The gibberellin biosynthetic genes AtKAO1 and AtKAO2 have overlapping roles throughout Arabidopsis development

The mutation of ent-kaurenoic acid oxidase, a key enzyme involved in gibberellin biosynthesis, confers a dwarf phenotype to cucumber

KEY MESSAGE

A dwarf mutant with short branches (csdf) was identified from EMS-induced mutagenesis. Bulked segregant analysis sequencing and map-based cloning revealed CsKAO encoding ent-kaurenoic acid oxidase as the causal gene. Plant architecture is the primary target of artificial selection during domestication and improvement based on the determinate function for fruit yield. Plant architecture is regulated by complicated genetic networks, more underlying mechanism remains to be elucidated. Here, we identified a dwarf mutant (csdf) in an EMS-induced cucumber population, and genetic analysis revealed the mutated phenotype is controlled by a single recessive gene. Optical microanalysis showed the decrease in cell length is mainly contribute to the dwarf phenotype. By strategy of BSA-seq combined with map-based cloning, CsaV3_6G006520 (CsKAO) on chromosome 6 was identified as the candidate gene for csdf. Gene cloning and sequence alignment revealed a G to A mutation in the sixth exon, which causes the premature stop codon in CsKAO of csdf. Expression analysis revealed CsKAO was expressed in various tissues with abundant transcripts, and has significant differences between WT and csdf. Gene annotation indicated CsKAO encodes a cytochrome P450 family ent-kaurenoic acid oxidase which functioned in GA biosynthesis. GA-relevant analysis showed that endogenous GA contents were significantly decreased and the dwarfism phenotype could be restored by exogenous GA3 treatment; while, some of the representative enzyme genes involved in the GA pathway were up-regulated in csdf. Besides, IAA content is decreased in the terminal bud and increased in the lateral bud in csdf as well as several IAA-related genes are differentially expressed. Overall, those findings suggest that CsKAO regulated plant height via the influence on GAs pathways, and IAA might interact with GAs on plant architecture morphogenesis in cucumber.

A multi-omics approach reveals a link between ribosomal protein alterations and proteome rebalancing in Arabidopsis thaliana seeds

The ability of seeds to restore their amino acid content and composition after the elimination of the most abundant seed storage proteins (SSPs) is well-documented, yet the underlying mechanisms remain unclear. To better understand how seeds compensate for major proteomic disruptions, we conducted a comprehensive analysis on an Arabidopsis mutant lacking the three most abundant SSPs, the cruciferins. Our initial findings indicated that carbon, nitrogen, and sulfur levels, as well as total protein and oil content, remained unchanged in these mutants suggesting rebalanced seeds. Transcriptomics and proteomics performed during seed maturation of Col-0 and the triple mutant revealed significant modulation in many components of the translational machinery, especially ribosomal proteins (RPs), and in the antioxidation response in the mutant. These findings suggest that RPs play a critical role in facilitating proteomic homeostasis during seed maturation when proteomic perturbation occurs. Biochemical and metabolic analyses of the triple mutant dry seeds revealed increased protein carbonylation and elevated glutathione levels further supporting the link between SSP accumulation and seed redox homeostasis. Overall, we propose that in response to significant proteomic perturbations, changes in the proteome and amino acid composition of seeds are accompanied by a broad remodeling of the translation apparatus. We postulate that these alterations are key elements in seed adaptability and robustness to large proteomic perturbations during seed maturation.

Biomass enhancement and activation of transcriptional regulation in sorghum seedling by plasma-activated water

Introduction

Recent advancements in agricultural technology have highlighted the potential of eco-friendly innovations, such as plasma-activated water (PAW), for enhancing seed germination, growth, and biomass production.

Methods

In this study, we investigated the effects of PAW irrigation on young sorghum seedlings through phenotypic and transcriptional analyses. We measured growth parameters, including seedling height, stem thickness, and biomass, across five sorghum varieties: BTx623, Sodamchal, Noeulchal, Baremae, and Hichal. Additionally, we performed detailed analyses of stem cross-sections to evaluate the structural changes induced by PAW. Whole transcriptome analysis was conducted to identify differentially expressed genes (DEGs) and to perform Gene Ontology (GO) analysis.

Results

Phenotypic analysis revealed significant growth enhancements in PAW-treated seedlings compared to the control group, with notable increases in seedling height, stem thickness, and biomass. Stem cross-section analysis confirmed that PAW treatment led to the enlargement of primordia tissue, leaf sheath (LS1 and LS2), and overall stem tissue area. Transcriptomic analysis revealed that 78% of the DEGs were upregulated in response to PAW, indicating that PAW acts as a positive regulator of gene expression. Gene Ontology (GO) analysis further showed that PAW treatment predominantly upregulated genes associated with transmembrane transport, response to light stimulus, oxidoreductase activity, and transcriptional regulation. Additionally, an enriched AP2/EREBP transcription binding motif was identified.

Conclusion

These findings suggest that PAW not only enhances sorghum seedling growth through transcriptional regulation but also has the potential to optimize agricultural practices by increasing crop yield. The upregulation of genes involved in critical biological processes underscores the need for further exploration of PAW's potential in improving the productivity of sorghum and possibly other crops.

Integrative transcriptome analysis uncovers common components containing CPS2 regulated by maize lncRNA GARR2 in gibberellin response

MAIN CONCLUSION

The combined transcriptome outcome provides an important clue to the regulatory cascade centering on lncRNA GARR2 and CPS2 gene in GA response. Long non-coding RNAs (lncRNAs) serve as regulatory components in transcriptional hierarchy governing multiple aspects of biological processes. Dissecting regulatory mechanisms underpinning tetracyclic diterpenoid gibberellin (GA) cascade holds both theoretical and applied significance. However, roles of lncRNAs in transcriptional modulation of GA pathway remain largely elusive. Gypsy retrotransposon-derived GIBBERELLIN RESPONSIVE lncRNA2 (GARR2) has been reported as GA-responsive maize lncRNA. Here a novel GARR2-edited line garr2-1 was identified, characteristic of GA-induced phenotype of increased seedling height and elongated leaf sheath. Transcriptome analysis indicated that transcriptional abundance of five genes [ent-copalyl diphosphate synthase2 (CPS2), ent-kaurene synthase4 (KS4), ent-kaurene synthase6 (KS6), ent-kaurene oxidase2 (KO2), and ent-kaurenoic acid oxidase1/Dwarf3 (KAO1/D3)] was elevated in garr2-1 for early steps of GA biosynthesis. Five GA biosynthetic genes as hub regulators were interlaced to shape regulatory network of GA response. Different transcriptome resources were integrated to discover common differentially expressed genes (DEGs) in the independent GARR2-edited lines GARR2KO and garr2-1. A total of 320 common DEGs were retrieved. These common DEGs were enriched in diterpenoid biosynthetic pathway. Integrative transcriptome analysis revealed the common CPS2 encoding the CPS enzyme that catalyzes the conversion of the precursor trans-geranylgeranyl diphosphate to ent-copalyl diphosphate. The up-regulated CPS2 supported the GA-induced phenotype of slender seedlings observed in the independent GARR2-edited lines GARR2KO and garr2-1. Our integrative transcriptome analysis uncovers common components of the GA pathway regulated by lncRNA GARR2. These common components, especially for the GA biosynthetic gene CPS2, provide a valuable resource for further delineating the underlying mechanisms of lncRNA GARR2 in GA response.

Highlights in gibberellin research: A tale of the dwarf and the slender

It has been almost a century since biologically active gibberellin (GA) was isolated. Here, we give a historical overview of the early efforts in establishing the GA biosynthesis and catabolism pathway, characterizing the enzymes for GA metabolism, and elucidating their corresponding genes. We then highlight more recent studies that have identified the GA receptors and early GA signaling components (DELLA repressors and F-box activators), determined the molecular mechanism of DELLA-mediated transcription reprograming, and revealed how DELLAs integrate multiple signaling pathways to regulate plant vegetative and reproductive development in response to internal and external cues. Finally, we discuss the GA transporters and their roles in GA-mediated plant development.

Molecular Insights into the Accelerated Sprouting of and Apical Dominance Release in Potato Tubers Subjected to Post-Harvest Heat Stress

Climate change-induced heat stress (HS) increasingly threatens potato (Solanum tuberosum L.) production by impacting tuberization and causing the premature sprouting of tubers grown during the hot season. However, the effects of post-harvest HS on tuber sprouting have yet to be explored. This study aims to investigate the effects of post-harvest HS on tuber sprouting and to explore the underlying transcriptomic changes in apical bud meristems. The results show that post-harvest HS facilitates potato tuber sprouting and negates apical dominance. A meticulous transcriptomic profiling of apical bud meristems unearthed a spectrum of differentially expressed genes (DEGs) activated in response to HS. During the heightened sprouting activity that occurred at 15-18 days of HS, the pathways associated with starch metabolism, photomorphogenesis, and circadian rhythm were predominantly suppressed, while those governing chromosome organization, steroid biosynthesis, and transcription factors were markedly enhanced. The critical DEGs encompassed the enzymes pivotal for starch metabolism, the genes central to gibberellin and brassinosteroid biosynthesis, and influential developmental transcription factors, such as SHORT VEGETATIVE PHASE, ASYMMETRIC LEAVES 1, SHOOT MERISTEMLESS, and MONOPTEROS. These findings suggest that HS orchestrates tuber sprouting through nuanced alterations in gene expression within the meristematic tissues, specifically influencing chromatin organization, hormonal biosynthesis pathways, and the transcription factors presiding over meristem fate determination. The present study provides novel insights into the intricate molecular mechanisms whereby post-harvest HS influences tuber sprouting. The findings have important implications for developing strategies to mitigate HS-induced tuber sprouting in the context of climate change.

Overexpression of SlCRF6 in tomato inhibits leaf development and affects plant morphology

Cytokinin response factors (CRFs) are transcription factors (TFs) that are specific to plants and have diverse functions in plant growth and stress responses. However, the precise roles of CRFs in regulating tomato plant architecture and leaf development have not been comprehensively investigated. Here, we identified a novel CRF, SlCRF6, which is involved in the regulation of plant growth via the gibberellin (GA) signaling pathway. SlCRF6-overexpressing (SlCRF6-OE) plants displayed pleiotropic phenotypic changes, including reduced internode length and leaf size, which caused dwarfism in tomato plants. This dwarfism could be alleviated by application of exogenous GA3. Remarkably, quantitative real-time PCR (qRTPCR), a dual luciferase reporter assay and a yeast one-hybrid (Y1H) assay revealed that SlCRF6 promoted the expression of SlDELLA (a GA signal transduction inhibitor) in vivo. Furthermore, transgenic plants displayed variegated leaves and diminished chlorophyll content, resulting in decreased photosynthetic efficiency and less starch than in wild-type (WT) plants. The results of transient expression assays and Y1H assays indicated that SlCRF6 suppressed the expression of SlPHAN (leaf morphology-related gene). Collectively, these findings suggest that SlCRF6 plays a crucial role in regulating tomato plant morphology, leaf development, and the accumulation of photosynthetic products.

Combined transcriptome and proteome analysis reveal the key physiological processes in seed germination stimulated by decreased salinity in the seagrass Zostera marina L

BACKGROUND

Zostera marina L., or eelgrass, is the most widespread seagrass species throughout the temperate northern hemisphere. Unlike the dry seeds of terrestrial plants, eelgrass seeds must survive in water, and salinity is the key factor influencing eelgrass seed germination. In the present study, transcriptome and proteome analysis were combined to investigate the mechanisms via which eelgrass seed germination was stimulated by low salinity, in addition to the dynamics of key metabolic pathways under germination.

RESULTS

According to the results, low salinity stimulated the activation of Ca2+ signaling and phosphatidylinositol signaling, and further initiated various germination-related physiological processes through the MAPK transduction cascade. Starch, lipids, and storage proteins were mobilized actively to provide the energy and material basis for germination; abscisic acid synthesis and signal transduction were inhibited whereas gibberellin synthesis and signal transduction were activated, weakening seed dormancy and preparing for germination; cell wall weakening and remodeling processes were activated to provide protection for cotyledon protrusion; in addition, multiple antioxidant systems were activated to alleviate oxidative stress generated during the germination process; ERF transcription factor has the highest number in both stages suggested an active role in eelgrass seed germination.

CONCLUSION

In summary, for the first time, the present study investigated the mechanisms by which eelgrass seed germination was stimulated by low salinity and analyzed the transcriptomic and proteomic features during eelgrass seed germination comprehensively. The results of the present study enhanced our understanding of seagrass seed germination, especially the molecular ecology of seagrass seeds.

o-Nitrobenzyl-Based Caged exo-16,17-Dihydro-gibberellin A5-13-acetate for Photocontrolled Release of Plant Growth Regulators

Caged plant growth regulators (caged PGRs) that release bioactive molecules under irradiation are critical in enhancing the efficacy and mitigating the negative environmental effects of PGRs. The synthetically derived plant growth inhibitor exo-16,17-dihydro-gibberellin A5-13-acetate (DHGA5) regulates the development and stress resilience of plants. We report here the conception of novel caged DHGA5 derivatives wherein the photoremovable protecting groups (PRPGs) serve not only to enable light-controlled release but also to protect the carboxyl group during chemical synthesis. Three o-nitrobenzyl-based caged DHGA5 derivatives with different substituents on the nitrobenzyl moiety were obtained and evaluated for their properties in vitro and in vivo. The photolysis half-life values of caged DHGA5 derivatives 7a, 7b, and 7c under a UV lamp were 15.6 h, 1.2 h, and 28.2 h, respectively. Experiments in vivo showed that 0.2 mM of the caged compounds significantly inhibited the growth of the model plant Arabidopsis thaliana and important crop rice in a precise photoactivated form.

Genome-wide transcriptomic and functional analyses provide new insights into the response of spring barley to drought stress

Drought is a major abiotic stress that impairs the physiology and development of plants, ultimately leading to crop yield losses. Drought tolerance is a complex quantitative trait influenced by multiple genes and metabolic pathways. However, molecular intricacies and subsequent morphological and physiological changes in response to drought stress remain elusive. Herein, we combined morpho-physiological and comparative RNA-sequencing analyses to identify core drought-induced marker genes and regulatory networks in the barley cultivar 'Giza134'. Based on field trials, drought-induced declines occurred in crop growth rate, relative water content, leaf area duration, flag leaf area, concentration of chlorophyll (Chl) a, b and a + b, net photosynthesis, and yield components. In contrast, the Chl a/b ratio, stoma resistance, and proline concentration increased significantly. RNA-sequence analysis identified a total of 2462 differentially expressed genes (DEGs), of which 1555 were up-regulated and 907 were down-regulated in response to water-deficit stress (WD). Comparative transcriptomics analysis highlighted three unique metabolic pathways (carbohydrate metabolism, iron ion binding, and oxidoreductase activity) as containing genes differentially expressed that could mitigate water stress. Our results identified several drought-induced marker genes belonging to diverse physiochemical functions like chlorophyll concentration, photosynthesis, light harvesting, gibberellin biosynthetic, iron homeostasis as well as Cis-regulatory elements. These candidate genes can be utilized to identify gene-associated markers to develop drought-resilient barley cultivars over a short period of time. Our results provide new insights into the understanding of water stress response mechanisms in barley.

Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation

Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.

MsCYP71 is a positive regulator for drought resistance in alfalfa

Cytochrome P450 (CYP450) family proteins play key roles in plant growth, development, stress responses, and other physiological processes. Here, we cloned the cytochrome P450 gene MsCYP71 in alfalfa and found that the expression of MsCYP71 was induced by drought stress. Silencing the MsCYP71 gene using virus-induced gene silencing technology significantly decreased the drought resistance of alfalfa, as indicated by their lower relative water content, net photosynthetic rate, and chlorophyll fluorescence maximum (Fm); further, the heterologous overexpression of MsCYP71 in tobacco significantly enhanced the drought resistance and Fm of transgenic tobacco. Furthermore, the expression of MsCYP71 across 45 alfalfa accessions under drought stress was investigated. A significant positive correlation between drought resistance and MsCYP71 expression was observed. The 45 alfalfa accessions were clustered into four groups, and drought resistance, Fm, and MsCYP71 were higher in group I than in the other groups, indicating that group I accessions can be used as candidate germplasm resources for the breeding of drought-resistant alfalfa varieties. Overall, our findings indicated that MsCYP71 is a positive regulator of drought resistance in alfalfa, and its expression can be used to evaluate the drought resistance of alfalfa.

High-resolution genetic linkage map and height-related QTLs in an oil palm (Elaeis guineensis) family planted across multiple sites

A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01360-2.

Transcription elongation factors OsSPT4 and OsSPT5 are essential for rice growth and development and act with APO2

KEY MESSAGE

The transcription elongation factor SPT4/SPT5 complex is essential for rice vegetative and reproductive growth and that OsSPT5-1, with its interactor APO2, is involved in multiple phytohormone pathways. The SPT4/SPT5 complex is a transcription elongation factor that regulates the processivity of transcription elongation. However, our understanding of the role of SPT4/SPT5 complex in developmental regulation remains limited. Here, we identified three SPT4/SPT5 genes (OsSPT4, OsSPT5-1, and OsSPT5-2) in rice, and investigated their roles in vegetative and reproductive growth. These genes are highly conserved with their orthologs in other species. OsSPT4 and OsSPT5-1 are widely expressed in various tissues. By contrast, OsSPT5-2 is expressed at a relatively low level, which could cause osspt5-2 null mutants have no phenotypes. Loss-of-function mutants of OsSPT4 and OsSPT5-1 could not be obtained; their heterozygotes showed severe reproductive growth defects. An incomplete mutant line (osspt5-1#12) displayed gibberellin-related dwarfed defects and a weak root system at an early vegetative phase, and a short life cycle in different planting environments. Furthermore, OsSPT5-1 interacts with the transcription factor ABERRANT PANICLE ORGANIZATION 2 (APO2) and plays a similar role in regulating the growth of rice shoots. RNA sequencing analysis verified that OsSPT5-1 is involved in multiple phytohormone pathways, including gibberellin, auxin, and cytokinin. Therefore, the SPT4/SPT5 complex is essential for both vegetative and reproductive growth in rice.

Thermosensitivity of pollen: a molecular perspective

A current trend in climate comprises adverse weather anomalies with more frequent and intense temperature events. Heatwaves are a serious threat to global food security because of the susceptibility of crop plants to high temperatures. Among various developmental stages of plants, even a slight rise in temperature during reproductive development proves detrimental, thus making sexual reproduction heat vulnerable. In this context, male gametophyte or pollen development stages are the most sensitive ones. High-temperature exposure induces pollen abortion, reducing pollen viability and germination rate with a concomitant effect on seed yield. This review summarizes the ultrastructural, morphological, biochemical, and molecular changes underpinning high temperature-induced aberrations in male gametophytes. Specifically, we highlight the temperature sensing cascade operating in pollen, involving reactive oxygen species (ROS), heat shock factors (HSFs), a hormones and transcriptional regulatory network. We also emphasize integrating various omics approaches to decipher the molecular events triggered by heat stress in pollen. The knowledge of genes, proteins, and metabolites conferring thermotolerance in reproductive tissues can be utilized to breed/engineer thermotolerant crops to ensure food security.

SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway

Plant height is an important target trait for crop genetic improvement. Our previous work has identified a salt-tolerant C2H2 zinc finger, SlZF3, and its overexpression lines also showed a semi-dwarf phenotype, but the molecular mechanism remains to be elucidated. Here, we characterized the dwarf phenotype in detail. The dwarfism is caused by a decrease in stem internode cell elongation and deficiency of bioactive gibberellic acids (GAs), and can be rescued by exogenous GA3 treatment. Gene expression assays detected reduced expression of genes in the GA biosynthesis pathway of the overexpression lines, including SlGA20ox4. Several protein-DNA interaction methods confirmed that SlZF3 can directly bind to the SlGA20ox4 promoter and inhibit its expression, and the interaction can also occur for SlKS and SlKO. Overexpression of SlGA20ox4 in the SlZF3-overexpressing line can recover the dwarf phenotype. Therefore, SlZF3 regulates plant height by directly repressing genes in the tomato GA biosynthesis pathway.

A tracking work on how Sm4CL2 re-directed the biosynthesis of salvianolic acids and tanshinones in Salvia miltiorrhiza hairy roots

Overexpression and antisense expression of Sm4CL2 re-directed the biosynthesis of salvianolic acids and tanshinones in Salvia miltiorrhiza hairy roots. Danshen (Salvia miltiorrhiza Bunge) is a widely used traditional Chinese medicine and its main active ingredients are water-soluble phenolic acids and lipophilic diterpenoids which are produced through the phenylpropanoid pathway and terpenoid pathway, respectively. 4-Coumaric acid: Coenzyme A ligase (4CL) is a key enzyme in the phenylpropanoid metabolism. We had obtained Sm4CL2-overexpressing (Sm4CL2-OE) and antisense Sm4CL2-expressing (anti-Sm4CL2) danshen hairy roots over ten years ago. In the follow-up study, we found that total salvianolic acids in Sm4CL2-OE-4 hairy roots increased to 1.35 times of the control-3, and that in anti-Sm4CL2-1 hairy roots decreased to 37.32% of the control-3, but tanshinones in anti-Sm4CL2-1 was accumulated to 1.77 ± 0.16 mg/g of dry weight, compared to undetectable in Sm4CL2-OE-4 and the control-3 hairy roots. Interestingly, Sm4CL2-OE-4 hairy roots contained more lignin, 1.36 times of the control-3, and enhanced cell wall and xylem lignification. Transcriptomic analysis revealed that overexpression of Sm4CL2 caused the upregulation of other phenylpropanoid pathway genes and antisense Sm4CL2 expression resulted in the downregulation of other phenylpropanoid pathway genes but activated the expression of terpenoid pathway genes like SmCYP76AK5, SmGPPS.SSUII.1 and SmDXS2. Protein-protein interaction analysis suggested that Sm4CL2 might interact with PAL, PAL4, CSE, CCoAOMT and SmCYP84A60, and appeared to play a key role in the interaction network. The tracking work in this study proved that Sm4CL2 could redirect both salvianolic acids and tanshinones biosynthesis possibly through synergistically regulating other pathway genes. It also indicated that genetic modification of plant secondary metabolism with biosynthetic gene might cause other responses through protein-protein interactions.

Responses of roots and rhizosphere of female papaya to the exogenous application of GA3

Exogenous GAs have an indeterminate effect on root development. Our current study used female papaya to reveal how the roots and rhizosphere respond to the exogenous application of GA₃ by investigating the transcriptome profile in roots, metabolic profile and microbial community in both roots and rhizosphere of GA₃-treated and control female papaya. The results demonstrated that exogenous GA₃ treatment enhanced female papaya lateral root development, which gave plants physical advantages of water and nutrient uptake. In addition, it was likely that GA₃ spraying in papaya shoot apices increased the level of auxin, which was transported to roots by CpPIN1, where auxin upregulated CpLBD16 and repressed CpBP to promote the lateral root initiation and development. In papaya roots, corresponding transporters (CpTMT3, CpNRT1:2, CpPHT1;4, CpINT2, CpCOPT2, CpABCB11, CpNIP4;1) were upregulated and excretion transporters were downregulated such as CpNAXT1 for water and nutrients uptake with exogenous GA₃ application. Moreover, in GA₃-treated papaya roots, CpALS3 and CpMYB62 were downregulated, indicating a stronger abiotic resistance to aluminum toxic and phosphate starvation. On the other hand, BRs and JAs, which involve in defense responses, were enriched in the roots and rhizosphere of GA₃-treated papayas. The upregulation of the two hormones might result in the reduction of pathogens in roots and rhizosphere such as Colletotrichum and Verticillium. GA₃-treated female papaya increased the abundance of beneficial bacteria species including Mycobacterium, Mitsuaria, and Actinophytocola, but decreased that of the genera Candidatus and Bryobacter for that it required less nitrate. Overall, the roots and rhizosphere of female papaya positively respond to exogenous application of GA₃ to promote development and stress tolerance. Treatment of female papaya with GA3 might result in the promotion of lateral root formation and development by upregulating CpLBD16 and downregulating CpBP. GA₃-treated papaya roots exhibited feedback control of brassinolide and jasmonate signaling in root development and defense. These findings revealed complex response to a growth hormone treatment in papaya roots and rhizosphere and will lead to investigations on the impact of other plant hormones on belowground development in papaya.

Genome-Wide Identification of the Cytochrome P450 Superfamily Genes and Targeted Editing of BnCYP704B1 Confers Male Sterility in Rapeseed

The cytochrome P450 (CYP450) monooxygenase superfamily, which is involved in the biosynthesis pathways of many primary and secondary metabolites, plays prominent roles in plant growth and development. However, systemic information about CYP450s in Brassica napus (BnCYP450) was previously undiscovered and their biological significance are far from understood. Members of clan 86 CYP450s, such as CYP704Bs, are essential for the formation of pollen exine in plant male reproduction, and the targeted mutagenesis of CYP704B genes has been used to create new male sterile lines in many crops. In the present study, a total of 687 BnCYP450 genes were identified in Brassica napus cultivar "Zhongshuang 11" (ZS11), which has nearly 2.8-fold as many CYP450 members as in Arabidopsis thaliana. It is rationally estimated since Brassica napus is a tetraploid oil plant with a larger genome compared with Arabidopsis thaliana. The BnCYP450 genes were divided into 47 subfamilies and clustered into nine clans. Phylogenetic relationship analysis reveals that CYP86 clan consists of four subfamilies and 109 BnCYP450s. Members of CYP86 clan genes display specific expression profiles in different tissues and in response to ABA and abiotic stresses. Two BnCYP450s within the CYP704 subfamily from CYP86 clan, BnCYP704B1a and BnCYP704B1b, display high similarity to MS26 (Male Sterility 26, also known as CYP704B1). These two BnCYP704B1 genes were specifically expressed in young buds. We then simultaneously knocked-out these two BnCYP704B1 genes through a clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) genome engineering system. The edited plants displayed a pollenless, sterile phenotype in mature anthers, suggesting that we successfully reproduced genic male sterility (GMS, also known as nuclear male sterility) lines in Brassica napus. This study provides a systemic view of BnCYP450s and offers a strategy to facilitate the commercial utility of the CRISPR/Cas9 system for the rapid generation of GMS in rapeseed via knocking-out GMS controlling genes.

Effects of gibberellins on important agronomic traits of horticultural plants

Horticultural plants such as vegetables, fruits, and ornamental plants are crucial to human life and socioeconomic development. Gibberellins (GAs), a class of diterpenoid compounds, control numerous developmental processes of plants. The roles of GAs in regulating growth and development of horticultural plants, and in regulating significant progress have been clarified. These findings have significant implications for promoting the quality and quantity of the products of horticultural plants. Here we review recent progress in determining the roles of GAs (including biosynthesis and signaling) in regulating plant stature, axillary meristem outgrowth, compound leaf development, flowering time, and parthenocarpy. These findings will provide a solid foundation for further improving the quality and quantity of horticultural plants products.

Harnessing hormone gibberellin knowledge for plant height regulation

Harnessing hormone GA knowledge is a potential means to develop plant height ideotypes. Plant height holds significance for natural beauty and agricultural revolution. The increased grain productivity during the Green Revolution of the 1960s is partly attributed to the reshaping of plant stature, which is conferred by changes in phytohormone gibberellin (GA) metabolism or signaling. GA fine-tunes multiple aspects of biological events and plays a pivotal role in plant height determinant. Harnessing hormone GA knowledge is a potential means to develop ideal plant height to meet the future demand. Here, we present an overview of characterized GA pathway genes for plant height regulation. Novel alleles of Green Revolution genes sd1 and Rht are specially delineated. Through interactome analysis, we uncover GA20ox and GA3ox family members as central hub modulators of GA pathway. Empowered by GA knowledge, we suggest ways towards design breeding of plant height ideotypes through harnessing the alterations of GA cascade. We highlight the utility of genome editing to generate weak alleles to circumvent side effects of GA pathway perturbation.

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.

BrKAO2 mutations disrupt leafy head formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

The role of BrKAO2 in leafy head formation was confirmed by using two allelic Chinese cabbage mutants. Chinese cabbage yield and quality are determined by leafy head formation. Cloning and characterising the key genes regulating leafy head formation are essential for its varietal improvement. We used an EMS-mutagenised population of the heading type 'FT' Chinese cabbage line and identified two allelic non-heading mutants, i.e. nhm3-1 and nhm3-2. Genetic analysis showed that the mutant trait was controlled by a single recessive gene. MutMap and Kompetitive Allele Specific PCR genotyping revealed that BraA05g012440.3C was the candidate gene, which encodes ent-kaurenoic acid oxidase 2 in gibberellin (GA) biosynthetic pathway. It was named BrKAO2. Two non-synonymous mutations in the second BrKAO2 exon, respectively, accounted for the mutant phenotypes of nhm3-1 and nhm3-2. BrKAO2 was expressed during all leaf development stages, and there were no significant differences between the wild type and mutants in terms of BrKAO2 expression. The mutant phenotypes were restored to the wild type via exogenous GA3 application. RNA-Seq was performed on wild-type 'FT', nhm3-1, and nhm3-1 + GA3 rosette leaves, and several key genes involved in GA biosynthesis, signal transduction, and leafy head development were identified. These findings indicate that BrKAO2 is responsible for the leafy head formation in nhm3 mutants.

Overexpression of SlPRE5, an atypical bHLH transcription factor, affects plant morphology and chlorophyll accumulation in tomato

The basic helix-loop-helix (bHLH) transcription factors play vital regulatory roles in a series of metabolic, physiological, and developmental processes of plants. Here, SlPRE5, an atypical bHLH gene, was isolated from tomato. SlPRE5 was noticeably expressed in young leaves, sepals, and flowers. SlPRE5-overexpressing plants exhibited rolling leaves with reduced chlorophyll content, increased stem internode length, leaf angle, and compound leaf length. The water loss rate of mature leaves and the content of starch were significantly reduced, while the content of gibberellin was significantly increased in transgenic plants. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) showed that SlPRE5 could interact with SlAIF1, SlAIF2, and SlPAR1. qRT-PCR and RNA-seq results revealed that the expression levels of genes related to chloroplast development, chlorophyll metabolism, gibberellin metabolism and signal transduction, starch, photosynthesis, and cell expansion were significantly altered in SlPRE5-overexpression plants. Collectively, our results suggest that SlPRE5 is a crucial transcription factor involved in plant morphology and chlorophyll accumulation in tomato leaves.

The Metabolism of a Novel Cytochrome P450 (CYP77B34) in Tribenuron-Methyl-Resistant Descurainia sophia L. to Herbicides with Different Mode of Actions

Descurainia sophia L. (flixweeds) is a noxious broad-leaf weed infesting winter wheat fields in China that has evolved high resistance to tribenuron-methyl. In this work, a brand new gene CYP77B34 was cloned from tribenuron-methyl-resistant (TR) D. sophia and transferred into Arabidopsis thaliana, and the sensitivities of Arabidopsis with or without the CYP77B34 transgene to herbicides with a different mode of actions (MoAs) were tested. Compared to Arabidopsis expressing pCAMBIA1302-GFP (empty plasmid), Arabidopsis transferring pCAMBIA1302-CYP77B34 (recombinant plasmid) became resistant to acetolactate synthase (ALS)-inhibiting herbicide tribenuron-methyl, protoporphyrinogen oxidase (PPO)-inhibiting herbicides carfentrazone-ethyl and oxyfluorfen. Cytochrome P450 inhibitor malathion could reverse the resistance to tribenuron-methyl, carfentrazone-ethyl and oxyfluorfen in transgenic Arabidopsis plants. In addition, the metabolic rates of tribenuron-methyl in Arabidopsis expressing CYP77B34 were significantly higher than those in Arabidopsis expressing pCAMBIA1302-GFP. Other than that, the transgenic plants showed some tolerance to very-long-chain fatty acid synthesis (VLCFAs)-inhibiting herbicide pretilachlor and photosystem (PS) II-inhibiting herbicide bromoxynil. Subcellular localization revealed that the CYP77B34 protein was located in the endoplasmic reticulum (ER). These results clearly indicated that CYP77B34 mediated D. sophia resistance to tribenuron-methyl and may have been involved in D. sophia cross-resistance to carfentrazone-ethyl, oxyfluorfen, pretilachlor and bromoxynil.

Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera

Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms "amino acid binding," "cellulase activity," and "DNA beta-glucosyltransferase activity". Further, KEGG pathway annotation showed significant enrichment in "fatty acid elongation" and "biosynthesis of unsaturated fatty acids". These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.

Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.

Integrated Bioinformatics Analyses of PIN1, CKX, and Yield-Related Genes Reveals the Molecular Mechanisms for the Difference of Seed Number Per Pod Between Soybean and Cowpea

There is limited advancement on seed number per pod (SNPP) in soybean breeding, resulting in low yield in China. To address this issue, we identified PIN1 and CKX gene families that regulate SNPP in Arabidopsis, analyzed the differences of auxin and cytokinin pathways, and constructed interaction networks on PIN1, CKX, and yield-related genes in soybean and cowpea. First, the relative expression level (REL) of PIN1 and the plasma membrane localization and phosphorylation levels of PIN1 protein were less in soybean than in cowpea, which make auxin transport efficiency lower in soybean, and its two interacted proteins might be involved in serine hydrolysis, so soybean has lower SNPP than cowpea. Then, the CKX gene family, along with its positive regulatory factor ROCK1, had higher REL and less miRNA regulation in soybean flowers than in cowpea ones. These lead to higher cytokinin degradation level, which further reduces the REL of PIN1 and decreases soybean SNPP. We found that VuACX4 had much higher REL than GmACX4, although the two genes essential in embryo development interact with the CKX gene family. Next, a tandem duplication experienced by legumes led to the differentiation of CKX3 into CKX3a and CKX3b, in which CKX3a is a key gene affecting ovule number. Finally, in the yield-related gene networks, three cowpea CBP genes had higher RELs than two soybean CBP genes, low RELs of three soybean-specific IPT genes might lead to a decrease in cytokinin synthesis, and some negative and positive SNPP regulation were found, respectively, in soybean and cowpea. These networks may explain the SNPP difference in the two crops. We deduced that ckx3a or ckx3a ckx6 ckx7 mutants, interfering CYP88A, and over-expressed DELLA increase SNPP in soybean. This study reveals the molecular mechanism for the SNPP difference in the two crops, and provides an important idea for increasing soybean yield.

Genome and transcriptome analysis to understand the role diversification of cytochrome P450 gene under excess nitrogen treatment

BACKGROUND

Panax notoginseng (Burk.) F. H. Chen (P. notoginseng) is a medicinal plant. Cytochrome P450 (CYP450) monooxygenase superfamily is involved in the synthesis of a variety of plant hormones. Studies have shown that CYP450 is involved in the synthesis of saponins, which are the main medicinal component of P. notoginseng. To date, the P. notoginseng CYP450 family has not been systematically studied, and its gene functions remain unclear.

RESULTS

In this study, a total of 188 PnCYP genes were identified, these genes were divided into 41 subfamilies and clustered into 9 clans. Moreover, we identified 40 paralogous pairs, of which only two had Ka/Ks ratio greater than 1, demonstrating that most PnCYPs underwent purification selection during evolution. In chromosome mapping and gene replication analysis, 8 tandem duplication and 11 segmental duplication events demonstrated that PnCYP genes were continuously replicating during their evolution. Gene ontology (GO) analysis annotated the functions of 188 PnCYPs into 21 functional subclasses, suggesting the functional diversity of these gene families. Functional divergence analyzed the members of the three primitive branches of CYP51, CYP74 and CYP97 at the amino acid level, and found some critical amino acid sites. The expression pattern of PnCYP450 related to nitrogen treatment was studied using transcriptome sequencing data, 10 genes were significantly up-regulated and 37 genes were significantly down-regulated. Combined with transcriptome sequencing analysis, five potential functional genes were screened. Quantitative real-time PCR (qRT-PCR) indicated that these five genes were responded to methyl jasmonate (MEJA) and abscisic acid (ABA) treatment.

CONCLUSIONS

These results provide a valuable basis for comprehending the classification and biological functions of PnCYPs, and offer clues to study their biological functions in response to nitrogen treatment.

A mutation in LacDWARF1 results in a GA-deficient dwarf phenotype in sponge gourd (Luffa acutangula)

KEY MESSAGE

A dwarfism gene LacDWARF1 was mapped by combined BSA-Seq and comparative genomics analyses to a 65.4 kb physical genomic region on chromosome 05. Dwarf architecture is one of the most important traits utilized in Cucurbitaceae breeding because it saves labor and increases the harvest index. To our knowledge, there has been no prior research about dwarfism in the sponge gourd. This study reports the first dwarf mutant WJ209 with a decrease in cell size and internodes. A genetic analysis revealed that the mutant phenotype was controlled by a single recessive gene, which is designated Lacdwarf1 (Lacd1). Combined with bulked segregate analysis and next-generation sequencing, we quickly mapped a 65.4 kb region on chromosome 5 using F2 segregation population with InDel and SNP polymorphism markers. Gene annotation revealed that Lac05g019500 encodes a gibberellin 3β-hydroxylase (GA3ox) that functions as the most likely candidate gene for Lacd1. DNA sequence analysis showed that there is an approximately 4 kb insertion in the first intron of Lac05g019500 in WJ209. Lac05g019500 is transcribed incorrectly in the dwarf mutant owing to the presence of the insertion. Moreover, the bioactive GAs decreased significantly in WJ209, and the dwarf phenotype could be restored by exogenous GA3 treatment, indicating that WJ209 is a GA-deficient mutant. All these results support the conclusion that Lac05g019500 is the Lacd1 gene. In addition, RNA-Seq revealed that many genes, including those related to plant hormones, cellular process, cell wall, membrane and response to stress, were significantly altered in WJ209 compared with the wild type. This study will aid in the use of molecular marker-assisted breeding in the dwarf sponge gourd.

Cytochrome P450 Superfamily: Evolutionary and Functional Divergence in Sorghum (Sorghum bicolor) Stress Resistance

Cytochrome P450 (CYP) genes encode enzymes that catalyze various growth-, development-, and stress-related reactions. Sorghum (Sorghum bicolor) is a type of C4 plant and an important cash crop. However, systematic identification and analysis of functional differentiation and evolution of CYP genes have not been carried out in this species. In the present study, we revealed that the sorghum genome contains 351 CYP genes, which can be divided into nine classes. These genes are from ancestors and repeated segments, rather than tandem repeats. Based on collinearity results, a large number of CYPs were extended before cotyledon differentiation, during the emergence of Gramineae, suggesting that genomewide duplication events and stress adaptation processes were important for the expansion of CYP genes. Their gene structure and motifs contain conserved regions and include various changes and loci. The expression characteristics and functional annotation of CYP genes indicated tissue specificity and selective expression. Overall, we identified all CYP genes in the sorghum genome and preliminarily explored their naming, structure, evolution, expression, and functional differentiation. The results advanced our understanding of plant gene family evolution and functional differentiation.

The GA 20-Oxidase Encoding Gene MSD1 Controls the Main Stem Elongation in Medicago truncatula

Plant height is an important agronomic trait that is closely related to biomass yield and crop production. Despite legumes comprise one of the largest monophyletic families that are second only to grasses in terms of economic and nutritional values, due to an ancient genome duplication event, most legume plants have complex genomes, thus the molecular mechanisms that determine plant height are less known in legumes. Here, we report the identification and characterization of MAIN STEM DWARF1 (MSD1), which is required for the plant height in the model legume Medicago truncatula. Loss of function of MSD1 leads to severely reduced main stem height but normal lateral branch elongation in M. truncatula. Histological analysis revealed that the msd1-1 main stem has shorter internodes with reduced cell size and number compared with the wild type, indicating that MSD1 affects cell elongation and cell proliferation. MSD1 encodes a putative GA 20-oxidase that is expressed at significantly higher levels in the main shoot apex than in the lateral shoot apices, suggesting that MSD1 expression is associated with its effect on the main stem elongation. UPLC-MS/MS analysis showed that GA₉ and GA₄, two identified products of the GA 20-oxidase, were severely reduced in msd1-1, and the dwarf phenotype of msd1-1 could be rescued by supplementation with gibberellic acid GA₃, confirming that MSD1 functions as a biologically active GA 20-oxidase. Moreover, we found that disruption of either MtGA20ox7 or MtGA20ox8, homologs of MSD1, has little effects on the elongation of the main stem, while the msd1-1 mtga20ox7-1 mtga20ox8 triple mutants exhibits a severe short main shoot and lateral branches, as well as reduced leaf size, suggesting that MSD1 and its homologs MtGA20ox7 and MtGA20ox8, redundantly regulate M. truncatula shoot elongation and leaf development. Taken together, our findings demonstrate the molecular mechanism of MSD1-mediated regulation of main stem elongation in M. truncatula and provide insights into understanding the functional diversity of GA 20-oxidases in optimizing plant architecture in legumes.

Transcriptomic Analysis of Radish (Raphanus sativus L.) Spontaneous Tumor

Spontaneous tumors can develop in different organs of various plant species without any pathogen infection and, as a rule, appear in plants with a certain genotype: Mutants, interspecific hybrids, etc. In particular, among the inbred lines of radish (Raphanus sativus L.), lines that form spontaneous tumors on the taproot during the flowering period were obtained many years ago. In this work, we analyzed the differential gene expression in the spontaneous tumors of radish versus the lateral roots using the RNA-seq method. Data were obtained indicating the increased expression of genes associated with cell division and growth (especially genes that regulate G2-M transition and cytokinesis) in the spontaneous tumor. Among genes downregulated in the tumor tissue, genes participating in the response to stress and wounding, mainly involved in the biosynthesis of jasmonic acid and glucosinolates, were enriched. Our data will help elucidate the mechanisms of spontaneous tumor development in higher plants.

ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses

The diversity and environmental plasticity of plant growth results from variations of repetitive modules, such as the basic shoot units made of a leaf, axillary bud, and internode. Internode elongation is regulated both developmentally and in response to environmental conditions, such as light quality, but the integration of internal and environmental signals is poorly understood. Here, we show that the compressed rosette growth habit of Arabidopsis is maintained by the convergent activities of the organ boundary gene ARABIDOPSIS THALIANA HOMEOBOX GENE 1 (ATH1) and of the gibberellin-signaling DELLA genes. Combined loss of ATH1 and DELLA function activated stem development during the vegetative phase and changed the growth habit from rosette to caulescent. Chromatin immunoprecipitation high-throughput sequencing and genetic analysis indicated that ATH1 and the DELLA gene REPRESSOR OF GA1-3 (RGA) converge on the regulation of light responses, including the PHYTOCHROME INTERACTING FACTORS (PIF) pathway, and showed that the ATH1 input is mediated in part by direct activation of BLADE ON PETIOLE (BOP1 and BOP2) genes, whose products destabilize PIF proteins. We conclude that an organ-patterning gene converges with hormone signaling to spatially restrict environmental responses and establish a widespread type of plant architecture.

Gibberellins are required for dimorphic flower development in Viola philippica

Photoperiod is a major determinant of chasmogamous (CH)-cleistogamous (CL) dimorphic flower development in Viola philippica, and only long-day (LD) conditions induce CL flowers. In this study, it was found that the active gibberellin (GA) content in CL floral buds was higher than in CH floral buds formed under short-day (SD) conditions, suggesting that the biosynthesis of active GAs is enhanced by a longer photoperiod and may be associated with dimorphic flower development. Thus, the next step was to molecularly characterize the key V. philippica GA synthesis genes GA 20-oxidase (VpGA20ox) and GA 3-oxidase (VpGA3ox). In terms of the expression of VpGA20ox and VpGA3ox, it was found that the active GAs could be upregulated in developing pistils under both LD and SD conditions to develop functional pistils, and GAs could also accumulate in the stamens under SD conditions. The anthers and the adjacent petals were well developed under SD conditions. In contrast, the above-mentioned floral organs displayed low GA contents under LD conditions and were poorly developed. Although the application of paclobutrazol, an inhibitor of GA synthesis, did not reverse CL development under LD conditions, exogenous GAs could partially trigger the transition from CH to CL flowers under relative SD conditions (≤12 h daylight). This was coupled with the downregulation of B-class MADS-box genes, thereby restraining stamen and petal development. Both VpGA20ox and VpGA3ox exhibited similar expression profiles with B-class MADS-box genes in the development of the stamens and petals. Therefore, in response to photoperiod, GA signaling could affect the expression of B-class homeotic genes and regulate dimorphic flower development in Viola. As a compensation for poorly-developed nectaries, anthers, and petals, filament elongation, style shortness, and inward bending could ensure self-pollination in CL flowers. This work provides new insights into the regulation of CH-CL floral development and the evolutionary significance of the formation of dimorphic flowers.

CRISPR-based assessment of genomic structure in the conserved SQUAMOSA promoter-binding-like gene clusters in rice

Although SQUAMOSA promoter-binding-like (SPL) transcription factors are important regulators of development in rice (Oryza sativa), prior assessments of the SPL family have been limited to single genes. A functional comparison across the full gene family in standardized genetic backgrounds has not been reported previously. Here, we demonstrate that the SPL gene family in rice is enriched due to the most recent whole genome duplication (WGD). Notably, 10 of 19 rice SPL genes (52%) cluster in four units that have persisted for at least 50 million years. We show that SPL gene grouping and retention following WGD is widespread in angiosperms, suggesting the conservatism and importance of this gene arrangement. We used Cas9 editing to generate transformation lines for all 19 SPL genes in a common set of backgrounds, and found that knockouts of 14 SPL genes exhibited defects in plant height, 10 exhibited defects in panicle size, and nine had altered grain lengths. We observed subfunctionalization of genes in the paleoduplicated pairs, but little evidence of neofunctionalization. Expression of OsSPL3 was negatively correlated with that of its closest neighbor in its synteny group, OsSPL4, and its sister paired gene, OsSPL12, in the opposing group. Nucleotide diversity was lower in eight of the nine singleton genes in domesticated rice, relative to wild rice, whereas the reverse was true for the paired genes. Together, these results provide functional information on eight previously unexamined OsSPL family members and suggest that paleoduplicate pair redundancy benefits plant survival and innovation.

Dwarf and Increased Branching 1 controls plant height and axillary bud outgrowth in Medicago truncatula

Optimizing plant architecture is an efficient approach for breeders to increase crop yields, and phytohormones such as gibberellins (GAs) play an important role in controlling growth. Medicago truncatula is a model legume species, but the molecular mechanisms underlying its architecture are largely unknown. In this study, we examined a tobacco retrotransposon Tnt1-tagged mutant collection of M. truncatula and identified dwarf and increased branching 1 (dib1), which exhibited extreme dwarfism and increased numbers of lateral branches. By analysis of the flanking sequences of Tnt1 insertions in different alleles of the tagged lines, we were able to clone DIB1. Linkage analysis and reverse screening of the flanking-sequence tags identified Medtr2g102570 as the gene corresponding to the DIB1 locus in the dib1 loss-of-function mutants. Phylogenetic analysis indicated that DIB1 was the ortholog of PsGA3ox1/Le in Pisum sativum. Expression analysis using a GUS-staining reporter line showed that DIB1 was expressed in the root apex, pods, and immature seeds. Endogenous GA4 concentrations were markedly decreased whilst some of representative GA biosynthetic enzymes were up-regulated in the dib1 mutant. In addition, exogenous application of GA3 rescued the dib1 mutant phenotypes. Overall, our results suggest that DIB1 controls plant height and axillary bud outgrowth via an influence on the biosynthesis of bioactive GAs. DIB1 could therefore be a good candidate gene for breeders to optimize plant architecture for crop improvement.

Cloning and Functional Analysis of Dwarf Gene Mini Plant 1 (MNP1) in Medicago truncatula

Plant height is a vital agronomic trait that greatly determines crop yields because of the close relationship between plant height and lodging resistance. Legumes play a unique role in the worldwide agriculture; however, little attention has been given to the molecular basis of their height. Here, we characterized the first dwarf mutant mini plant 1 (mnp1) of the model legume plant Medicago truncatula. Our study found that both cell length and the cell number of internodes were reduced in a mnp1 mutant. Using the forward genetic screening and subsequent whole-genome resequencing approach, we cloned the MNP1 gene and found that it encodes a putative copalyl diphosphate synthase (CPS) implicated in the first step of gibberellin (GA) biosynthesis. MNP1 was highly homologous to Pisum sativum LS. The subcellular localization showed that MNP1 was located in the chloroplast. Further analysis indicated that GA3 could significantly restore the plant height of mnp1-1, and expression of MNP1 in a cps1 mutant of Arabidopsis partially rescued its mini-plant phenotype, indicating the conservation function of MNP1 in GA biosynthesis. Our results provide valuable information for understanding the genetic regulation of plant height in M. truncatula.

Transcriptomic analysis of cytochrome P450 genes and pathways involved in chromium toxicity in Oryza sativa

In plants, cytochrome P450 monooxygenase (CYP) plays an important role in detoxifying xenobiotic chemicals and coordinating abiotic stresses. Agilent 44 K rice microarray has been used to focus on the transcriptional profile of osCYP genes in rice seedling exposed to Cr solution containing K₂CrO₄ or Cr(NO₃)₃. Our study showed that expression profiles of 264 osCYP genes identified were tissue, dose and stimulus specific in rice seedlings. Comparative genomics analysis revealed that more differentially expressed osCYP genes were discovered in roots than in shoots under both Cr exposures. Results from Venn diagram analysis of differentially expressed osCYP genes demonstrated that there were common osCYP genes and unique osCYP genes present in different rice tissue as well as in different Cr treatments, which may control and/or regulate involvement of different CYP isoenzymes under Cr exposure individually or combinedly. KEGG analysis indicated that significant up- and down-regulated osCYP genes in rice tissues were chiefly related to "biosynthesis of secondary metabolites". However, involvements of osCYP genes mapped in the "biosynthesis of secondary metabolites" were tissue and dose specific, implying their distinctly responsive and adaptive mechanisms during Cr exposure. Overall, our findings are evident to describe and clarify their individual roles of specific osCYP genes in regulating involvement of CYP isoforms in Cr detoxification by rice seedlings.

Comparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize

BACKGROUND

The cytochrome P450s (CYP450s) as the largest enzyme family of plant metabolism participate in various physiological processes, whereas no study has demonstrated interest in comprehensive comparison of the genes in wheat and maize. Genome-wide survey, characterization and comparison of wheat and maize CYP450 gene superfamily are useful for genetic manipulation of the Gramineae crops.

RESULTS

In total, 1285 and 263 full-length CYP450s were identified in wheat and maize, respectively. According to standard nomenclature, wheat CYP450s (TaCYP450s) were categorized into 45 families, while maize CYP450s (ZmCYP450s) into 43 families. A comprehensive analysis of wheat and maize CYP450s, involved in functional domains, conserved motifs, phylogeny, gene structures, chromosome locations and duplicated events was performed. The result showed that each family/subfamily in both species exhibited characteristic features, suggesting their phylogenetic relationship and the potential divergence in their functions. Functional divergence analysis at the amino acid level of representative clans CYP51, CYP74 and CYP97 in wheat, maize and rice identified some critical amino acid sites that are responsible for functional divergence of a gene family. Expression profiles of Ta-, ZmCYP450s were investigated using RNA-seq data, which contribute to infer the potential functions of the genes during development and stress responses. We found in both species CYP450s had preferential expression in specific tissues, and many tissue-specific genes were identified. Under water-deficit condition, 82 and 39 significantly differentially expressed CYP450s were respectively detected in wheat and maize. These genes may have some roles in protecting plants against drought damage. Thereinto, fourteen CYP450s were selected to validate their expression level through qRT-PCR. To further elucidating molecular mechanisms of CYP450 action, gene co-expression network was constructed. In total, 477 TaCYP450s were distributed in 22 co-expression modules, and some co-expressed genes that likely take part in the same biochemical pathway were identified. For instance, the expression of TaCYP74A98_4D was highly correlated with TaLOX9, TaLOX36, TaLOX39, TaLOX44 and TaOPR8, and all of them may be involved in jasmonate (JA) biosynthesis. TaCYP73A201_3A showed coexpression with TaPAL1.25, TaCCoAOMT1.2, TaCOMT.1, TaCCR1.6 and TaLAC5, which probably act in the wheat stem and/or root lignin synthesis pathway.

CONCLUSION

Our study first established systematic information about evolutionary relationship, expression pattern and function characterization of CYP450s in wheat and maize.

Plant growth-regulating molecules as thermoprotectants: functional relevance and prospects for improving heat tolerance in food crops

Among various abiotic stresses, heat stress is one of the most damaging, threatening plant productivity and survival all over the world. Warmer temperatures due to climatic anomalies above optimum growing temperatures have detrimental impacts on crop yield potential as well as plant distribution patterns. Heat stress affects overall plant metabolism in terms of physiology, biochemistry, and gene expression. Membrane damage, protein degradation, enzyme inactivation, and the accumulation of reactive oxygen species are some of the harmful effects of heat stress that cause injury to various cellular compartments. Although plants are equipped with various defense strategies to counteract these adversities, their defensive means are not sufficient to defend against the ever-rising temperatures. Hence, substantial yield losses have been observed in all crop species under heat stress. Here, we describe the involvement of various plant growth-regulators (PGRs) (hormones, polyamines, osmoprotectants, antioxidants, and other signaling molecules) in thermotolerance, through diverse cellular mechanisms that protect cells under heat stress. Several studies involving the exogenous application of PGRs to heat-stressed plants have demonstrated their role in imparting tolerance, suggesting the strong potential of these molecules in improving the performance of food crops grown under high temperature.

Root-derived GA12 contributes to temperature-induced shoot growth in Arabidopsis

Plants are able to sense a rise in temperature of several degrees, and appropriately adapt their metabolic and growth processes. To this end, plants produce various signalling molecules that act throughout the plant body. Here, we report that root-derived GA₁₂, a precursor of the bioactive gibberellins, mediates thermo-responsive shoot growth in Arabidopsis. Our data suggest that root-to-shoot translocation of GA₁₂ enables a flexible growth response to ambient temperature changes.

The viral F-box protein P0 induces an ER-derived autophagy degradation pathway for the clearance of membrane-bound AGO1

The viral suppressor of RNA silencing P0 is known to target plant antiviral ARGONAUTE (AGO) proteins for degradation via an autophagy-related process. Here we utilized P0 to gain insight into the cellular degradation dynamics of AGO1, the major plant effector of RNA silencing. We revealed that P0 targets endoplasmic reticulum (ER)-associated AGO1 by inducing the formation of ER-related bodies that are delivered to the vacuole with both P0 and AGO1 as cargos. This process involves ATG8-interacting proteins 1 and 2 (ATI1 and ATI2) that interact with AGO1 and negatively regulate its transgene-silencing activity. Together, our results reveal a layer of ER-bound AGO1 posttranslational regulation that is manipulated by P0 to subvert plant antiviral defense.

RNA silencing is a major antiviral defense mechanism in plants and invertebrates. Plant ARGONAUTE1 (AGO1) is pivotal in RNA silencing, and hence is a major target for counteracting viral suppressors of RNA-silencing proteins (VSRs). P0 from Turnip yellows virus (TuYV) is a VSR that was previously shown to trigger AGO1 degradation via an autophagy-like process. However, the identity of host proteins involved and the cellular site at which AGO1 and P0 interact were unknown. Here we report that P0 and AGO1 associate on the endoplasmic reticulum (ER), resulting in their loading into ER-associated vesicles that are mobilized to the vacuole in an ATG5- and ATG7-dependent manner. We further identified ATG8-Interacting proteins 1 and 2 (ATI1 and ATI2) as proteins that associate with P0 and interact with AGO1 on the ER up to the vacuole. Notably, ATI1 and ATI2 belong to an endogenous degradation pathway of ER-associated AGO1 that is significantly induced following P0 expression. Accordingly, ATI1 and ATI2 deficiency causes a significant increase in posttranscriptional gene silencing (PTGS) activity. Collectively, we identify ATI1 and ATI2 as components of an ER-associated AGO1 turnover and proper PTGS maintenance and further show how the VSR P0 manipulates this pathway.

Distributed phenomics with the unPAK project reveals the effects of mutations

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance. These phenotypes are placed in the context of the wild-type and also natural accessions (phytometers), and standardized for environmental differences between assays. Data from the unPAK project are used to describe broad patterns in the phenotypic consequences of insertion mutation, and to identify individual mutant lines with distinct phenotypes as candidates for further study. Inclusion of undergraduate researchers is at the core of unPAK activities, and an important broader impact of the project is providing students an opportunity to obtain research experience.

A point mutation resulting in a 13 bp deletion in the coding sequence of Cldf leads to a GA-deficient dwarf phenotype in watermelon

The dwarf architecture is an important and valuable agronomic trait in watermelon breeding and has the potential to increase fruit yield and reduce labor cost in crop cultivation. However, the molecular basis for dwarfism in watermelon remains largely unknown. In this study, a recessive dwarf allele (designated as Cldf (Citrullus lanatus dwarfism)) was fine mapped in a 32.88 kb region on chromosome 09 using F₂ segregation populations derived from reciprocal crossing of a normal line M08 and a dwarf line N21. Gene annotation of the corresponding region revealed that the Cla015407 gene encoding a gibberellin 3β-hydroxylase functions as the best possible candidate gene for Cldf. Sequence analysis showed that the fourth polymorphism site (a G to A point mutation) at the 3' AG splice receptor site of the intron leads to a 13 bp deletion in the coding sequence of Cldf in dwarf line N21 and thus results in a truncated protein lacking the conserved domain for binding 2-oxoglutarate. In addition, the dwarf phenotype of Cldf could be rescued by exogenous GA₃ application. Phylogenetic analysis suggested that the small multigene family GA3ox (GA3 oxidase) in cucurbit species may originate from three ancient lineages in Cucurbitaceae. All these data support the conclusion that Cldf is a GA-deficient mutant, which together with the cosegregated marker can be used for breeding new dwarf cultivars.

Overexpression of the MADS-box gene K-domain increases the yield potential of blueberry

MADS-box genes play a significant role for plant flowering. Keratin-like (K) domains are involved in protein-to-protein interactions in the formation of the MIKC-type MADS-box domain proteins. In this study, the potential of utilizing the K domain of a Vaccinium corymbosum SOC1-like gene (VcSOC1K) was investigated to modulate expression of other blueberry MADS-box genes for increasing blueberry productivity. Chilled transgenic blueberry plants overexpressing the VcSOC1K showed a significant increase in the number of canes, floral buds, and flower and fruit clusters compared to chilled non-transgenic plants. Additionally, nonchilled transgenic plants flowered whereas nonchilled non-transgenic plants did not. Transgenic plants showed an increase in tolerance to high soil pH. Comparative transcriptome analysis of transgenic and non-transgenic leaves showed differential expression of 17% of the MADS-box genes identified in blueberry. These differentially expressed (DE) MADS-box genes were associated with genes related to plant flowering, phytohormones, and response to various biotic and abiotic stimuli. The phenotypic changes and the DE MADS-box genes caused by the overexpression of VcSOC1K not only reveal that the MADS-box genes are involved in chilling/vernalization-mediated flowering in blueberry but also demonstrated that the overexpression of the K domain can effectively modulate plant reproductive processes.

Comparative transcriptome analysis of nonchilled, chilled, and late-pink bud reveals flowering pathway genes involved in chilling-mediated flowering in blueberry

BACKGROUND

Blueberry cultivars require a fixed quantity of chilling hours during winter endo-dormancy for vernalization. In this study, transcriptome analysis using RNA sequencing data from nonchilled, chilled, and late pink buds of southern highbush blueberry 'Legacy' was performed to reveal genes associated with chilling accumulation and bud break.

RESULTS

Fully chilled 'Legacy' plants flowered normally whereas nonchilled plants could not flower. Compared to nonchilled flower buds, chilled flower buds showed differential expression of 89% of flowering pathway genes, 86% of MADS-box genes, and 84% of cold-regulated genes. Blueberry orthologues of FLOWERING LOCUS T (FT) did not show a differential expression in chilled flower buds (compared to nonchilled flower bud) but were up-regulated in late-pink buds (compared to chilled flower bud). Orthologoues of major MADS-box genes were significantly up-regulated in chilled flower buds and down-regulated in late-pink buds. Functional orthologues of FLOWERING LOCUS C (FLC) were not found in blueberry. Orthologues of Protein FD (FD), TERMINAL FLOWER 1 (TFL1), and LEAFY (LFY) were down-regulated in chilled flower buds and in late-pink buds compared to nonchilled flower bud.

CONCLUSIONS

The changes from nonchilled to chilled and chilled to late-pink buds are associated with transcriptional changes in a large number of differentially expressed (DE) phytohormone-related genes and DE flowering pathway genes. The profile of DE genes suggests that orthologues of FT, FD, TFL1, LFY, and MADS-box genes are the major genes involved in chilling-mediated blueberry bud-break. The results contribute to the comprehensive investigation of the vernalization-mediated flowering mechanism in woody plants.

Differential expression of gibberellin- and abscisic acid-related genes implies their roles in the bud activity-dormancy transition of tea plants

Thirty genes involved in GA and ABA metabolism and signalling were identified, and the expression profiles indicated that they play crucial roles in the bud activity-dormancy transition in tea plants. Gibberellin (GA) and abscisic acid (ABA) are fundamental phytohormones that extensively regulate plant growth and development, especially bud dormancy and sprouting transition in perennial plants. However, there is little information on GA- and ABA-related genes and their expression profiles during the activity-dormancy transition in tea plants. In the present study, 30 genes involved in the metabolism and signalling pathways of GA and ABA were first identified, and their expression patterns in different tissues were assessed. Further evaluation of the expression patterns of selected genes in response to GA₃ and ABA application showed that CsGA3ox, CsGA20ox, CsGA2ox, CsZEP and CsNCED transcripts were differentially expressed after exogenous treatment. The expression profiles of the studied genes during winter dormancy and spring sprouting were investigated, and somewhat diverse expression patterns were found for GA- and ABA-related genes. This diversity was associated with the bud activity-dormancy cycle of tea plants. These results indicate that the genes involved in the metabolism and signalling of GA and ABA are important for regulating the bud activity-dormancy transition in tea plants.

Characterization of a Transcriptional Regulator, BrWRKY6, Associated with Gibberellin-Suppressed Leaf Senescence of Chinese Flowering Cabbage

Phytohormone gibberellin (GA) and plant-specific WRKY transcription factors (TFs) are reported to play important roles in leaf senescence. The association of WRKY TFs with GA-mediated leaf senescence of economically important leafy vegetables like Chinese flowering cabbage, however, remains largely unknown. In this study, we showed that exogenous application of GA₃ suppressed Chinese flowering cabbage leaf senescence, with GA₃-treated cabbages maintaining a higher level of maximum quantum yield (Fv/Fm) and total chlorophyll content. GA₃ treatment also led to lower electrolyte leakage and expression level of a series of senescence-associated genes (SAGs) including BrSAG12 and BrSAG19, and chlorophyll catabolic genes (CCGs) BrPPH1, BrNYC1, and BrSGRs. In addition, higher transcription levels of GA biosynthetic genes BrKAO2 and BrGA20ox2 were found after GA₃ treatment. More importantly, a GA-repressible, nuclear-localized WRKY TF, BrWRKY6, a homologue of the Arabidopsis AtWRKY6, was identified and characterized. BrWRKY6 was GA-repressible and localized in the nucleus. Further experiments revealed that BrWRKY6 repressed the expression of BrKAO2 and BrGA20ox2, while it activated BrSAG12, BrNYC1, and BrSGR1, through binding to their promoters via the W-box cis-element. Together, the novel GA-WRKY link reported in our study provides new insight into the transcriptional regulation of GA-suppressed leaf senescence in Chinese flowering cabbage.

Silencing SlMED18, tomato Mediator subunit 18 gene, restricts internode elongation and leaf expansion

Mediator complex, a conserved multi-protein, is necessary for controlling RNA polymerase II (Pol II) transcription in eukaryotes. Given little is known about them in tomato, a tomato Mediator subunit 18 gene was isolated and named SlMED18. To further explore the function of SlMED18, the transgenic tomato plants targeting SlMED18 by RNAi-mediated gene silencing were generated. The SlMED18-RNAi lines exhibited multiple developmental defects, including smaller size and slower growth rate of plant and significantly smaller compound leaves. The contents of endogenous bioactive GA3 in SlMED18 silenced lines were slightly less than that in wild type. Furthermore, qRT-PCR analysis indicated that expression of gibberellins biosynthesis genes such as SlGACPS and SlGA20x2, auxin transport genes (PIN1, PIN4, LAX1 and LAX2) and several key regulators, KNOX1, KNOX2, PHAN and LANCEOLATE(LA), which involved in the leaf morphogenesis were significantly down-regulated in SlMED18-RNAi lines. These results illustrated that SlMED18 plays an essential role in regulating plant internode elongation and leaf expansion in tomato plants and it acts as a key positive regulator of gibberellins biosynthesis and signal transduction as well as auxin proper transport signalling. These findings are the basis for understanding the function of the individual Mediator subunits in tomato.