Mutants at the Slender1 locus of barley cv Himalaya. Molecular and physiological characterization

Genome-wide analysis of GRAS gene family and functional identification of a putative development and maintenance of axillary meristematic tissue gene PlGRAS22 in Paeonia ludlowii

The GRAS gene family, is instrumental in a myriad of biological processes, including plant growth and development. Our findings revealed that Paeonia ludlowii (Stern & G.Taylor) D.Y.Hong) harbored 45 PlGRAS genes, which are categorized into eight subfamilies. These genes are distributed across chromosomes 1 through 5, with their encoded proteins exhibiting variation in physicochemical properties. The promoter regions of the Paeonia ludlowii GRAS genes are enriched with cis-acting elements associated with growth and development, hormonal responses, and light signaling, among others. Among these genes, we have pinpointed PlGRAS22, which bears the closest resemblance to the AtLAS gene in Arabidopsis. Notably, this gene exhibits heightened expression levels within the LAS subfamily across a range of tissues, and it demonstrates an exceptionally robust response to treatments with exogenous gibberellins and cytokinins. The subdued expression of TRV2-PlGRAS22 within the flower buds of the Paeonia ludlowii has resulted in a diminished development of axillary bud primordia. Intriguingly, overexpression of PlGRAS22 in Arabidopsis led to an increase in the number of branches, highlighting its potential role in developmental processes. Furthermore, through the use of luciferase and yeast one-hybrid assays, we have demonstrated that PlGRAS22 interacts with the SPL transcription factor PlSPL3. The comprehensive analysis presented in this study lays a solid foundation for future investigations into the functional roles of Paeonia ludlowii GRAS genes and elucidates the underlying mechanisms governing growth and development in this species.

CsIREH1 phosphorylation regulates DELLA protein affecting plant height in cucumber (Cucumis sativus)

Plant height is a critical agronomic trait that affects crop yield, plant architecture, and environmental adaptability. Gibberellins (GAs) regulate plant height, with DELLA proteins acting as key repressors in the GA signaling pathway by inhibiting GA-induced growth. While DELLA phosphorylation is essential for regulating plant height, the precise mechanisms underlying this process remain incompletely understood. In this study, we identified a cucumber mutant with delayed growth, which exhibited reduced sensitivity to GA treatment. Through bulked segregant analysis (BSA-seq) combined with molecular marker linkage analysis, we successfully identified and cloned the gene responsible for the dwarf phenotype, CsIREH1 (INCOMPLETE ROOT HAIR ELONGATION 1), which encodes an AGC protein kinase. Further research revealed that CsIREH1 interacts with and phosphorylates DELLA proteins, specifically targeting CsGAIP and CsGAI2. We propose that IREH1-dependent phosphorylation of DELLA proteins prevents their excessive accumulation, thereby maintaining normal plant growth. Therefore, investigating the role of IREH1-mediated DELLA phosphorylation provides valuable insights and theoretical foundations for understanding how plants regulate growth mechanisms.

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.

Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions

The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.

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.

Role of BraRGL1 in regulation of Brassica rapa bolting and flowering

Gibberellin (GA) plays a major role in controlling Brassica rapa stalk development. As an essential negative regulator of GA signal transduction, DELLA proteins may exert significant effects on stalk development. However, the regulatory mechanisms underlying this regulation remain unclear. In this study, we report highly efficient and inheritable mutagenesis using the CRISPR/Cas9 gene editing system in BraPDS (phytoene desaturase) and BraRGL1 (key DELLA protein) genes. We observed a loss-of-function mutation in BraRGL1 due to two amino acids in GRAS domain. The flower bud differentiation and bolting time of BraRGL1 mutants were significantly advanced. The expression of GA-regulatory protein (BraGASA6), flowering related genes (BraSOC1, BraLFY), expansion protein (BraEXPA11) and xyloglucan endotransferase (BraXTH3) genes was also significantly upregulated in these mutants. BraRGL1-overexpressing plants displayed the contrasting phenotypes. BraRGL1 mutants were more sensitive to GA signaling. BraRGL1 interacted with BraSOC1, and the interaction intensity decreased after GA3 treatment. In addition, BraRGL1 inhibited the transcription-activation ability of BraSOC1 for BraXTH3 and BraLFY genes, but the presence of GA3 enhanced the activation ability of BraSOC1, suggesting that the BraRGL1-BraSOC1 module regulates bolting and flowering of B. rapa through GA signal transduction. Thus, we hypothesized that BraRGL1 is degraded, and BraSOC1 is released in the presence of GA3, which promotes the expression of BraXTH3 and BraLFY, thereby inducing stalk development in B. rapa. Further, the BraRGL1-M mutant promoted the flower bud differentiation without affecting the stalk quality. Thus, BraRGL1 can serve as a valuable target for the molecular breeding of early maturing varieties.

Uncovering the involvement of DoDELLA1-interacting proteins in development by characterizing the DoDELLA gene family in Dendrobium officinale

BACKGROUND

Gibberellins (GAs) are widely involved in plant growth and development. DELLA proteins are key regulators of plant development and a negative regulatory factor of GA. Dendrobium officinale is a valuable traditional Chinese medicine, but little is known about D. officinale DELLA proteins. Assessing the function of D. officinale DELLA proteins would provide an understanding of their roles in this orchid's development.

RESULTS

In this study, the D. officinale DELLA gene family was identified. The function of DoDELLA1 was analyzed in detail. qRT-PCR analysis showed that the expression levels of all DoDELLA genes were significantly up-regulated in multiple shoots and GA3-treated leaves. DoDELLA1 and DoDELLA3 were significantly up-regulated in response to salt stress but were significantly down-regulated under drought stress. DoDELLA1 was localized in the nucleus. A strong interaction was observed between DoDELLA1 and DoMYB39 or DoMYB308, but a weak interaction with DoWAT1.

CONCLUSIONS

In D. officinale, a developmental regulatory network involves a close link between DELLA and other key proteins in this orchid's life cycle. DELLA plays a crucial role in D. officinale development.

Manipulating GA-Related Genes for Cereal Crop Improvement

The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na⁺ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.

PavGA2ox-2L inhibits the plant growth and development interacting with PavDWARF in sweet cherry (Prunus avium L.)

Dwarf dense planting is helpful to improve the yield and quality of sweet cherry, which has enormous market demand. GA2oxs (GA oxidases) affect plant height, dormancy release, flower development, and seed germination by participating in the metabolic regulation and signal transduction of GA (Gibberellin). However, the research on GA2ox in sweet cherry is little and worthy of further investigation. Therefore, we identified the PavGA2ox-2L gene from sweet cherry, close to PynGA2ox-2 from Prunus yedoensis var. Nudiflora. The phylogenetic analysis indicated conserved functions with these evolutionarily closer GA2ox subfamily genes. Subcellular localization forecast analysis indicated that PavGA2ox-2L was localized in the nucleus or cytoplasm. The expression levels of PavGA2ox-2L were higher in winter, indicating that PavGA2ox-2L promoted maintained flower bud dormancy. The expression levels of PavGA2ox-2L were significantly increased after GA₄₊₇ treatment while decreased after GR24 (a synthetic analog of SLs (Strigolactones)) or TIS108 (a triazole-type SL-biosynthesis inhibitor) treatments. Over-expression of PavGA2ox-2L resulted in decreased plant height, delayed flowering time, and low seed germination rate in Arabidopsis thaliana. Furthermore, the interaction between PavGA2ox-2L and PavDWARF was verified by Y2H and BiFC assays. In the current investigation, PavGA2ox-2L functions as a GA metabolic gene that promotes dwarf dense planting, delays flowering time, and inhibits seed germination. In addition, it also participates in regulating plant growth and development through the interaction with the critical negative regulator PavDWARF of Gibberellin. These results will help us better explore the molecular mechanism of GA2ox-mediated dwarf and late-maturing varieties for fruit trees.

Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review

The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.

Late-maturity α-amylase (LMA): exploring the underlying mechanisms and end-use quality effects in wheat

MAIN CONCLUSION

A comprehensive understanding of LMA from the underlying molecular aspects to the end-use quality effects will greatly benefit the global wheat industry and those whose livelihoods depend upon it. Late-maturity α-amylase (LMA) leads to the expression and protein accumulation of high pI α-amylases during late grain development. This α-amylase is maintained through harvest and leads to an unacceptable low falling number (FN), the wheat industry's standard measure for predicting end-use quality. Unfortunately, low FN leads to significant financial losses for growers. As a result, wheat researchers are working to understand and eliminate LMA from wheat breeding programs, with research aims that include unraveling the genetic, biochemical, and physiological mechanisms that lead to LMA expression. In addition, cereal chemists and quality scientists are working to determine if and how LMA-affected grain impacts end-use quality. This review is a comprehensive overview of studies focused on LMA and includes open questions and future directions.

Identification of DELLA Genes and Key Stage for GA Sensitivity in Bolting and Flowering of Flowering Chinese Cabbage

Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) is an important and extensively cultivated vegetable in south China, and its stalk development is mainly regulated by gibberellin (GA). DELLA proteins negatively regulate GA signal transduction and may play an important role in determining bolting and flowering. Nevertheless, no systematic study of the DELLA gene family has been undertaken in flowering Chinese cabbage. In the present study, we found that the two-true-leaf spraying of gibberellin A3 (GA₃) did not promote bolting but did promote flowering, whereas the three-true-leaf spraying of GA₃ promoted both bolting and flowering. In addition, we identified five DELLA genes in flowering Chinese cabbage. All five proteins contained DELLA, VHYNP, VHIID, and SAW conserved domains. Protein-protein interaction results showed that in the presence of GA₃, all five DELLA proteins interacted with BcGID1b (GA-INSENSITIVE DWARF 1b) but not with BcGID1a (GA-INSENSITIVE DWARF 1a) or BcGID1c (GA-INSENSITIVE DWARF 1c). Their expression analysis showed that the DELLA genes exhibited tissue-specific expression, and their reversible expression profiles responded to exogenous GA₃ depending on the treatment stage. We also found that the DELLA genes showed distinct expression patterns in the two varieties of flowering Chinese cabbage. BcRGL1 may play a major role in the early bud differentiation process of different varieties, affecting bolting and flowering. Taken together, these results provide a theoretical basis for further dissecting the DELLA regulatory mechanism in the bolting and flowering of flowering Chinese cabbage.

The Breeding of Winter-Hardy Malting Barley

In breeding winter malting barley, one recurring strategy is to cross a current preferred spring malting barley to a winter barley. This is because spring malting barleys have the greatest amalgamation of trait qualities desirable for malting and brewing. Spring barley breeding programs can also cycle their material through numerous generations each year-some managing even six-which greatly accelerates combining desirable alleles to generate new lines. In a winter barley breeding program, a single generation per year is the limit when the field environment is used and about two generations per year if vernalization and greenhouse facilities are used. However, crossing the current favored spring malting barley to a winter barley may have its downsides, as winter-hardiness too may be an amalgamation of desirable alleles assembled together that confers the capacity for prolonged cold temperature conditions. In this review I touch on some general criteria that give a variety the distinction of being a malting barley and some of the general trends made in the breeding of spring malting barleys. But the main objective of this review is to pull together different aspects of what we know about winter-hardiness from the seemingly most essential aspect, which is survival in the field, to molecular genetics and gene regulation, and then finish with ideas that might help further our insight for predictability purposes.

Major flowering time genes of barley: allelic diversity, effects, and comparison with wheat

This review summarizes the allelic series, effects, interactions between genes and with the environment, for the major flowering time genes that drive phenological adaptation of barley. The optimization of phenology is a major goal of plant breeding addressing the production of high-yielding varieties adapted to changing climatic conditions. Flowering time in cereals is regulated by genetic networks that respond predominately to day length and temperature. Allelic diversity at these genes is at the basis of barley wide adaptation. Detailed knowledge of their effects, and genetic and environmental interactions will facilitate plant breeders manipulating flowering time in cereal germplasm enhancement, by exploiting appropriate gene combinations. This review describes a catalogue of alleles found in QTL studies by barley geneticists, corresponding to the genetic diversity at major flowering time genes, the main drivers of barley phenological adaptation: VRN-H1 (HvBM5A), VRN-H2 (HvZCCTa-c), VRN-H3 (HvFT1), PPD-H1 (HvPRR37), PPD-H2 (HvFT3), and eam6/eps2 (HvCEN). For each gene, allelic series, size and direction of QTL effects, interactions between genes and with the environment are presented. Pleiotropic effects on agronomically important traits such as grain yield are also discussed. The review includes brief comments on additional genes with large effects on phenology that became relevant in modern barley breeding. The parallelisms between flowering time allelic variation between the two most cultivated Triticeae species (barley and wheat) are also outlined. This work is mostly based on previously published data, although we added some new data and hypothesis supported by a number of studies. This review shows the wide variety of allelic effects that provide enormous plasticity in barley flowering behavior, which opens new avenues to breeders for fine-tuning phenology of the barley crop.

Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus

BACKGROUND

Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed.

RESULTS

In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses.

CONCLUSION

In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.

The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.

Understanding Omics Driven Plant Improvement and de novo Crop Domestication: Some Examples

In the current era, one of biggest challenges is to shorten the breeding cycle for rapid generation of a new crop variety having high yield capacity, disease resistance, high nutrient content, etc. Advances in the "-omics" technology have revolutionized the discovery of genes and bio-molecules with remarkable precision, resulting in significant development of plant-focused metabolic databases and resources. Metabolomics has been widely used in several model plants and crop species to examine metabolic drift and changes in metabolic composition during various developmental stages and in response to stimuli. Over the last few decades, these efforts have resulted in a significantly improved understanding of the metabolic pathways of plants through identification of several unknown intermediates. This has assisted in developing several new metabolically engineered important crops with desirable agronomic traits, and has facilitated the de novo domestication of new crops for sustainable agriculture and food security. In this review, we discuss how "omics" technologies, particularly metabolomics, has enhanced our understanding of important traits and allowed speedy domestication of novel crop plants.

Pre-harvest sprouting in cereals: genetic and biochemical mechanisms

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

Virus-Mediated Transient Expression Techniques Enable Functional Genomics Studies and Modulations of Betalain Biosynthesis and Plant Height in Quinoa

Quinoa (Chenopodium quinoa), native to the Andean region of South America, has been recognized as a potentially important crop in terms of global food and nutrition security since it can thrive in harsh environments and has an excellent nutritional profile. Even though challenges of analyzing the complex and heterogeneous allotetraploid genome of quinoa have recently been overcome, with the whole genome-sequencing of quinoa and the creation of genotyped inbred lines, the lack of technology to analyze gene function in planta is a major limiting factor in quinoa research. Here, we demonstrate that two virus-mediated transient expression techniques, virus-induced gene silencing (VIGS) and virus-mediated overexpression (VOX), can be used in quinoa. We show that apple latent spherical virus (ALSV) can induce gene silencing of quinoa phytoene desaturase (CqPDS1) in a broad range of quinoa inbred lines derived from the northern and southern highland and lowland sub-populations. In addition, we show that ALSV can be used as a VOX vector in roots. Our data also indicate that silencing a quinoa 3,4-dihydroxyphenylalanine 4,5-dioxygenase gene (CqDODA1) or a cytochrome P450 enzyme gene (CqCYP76AD1) inhibits betalain production and that knockdown of a reduced-height gene homolog (CqRHT1) causes an overgrowth phenotype in quinoa. Moreover, we show that ALSV can be transmitted to the progeny of quinoa plants. Thus, our findings enable functional genomics in quinoa, ushering in a new era of quinoa research.

Identification of Fusarium head blight resistance loci in two Brazilian wheat mapping populations

Fusarium head blight (FHB) is a disease of wheat (Triticum aestivum L.) that causes major yield losses in South America, as well as many other wheat growing regions around the world. FHB results in low quality, contaminated grain due to the production of mycotoxins such as deoxynivalenol (DON). In Brazil, FHB outbreaks are increasing in frequency and are currently controlled by fungicides which are costly and potentially harmful to the wider environment. To identify the genetic basis of resistance to FHB in Brazilian wheat, two mapping populations (Anahuac 75 × BR 18-Terena and BR 18-Terena × BRS 179) segregating for FHB resistance were phenotyped and quantitative trait loci (QTL) analysis was undertaken to identify genomic regions associated with FHB-related traits. A total of 14 QTL associated with FHB visual symptoms were identified, each of which explained 3.7–17.3% of the phenotypic variance. Two of these QTL were stable across environments. This suggests FHB resistance in Anahuac 75, BR 18-Terena and BRS 179 is controlled by multiple genetic loci that confer relatively minor differences in resistance. A major, novel QTL associated with DON accumulation was also identified on chromosome 4B (17.8% of the phenotypic variance), as well as a major QTL associated with thousand-grain weight on chromosome 6B (16.8% phenotypic variance). These QTL could be useful breeding targets, when pyramided with major sources of resistance such as Fhb1, to improve grain quality and reduce the reliance on fungicides in Brazil and other countries affected by FHB.

Light contributes to salt resistance through GAI protein regulation in Arabidopsis thaliana

The role of DELLAs in response to light intensity under salt stress is largely unknown. Therefore, the effect of three light intensities-low (35), medium (60), and high (155) μmol m^-2 s^-1 on Arabidopsis plants growth under saline condition (150 mM NaCl) was evaluated. High light intensity exhibited significant growth in the number of lateral roots related to the low light. Immunoblot assay revealed increased DELLA accumulation at the seedling stage under high light intensity. High light promotes seed germination by 24-44%, whilst, lateral roots by 25-90% in wild-type ecotypes. The lateral roots increased significantly in gai (gibberellic acid insensitive mutant) as compared with gai-t6 (wild type like gibberellic acid insensitive mutant) in response to low to medium and high to medium light intensity. High light increased seedling survival rate by 67% in Col-0 (Columbia) and 60% in Ler (Landsberg erecta) and showed a 28% increase in survival rate in gai mutant under salt stress as compared to gai-t6. Furthermore, salt-stress responsive genes' expression in gai-mutant establishes the relationship of DELLA proteins with salt resistance. Together, light is a cardinal element, its optimum quantity is highly beneficial and promotes salt stress resistance through DELLA protein at seedling stage in plants.

Gibberellin Metabolism and Signaling: Targets for Improving Agronomic Performance of Crops

Gibberellins (GAs) are a class of tetracyclic diterpenoid phytohormones that regulate many aspects of plant development, including seed germination, stem elongation, leaf expansion, pollen maturation, and the development of flowers, fruits and seeds. During the past decades, the primary objective of crop breeding programs has been to increase productivity or yields. 'Green Revolution' genes that can produce semidwarf, high-yielding crops were identified as GA synthesis or response genes, confirming the value of research on GAs in improving crop productivity. The manipulation of GA status either by genetic alteration or by exogenous application of GA or GA biosynthesis inhibitors is often used to optimize plant growth and yields. In this review, we summarize the roles of GAs in major aspects of crop growth and development and present the possible targets for the fine-tuning of GA metabolism and signaling as a promising strategy for crop improvement.

Modeling vegetative vigour in grapevine: unraveling underlying mechanisms

Mechanistic modeling constitutes a powerful tool to unravel complex biological phenomena. This study describes the construction of a mechanistic, dynamic model for grapevine plant growth and canopy biomass (vigor). To parametrize and validate the model, the progeny from a cross of Ramsey (Vitis champinii) × Riparia Gloire (V. riparia) was evaluated. Plants with different vigor were grown in a greenhouse during the summer of 2014 and 2015. One set of plants was grafted with Cabernet Sauvignon. Shoot growth rate (b), leaf area (LA), dry biomass, whole plant and root specific hydraulic conductance (k_H and L_pr), stomatal conductance (g_s), and water potential (Ψ) were measured. Partitioning indices and specific leaf area (SLA) were calculated. The model includes an empirical fit of a purported seasonal pattern of bioactive GAs based on published seasonal evolutionary levels and reference values. The model provided a good fit of the experimental data, with R = 0.85. Simulation of single trait variations defined the individual effect of each variable on vigor determination. The model predicts, with acceptable accuracy, the vigor of a young plant through the measurement of L_pr and SLA. The model also permits further understanding of the functional traits that govern vigor, and, ultimately, could be considered useful for growers, breeders and those studying climate change.

Herbaceous peony (Paeonia lactiflora Pall.) PlDELLA gene negatively regulates dormancy release and plant growth

DELLA protein plays a significant role in plant growth and development. In this study, PlDELLA with the open reading frame of 1866 bp in length was isolated from Paeonia lactiflora. Overexpression of PlDELLA in Arabidopsis thaliana showed that seed germination was significantly repressed as it took 144∼192 h for the OEs to reach 100 % germination and it required only 60 h for the WT. The OEs were also inhibited in bolting time and in plant vegetative growth. When PlDELLA was silenced in peony by virus-induced gene silencing method, peony budbreak occurred earlier by 8∼10 d and the vegetative growth was significantly accelerated compared with the control group. These results collectively indicated that PlDELLA negatively regulated dormancy release and plant growth. During chilling process to release peony endodormancy, PlDELLA expression down-regulated, and the content of both endogenous active GAs and ABA decreased, indicating decreasing of PlDELLA expression under chilling was not caused by the known gibberellin signal transduction pathway. Besides, PlDELLA had no interaction with the four screened PlWRKYs, PlWRKY13, PlWRKY18, PlWRKY40 or PlWRKY50. These findings not only enrich the knowledge of DELLA protein family, but also provide insights into understanding the function of PlDELLA protein in endodormancy release in peony.

Generation and Transcriptome Profiling of Slr1-d7 and Slr1-d8 Mutant Lines with a New Semi-Dominant Dwarf Allele of SLR1 Using the CRISPR/Cas9 System in Rice

The rice SLR1 gene encodes the DELLA protein (protein with DELLA amino acid motif), and a loss-of-function mutation is dwarfed by inhibiting plant growth. We generate slr1-d mutants with a semi-dominant dwarf phenotype to target mutations of the DELLA/TVHYNP domain using CRISPR/Cas9 genome editing in rice. Sixteen genetic edited lines out of 31 transgenic plants were generated. Deep sequencing results showed that the mutants had six different mutation types at the target site of the TVHYNP domain of the SLR1 gene. The homo-edited plants selected individuals without DNA (T-DNA) transcribed by segregation in the T1 generation. The slr1-d7 and slr1-d8 plants caused a gibberellin (GA)-insensitive dwarf phenotype with shrunken leaves and shortened internodes. A genome-wide gene expression analysis by RNA-seq indicated that the expression levels of two GA-related genes, GA₂₀OX₂ (Gibberellin oxidase) and GA₃OX₂, were increased in the edited mutant plants, suggesting that GA₂₀OX₂ acts as a convert of GA₁₂ signaling. These mutant plants are required by altering GA responses, at least partially by a defect in the phytohormone signaling system process and prevented cell elongation. The new mutants, namely, the slr1-d7 and slr1-d8 lines, are valuable semi-dominant dwarf alleles with potential application value for molecule breeding using the CRISPR/Cas9 system in rice.

Genome-Wide Analysis of the GRAS Gene Family in Barley (Hordeum vulgare L.)

The GRAS (named after first three identified proteins within this family, GAI, RGA, and SCR) family contains plant-specific genes encoding transcriptional regulators that play a key role in gibberellin (GA) signaling, which regulates plant growth and development. Even though GRAS genes have been characterized in some plant species, little research is known about the GRAS genes in barley (Hordeum vulgare L.). In this study, we observed 62 GRAS members from barley genome, which were grouped into 12 subgroups by using phylogenomic analysis together with the GRAS genes from Arabidopsis (Arabidopsis thaliana), maize (Zea mays), and rice (Oryza sativa). Chromosome localization and gene structure analysis suggested that duplication events and abundant presence of intronless genes might account for the massive expansion of GRAS gene family in barley. The analysis of RNA-seq data indicates the expression pattern of GRAS genes in various tissues at different stages in barley. Noteworthy, our qRT-PCR analysis showed the expression of 18 candidate GRAS genes abundantly in the developing inflorescence, indicating their potential roles in the barley inflorescence development and reproduction. Collectively, our evolutionary and expression analysis of GRAS family are useful for future functional characterization of GA signaling in barley and agricultural improvement.

SLENDER RICE1 and Oryza sativa INDETERMINATE DOMAIN2 Regulating OsmiR396 Are Involved in Stem Elongation

GAs play key roles in controlling cell proliferation through the GIBBERELLIN INSENSITIVE DWARF1/DELLA-mediated pathway. However, how DELLA proteins affect downstream pathways is not well understood. Therefore, discovering the signaling events downstream of DELLAs is key to better understanding the roles of GAs in plant development. Here, we discovered that miR396 is regulated by SLENDER RICE1 (SLR1) in controlling cell proliferation. The positive response of rice (Oryza sativa) GROWTH-REGULATING FACTORs (OsGRFs) to GAs was found to be caused by a negative response of miR396 to GAs. miR396 acts downstream of SLR1 and upstream of GA-induced cell-cycle genes. Rice INDETERMINATE DOMAIN2 (OsIDD2) directly binds the promoter of OsmiR396a and can interact with SLR1 in vivo and in vitro. Rice lines overexpressing miR396a (miR396OE) or OsIDD2 (OsIDD2OE) displayed dwarfism resulting from higher abundance of miR396 RNA. However, the stem elongation of OsIDD2OE plants could be significantly stimulated by applying exogenous GA₃, while that of miR396OE plants could not. Rice with OsIDD2 knocked down by RNA interference showed a slr1-like phenotype, in which the expression of miR396 was inhibited while its targets were enhanced. The protein levels of OsIDD2 were unaffected by GA in wild-type and OsIDD2OE plants, implying that OsIDD2 promotes the expression of miR396 and likely requires the coactivator of SLR1. Taken together, these results provided a close link between SLR1/OsIDD2 and GRFs via a negative regulator, miR396, and thus highlighted a molecular mechanism of GA-mediated cell proliferation in rice.

Transcriptional and biochemical analyses of gibberellin expression and content in germinated barley grain

Mobilization of reserves in germinated cereal grains is critical for early seedling vigour, global crop productivity, and hence food security. Gibberellins (GAs) are central to this process. We have developed a spatio-temporal model that describes the multifaceted mechanisms of GA regulation in germinated barley grain. The model was generated using RNA sequencing transcript data from tissues dissected from intact, germinated grain, which closely match measurements of GA hormones and their metabolites in those tissues. The data show that successful grain germination is underpinned by high concentrations of GA precursors in ungerminated grain, the use of independent metabolic pathways for the synthesis of several bioactive GAs during germination, and a capacity to abort bioactive GA biosynthesis. The most abundant bioactive form is GA1, which is synthesized in the scutellum as a glycosyl conjugate that diffuses to the aleurone, where it stimulates de novo synthesis of a GA3 conjugate and GA4. Synthesis of bioactive GAs in the aleurone provides a mechanism that ensures the hormonal signal is relayed from the scutellum to the distal tip of the grain. The transcript data set of 33 421 genes used to define GA metabolism is available as a resource to analyse other physiological processes in germinated grain.

Manipulating Gibberellin Control Over Growth and Fertility as a Possible Target for Managing Wild Radish Weed Populations in Cropping Systems

Wild radish is a major weed of Australian cereal crops. A rapid establishment, fast growth, and abundant seed production are fundamental to its success as an invasive species. Wild radish has developed resistance to a number of commonly used herbicides increasing the problem. New innovative approaches are needed to control wild radish populations. Here we explore the possibility of pursuing gibberellin (GA) biosynthesis as a novel molecular target for controlling wild radish, and in doing so contribute new insights into GA biology. By characterizing ga 3-oxidase (ga3ox) mutants in Arabidopsis, a close taxonomic relative to wild radish, we showed that even mild GA deficiencies cause considerable reductions in growth and fecundity. This includes an explicit requirement for GA biosynthesis in successful female fertility. Similar defects were reproducible in wild radish via chemical inhibition of GA biosynthesis, confirming GA action as a possible new target for controlling wild radish populations. Two possible targeting approaches are considered; the first would involve developing a species-specific inhibitor that selectively inhibits GA production in wild radish over cereal crops. The second, involves making crop species insensitive to GA repression, allowing the use of existing broad spectrum GA inhibitors to control wild radish populations. Toward the first concept, we cloned and characterized two wild radish GA3OX genes, identifying protein differences that appear sufficient for selective inhibition of dicot over monocot GA3OX activity. We developed a novel yeast-based approach to assay GA3OX activity as part of the molecular characterization, which could be useful for future screening of inhibitory compounds. For the second approach, we demonstrated that a subset of GA associated sln1/Rht-1 overgrowth mutants, recently generated in cereals, are insensitive to GA reductions brought on by the general GA biosynthesis inhibitor, paclobutrazol. The location of these mutations within sln1/Rht-1, offers additional insight into the functional domains of these important GA signaling proteins. Our early assessment suggests that targeting the GA pathway could be a viable inclusion into wild radish management programs that warrants further investigation. In drawing this conclusion, we provided new insights into GA regulated reproductive development and molecular characteristics of GA metabolic and signaling proteins.

Gibberellin Signaling Repressor LlDELLA1 Controls the Flower and Pod Development of Yellow Lupine (Lupinus luteus L.)

Precise control of generative organ development is of great importance for the productivity of crop plants, including legumes. Gibberellins (GAs) play a key role in the regulation of flowering, and fruit setting and development. The major repressors of GA signaling are DELLA proteins. In this paper, the full-length cDNA of LlDELLA1 gene in yellow lupine (Lupinus luteus L.) was identified. Nuclear-located LlDELLA1 was clustered in a second phylogenetic group. Further analyses revealed the presence of all conserved motifs and domains required for the GA-dependent interaction with Gibberellin Insensitive Dwarf1 (GID1) receptor, and involved in the repression function of LlDELLA1. Studies on expression profiles have shown that fluctuating LlDELLA1 transcript level favors proper flower and pod development. Accumulation of LlDELLA1 mRNA slightly decreases from the flower bud stage to anther opening (dehiscence), while there is rapid increase during pollination, fertilization, as well as pod setting and early development. LlDELLA1 expression is downregulated during late pod development. The linkage of LlDELLA1 activity with cellular and tissue localization of gibberellic acid (GA₃) offers a broader insight into the functioning of the GA pathway, dependent on the organ and developmental stage. Our analyses provide information that may be valuable in improving the agronomic properties of yellow lupine.

Molecular and functional characterization of two DELLA protein-coding genes in litchi

DELLA proteins are members of the plant-specific GRAS family, acting as negative regulators of plant growth. In this study, we identified two DELLA protein-coding genes in litchi, denoted as LcGAI and LcRGL1. Motif analysis showed that LcGAI and LcRGL1 proteins both contain a conserved DELLA and TVHYNP motif at the N-terminus as well as LHR1, VHIID, LHR2, PFYRE, and SAW motifs at the C terminus. The fused proteins of LcGAI-GFP and LcRGL1-GFP were both localized in the nucleus. Overexpression of LcGAI and LcRGL1 in Arabidopsis substantially inhibits leaf growth. Expression analysis showed that HLH factors, PRE1 and PRE5, were restrained, whereas gibberellin (GA) receptors GID1a and LcGID1b were enhanced in LcGAI and LcRGL1 overexpression lines. Results of the yeast two-hybrid assay showed that LcGAI and LcRGL1 interact with LcGID1b/LcGID1c in a GA dose-dependent manner, whereas LcGAI and LcRGL1 had a greater binding capacity to LcGID1b than LcGID1c. These observations suggested that LcGAI and LcRGL1 proteins are nuclear growth repressors.

Antioxidant and the Dwarfing Candidate Gene of "Nantongxiaofangshi" (Diospyros kaki Thunb.)

The aims of this work were to identify genes related to dwarfing for subsequent dwarfing-related research in persimmon and evaluate the relationship between antioxidant activity, dwarf, and hormones of persimmon trees for analyzing the possible dwarf mechanism oxidation factors. In the present study, a transcriptome analysis of “Nantongxiaofangshi” was used to identify and clone 22 candidate genes related to gibberellin signal transduction pathways and synthetic pathway. The expression of these genes was assessed in two persimmon cultivars, “Dafangshi” and “Nantongxiaofangshi,” by RT-qPCR at different phenological stages and in response to the exogenous application of GA₃ (GA treatment) and PAZ (paclobutrazol, a plant growth inhibitor, also called PP₃₃₃). The results revealed differential expression of 14 of these 22 genes in the two varieties. Subsequently, endogenous hormone levels were assessed of the two varieties, along with the number of internodes and internode length. The results suggested that the persimmon could be used as a valuable and powerful natural candidate for providing information on the functional role of dwarfing.

Comprehensive Insight into Gibberellin- and Jasmonate-Mediated Stamen Development

In flowering plants, proper development of male generative organs is required for successful sexual reproduction. Stamen primordia arise in the third whorl of floral organs and subsequently differentiate into filaments and anthers. The early phase of stamen development, in which meiosis occurs, is followed by a late developmental phase, which consists of filament elongation coordinated with pollen maturation, anther dehiscence and finally viable pollen grain release. Stamen development and function are modulated by phytohormones, with a key role of gibberellins (GAs) and jasmonates (JAs). Long-term, extensive investigations, mainly involving GA/JA-deficient and GA/JA-response mutants, have led to a better understanding of the hormone-dependent molecular mechanisms of stamen development. In several species, the principal functions of GAs are to stimulate filament elongation through increased cell elongation and to promote anther locule opening. In the GA-dependent regulation of early stamen development, both the tapetum and developing pollen were identified as major targets. JAs mainly control the late stages of stamen development, such as filament elongation, viable pollen formation and anther dehiscence. A hierarchical relationship between GAs and JAs was recognized mainly in the control of late stamen development. By repressing DELLA proteins, GAs modulate the transcriptional activity of JA biosynthesis genes to promote JA production. A high level of JAs induces a complex of transcription factors crucial for normal stamen development.

Piriformospora indica-induced phytohormone changes and root colonization strategies are highly host-specific

Piriformospora indica, an endophytic fungus of Sebacinales, has a wide host range and promotes the performance of mono- and eudicot plants. Here, we compare the interaction of P. indica with the roots of seven host plants (Anthurium andraeanum, Arabidopsis thaliana, Brassica campestris, Lycopersicon esculentum, Oncidium orchid, Oryza sativa, and Zea mays). Microscopical analyses showed that the colonization time and the mode of hyphal invasion into the roots differ in the symbiotic interactions. Substantial differences between the species were also observed for the levels and accumulation of jasmonate (JA) and gibberellin (GA) and the transcript levels for genes involved in their syntheses. No obvious correlation could be detected between the endogenous JA and/or GA levels and the time point of root colonization in a given plant species. Our results suggest that root colonization strategies and changes in the two phytohormone levels are highly host-specific.

Unraveling Molecular and Genetic Studies of Wheat (Triticum aestivum L.) Resistance against Factors Causing Pre-Harvest Sprouting

Pre-harvest sprouting (PHS) is one of the most important factors having adverse effects on yield and grain quality all over the world, particularly in wet harvest conditions. PHS is controlled by both genetic and environmental factors and the interaction of these factors. Breeding varieties with high PHS resistance have important implications for reducing yield loss and improving grain quality. The rapid advancements in the wheat genomic database along with transcriptomic and proteomic technologies have broadened our knowledge for understanding the regulatory mechanism of PHS resistance at transcriptomic and post-transcriptomic levels. In this review, we have described in detail the recent advancements on factors influencing PHS resistance, including grain color, seed dormancy, α-amylase activity, plant hormones (especially abscisic acid and gibberellin), and QTL/genes, which are useful for mining new PHS-resistant genes and developing new molecular markers for multi-gene pyramiding breeding of wheat PHS resistance, and understanding the complicated regulatory mechanism of PHS resistance.

Root phenotypes of dwarf and "overgrowth" SLN1 barley mutants, and implications for hypoxic stress tolerance

Gibberellins are central to the regulation of plant development and growth. Action of gibberellins involves the degradation of DELLA proteins, which are negative regulators of growth. In barley (Hordeum vulgare), certain mutations affecting genes involved in gibberellin synthesis or coding for the barley DELLA protein (Sln1) confer dwarfism. Recent studies have identified new alleles of Sln1 with the capacity to revert the dwarf phenotype back to the taller phenotypes. While the effect of these overgrowth alleles on shoot phenotypes has been explored, no information is available for roots. Here, we examined aspects of the root phenotypes displayed by plants with various Sln1 gene alleles, and tested responses to growth in an O₂-deficient root-zone as occurs during soil waterlogging. One overgrowth line, bearing the Sln1d.8 allele carrying two amino acid substitutions (one in the amino terminus and one in the GRAS domain of the encoded DELLA protein), displays profound and opposite effects on shoot height and root length. While it stimulates shoot height, it severely compromises root length by a reduction of cell size in zones distal to the root apex. In addition, Sln1d.8 plants counteract the negative effect of the original mutation on the formation of adventitious roots. Interestingly, plants bearing this allele display enhanced resistance to flooding stress in a way non-related with increased root porosity. Thus, various Sln1 gene alleles contribute to root phenotypes and can also influence plant responses to root-zone O₂-deficiency stress.

Genetic pathways controlling inflorescence architecture and development in wheat and barley

Modifications of inflorescence architecture have been crucial for the successful domestication of wheat and barley, which are central members of the Triticeae tribe that provide essential grains for the human diet. Investigation of the genes and alleles that underpin domestication-related traits has provided valuable insights into the molecular regulation of inflorescence development of the Triticeae, and further investigation of modified forms of architecture are proving to be equally fruitful. The identified genes are involved in diverse biological processes, including transcriptional regulation, hormone biosynthesis and metabolism, post-transcriptional and post-translational regulation, which alter inflorescence architecture by modifying the development and fertility of lateral organs, called spikelets and florets. Recent advances in sequencing capabilities and the generation of mutant populations are accelerating the identification of genes that influence inflorescence development, which is important given that genetic variation for this trait promises to be a valuable resource for optimizing grain production. This review assesses recent advances in our understanding of the genes controlling inflorescence development in wheat and barley, with the aim of highlighting the importance of improvements in developmental biology for optimizing the agronomic performance of staple crop plants.

Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele

The tomato PROCERA gene encodes a DELLA protein, and loss-of-function mutations derepress growth. We used CRISPR/Cas9 and a single guide RNAs (sgRNA) to target mutations to the PROCERA DELLA domain, and recovered several loss-of-function mutations and a dominant dwarf mutation that carries a deletion of one amino acid in the DELLA domain. This is the first report of a dominant dwarf PROCERA allele. This allele retains partial responsiveness to exogenously applied gibberellin. Heterozygotes show an intermediate phenotype at the seedling stage, but adult heterozygotes are as dwarfed as homozygotes.

Inheritance and Genetic Mapping of the Reduced Height (Rht18) Gene in Wheat

Short-statured plants revolutionized agriculture during the 1960s due to their ability to resist lodging, increased their response to fertilizers, and improved partitioning of assimilates which led to yield gains. Of more than 21 reduced-height (Rht) genes reported in wheat, only three-Rht-B1b, Rht-D1b, and Rht8-were extensively used in wheat breeding programs. The remaining reduced height mutants have not been utilized in breeding programs due to the lack of characterization. In the present study, we determined the inheritance of Rht18 and developed a genetic linkage map of the region containing Rht18. The height distribution of the F₂ population was skewed towards the mutant parent, indicating that the dwarf allele (Rht18) is semi-dominant over the tall allele (rht18). Rht18 was mapped on chromosome 6A between markers barc146 and cfd190 with a genetic distance of 26.2 and 17.3 cM, respectively. In addition to plant height, agronomically important traits, like awns and tiller numbers, were also studied in the bi-parental population. Although the average tiller number was very similar in both parents, the F₂ population displayed a normal distribution for tiller number with the majority of plants having phenotype similar to the parents. Transgressive segregation was observed for plant height and tiller number in F₂ population. This study enabled us to select a semi-dwarf line with superior agronomic characteristics that could be utilized in a breeding program. The identification of SSRs associated with Rht18 may improve breeders' effectiveness in selecting desired semi-dwarf lines for developing new wheat cultivars.

FveRGA1, encoding a DELLA protein, negatively regulates runner production in Fragaria vesca

FveRGA1 was highly expressed in tender tissues such as young leaves and stem apices and was localized in the nucleus. RNAi silencing of FveRGA1 in non-runnering woodland strawberry produced many runners. FveRGA1 is thus a key gene controlling strawberry runner formation. The propagation of strawberry is mainly based on runners, while the genes controlling runner production have not been well characterized. Exogenous applications of optimum concentration gibberellins (GAs) promote runner formation in strawberry cultivation and GA can accelerate the degradation of DELLA proteins. To investigate whether DELLA proteins are responsible for runner production, we analyzed all the DELLA genes in Fragaria vesca and cloned a DELLA protein-encoding gene FveRGA1 in woodland strawberry using RT-PCR. Subcellular localization analysis indicated that FveRGA1 was localized in the nucleus. A transcription analysis suggested that FveRGA1 was expressed ubiquitously in all examined strawberry organs, especially in young leaves, petioles, and stem apices. RNA interference (RNAi) technology was carried out to investigate the function of FveRGA1 in woodland strawberry 'Yellow Wonder' (YW) and 'Ruegen' (RG) via an Agrobacterium-mediated transformation. Interestingly, the RNAi silencing transgenic plants in the naturally non-runnering YW and RG strains produced many runners, suggesting FveRGA1 as a key gene controlling strawberry runner formation. Our study lays a solid basis for unraveling the detailed molecular mechanism of runner formation in strawberry.

Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria

Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.

Molecular Mechanisms Underlying Abscisic Acid/Gibberellin Balance in the Control of Seed Dormancy and Germination in Cereals

Seed dormancy is an adaptive trait that does not allow the germination of an intact viable seed under favorable environmental conditions. Non-dormant seeds or seeds with low level of dormancy can germinate readily under optimal environmental conditions, and such a trait leads to preharvest sprouting, germination of seeds on the mother plant prior to harvest, which significantly reduces the yield and quality of cereal crops. High level of dormancy, on the other hand, may lead to non-uniform germination and seedling establishment. Therefore, intermediate dormancy is considered to be a desirable trait as it prevents the problems of sprouting and allows uniformity of postharvest germination of seeds. Induction, maintenance, and release of seed dormancy are complex physiological processes that are influenced by a wide range of endogenous and environmental factors. Plant hormones, mainly abscisic acid (ABA) and gibberellin (GA), are the major endogenous factors that act antagonistically in the control of seed dormancy and germination; ABA positively regulates the induction and maintenance of dormancy, while GA enhances germination. Significant progress has been made in recent years in the elucidation of molecular mechanisms regulating ABA/GA balance and thereby dormancy and germination in cereal seeds, and this review summarizes the current state of knowledge on the topic.

Identification and expression of GRAS family genes in maize (Zea mays L.)

GRAS transcriptional factors have diverse functions in plant growth and development, and are named after the first three transcription factors, namely, GAI (GIBBERELLIC ACID INSENSITIVE), RGA (REPRESSOR OF GAI) and SCR (SCARECROW) identified in this family. Knowledge of the GRAS gene family in maize remains was largely unknown, and their characterization is necessary to understand their importance in the maize life cycle. This study identified 86 GRAS genes in maize, and further characterized with phylogenetics, gene structural analysis, genomic loci, and expression patterns. The 86 GRAS genes were divided into 8 groups (SCL3, HAM, LS, SCR, DELLA, SHR, PAT1 and LISCL) by phylogenetic analysis. Most of the maize GRAS genes contain one exon (80.23%) and closely related members in the phylogenetic tree had similar structure and motif composition. Different motifs especially in the N-terminus might be the sources of their functional divergence. Segmental- and tandem-duplication occurred in this family leading to expansion of maize GRAS genes and the expression patterns of the duplicated genes in the heat map according to the published microarray data were very similar. Quantitative RT-PCR (qRT-PCR) results demonstrated that the expression level of genes in different tissues were different, suggesting their differential roles in plant growth and development. The data set expands our knowledge to understanding the function of GRAS genes in maize, an important crop plant in the world.

Wheat and rye genome confer specific phytohormone profile features and interplay under water stress in two phenotypes of triticale

The aim of the experiment was to determine phytohormone profile of triticale and quality-based relationships between the analyzed groups of phytohormones. The study involved two triticale phenotypes, a long-stemmed one and a semi-dwarf one with Dw1 gene, differing in mechanisms of acclimation to drought and controlled by wheat or rye genome. Water deficit in the leaves triggered a specific phytohormone response in both winter triticale phenotypes attributable to the dominance of wheat (semi-dwarf cultivar) or rye (long-stemmed cultivar) genome. Rye genome in long-stemmed triticale was responsible for specific increase (tillering: gibberellic acid; heading: N6-isopentenyladenine, trans-zeatin-9-riboside, cis-zeatin-9-riboside; flowering: N6-isopentenyladenine, indolebutyric acid, salicylic acid) or decrease (heading: trans-zeatin) in the content of some phytohormones. Wheat genome in semi-dwarf triticale controlled a specific increase in trans-zeatin content at heading and anthesis in gibberellin A1 during anthesis. The greatest number of changes in the phytohormone levels was observed in the generative phase. In both triticale types, the pool of investigated phytohormones was dominated by abscisic acid and gibberellins. The semi-dwarf cultivar with Dw1 gene was less sensitive to gibberellins and its mechanisms of acclimation to water stress were mainly ABA-dependent. An increase in ABA and gibberellins during drought and predominance of these hormones in the total pool of analyzed phytohormones indicated their equal share in drought acclimation mechanisms in long-stemmed cultivar.

A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa)

Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, , which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single-nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37-0.53); however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice.

Brachytic 1 of barley (Hordeum vulgare L.) encodes the α subunit of heterotrimeric G protein

Physiological and molecular biological analysis of the dwarf barley (Hordeum vulgare L.) mutant brachytic 1 (brh1) was conducted. The root responses of brh1 to brassinolide were weaker than those of wild type, but the responses of leaf segments of dark-grown plants were not. Responses of brh1 to gibberellin A₃ were similar to or slightly stronger than those of wild type. Endogenous levels of these hormones in young seedlings were not clearly different between brh1 and wild type. Skotomorphogeneses of brh1 were similar to those of wild type. Some of these physiological characteristics of brh1 resemble those of the dwarf rice (Oryza sativa L.) mutant daikoku (dwarf1; d1), whose dwarfism is caused by a mutation in the heterotrimeric G protein α (Gα) subunit. A database search indicated that the barley Gα gene is located near the locus where Brh1 has already been genetically mapped. Sequences of the Gα gene and cDNAs of five brh1 alleles contained substitutions and a deletion that lead to the production of abnormal Gα proteins. These results indicate that the phenotype of brh1, similarly to that of d1, is caused by mutations in an orthologous gene encoding Gα.

Major genes determining yield-related traits in wheat and barley

Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.