaccharides in peanut (Arachis hypogaea L.) seed

Raffinose family oligosaccharides (RFOs) are known to have important physiological functions in plants. However, the presence of RFOs in legumes causes flatulence, hence are considered antinutrients. To reduce the RFOs content to a desirable limit without compromising normal plant development and functioning, the identification of important regulatory genes associated with the biosynthetic pathway is a prerequisite. In the present study, through comparative RNA sequencing in contrasting genotypes for seed RFOs content at different seed maturity stages, differentially expressed genes (DEGs) associated with the pathway were identified. The DEGs exhibited spatio-temporal expression patterns with high RFOs variety showing early induction of RFOs biosynthetic genes and low RFOs variety showing a late expression at seed maturity. Selective and seed-specific differential expression of raffinose synthase genes (AhRS14 and AhRS6) suggested their regulatory role in RFOs accumulation in peanut seeds, thereby serving as promising targets in low RFOs peanut breeding programs. Despite stachyose being the major seed RFOs fraction, differential expression of raffinose synthase genes indicated the complex metabolic regulation of this pathway. The transcriptomic resource and the genes identified in this study could be studied further to develop low RFOs varieties, thus improving the overall nutritional quality of peanuts.

Alterations in Carbohydrate Quantities in Freeze-Dried, Relative to Fresh or Frozen Maize Leaf Disks

For various reasons, leaves are occasionally lyophilized prior to storage at -80 °C and preparing extracts. Soluble carbohydrate identity and quantity from maize leaf disks were ascertained in two separate years using anion exchange HPLC with pulsed electrochemical detection. Analyses were made from disks after freezing in liquid nitrogen with or without subsequent lyophilization (both years) or directly after removal from plants with or without lyophilization (only in the second year). By adding the lyophilizing step, galactose content consistently increased and, frequently, so did galactoglycerols. The source of the galactose increase with the added lyophilizing step was not due to metabolizing raffinose, as the raffinose synthase (rafs) null mutant leaves, which do not make that trisaccharide, also had a similar increase in galactose content with lyophilization. Apparently, the ester linkages attaching free fatty acids to galactoglycerolipids of the chloroplast are particularly sensitive to cleavage during lyophilization, resulting in increases in galactoglycerols. Regardless of the galactose source, a systematic error is introduced for carbohydrate (and, most likely, also chloroplast mono- or digalactosyldiacylglycerol) amounts when maize leaf samples are lyophilized prior to extraction. The recognition of lyophilization as a source of galactose increase provides a cautionary note for investigators of soluble carbohydrates.

Cucumber STACHYOSE SYNTHASE is regulated by its cis-antisense RNA asCsSTS to balance source-sink carbon partitioning

Photosynthate partitioning between source and sink is a key determinant of crop yield. In contrast to sucrose-transporting plants, cucumber (Cucumis sativus) plants mainly transport stachyose and stachyose synthase (CsSTS) synthesizes stachyose in the vasculature for loading. Therefore, CsSTS is considered a key regulator of carbon partitioning. We found that CsSTS expression and CsSTS enzyme activity were upregulated in the vasculature and downregulated in mesophyll tissues at fruiting. In situ hybridization and tissue enrichment experiments revealed that a cis-natural antisense noncoding transcript of CsSTS, named asCsSTS, is mainly expressed in mesophyll tissues. In vitro overexpression (OE), RNA interference (RNAi), and dual luciferase reporter experiments indicated that CsSTSs are negatively regulated by asCsSTS. Fluorescence in situ hybridization revealed that asCsSTS transcript localized in leaf cytoplasm, indicating that the regulation of CsSTS by asCsSTS is a posttranscriptional process. Further investigation revealed that this regulation occurred by reducing CsSTS transcript stability through a DICER-like protein-mediated pathway. Chemically induced OE and RNAi of asCsSTS led to promotion or inhibition, respectively, of assimilate export from leaves and altered fruit growth rates. Our results suggest that the regulation of CsSTSs between the mesophyll and vasculature reduces sugar storage in mesophyll tissue and promotes assimilate export from the leaf when the plant carries fruit.

An alternative pathway to plant cold tolerance in the absence of vacuolar invertase activity

To cope with cold stress, plants have developed antioxidation strategies combined with osmoprotection by sugars. In potato (Solanum tuberosum) tubers, which are swollen stems, exposure to cold stress induces starch degradation and sucrose synthesis. Vacuolar acid invertase (VInv) activity is a significant part of the cold-induced sweetening (CIS) response, by rapidly cleaving sucrose into hexoses and increasing osmoprotection. To discover alternative plant tissue pathways for coping with cold stress, we produced VInv-knockout lines in two cultivars. Genome editing of VInv in 'Désirée' and 'Brooke' was done using stable and transient expression of CRISPR/Cas9 components, respectively. After storage at 4°C, sugar analysis indicated that the knockout lines showed low levels of CIS and maintained low acid invertase activity in storage. Surprisingly, the tuber parenchyma of vinv lines exhibited significantly reduced lipid peroxidation and reduced H2 O2 levels. Furthermore, whole plants of vinv lines exposed to cold stress without irrigation showed normal vigor, in contrast to WT plants, which wilted. Transcriptome analysis of vinv lines revealed upregulation of an osmoprotectant pathway and ethylene-related genes during cold temperature exposure. Accordingly, higher expression of antioxidant-related genes was detected after exposure to short and long cold storage. Sugar measurements showed an elevation of an alternative pathway in the absence of VInv activity, raising the raffinose pathway with increasing levels of myo-inositol content as a cold tolerance response.

Identification, Characterization and Expression Profiling of the RS Gene Family during the Withering Process of White Tea in the Tea Plant (Camellia sinensis) Reveal the Transcriptional Regulation of CsRS8

Raffinose synthetase (RS) is a key enzyme in the process of raffinose (Raf) synthesis and is involved in plant development and stress responses through regulating Raf content. As a sweetener, Raf makes an important contribution to the sweet taste of white tea. However, studies on the identification, analysis and transcriptional regulation of CsRSs (Camellia sinensis RS genes) are still lacking. In this study, nine CsRSs were identified from the tea plant (Camellia sinensis) genome database. The CsRSs were classified into five groups in the phylogenetic tree. Expression level analysis showed that the CsRSs varied in different parts of the tea plant. Transcriptome data showed that CsRSs could respond to persistent drought and cold acclimation. Except for CsRS5 and CsRS9, the expression pattern of all CsRSs increased at 12 h and decreased at 30 h during the withering process of white tea, consistent with the change trend of the Raf content. Furthermore, combining yeast one-hybrid assays with expression analysis, we found that CsDBB could potentially regulate the expression of CsRS8. Our results provide a new perspective for further research into the characterization of CsRS genes and the formation of the white tea flavour.

Ectopic expression of a grapevine alkaline α-galactosidase seed imbibition protein VvSIP enhanced salinity tolerance in transgenic tobacco plants

Alpha-galactosidase seed imbibition protein (VvSIP) isolated from Vitis vinifera is up-regulated upon salt stress and mediates osmotic stress responses in a tolerant grapevine cultivar. So far, little is known about the putative role of this stress-responsive gene. In the present study, VvSIP function was investigated in model tobacco plants via Agrobacterium-mediated genetic transformation. Our results showed that overexpression of VvSIP exhibited increased tolerance to salinity at germination and late vegetative stage in transgenic Nicotiana benthamiana compared to the nontransgenic plants based on the measurement of the germination rate and biomass production. High salt concentrations of 200 and 400 mM NaCl in greenhouse-grown pot assay resulted in better relative water content, higher leaf osmotic potential, and leaf water potential in transgenic lines when compared to the wild-type (WT) plants. These physiological changes attributed to efficient osmotic adjustment improved plant performance and tolerance to salinity compared to the WT. Moreover, the VvSIP-expressing lines SIP1 and SIP2 showed elevated amounts of chlorophyll with lower malondialdehyde content indicating a reduced lipid peroxidation required to maintain membrane stability. When subjected to high salinity conditions, the transgenic tobacco VvSIP exhibited higher soluble sugar content, which may suggest an enhancement of the carbohydrate metabolism. Our findings indicate that the VvSIP is involved in plant salt tolerance by functioning as a positive regulator of osmotic adjustment and sugar metabolism, both of which are responsible for stress mitigation. Such a candidate gene is highly suitable to alleviate environmental stresses and thus could be a promising candidate for crop improvement.

Transcriptional regulation of the raffinose family oligosaccharides pathway in Sorghum bicolor reveals potential roles in leaf sucrose transport and stem sucrose accumulation

Bioenergy sorghum hybrids are being developed with enhanced drought tolerance and high levels of stem sugars. Raffinose family oligosaccharides (RFOs) contribute to plant environmental stress tolerance, sugar storage, transport, and signaling. To better understand the role of RFOs in sorghum, genes involved in myo-inositol and RFO metabolism were identified and relative transcript abundance analyzed during development. Genes involved in RFO biosynthesis (SbMIPS1, SbInsPase, SbGolS1, SbRS) were more highly expressed in leaves compared to stems and roots, with peak expression early in the morning in leaves. SbGolS, SbRS, SbAGA1 and SbAGA2 were also expressed at high levels in the leaf collar and leaf sheath. In leaf blades, genes involved in myo-inositol biosynthesis (SbMIPS1, SbInsPase) were expressed in bundle sheath cells, whereas genes involved in galactinol and raffinose synthesis (SbGolS1, SbRS) were expressed in mesophyll cells. Furthermore, SbAGA1 and SbAGA2, genes that encode neutral-alkaline alpha-galactosidases that hydrolyze raffinose, were differentially expressed in minor vein bundle sheath cells and major vein and mid-rib vascular and xylem parenchyma. This suggests that raffinose synthesized from sucrose and galactinol in mesophyll cells diffuses into vascular bundles where hydrolysis releases sucrose for long distance phloem transport. Increased expression (>20-fold) of SbAGA1 and SbAGA2 in stem storage pith parenchyma of sweet sorghum between floral initiation and grain maturity, and higher expression in sweet sorghum compared to grain sorghum, indicates these genes may play a key role in non-structural carbohydrate accumulation in stems.

The Use of DArTseq Technology to Identify Markers Linked to Genes Responsible for Seed Germination and Seed Vigor in Maize

Seed vigor and seed germination are very important traits, determined by several factors including genetic and physical purity, mechanical damage, and physiological condition, characterized by maintaining a high seed vigor and stable content after storage. The search for molecular markers related to improvement in seed vigor under adverse condition is an important issue in maize breeding currently. Higher sowing quality of seeds is necessary for the development of the agriculture production and better ability to resist all kinds of adversity in the seeds’ storage. Condition is a very important factor affecting the yield of plants, thanks to the construction of their vitality. Identification of molecular markers associated with seed germination and seed vigor may prove to be very important in the selection of high-yielding maize varieties. The aim of this study was to identify and select new markers for maize (SNP and SilicoDArT) linked to genes influencing the seed germination and seed vigor in inbred lines of maize (Zea mays L.). The plant material used for the research was 152 inbred maize lines. The seed germination and seed vigor were analyzed. For identification of SNP and SilicoDArT markers related to the seed germination and seed vigor, the SilicoDarT technique developed by Diversity Arrays Technology was used. The analysis of variance indicated a statistically significant differentiation between genotypes for both observed traits. Positive (r = 0.41) correlation (p < 0.001) between seed germination and seed vigor was observed. As a result of next-generation sequencing, the molecular markers SilicoDArT (53,031) and SNP (28,571) were obtained. Out of 81,602 identified SilicoDArT and SNP markers, 15,409 (1559 SilicoDArT and 13,850 SNP) were selected as a result of association mapping, which showed them to be significantly related to the analyzed traits. The 890 molecular markers were associated with seed vigor, and 1323 with seed germination. Fifty-six markers (47 SilicoDArT and nine SNP) were significant for both traits. Of these 56 markers, the 20 most significant were selected (five of these markers were significant at the level of 0.001 for seed vigor and at the level of 0.05 for seed germination, another five markers were significant at the level of 0.001 for seed germination and at the level of 0.05 for seed vigor, five markers significant at the level of 0.001 only for seed vigor and five significant at the level of 0.001 only for seed germination also selected). These markers were used for physical mapping to determine their location on the genetic map. Finally, it was found that six of these markers (five silicoDArT—2,435,784, 4,772,587, 4,776,334, 2,507,310, 25,981,291, and one SNP—2,386,217) are located inside genes, the action of which may affect both seed germination and seed vigor. These markers can be used to select genotypes with high vigor and good seed germination.

Raffinose family oligosaccharides (RFOs): role in seed vigor and longevity

Seed vigor and longevity are important agronomic attributes, as they are essentially associated with crop yield and thus the global economy. Seed longevity is a measure of seed viability and the most essential property in gene bank management since it affects regeneration of seed recycling. Reduced seed life or storability is a serious issue in seed storage since germplasm conservation and agricultural enhancement initiatives rely on it. The irreversible and ongoing process of seed deterioration comprises a complex gene regulatory network and altered metabolism that results in membrane damage, DNA integrity loss, mitochondrial dysregulation, protein damage, and disrupted antioxidative machinery. Carbohydrates and/or sugars, primarily raffinose family oligosaccharides (RFOs), have emerged as feasible components for boosting or increasing seed vigor and longevity in recent years. RFOs are known to perform diverse functions in plants, including abiotic and biotic stress tolerance, besides being involved in regulating seed germination, desiccation tolerance, vigor, and longevity. We emphasized and analyzed the potential impact of RFOs on seed vigor and longevity in this review. Here, we comprehensively reviewed the molecular mechanisms involved in seed longevity, RFO metabolism, and how RFO content is critical and linked with seed vigor and longevity. Further molecular basis, biotechnological approaches, and CRISPR/Cas applications have been discussed briefly for the improvement of seed attributes and ultimately crop production. Likewise, we suggest advancements, challenges, and future possibilities in this area.

Identification of miRNAs Mediating Seed Storability of Maize during Germination Stage by High-Throughput Sequencing, Transcriptome and Degradome Sequencing

Seed storability is an important trait for improving grain quality and germplasm conservation, but little is known about the regulatory mechanisms and gene networks involved. MicroRNAs (miRNAs) are small non-coding RNAs regulating the translation and accumulation of their target mRNAs by means of sequence complementarity and have recently emerged as critical regulators of seed germination. Here, we used the germinating embryos of two maize inbred lines with significant differences in seed storability to identify the miRNAs and target genes involved. We identified a total of 218 previously known and 448 novel miRNAs by miRNA sequencing and degradome analysis, of which 27 known and 11 newly predicted miRNAs are differentially expressed in two maize inbred lines, as measured by Gene Ontology (GO) enrichment analysis. We then combined transcriptome sequencing and real-time quantitative polymerase chain reaction (RT-PCR) to screen and confirm six pairs of differentially expressed miRNAs associated with seed storability, along with their negative regulatory target genes. The enrichment analysis suggested that the miRNAs/target gene mediation of seed storability occurs via the ethylene activation signaling pathway, hormone synthesis and signal transduction, as well as plant organ morphogenesis. Our results should help elucidate the mechanisms through which miRNAs are involved in seed storability in maize.

Genome-Wide Expression Profiling Analysis of Kiwifruit GolS and RFS Genes and Identification of AcRFS4 Function in Raffinose Accumulation

The raffinose synthetase (RFS) and galactinol synthase (GolS) are two critical enzymes for raffinose biosynthesis, which play an important role in modulating plant growth and in response to a variety of biotic or abiotic stresses. Here, we comprehensively analyzed the RFS and GolS gene families and their involvement in abiotic and biotic stresses responses at the genome-wide scale in kiwifruit. A total of 22 GolS and 24 RFS genes were identified in Actinidia chinensis and Actinidia eriantha genomes. Phylogenetic analysis showed that the GolS and RFS genes were clustered into four and six groups, respectively. Transcriptomic analysis revealed that abiotic stresses strongly induced some crucial genes members including AcGolS1/2/4/8 and AcRFS2/4/8/11 and their expression levels were further confirmed by qRT-PCR. The GUS staining of AcRFS4Pro::GUS transgenic plants revealed that the transcriptionlevel of AcRFS4 was significantly increased by salt stress. Overexpression of AcRFS4 in Arabidopsis demonstrated that this gene enhanced the raffinose accumulation and the tolerance to salt stress. The co-expression networks analysis of hub transcription factors targeting key AcRFS4 genes indicated that there was a strong correlation between AcNAC30 and AcRFS4 expression under salt stress. Furthermore, the yeast one-hybrid assays showed that AcNAC30 could bind the AcRFS4 promoter directly. These results may provide insights into the evolutionary and functional mechanisms of GolS and RFS genes in kiwifruit.

Energy homeostasis mediated by the LcSnRK1α-LcbZIP1/3 signaling pathway modulates litchi fruit senescence

Cellular energy status is a key factor deciding the switch-on of the senescence of horticultural crops. Despite the established significance of the conserved energy master regulator sucrose non-fermenting 1 (SNF1)-related protein kinase 1 (SnRK1) in plant development, its working mechanism and related signaling pathway in the regulation of fruit senescence remain enigmatic. Here, we demonstrate that energy deficit accelerates fruit senescence, whereas exogenous ATP treatment delays it. The transient suppression of LcSnRK1α in litchi (Litchi chinensis Sonn.) fruit inhibited the expression of energy metabolism-related genes, while its ectopic expression in tomato (Solanum lycopersicum) promoted ripening and a high energy level. Biochemical analyses revealed that LcSnRK1α interacted with and phosphorylated the transcription factors LcbZIP1 and LcbZIP3, which directly bound to the promoters to activate the expression of DARK-INDUCIBLE 10 (LcDIN10), ASPARAGINE SYNTHASE 1 (LcASN1), and ANTHOCYANIN SYNTHASE (LcANS), thereby fine-tuning the metabolic reprogramming to ensure energy and redox homeostasis. Altogether, these observations reveal a post-translational modification mechanism by which LcSnRK1α-mediated phosphorylation of LcbZIP1 and LcbZIP3 regulates the expression of metabolic reprogramming-related genes, consequently modulating litchi fruit senescence.

Alkaline α-galactosidase 2 (CsAGA2) plays a pivotal role in mediating source-sink communication in cucumber

Sugars are necessary for plant growth and fruit development. Cucumber (Cucumis sativus L.) transports sugars, mainly raffinose family oligosaccharides (RFOs), in the vascular bundle. As the dominant sugars in cucumber fruit, glucose and fructose are derived from sucrose, which is the product of RFO hydrolysis by α-galactosidase (α-Gal). Here, we characterized the cucumber alkaline α-galactosidase 2 (CsAGA2) gene and found that CsAGA2 has undergone human selection during cucumber domestication. Further experiments showed that the expression of CsAGA2 increases gradually during fruit development, especially in fruit vasculature. In CsAGA2-RNA interference (RNAi) lines, fruit growth was delayed because of lower hexose production in the peduncle and fruit main vascular bundle (MVB). In contrast, CsAGA2-overexpressing (OE) plants displayed bigger fruits. Functional enrichment analysis of transcriptional data indicated that genes related to sugar metabolism, cell wall metabolism, and hormone signaling were significantly downregulated in the peduncle and fruit MVBs of CsAGA2-RNAi plants. Moreover, downregulation of CsAGA2 also caused negative feedback regulation on source leaves, which was shown by reduced photosynthetic efficiency, fewer plasmodesmata at the surface between mesophyll cell and intermediary cell (IC) or between IC and sieve element, and downregulated gene expression and enzyme activities related to phloem loading, as well as decreased sugar production and exportation from leaves and petioles. The opposite trend was observed in CsAGA2-OE lines. Overall, we conclude that CsAGA2 is essential for cucumber fruit set and development through mediation of sugar communication between sink strength and source activity.

Transcriptome-Wide Characterization of Seed Aging in Rice: Identification of Specific Long-Lived mRNAs for Seed Longevity

Various long-lived mRNAs are stored in seeds, some of which are required for the initial phase of germination and are critical to seed longevity. However, the seed-specific long-lived mRNAs involved in seed longevity remain poorly understood in rice. To identify these mRNAs in seeds, we first performed aging experiment with 14 rice varieties, and categorized them as higher longevity (HL) and lower longevity (LL) rice varieties in conventional rice and hybrid rice, respectively. Second, RNA-seq analysis showed that most genes showed similar tendency of expression changes during natural and artificial aging, suggesting that the effects of these two aging methods on transcription are comparable. In addition, some differentially expressed genes (DEGs) in the HL and LL varieties differed after natural aging. Furthermore, several specific long-lived mRNAs were identified through a comparative analysis of HL and LL varieties after natural aging, and similar sequence features were also identified in the promoter of some specific long-lived mRNAs. Overall, we identified several specific long-lived mRNAs in rice, including gibberellin receptor gene GID1, which may be associated with seed longevity.

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.

Sugar transporters and their molecular tradeoffs during abiotic stress responses in plants

Sugars as photosynthates are well known as energy providers and as building blocks of various structural components of plant cells, tissues and organs. Additionally, as a part of various sugar signaling pathways, they interact with other cellular machinery and influence many important cellular decisions in plants. Sugar signaling is further reliant on the differential distribution of sugars throughout the plant system. The distribution of sugars from source to sink tissues or within organelles of plant cells is a highly regulated process facilitated by various sugar transporters located in plasma membranes and organelle membranes, respectively. Sugar distribution, as well as signaling, is impacted during unfavorable environments such as extreme temperatures, salt, nutrient scarcity, or drought. Here, we have discussed the mechanism of sugar transport via various types of sugar transporters as well as their differential response during environmental stress exposure. The functional involvement of sugar transporters in plant's abiotic stress tolerance is also discussed. Besides, we have also highlighted the challenges in engineering sugar transporter proteins as well as the undeciphered modules associated with sugar transporters in plants. Thus, this review provides a comprehensive discussion on the role and regulation of sugar transporters during abiotic stresses and enables us to target the candidate sugar transporter(s) for crop improvement to develop climate-resilient crops.

The Orthodox Dry Seeds Are Alive: A Clear Example of Desiccation Tolerance

To survive in the dry state, orthodox seeds acquire desiccation tolerance. As maturation progresses, the seeds gradually acquire longevity, which is the total timespan during which the dry seeds remain viable. The desiccation-tolerance mechanism(s) allow seeds to remain dry without losing their ability to germinate. This adaptive trait has played a key role in the evolution of land plants. Understanding the mechanisms for seed survival after desiccation is one of the central goals still unsolved. That is, the cellular protection during dry state and cell repair during rewatering involves a not entirely known molecular network(s). Although desiccation tolerance is retained in seeds of higher plants, resurrection plants belonging to different plant lineages keep the ability to survive desiccation in vegetative tissue. Abscisic acid (ABA) is involved in desiccation tolerance through tight control of the synthesis of unstructured late embryogenesis abundant (LEA) proteins, heat shock thermostable proteins (sHSPs), and non-reducing oligosaccharides. During seed maturation, the progressive loss of water induces the formation of a so-called cellular "glass state". This glassy matrix consists of soluble sugars, which immobilize macromolecules offering protection to membranes and proteins. In this way, the secondary structure of proteins in dry viable seeds is very stable and remains preserved. ABA insensitive-3 (ABI3), highly conserved from bryophytes to Angiosperms, is essential for seed maturation and is the only transcription factor (TF) required for the acquisition of desiccation tolerance and its re-induction in germinated seeds. It is noteworthy that chlorophyll breakdown during the last step of seed maturation is controlled by ABI3. This update contains some current results directly related to the physiological, genetic, and molecular mechanisms involved in survival to desiccation in orthodox seeds. In other words, the mechanisms that facilitate that an orthodox dry seed is a living entity.

Contrasting Metabolic Fingerprints and Seed Protein Profiles of Cucurbita foetidissima and C. radicans Fruits from Feral Plants Sampled in Central Mexico

Cucurbita foetidissima and C. radicans are scarcely studied wild pumpkin species that grow in arid and semi-arid areas of Mexico and the United States. This study describes the morphological, proximal composition, metabolic finger-prints and seed protein profiles of C. foetidissima and C. radicans fruits collected in the wild during a one-year period in different locations of central-western Mexico. The results obtained complement the limited information concerning the fruit composition of C. foetidissima and greatly expand information in this respect regarding C. radicans. Morphology and proximal composition of their fruits varied significantly. Different metabolic fingerprints and seed protein profiles were detected between them and also with the chemical composition of domesticated Cucurbita fruits. The neutral lipids in seed, pulp and peels were rich in wax content and in unsaturated compounds, probably carotenoids and tocopherols, in addition to tri-, di- and mono-acylglycerols. The tri- and diacylglycerol profiles of their seed oils were different from commercial seed oils and between each other. They also showed unusual fatty acid compositions. Evidence of a possible alkaloid in the pulp and peel of both species was obtained in addition to several putative cucurbitacins. An abundance of phenolic acids was found in all fruit parts, whereas flavonoids were only detected in the peels. Unlike most cucurbits, globulins were not the main protein fraction in the seeds of C. radicans, whereas the non-structural carbohydrate and raffinose oligosaccharide content in their fruit parts was lower than in other wild cucurbit species. These results emphasize the significantly different chemical composition of these two marginally studied Cucurbita species, which was more discrepant in C. radicans, despite the notion regarding C. foetidissima as an aberrant species with no affinity to any other Cucurbita species.

A conserved NAG motif is critical to the catalytic activity of galactinol synthase, a key regulatory enzyme of RFO biosynthesis

Galactinol synthase (GolS) catalyzes the key regulatory step in the biosynthesis of Raffinose Family Oligosaccharides (RFOs). Even though the physiological role and regulation of this enzyme has been well studied, little is known about active site amino acids and the structure-function relationship with substrates of this enzyme. In the present study, we investigate the active site amino acid and structure-function relationship for this enzyme. Using a combination of three-dimensional homology modeling, molecular docking along with a series of deletion, site-directed mutagenesis followed by in vitro biochemical and in vivo functional analysis; we have studied active site amino acids and their interaction with the substrate of chickpea and Arabidopsis GolS enzyme. Our study reveals that the GolS protein possesses GT8 family-specific several conserved motifs in which NAG motif plays a crucial role in substrate binding and catalytic activity of this enzyme. Deletion of entire NAG motif or deletion or the substitution (with alanine) of any residues of this motif results in complete loss of catalytic activity in in vitro condition. Furthermore, disruption of NAG motif of CaGolS1 enzyme disrupts it's in vivo cellular function in yeast as well as in planta. Together, our study offers a new insight into the active site amino acids and their substrate interaction for the catalytic activity of GolS enzyme. We demonstrate that NAG motif plays a vital role in substrate binding for the catalytic activity of galactinol synthase that affects overall RFO synthesis.

ZmAGA1 Hydrolyzes RFOs Late during the Lag Phase of Seed Germination, Shifting Sugar Metabolism toward Seed Germination Over Seed Aging Tolerance

Raffinose family oligosaccharides (RFOs) are accumulated during the late stage of seed development and hydrolyzed during seed germination. The process of raffinose hydrolysis during seed germination and how this process affects seed vigor remains unknown. We report here that maize alkaline α-galactosidase 1 (ZmAGA1) protein is translationally induced and is capable of hydrolyzing RFOs as well as a precursor, galactinol, during seed germination. Constitutively overexpressing ZmAGA1 in Arabidopsis decreased both RFOs and galactinol contents of mature, desiccated, and 30 hours after imbibition (HAI) seeds, yet enhanced the seed germination percentage under either salt or somewhat osmotic-stress conditions at earlier times during the time course. However, ZmAGA1 overexpression also decreased the seed aging tolerance of mature, desiccated seeds as compared with wild type (WT) or those overexpressing GFP. Compared to that of WT control seeds, the atsip2 (mutant of Arabidopsis AtSIP2 (seed imbibition protein 2, encoding alkaline α-galactosidase)) seeds have similar RFOs and galactinol contents in mature, desiccated seeds but significantly increased the amount of these metabolites at 30 HAI. This retention of RFOs and galactinol in atsip2 results in seeds that exhibit lowered seed germination percentage under either salt or osmotic stress conditions, and yet, increased seed aging tolerance relative to WT. Similarly, when maize seeds were imbibed in the presence of a specific α-galactosidase inhibitor (1-deoxygalactonojirimycin) as compared to those imbibed in water, greater amounts of raffinose and galactinol were detected; the seeds exhibited decreased seed germination percentages but increased seed aging tolerance. Taken together, these data suggest that both maize seed germination and seed aging tolerance can be simultaneously regulated through careful temporal manipulation of ZmAGA1 expression.

Comparative Proteomics at the Critical Node of Vigor Loss in Wheat Seeds Differing in Storability

The critical node (CN, 85% germination) of seed viability is an important threshold for seed regeneration decisions after long-term conservation. Dependent on the germplasm, the storage period until CN is reached varies and information on the divergence of the proteomic profiles is limited. Therefore, the study aims to identify key proteins and mechanisms relevant for a long plateau phase and a late CN during artificial seed aging of wheat. Seeds of the storage-tolerant genotype (ST) TRI 23248, and the storage-sensitive genotype (SS) TRI 10230 were exposed to artificial ageing (AA) and extracted embryos of imbibed seeds were analyzed using an iTRAQ-based proteomic technique. ST and SS required AA for 24 and 18 days to reach the CN, respectively. Fifty-seven and 165 differentially abundant proteins (DAPs) were observed in the control and aged groups, respectively. Interestingly, a higher activity in metabolic processes, protein synthesis, transcription, cell growth/division, and signal transduction were already found in imbibed embryos of control ST seeds. After AA, 132 and 64 DAPs were accumulated in imbibed embryos of both aged ST and SS seeds, respectively, which were mainly associated with cell defense, rescue, and metabolism. Moreover, 78 DAPs of ST appeared before CN and were mainly enriched in biological pathways related to the maintenance of redox and carbon homeostasis and they presented a stronger protein translation ability. In contrast, in SS, only 3 DAPs appeared before CN and were enriched only in the structural constituents of the cytoskeleton. In conclusion, a longer span of plateau phase might be obtained in seeds when proteins indicate an intense stress response before CN and include the effective maintenance of cellular homeostasis, and avoidance of excess accumulation of cytotoxic compounds. Although key proteins, inherent factors and the precise regulatory mechanisms need to be further investigated, the found proteins may also have functional potential roles during long-term seed conservation.

Transcriptomic and Metabolic Analysis of Fruit Development and Identification of Genes Involved in Raffinose and Hydrolysable Tannin Biosynthesis in Walnuts

Walnut (Juglans regia L.) is an important fruit tree with high nutrition in its nuts. Here, the development of walnut fruits was monitored, and nine biological samples at five developmental stages were collected and analyzed by transcriptomic and metabolic assays. Many phenolic metabolites accumulated in the peel of mature fruits, while lipids, carbohydrates, and amino acids and their derivatives mainly accumulated in the kernel. Fatty acid biosynthesis occurred at 13 weeks after pollination, and photosynthesis might occur in the exocarp of walnuts. By coexpression analysis of the transcriptome and metabolome, genes responsible for some metabolic pathways were predicted. Three genes encoding shikimate dehydrogenases (SDHs) that convert 3-dehydroshikimic acid to gallic acid (GA) and four genes encoding UDP-glycosyltransferase (UGT) that convert GA to β-glucogallin in the biosynthesis of hydrolysable tannins (HTs) were selected for functional confirmation. These three SDH genes were then expressed in Escherichia coli, and their recombinant proteins showed GA formation activity. Moreover, heterologous expression of the three SDH and four UGT genes in poplar hairy roots also showed a significant increase in GA and β-glucogallin accumulation, respectively. Taken together, we have provided an overview of walnut fruit development and uncovered genes involved in HT biosynthesis.