An efficient and reproducible Agrobacterium-mediated transformation method for hexaploid wheat (Triticum aestivum L.)

Progress and innovations of gene cloning in wheat and its close relatives

KEY MESSAGE

Wheat and its close relatives have large and complex genomes, making gene cloning difficult. Nevertheless, developments in genomics over the past decade have made it more feasible. The large and complex genomes of cereals, especially bread wheat, have always been a challenge for gene mapping and cloning. Nevertheless, recent advances in genomics have led to significant progress in this field. Currently, high-quality reference sequences are available for major wheat species and their relatives. New high-throughput genotyping platforms and next-generation sequencing technologies combined with genome complexity reduction techniques and mutagenesis have opened new avenues for gene cloning. In this review, we provide a comprehensive overview of the genes cloned in wheat so far and discuss the strategies used for cloning these genes. We highlight the advantages and drawbacks of individual approaches and show how particular genomic progress contributed to wheat gene cloning. A wide range of new resources and approaches have led to a significant increase in the number of successful cloning projects over the past decade, demonstrating that it is now feasible to perform rapid gene cloning of agronomically important genes, even in a genome as large and complex as that of wheat.

Evolutionary characteristics, expression patterns of wheat receptor-like kinases and functional analysis of TaCrRLK1L16

Reverse genetics research in complex hexaploid wheat often encounters challenges in determining the priority of gene functional characterization. This study aims to systematically analyze the wheat (Triticum aestivum) receptor-like kinase (TaRLK) gene family and develop an effective strategy to identify key candidate genes for further investigation. We identified 3,424 TaRLKs using bioinformatics methods and analyzed the diverse and conserved evolutionary relationships of RLKs among Arabidopsis, rice and wheat. Based on publicly available and our laboratory's transcriptome data, we comprehensively analyzed the transcriptional expression patterns of TaRLKs in response to various stresses, particularly Puccinia striiformis f. sp. tritici (Pst). The TaCrRLK1L16, which is upregulated during Pst infection and triggered cell death in Nicotiana benthamiana, has been identified as a key candidate gene for further functional characterization. Furthermore, our results suggested that the transgenic wheat overexpressing TaCrRLK1L16 significantly enhanced resistance to Pst. This study will provide valuable insights into understanding the evolutionary characteristics and expression patterns of TaRLKs while offering a novel strategy for determining the priority of key candidate TaRLKs.

Isolation of OSCAs in wheat and over-expression of TaOSCA14D increased salt stress tolerance

Salt stress is a major environmental factor that limits plant growth and productivity. In the early stage of salt stress, the intracellular Ca2+ concentration elevates, thereby triggering osmotic stress tolerance signaling pathway. OSCAs encode hyperosmotic gated calcium channels and function as osmotic sensors in Arabidopsis. But the functions of OSCAs in wheat responding to salt stress have not been elucidated. In this study, we identified 42 TaOSCAs and examined their expression pattern in 12 tissues and under salt stress. Further, the salt inducible TaOSCA14D was selected for functional study in response to salt stress. TaOSCA14D was induced by NaCl, PEG, exogenous ABA treatment. Over-expression of TaOSCA14D in Arabidopsis and wheat increased salt stress tolerance. Salt stress related marker genes SnRK2s, ABFs, RD29B were higher expressed in TaOSCA14D transgenic plants than in the wild type under NaCl treatment. Furthermore, the soluble sugar and proline content were higher in transgenic plants than in wild-type ones. Over-expression of TaOSCA14D promoted flowering, decreased spike length and the grain number of per spike. All these results shed some light on the function of OSCAs in tolerance to salt stress and its roles in agronomic trait in wheat.

Soybean transcription factor GmNF-YB20 confers resistance to stripe rust in transgenic wheat by regulating nonspecific lipid transfer protein genes

Worldwide food security is severely threatened by the devastating wheat stripe rust disease. The utilization of resistant wheat cultivars represents the most cost-effective and efficient strategy for combating this disease. However, the lack of resistant resources has been a major bottleneck in breeding for wheat disease resistance. Therefore, revealing novel gene resources for combating stripe rust and elucidating the underlying resistance mechanism is of utmost urgency. In this study, we identified that the soybean NF-YB transcription factor GmNF-YB20 in wheat provides resistance to the stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst). Wheat lines with stable overexpression of the GmNF-YB20 enhanced resistance against multiple Pst races. Transcriptome profiling of GmNF-YB20 transgenic wheat under Pst infection unveiled its involvement in the lipid signaling pathway. RT-qPCR assays suggested that GmNF-YB20 increased transcript levels of multiple nonspecific lipid transfer protein (LTP) genes during wheat-Pst interaction, luciferase reporter analysis illustrates that it activates the transcription of TaLTP1.50 in wheat protoplast, and GmNF-YB20 overexpressed wheat plants had higher total LTP content in vivo during Pst infection. Overexpression of TaLTP1.50 in wheat significantly increased resistance to Pst, whereas knockdown of TaLTP1.50 exhibited the opposite trends, indicating that TaLTP1.50 plays a positive role in wheat resistance. Taken together, our findings provide perspective regarding the molecular mechanism of GmNF-YB20 in wheat and highlight the potential use for wheat breeding.

Chia (Salvia hispanica L.), a functional 'superfood': new insights into its botanical, genetic and nutraceutical characteristics

BACKGROUND

Chia (Salvia hispanica L.) seeds have become increasingly popular among health-conscious consumers owing to their high content of ω-3 fatty acids, which provide various health benefits. Comprehensive chemical analyses of the fatty acids and proteins in chia seeds have been conducted, revealing their functional properties. Recent studies have confirmed the high ω-3 content of chia seed oil and have hinted at additional functional characteristics.

SCOPE

This review article aims to provide an overview of the botanical, morphological and biochemical features of chia plants, seeds and seed mucilage. Additionally, we discuss the recent developments in genetic and molecular research on chia, including the latest transcriptomic and functional studies that examine the genes responsible for chia fatty acid biosynthesis. In recent years, research on chia seeds has shifted its focus from studying the physicochemical characteristics and chemical composition of seeds to understanding the metabolic pathways and molecular mechanisms that contribute to their nutritional benefits. This has led to a growing interest in various pharmaceutical, nutraceutical and agricultural applications of chia. In this context, we discuss the latest research on chia and the questions that remain unanswered, and we identify areas that require further exploration.

CONCLUSIONS

Nutraceutical compounds associated with significant health benefits, including ω-3 polyunsaturated fatty acids, proteins and phenolic compounds with antioxidant activity, have been measured in high quantities in chia seeds. However, comprehensive investigations through both in vitro experiments and in vivo animal and controlled human trials are expected to provide greater clarity on the medicinal, antimicrobial and antifungal effects of chia seeds. The recently published genome of chia and gene-editing technologies, such as CRISPR, facilitate functional studies deciphering molecular mechanisms of biosynthesis and metabolic pathways in this crop. This necessitates development of stable transformation protocols and creation of a publicly available lipid database, mutant collection and large-scale transcriptomic datasets for chia.

Multi-omics analysis reveals the positive impact of differential chloroplast activity during in vitro regeneration of barley

Existence of potent in vitro regeneration system is a prerequisite for efficient genetic transformation and functional genomics of crop plants. In this study, two contrasting cultivars differencing in their in vitro regeneration efficiency were identified. Tissue culture friendly cultivar Golden Promise (GP) and tissue culture resistant DWRB91(D91) were selected as contrasting cultivars to investigate the molecular basis of regeneration efficiency through multiomics analysis. Transcriptomics analysis revealed 1487 differentially expressed genes (DEGs), in which 795 DEGs were upregulated and 692 DEGs were downregulated in the GP-D91 transcriptome. Genes encoding proteins localized in chloroplast and involved in ROS generation were upregulated in the embryogenic calli of GP. Moreover, proteome analysis by LC-MS/MS revealed 3062 protein groups and 16,989 peptide groups, out of these 1586 protein groups were differentially expressed proteins (DEPs). Eventually, GC-MS based metabolomics analysis revealed the higher activity of plastids and alterations in key metabolic processes such as sugar metabolism, fatty acid biosynthesis, and secondary metabolism. TEM analysis also revealed differential plastid development. Higher accumulation of sugars, amino acids and metabolites corresponding to lignin biosynthesis were observed in GP as compared to D91. A comprehensive examination of gene expression, protein profiling and metabolite patterns unveiled a significant increase in the genes encompassing various functions, such as ion homeostasis, chlorophyll metabolic process, ROS regulation, and the secondary metabolic pathway.

Engineering a One Health Super Wheat

Wheat is the predominant crop worldwide, contributing approximately 20% of protein and calories to the human diet. However, the yield potential of wheat faces limitations due to pests, diseases, and abiotic stresses. Although conventional breeding has improved desirable traits, the use of modern transgenesis technologies has been limited in wheat in comparison to other crops such as maize and soybean. Recent advances in wheat gene cloning and transformation technology now enable the development of a super wheat consistent with the One Health goals of sustainability, food security, and environmental stewardship. This variety combines traits to enhance pest and disease resistance, elevate grain nutritional value, and improve resilience to climate change. In this review, we explore ways to leverage current technologies to combine and transform useful traits into wheat. We also address the requirements of breeders and legal considerations such as patents and regulatory issues.

Plant regeneration in the new era: from molecular mechanisms to biotechnology applications

Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.

The improvement of the in vitro plant regeneration in barley with the epigenetic modifier of histone acetylation, trichostatin A

Genotype-limited plant regeneration is one of the main obstacles to the broader use of genetic transformation in barley breeding. Thus, developing new approaches that might improve responses of in vitro recalcitrant genotypes remains at the center of barley biotechnology. Here, we analyzed different barley genotypes, including "Golden Promise," a genotype commonly used in the genetic transformation, and four malting barley cultivars of poor regenerative potential. The expression of hormone-related transcription factor (TF) genes with documented roles in plant regeneration was analyzed in genotypes with various plant-regenerating capacities. The results indicated differential expression of auxin-related TF genes between the barley genotypes in both the explants and the derived cultures. In support of the role of auxin in barley regeneration, distinct differences in the accumulation of free and oxidized auxin were observed in explants and explant-derived callus cultures of barley genotypes. Following the assumption that modifying gene expression might improve plant regeneration in barley, we treated the barley explants with trichostatin A (TSA), which affects histone acetylation. The effects of TSA were genotype-dependent as TSA treatment improved plant regeneration in two barley cultivars. TSA-induced changes in plant regeneration were associated with the increased expression of auxin biosynthesis-involved TFs. The study demonstrated that explant treatment with chromatin modifiers such as TSA might provide a new and effective epigenetic approach to improving plant regeneration in recalcitrant barley genotypes.

Modulation of Plant MicroRNA Expression: Its Potential Usability in Wheat (Triticum aestivum L.) Improvement

Wheat, a crucial crop for the pursuit of food security, is faced with a plateauing yield projected to fall short of meeting the demands of the exponentially increasing human population. To raise global wheat productivity levels, strong efforts must be made to overcome the problems of (1) climate change-induced heat and drought stress and (2) the genotype-dependent amenability of wheat to tissue culture, which limits the success of recovering genetically engineered plants, especially in elite cultivars. Unfortunately, the mainstream approach of genetically engineering plant protein-coding genes may not be effective in solving these problems as it is difficult to map, annotate, functionally verify, and modulate all existing homeologs and paralogs within wheat's large, complex, allohexaploid genome. Additionally, the quantitative, multi-genic nature of most agronomically important traits furthers the complications faced by this approach. miRNAs are small, noncoding RNAs (sncRNAs) that repress gene expression at the post-transcriptional level, regulating various aspects of plant growth and development. They are gaining popularity as alternative targets of genetic engineering efforts for crop improvement due to their (1) highly conserved nature, which facilitates reasonable prediction of their gene targets and phenotypic effects under different expression levels, and (2) the capacity to target multiple genes simultaneously, making them suitable for enhancing complex and multigenic agronomic traits. In this mini-review, we will discuss the biogenesis, manipulation, and potential applications of plant miRNAs in improving wheat's yield, somatic embryogenesis, thermotolerance, and drought-tolerance in response to the problems of plateauing yield, genotype-dependent amenability to tissue culture, and susceptibility to climate change-induced heat and drought stress.  © His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food, 2023.

Design principles for synthetic control systems to engineer plants

KEY MESSAGE

Synthetic control systems have led to significant advancement in the study and engineering of unicellular organisms, but it has been challenging to apply these tools to multicellular organisms like plants. The ability to predictably engineer plants will enable the development of novel traits capable of alleviating global problems, such as climate change and food insecurity. Engineering predictable multicellular phenotypes will require the development of synthetic control systems that can precisely regulate how the information encoded in genomes is translated into phenotypes. Many efficient control systems have been developed for unicellular organisms. However, it remains challenging to use such tools to study or engineer multicellular organisms. Plants are a good chassis within which to develop strategies to overcome these challenges, thanks to their capacity to withstand large-scale reprogramming without lethality. Additionally, engineered plants have great potential for solving major societal problems. Here we briefly review the progress of control system development in unicellular organisms, and how that information can be leveraged to characterize control systems in plants. Further, we discuss strategies for developing control systems designed to regulate the expression of transgenes or endogenous loci and generate dosage-dependent or discrete traits. Finally, we discuss the utility that mathematical models of biological processes have for control system deployment.

Wheat cis-zeatin-O-glucosyltransferase cZOGT1 interacts with the Ca2+-dependent lipid binding protein TaZIP to regulate senescence

Premature senescence is an important factor affecting wheat yield and quality. Wheat yield can be increased by delaying senescence and prolonging the effective photosynthetic time. Previously, we found that the cis-zeatin-O-glucosyltransferase (cZOGT1) gene plays an important role in the stay-green wheat phenotype. In this study, cZOGT1-overexpressing lines exhibited a delayed senescence phenotype, despite a significant reduction in the total cytokinin content. Further, we found that cZOGT1 interacted with the Ca2+-dependent lipid binding protein TaZIP (cZOGT1-interacting protein), and that a high level of cZOGT1 expression led to the suppression of TaZIP expression, which in turn, reduced abscisic acid (ABA) content. The synergistic reduction in cytokinins and ABA levels eventually caused the stay-green phenotype in cZOGT1-overexpressing lines. This study provides a new theoretical basis to explain the mechanism underlying the wheat stay-green phenotype and provides a genetic resource for wheat molecular-design breeding.

DMC1 stabilizes crossovers at high and low temperatures during wheat meiosis

Effective chromosome synapsis and crossover formation during meiosis are essential for fertility, especially in grain crops such as wheat. These processes function most efficiently in wheat at temperatures between 17-23 °C, although the genetic mechanisms for such temperature dependence are unknown. In a previously identified mutant of the hexaploid wheat reference variety 'Chinese Spring' lacking the long arm of chromosome 5D, exposure to low temperatures during meiosis resulted in asynapsis and crossover failure. In a second mutant (ttmei1), containing a 4 Mb deletion in chromosome 5DL, exposure to 13 °C led to similarly high levels of asynapsis and univalence. Moreover, exposure to 30 °C led to a significant, but less extreme effect on crossovers. Previously, we proposed that, of 41 genes deleted in this 4 Mb region, the major meiotic gene TaDMC1-D1 was the most likely candidate for preservation of synapsis and crossovers at low (and possibly high) temperatures. In the current study, using RNA-guided Cas9, we developed a new Chinese Spring CRISPR mutant, containing a 39 bp deletion in the 5D copy of DMC1, representing the first reported CRISPR-Cas9 targeted mutagenesis in Chinese Spring, and the first CRISPR mutant for DMC1 in wheat. In controlled environment experiments, wild-type Chinese Spring, CRISPR dmc1-D1 and backcrossed ttmei1 mutants were exposed to either high or low temperatures during the temperature-sensitive period from premeiotic interphase to early meiosis I. After 6-7 days at 13 °C, crossovers decreased by over 95% in the dmc1-D1 mutants, when compared with wild-type plants grown under the same conditions. After 24 hours at 30 °C, dmc1-D1 mutants exhibited a reduced number of crossovers and increased univalence, although these differences were less marked than at 13 °C. Similar results were obtained for ttmei1 mutants, although their scores were more variable, possibly reflecting higher levels of background mutation. These experiments confirm our previous hypothesis that DMC1-D1 is responsible for preservation of normal crossover formation at low and, to a certain extent, high temperatures. Given that reductions in crossovers have significant effects on grain yield, these results have important implications for wheat breeding, particularly in the face of climate change.

Opportunities and Challenges of In Vitro Tissue Culture Systems in the Era of Crop Genome Editing

Currently, the development of genome editing (GE) tools has provided a wide platform for targeted modification of plant genomes. However, the lack of versatile DNA delivery systems for a large variety of crop species has been the main bottleneck for improving crops with beneficial traits. Currently, the generation of plants with heritable mutations induced by GE tools mostly goes through tissue culture. Unfortunately, current tissue culture systems restrict successful results to only a limited number of plant species and genotypes. In order to release the full potential of the GE tools, procedures need to be species and genotype independent. This review provides an in-depth summary and insights into the various in vitro tissue culture systems used for GE in the economically important crops barley, wheat, rice, sorghum, soybean, maize, potatoes, cassava, and millet and uncovers new opportunities and challenges of already-established tissue culture platforms for GE in the crops.

Technological Development and Application of Plant Genetic Transformation

Genetic transformation is an important strategy for enhancing plant biomass or resistance in response to adverse environments and population growth by imparting desirable genetic characteristics. Research on plant genetic transformation technology can promote the functional analysis of plant genes, the utilization of excellent traits, and precise breeding. Various technologies of genetic transformation have been continuously discovered and developed for convenient manipulation and high efficiency, mainly involving the delivery of exogenous genes and regeneration of transformed plants. Here, currently developed genetic transformation technologies were expounded and compared. Agrobacterium-mediated gene delivery methods are commonly used as direct genetic transformation, as well as external force-mediated ways such as particle bombardment, electroporation, silicon carbide whiskers, and pollen tubes as indirect ones. The regeneration of transformed plants usually involves the de novo organogenesis or somatic embryogenesis pathway of the explants. Ectopic expression of morphogenetic transcription factors (Bbm, Wus2, and GRF-GIF) can significantly improve plant regeneration efficiency and enable the transformation of some hard-to-transform plant genotypes. Meanwhile, some limitations in these gene transfer methods were compared including genotype dependence, low transformation efficiency, and plant tissue damage, and recently developed flexible approaches for plant genotype transformation are discussed regarding how gene delivery and regeneration strategies can be optimized to overcome species and genotype dependence. This review summarizes the principles of various techniques for plant genetic transformation and discusses their application scope and limiting factors, which can provide a reference for plant transgenic breeding.

Uncovering the transcriptional regulatory network involved in boosting wheat regeneration and transformation

Genetic transformation is important for gene functional study and crop improvement. However, it is less effective in wheat. Here we employed a multi-omic analysis strategy to uncover the transcriptional regulatory network (TRN) responsible for wheat regeneration. RNA-seq, ATAC-seq and CUT&Tag techniques were utilized to profile the transcriptional and chromatin dynamics during early regeneration from the scutellum of immature embryos in the wheat variety Fielder. Our results demonstrate that the sequential expression of genes mediating cell fate transition during regeneration is induced by auxin, in coordination with changes in chromatin accessibility, H3K27me3 and H3K4me3 status. The built-up TRN driving wheat regeneration was found to be dominated by 446 key transcription factors (TFs). Further comparisons between wheat and Arabidopsis revealed distinct patterns of DNA binding with one finger (DOF) TFs in the two species. Experimental validations highlighted TaDOF5.6 (TraesCS6A02G274000) and TaDOF3.4 (TraesCS2B02G592600) as potential enhancers of transformation efficiency in different wheat varieties.

Agrobacterium-mediated direct transformation of wheat mature embryos through organogenesis

Transgenic plant production in monocotyledonous species has primarily relied on embryogenic callus induction from both immature and mature embryos as the pathway for plant regeneration. We have efficiently regenerated fertile transgenic wheat plants through organogenesis after Agrobacterium-mediated direct transformation of mechanically isolated mature embryos from field-grown seed. Centrifugation of the mature embryos in the presence of Agrobacterium was found to be essential for efficient T-DNA delivery to the relevant regenerable cells. The inoculated mature embryos formed multiple buds/shoots on high-cytokinin medium, which directly regenerated into transgenic shoots on hormone-free medium containing glyphosate for selection. Rooted transgenic plantlets were obtained within 10-12 weeks after inoculation. Further optimization of this transformation protocol resulted in significant reduction of chimeric plants to below 5%, as indicated by leaf GUS staining and T1 transgene segregation analysis. Direct transformation of wheat mature embryos has substantial advantages over traditional immature embryo-based transformation systems, including long-term storability of the mature dry explants, scalability, and greatly improved flexibility and consistency in transformation experiments.

ZIP4 is required for normal progression of synapsis and for over 95% of crossovers in wheat meiosis

Tetraploid (AABB) and hexaploid (AABBDD) wheat have multiple sets of similar chromosomes, with successful meiosis and preservation of fertility relying on synapsis and crossover (CO) formation only taking place between homologous chromosomes. In hexaploid wheat, the major meiotic gene TaZIP4-B2 (Ph1) on chromosome 5B, promotes CO formation between homologous chromosomes, whilst suppressing COs between homeologous (related) chromosomes. In other species, ZIP4 mutations eliminate approximately 85% of COs, consistent with loss of the class I CO pathway. Tetraploid wheat has three ZIP4 copies: TtZIP4-A1 on chromosome 3A, TtZIP4-B1 on 3B and TtZIP4-B2 on 5B. Here, we have developed single, double and triple zip4 TILLING mutants and a CRISPR Ttzip4-B2 mutant, to determine the effect of ZIP4 genes on synapsis and CO formation in the tetraploid wheat cultivar 'Kronos'. We show that disruption of two ZIP4 gene copies in Ttzip4-A1B1 double mutants, results in a 76-78% reduction in COs when compared to wild-type plants. Moreover, when all three copies are disrupted in Ttzip4-A1B1B2 triple mutants, COs are reduced by over 95%, suggesting that the TtZIP4-B2 copy may also affect class II COs. If this is the case, the class I and class II CO pathways may be interlinked in wheat. When ZIP4 duplicated and diverged from chromosome 3B on wheat polyploidization, the new 5B copy, TaZIP4-B2, could have acquired an additional function to stabilize both CO pathways. In tetraploid plants deficient in all three ZIP4 copies, synapsis is delayed and does not complete, consistent with our previous studies in hexaploid wheat, when a similar delay in synapsis was observed in a 59.3 Mb deletion mutant, ph1b, encompassing the TaZIP4-B2 gene on chromosome 5B. These findings confirm the requirement of ZIP4-B2 for efficient synapsis, and suggest that TtZIP4 genes have a stronger effect on synapsis than previously described in Arabidopsis and rice. Thus, ZIP4-B2 in wheat accounts for the two major phenotypes reported for Ph1, promotion of homologous synapsis and suppression of homeologous COs.

The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase

To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool¹. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum^2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.

An efficient transformation method for genome editing of elite bread wheat cultivars

An efficient genetic transformation protocol is necessary to edit genes for trait improvement directly in elite bread wheat cultivars. We used a protein fusion between a wheat growth-regulating factor 4 (GRF4) and its interacting factor (GIF1) to develop a reproducible genetic transformation and regeneration protocol, which we then used to successfully transform elite bread wheat cultivars Baj, Kachu, Morocco, Reedling, RL6077, and Sujata in addition to the experimental cultivar Fielder. Immature embryos were transformed with the vector using particle bombardment method. Transformation frequency increased nearly 60-fold with the GRF4-GIF1-containing vectors as compared to the control vector and ranged from ~5% in the cultivar Kachu to 13% in the cultivar RL6077. We then edited two genes that confer resistance against leaf rust and powdery mildew directly in the aforementioned elite cultivars. A wheat promoter, TaU3 or TaU6, to drive the expression of guide RNA was effective in gene editing whereas the OsU3 promoter failed to generate any edits. Editing efficiency was nearly perfect with the wheat promoters. Our protocol has made it possible to edit genes directly in elite wheat cultivars and would be useful for gene editing in other wheat varieties, which have been recalcitrant to transformation thus far.

Development of two protocols for Agrobacterium-mediated transformation of white clover (Trifolium repens) via the callus system

White clover (Trifolium repens) is one of the most widely cultivated livestock forage plants whose persistence is severely affected by abiotic stresses. For the white clover, efficient regeneration systems is still a great necessity. In this study, inoculating 4-day-old cotyledons into MS media fortified with 0.4 mg·L-1 6-BA and 2 mg·L-1 2,4-D significantly increased the callus induction rate. Roots and cotyledons proved to be better explants, followed by hypocotyls, leaves, and petioles for callus induction. The development of differentiated structures occurred effectively on MS supplemented with 1 mg·L-1 6-BA and 0.1 mg·L-1 NAA. To increase transformation, we investigated various factors affecting the Agrobacterium tumefaciens transformation in white clover. The optimal conditions for root-derived callus and 4-day-old cotyledons were as follows: Agrobacterium suspension density with OD600 of 0.5, 20 mg·L-1 AS, and 4 days of co-cultivation duration. Subsequently, we developed two transformation protocols: transformation after callus induction from 4-day-old roots (Protocol A) and transformation before initiation of callus from cotyledons (Protocol B). The transformation frequencies varied from 1.92 to 3.17% in Protocol A and from 2.76 to 3.47% in Protocol B. We report the possibility to regenerate multiple transgenic white clover plants from a single genetic background. Our research may also contribute to successful genetic manipulation and genome editing in white clover.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03591-2.

A bifunctional selectable marker for wheat transformation contributes to the characterization of male-sterile phenotype induced by a synthetic Ms2 gene

KEY MESSAGE

An engineered selectable marker combining herbicide resistance and yellow fluorescence contributes to the characterization of male-sterile phenotype in wheat, the severity of which correlates with expression levels of a synthetic Ms2 gene. Genetic transformation of wheat is conducted using selectable markers, such as herbicide and antibiotic resistance genes. Despite their proven effectiveness, they do not provide visual control of the transformation process and transgene status in progeny, which creates uncertainty and prolongs screening procedures. To overcome this limitation, this study developed a fusion protein by combining gene sequences encoding phosphinothricin acetyltransferase and mCitrine fluorescent protein. The fusion gene, introduced into wheat cells by particle bombardment, enabled herbicide selection, and visual identification of primary transformants along with their progeny. This marker was then used to select transgenic plants containing a synthetic Ms2 gene. Ms2 is a dominant gene whose activation in wheat anthers leads to male sterility, but the relationship between the expression levels and the male-sterile phenotype is unknown. The Ms2 gene was driven either by a truncated Ms2 promoter containing a TRIM element or a rice promoter OsLTP6. The expression of these synthetic genes resulted in complete male sterility or partial fertility, respectively. The low-fertility phenotype was characterized by smaller anthers than the wild type, many defective pollen grains, and low seed sets. The reduction in the size of anthers was observed at earlier and later stages of their development. Consistently, Ms2 transcripts were detected in these organs, but their levels were significantly lower than those in completely sterile Ms2TRIM::Ms2 plants. These results suggested that the severity of the male-sterile phenotype was modulated by Ms2 expression levels and that higher levels may be key to activating total male sterility.

Rapid and highly efficient morphogenic gene-mediated hexaploid wheat transformation

The successful employment of morphogenic regulator genes, Zm-Baby Boom (ZmBbm) and Zm-Wuschel2 (ZmWus2), for Agrobacterium-mediated transformation of maize (Zea mays L.) and sorghum (Sorghum bicolor L.) has been reported to improve transformation by inducing rapid somatic embryo formation. Here, we report two morphogenic gene-mediated wheat transformation methods, either with or without morphogenic and marker gene excision. These methods yield independent-transformation efficiency up to 58% and 75%, respectively. In both cases, the tissue culture duration for generating transgenic plants was significantly reduced from 80 to nearly 50 days. In addition, the transformation process was significantly simplified to make the procedure less labor-intensive, higher-throughput, and more cost-effective by eliminating the requirement for embryonic axis excision, bypassing the necessity for prolonged dual-selection steps for callus formation, and obviating the prerequisite of cytokinin for shoot regeneration. Furthermore, we have demonstrated the flexibility of the methods and generated high-quality transgenic events across multiple genotypes using herbicide (phosphinothricin, ethametsulfuron)- and antibiotic (G418)-based selections.

Recent advances in understanding of the epigenetic regulation of plant regeneration

Ever since the concept of "plant cell totipotency" was first proposed in the early twentieth century, plant regeneration has been a major focus of study. Regeneration-mediated organogenesis and genetic transformation are important topics in both basic research and modern agriculture. Recent studies in the model plant Arabidopsis thaliana and other species have expanded our understanding of the molecular regulation of plant regeneration. The hierarchy of transcriptional regulation driven by phytohormone signaling during regeneration is associated with changes in chromatin dynamics and DNA methylation. Here, we summarize how various aspects of epigenetic regulation, including histone modifications and variants, chromatin accessibility dynamics, DNA methylation, and microRNAs, modulate plant regeneration. As the mechanisms of epigenetic regulation are conserved in many plants, research in this field has potential applications in boosting crop breeding, especially if coupled with emerging single-cell omics technologies.

A two-gene strategy increases iron and zinc concentrations in wheat flour, improving mineral bioaccessibility

Dietary deficiencies of iron and zinc cause human malnutrition that can be mitigated by biofortified staple crops. Conventional breeding approaches to increase grain mineral concentrations in wheat (Triticum aestivum L.) have had only limited success, and our understanding of the genetic and physiological barriers to altering this trait is incomplete. Here we demonstrate that a transgenic approach combining endosperm-specific expression of the wheat VACUOLAR IRON TRANSPORTER gene TaVIT2-D with constitutive expression of the rice (Oryza sativa) NICOTIANAMINE SYNTHASE gene OsNAS2 significantly increases the total concentration of zinc and relocates iron to white-flour fractions. In two distinct bread wheat cultivars, we show that the so called VIT-NAS construct led to a two-fold increase in zinc in wholemeal flour, to ∼50 µg g-1. Total iron was not significantly increased, but redistribution within the grain resulted in a three-fold increase in iron in highly pure, roller-milled white flour, to ∼25 µg g-1. Interestingly, expression of OsNAS2 partially restored iron translocation to the aleurone, which is iron depleted in grain overexpressing TaVIT2 alone. A greater than three-fold increase in the level of the natural plant metal chelator nicotianamine in the grain of VIT-NAS lines corresponded with improved iron and zinc bioaccessibility in white flour. The growth of VIT-NAS plants in the greenhouse was indistinguishable from untransformed controls. Our results provide insights into mineral translocation and distribution in wheat grain and demonstrate that the individual and combined effects of the two transgenes can enhance the nutritional quality of wheat beyond what is possible by conventional breeding.

Potential abiotic stress targets for modern genetic manipulation

Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.

A stripe rust fungal effector PstSIE1 targets TaSGT1 to facilitate pathogen infection

Puccinia striiformis f. sp. tritici (Pst), the causal agent of stripe rust, is a destructive pathogen of Triticum aestivum (wheat), threatening wheat production worldwide. Pst delivers hundreds of effectors to manipulate processes in its hosts during infection. The SGT1 (suppressor of the G2 allele of skp1), RAR1 (required for Mla12 resistance) and HSP90 (heat-shock protein 90) proteins form a chaperone complex that acts as a core modulator in plant immunity. However, little is known about how Pst effectors target this immune component to suppress plant immunity. Here, we identified a Pst effector PstSIE1 that interacts with TaSGT1 in wheat and is upregulated during the early infection stage. Transient expression of PstSIE1 suppressed cell death in Nicotiana benthamiana induced by VmE02 and PcNLP2. Transgenic expression of PstSIE1-RNAi constructs in wheat significantly reduced the virulence of Pst. Overexpression of PstSIE1 in wheat increased the number of rust pustules and reduced the accumulation of reactive oxygen species (ROS), indicating that PstSIE1 functions as an important pathogenicity factor in Pst. PstSIE1 was found to compete with TaRAR1 to bind TaSGT1, thus disrupting the formation of the TaRAR1-TaSGT1 subcomplex. Taken together, PstSIE1 is an important Pst effector targeting the immune component TaSGT1 and involved in suppressing wheat defense.

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.

A serine-rich effector from the stripe rust pathogen targets a Raf-like kinase to suppress host immunity

Puccinia striiformis f. sp. tritici (Pst) is an important obligate pathogen in wheat (Triticum aestivum L.) and secretes effectors into plant cells to promote infection. Identifying host targets of effector proteins and clarifying their roles in pathogen infection is essential for understanding pathogen virulence. In this study, we identified a serine-rich effector, Pst27791, from Pst that suppresses cell death in Nicotiana benthamiana. Stable overexpression of Pst27791 in wheat suppressed reactive oxygen species accumulation and the salicylic acid-dependent defense response. Transgenic wheat expressing the RNA interference construct of Pst27791 exhibited high resistance to Pst virulent isolate CYR31, indicating its importance in pathogenesis. Pst27791 interacting with wheat rapidly accelerated fibrosarcoma (Raf)-like kinase TaRaf46 in yeast and in planta. Knocking down TaRaf46 expression in wheat attenuated Pst infection and increased wheat immunity. The overexpression of TaRaf46 decreased wheat resistance to Pst and repressed MAPK activation in wheat. Pst27791 may stabilize TaRaf46 through the inhibition of proteasome-mediated degradation in N. benthamiana. The ability of Pst27791 to enhance Pst colonization was compromised when TaRaf46 was silenced, suggesting that the virulence of Pst27791 is mediated by TaRaf46. Overall, these results indicate that Raf-like kinase TaRaf46 is exploited by the Pst effector as a negative regulator of plant immunity to promote infection in wheat.

Agrobacterium expressing a type III secretion system delivers Pseudomonas effectors into plant cells to enhance transformation

Agrobacterium-mediated plant transformation (AMT) is the basis of modern-day plant biotechnology. One major drawback of this technology is the recalcitrance of many plant species/varieties to Agrobacterium infection, most likely caused by elicitation of plant defense responses. Here, we develop a strategy to increase AMT by engineering Agrobacterium tumefaciens to express a type III secretion system (T3SS) from Pseudomonas syringae and individually deliver the P. syringae effectors AvrPto, AvrPtoB, or HopAO1 to suppress host defense responses. Using the engineered Agrobacterium, we demonstrate increase in AMT of wheat, alfalfa and switchgrass by ~250%-400%. We also show that engineered A. tumefaciens expressing a T3SS can deliver a plant protein, histone H2A-1, to enhance AMT. This strategy is of great significance to both basic research and agricultural biotechnology for transient and stable transformation of recalcitrant plant species/varieties and to deliver proteins into plant cells in a non-transgenic manner.

Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes

Meiotic recombination is not only fundamental to the adaptation of sexually reproducing eukaryotes in nature but increased recombination rates facilitate the combination of favourable alleles into a single haplotype in breeding programmes. The main objectives of this study were to (i) assess the extent and distribution of the recombination rate variation in cultivated barley (Hordeum vulgare L.), (ii) quantify the importance of the general and specific recombination effects, and (iii) evaluate a genomic selection approach's ability to predict the recombination rate variation. Genetic maps were created for the 45 segregating populations that were derived from crosses among 23 spring barley inbreds with origins across the world. The genome-wide recombination rate among populations ranged from 0.31 to 0.73 cM/Mbp. The crossing design used in this study allowed to separate the general recombination effects (GRE) of individual parental inbreds from the specific recombination effects (SRE) caused by the combinations of parental inbreds. The variance of the genome-wide GRE was found to be about eight times the variance of the SRE. This finding indicated that parental inbreds differ in the efficiency of their recombination machinery. The ability to predict the chromosome or genome-wide recombination rate of an inbred ranged from 0.80 to 0.85. These results suggest that a reliable screening of large genetic materials for their potential to cause a high extent of genetic recombination in their progeny is possible, allowing to systematically manipulate the recombination rate using natural variation.

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.

Biotechnological approach for improvement of Crambe species as valuable oilseed plants for industrial purposes

Boosting technological innovation for a sustainable and circular bioeconomy encompasses the use of renewable materials and development of highly effective biotechnological approaches to improve the quality of oilseed crops and facilitate their industrial deployment. The interest in cultivating Crambe as a potential crop is steadily growing due to its low propensity to crossbreeding with other oilseed crops, valuable seed oil composition and a high yield capacity. The main focus is located on Crambe abyssinica as the most adapted into the agriculture and well-studied Crambe species. At the same time, the Crambe genus is one of the most numerous of the Brassicaceae family featuring several underestimated (orphaned) species with useful traits (abiotic stress tolerance, wide range of practical applications). This review features progress in the biotechnological improvement of well-adapted and wild Crambe species starting with aseptic culture establishment and plant propagation in vitro reinforced with the use of genetic engineering and breeding techniques. The aim of the paper is to highlight and review the existing biotechnological methods of both underestimated and well-adapted Crambe species improvment, including the establishment of aseptic culture, in vitro cultivation, plant regeneration and genetic transformation to modify seed oil content and morphological traits of valuable species.

Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.

Characterization of a Novel TtLEA2 Gene From Tritipyrum and Its Transformation in Wheat to Enhance Salt Tolerance

Late embryogenesis-abundant (LEA) proteins are critical in helping plants cope with salt stress. "Y1805" is a salt-tolerant Tritipyrum. We identified a "Y1805"-specific LEA gene that was expressed highly and sensitively under salt stress using transcriptome analysis. The novel group 2 LEA gene (TtLEA2-1) was cloned from "Y1805." TtLEA2-1 contained a 453 bp open reading frame encoding an 151-amino-acid protein that showed maximum sequence identity (77.00%) with Thinopyrum elongatum by phylogenetic analysis. It was mainly found to be expressed highly in the roots by qRT-PCR analysis and was located in the whole cell. Forty-eight candidate proteins believed to interact with TtLEA2-1 were confirmed by yeast two-hybrid analysis. These interacting proteins were mainly enriched in "environmental information processing," "glycan biosynthesis and metabolism," and "carbohydrate metabolism." Protein-protein interaction analysis indicated that the translation-related 40S ribosomal protein SA was the central node. An efficient wheat transformation system has been established. A coleoptile length of 2 cm, an Agrobacteria cell density of 0.55-0.60 OD₆₀₀, and 15 KPa vacuum pressure were ideal for common wheat transformation, with an efficiency of up to 43.15%. Overexpression of TaLEA2-1 in wheat "1718" led to greater height, stronger roots, and higher catalase activity than in wild type seedlings. TaLEA2-1 conferred enhanced salt tolerance in transgenic wheat and may be a valuable gene for genetic modification in crops.

Transcription factor BZR2 activates chitinase Cht20.2 transcription to confer resistance to wheat stripe rust

The brassinosteroid pathway promotes a variety of physiological processes in plants and the brassinosteroid insensitive1-ethylmethane sulfonate suppressor (BES)/brassinazole-resistant (BZR) functions as one of its key regulators. We previously showed that the BES/BZR-type transcription factor TaBZR2 mediates the drought stress response in wheat (Triticum aestivum) by directly upregulating the transcriptional activity of glutathione S-transferase 1. However, the function of TaBZR2 in plants under biotic stresses is unknown. In this study, we found that transcript levels of TaBZR2 were upregulated in response to inoculation with wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, Pst) and treatment with flg22 or an elicitor-like protein of Pst, Pst322. Wheat lines overexpressing TaBZR2 conferred increased resistance, whereas TaBZR2-RNAi lines exhibited decreased resistance to multiple races of Pst. TaBZR2 targeted the promoter of the chitinase gene TaCht20.2, activating its transcription. Knockdown of TaCht20.2 in wheat resulted in enhanced susceptibility to Pst, indicating the positive role of TaCht20.2 in wheat resistance. Upon Pst infection in vivo, the overexpression of TaBZR2 increased total chitinase activity, whereas RNAi-mediated silencing of TaBZR2 reduced total chitinase activity. Taken together, our results suggest that TaBZR2 confers broad-spectrum resistance to the stripe rust fungus by increasing total chitinase activity in wheat.

Compendium of Plant-Specific CRISPR Vectors and Their Technical Advantages

CRISPR/Cas mediated genome editing is a revolutionary approach for manipulating the plant genome. However, the success of this technology is highly dependent on selection of a specific vector and the other components. A plant-specific CRISPR/Cas vector usually consists of a Cas gene, target-specific gRNA, leader sequence, selectable marker gene, precise promoters, and other accessories. It has always been challenging to select the specific vector for each study due to a lack of comprehensive information on CRISPR vectors in one place. Herein, we have discussed every technical aspect of various important elements that will be highly useful in vector selection and efficient editing of the desired plant genome. Various factors such as the promoter regulating the expression of Cas and gRNA, gRNA size, Cas variants, multicistronic gRNA, and vector backbone, etc. influence transformation and editing frequency. For example, the use of polycistronic tRNA-gRNA, and Csy4-gRNA has been documented to enhance the editing efficiency. Similarly, the selection of an efficient selectable marker is also a very important factor. Information on the availability of numerous variants of Cas endonucleases, such as Cas9, Cas12a, Cas12b, Casɸ, and CasMINI, etc., with diverse recognition specificities further broadens the scope of editing. The development of chimeric proteins such as Cas fused to cytosine or adenosine deaminase domain and modified reverse transcriptase using protein engineering enabled base and prime editing, respectively. In addition, the newly discovered Casɸ and CasMINI would increase the scope of genetic engineering in plants by being smaller Cas variants. All advancements would contribute to the development of various tools required for gene editing, targeted gene insertion, transcriptional activation/suppression, multiplexing, prime editing, base editing, and gene tagging. This review will serve as an encyclopedia for plant-specific CRISPR vectors and will be useful for researchers.

Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner

Flower development is an important determinant of grain yield in crops. In wheat (Triticum spp.), natural variation for the size of spikelet and floral organs is particularly evident in Triticum turgidum ssp. polonicum (also termed Triticum polonicum), a tetraploid subspecies of wheat with long glumes, lemmas, and grains. Using map-based cloning, we identified VEGETATIVE TO REPRODUCTIVE TRANSITION 2 (VRT2), which encodes a MADS-box transcription factor belonging to the SHORT VEGETATIVE PHASE family, as the gene underlying the T. polonicum long-glume (P1) locus. The causal P1 mutation is a sequence rearrangement in intron-1 that results in ectopic expression of the T. polonicum VRT-A2 allele. Based on allelic variation studies, we propose that the intron-1 mutation in VRT-A2 is the unique T. polonicum subspecies-defining polymorphism, which was later introduced into hexaploid wheat via natural hybridizations. Near-isogenic lines differing for the P1 locus revealed a gradient effect of P1 across spikelets and within florets. Transgenic lines of hexaploid wheat carrying the T. polonicum VRT-A2 allele show that expression levels of VRT-A2 are highly correlated with spike, glume, grain, and floral organ length. These results highlight how changes in expression profiles, through variation in cis-regulation, can affect agronomic traits in a dosage-dependent manner in polyploid crops.

Subcellular dynamics studies of iron reveal how tissue-specific distribution patterns are established in developing wheat grains

Understanding the mechanisms of iron trafficking in plants is key to enhancing the nutritional quality of crops. Because it is difficult to image iron in transit, we currently have an incomplete picture of the route(s) of iron translocation in developing seeds and how the tissue-specific distribution is established. We have used a novel approach, combining iron-57 (⁵⁷ Fe) isotope labelling and nanoscale secondary ion mass spectrometry (NanoSIMS), to visualize iron translocation between tissues and within cells in immature wheat grain, Triticum aestivum. This enabled us to track the main route of iron transport from maternal tissues to the embryo through the different cell types. Further evidence for this route was provided by genetically diverting iron into storage vacuoles, with confirmation provided by histological staining and transmission electron microscopy energy dispersive X-ray spectroscopy (TEM-EDS). Almost all iron in both control and transgenic grains was found in intracellular bodies, indicating symplastic rather than apoplastic transport. Furthermore, a new type of iron body, highly enriched in ⁵⁷ Fe, was observed in aleurone cells and may represent iron being delivered to phytate globoids. Correlation of the ⁵⁷ Fe enrichment profiles obtained by NanoSIMS with tissue-specific gene expression provides an updated model of iron homeostasis in cereal grains with relevance for future biofortification strategies.

Rapid Methodologies for Assessing Pseudomonas syringae pv. actinidiae Colonization and Effector-Mediated Hypersensitive Response in Kiwifruit

The infection of Pseudomonas syringae pv. actinidiae in kiwifruit is currently assessed by numerous methodologies, each with their own limitations. Most studies are based on either a laborious method of growth quantification of the pathogen or qualitative assessments by visual scoring following stem or cutting inoculation. Additionally, when assessing for resistance against specific pathogen effectors, confounding interactions between multiple genes in the pathogen can make mapping resistance phenotypes nearly impossible. Here, we present robust alternative methods to quantify pathogen load based on rapid bacterial DNA quantification by PCR, the use of Pseudomonas fluorescens, and a transient reporter eclipse assay for assessing resistance conferred by isolated bacterial avirulence genes. These assays compare well with bacterial plate counts to assess bacterial colonization as a result of plant resistance activation. The DNA-based quantification, when coupled with the P. fluorescens and reporter eclipse assays to independently identify bacterial avirulence genes, is rapid, highly reproducible, and scalable for high-throughput screens of multiple cultivars or genotypes. Application of these methodologies will allow rapid and high-throughput identification of resistant cultivars and the bacterial avirulence genes they recognize, facilitating resistance gene discovery for plant breeding programs.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome editing in cereal crops: an overview

Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.

Creation and judicious application of a wheat resistance gene atlas

Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing

Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.

Bioproduction process of natural products and biopharmaceuticals: Biotechnological aspects

Decades of research have been put in place for developing sustainable routes of bioproduction of high commercial value natural products (NPs) on the global market. In the last few years alone, we have witnessed significant advances in the biotechnological production of NPs. The development of new methodologies has resulted in a better understanding of the metabolic flux within the organisms, which have driven manipulations to improve production of the target product. This was further realised due to the recent advances in the omics technologies such as genomics, transcriptomics, proteomics, metabolomics and secretomics, as well as systems and synthetic biology. Additionally, the combined application of novel engineering strategies has made possible avenues for enhancing the yield of these products in an efficient and economical way. Invention of high-throughput technologies such as next generation sequencing (NGS) and toolkits for genome editing Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated 9 (CRISPR/Cas9) have been the game changers and provided unprecedented opportunities to generate rationally designed synthetic circuits which can produce complex molecules. This review covers recent advances in the engineering of various hosts for the production of bioactive NPs and biopharmaceuticals. It also highlights general approaches and strategies to improve their biosynthesis with higher yields in a perspective of plants and microbes (bacteria, yeast and filamentous fungi). Although there are numerous reviews covering this topic on a selected species at a time, our approach herein is to give a comprehensive understanding about state-of-art technologies in different platforms of organisms.

Agroinfiltration for transient gene expression and characterisation of fungal pathogen effectors in cool-season grain legume hosts

KEY MESSAGE

Modified pEAQ-HT-DEST1 vectors were used for agroinfiltration in legumes. We demonstrate protein expression and export in pea, lentil, and faba bean; however, the method for chickpea was not successful. Agroinfiltration is a valuable research method for investigating virulence and avirulence effector proteins from pathogens and pests, where heterologous effector proteins are transiently expressed in plant leaves and hypersensitive necrosis responses and other effector functions can be assessed. Nicotiana benthamiana is widely used for agroinfiltration and the characterisation of broad-spectrum effectors. The method has also been used in other plant species including field pea, but not yet developed for chickpea, lentil, or faba bean. Here, we have modified the pEAQ-HT-DEST1 vector for expression of 6 × histidine-tagged green-fluorescent protein (GFP) and the known necrosis-inducing broad-spectrum effector necrosis and ethylene-inducing peptide (Nep1)-like protein (NLP). Modified pEAQ-based vectors were adapted to encode signal peptide sequences for apoplast targeting of expressed proteins. We used confocal microscopy to assess the level of GFP expression in agroinfiltrated leaves. While at 3 days after infiltration in N. benthamiana, GFP was expressed at a relatively high level, expression in field pea and faba bean at the same time point was relatively low. In lentil, an expression level of GFP similar to field pea and faba bean at 3 days was only observed after 5 days. Chickpea leaf cells were transformed at low frequency and agroinfiltration was concluded to not be successful for chickpea. We concluded that the pEAQ vector is suitable for testing host-specific effectors in field pea, lentil, and faba bean, but low transformation efficiency limits the utility of the method for chickpea.

RNAi-mediated stable silencing of TaCSN5 confers broad-spectrum resistance to Puccinia striiformis f. sp. tritici

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a versatile regulator of plant growth, development, and response to diverse pathogens. However, little research has been done to understand the function of those CSN genes in broad-spectrum resistance to pathogens. In this study, we found that the transcript levels of wheat TaCSN5 were induced in response to inoculation with Puccinia striiformis f. sp. tritici (Pst) and treatment with salicylic acid (SA). Overexpression of TaCSN5 in Arabidopsis resulted in increased susceptibility to Pseudomonas syringae pv. tomato DC3000 infection accompanied by down-regulation of AtPR1 expression. Overexpression of TaCSN5 in wheat lines significantly increased susceptibility to Pst accompanied by decreased SA accumulation, whereas TaCSN5-RNAi wheat lines exhibited opposite trends. Moreover, we found that TaCSN5 negatively regulated TaG3NPR1 genes involved in the SA signalling pathway. In addition, TaCSN5-RNAi lines showed increased resistance to multiple races of Pst. Taken together, we demonstrate that TaCSN5 contributes to negative regulation of wheat resistance to Pst in an SA-dependent manner.

Establishment of Agrobacterium rhizogenes-mediated hairy root transformation of Crocus sativus L

Efficient transformation system for genetic improvement is essential in Crocus sativus, as it lacks sexual reproduction. This is the first report wherein an efficient protocol is developed for the transformation of Crocus sativus L. by Agrobacterium rhizogenes strain ARqua1 with a transformation efficiency of 78.51%. The ARqua1 strain harboring both Ri plasmid and binary vector plasmid pSITE-4NB, and marker genes for red fluorescent protein (RFP) and a β-glucuronidase (GUS) reporter gene were used for selection. Transformation was confirmed by RFP signal, GUS reporter assay and polymerase chain reaction (PCR) analysis of the test samples after 21 days post inoculation. These results confirm the establishment of protocol for hairy root transformation in C. sativus that can be further used for gene transfer or gene editing in Crocus for its genetic improvement.

An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat (Triticum aestivum L.)

Virus-induced gene silencing (VIGS) is a rapid and powerful method to evaluate gene function, especially for species like hexaploid wheat that have large, redundant genomes and are difficult and time-consuming to transform. The Brome mosaic virus (BMV)-based VIGS vector is widely used in monocotyledonous species but not wheat. Here we report the establishment of a simple and effective VIGS procedure in bread wheat using BMVCP5, the most recently improved BMV silencing vector, and wheat genes PHYTOENE DESATURASE (TaPDS) and PHOSPHATE2 (TaPHO2) as targets. Time-course experiments revealed that smaller inserts (~100 nucleotides, nt) were more stable in BMVCP5 and conferred higher silencing efficiency and longer silencing duration, compared with larger inserts. When using a 100-nt insert and a novel coleoptile inoculation method, BMVCP5 induced extensive silencing of TaPDS transcript and a visible bleaching phenotype in the 2nd to 5th systemically-infected leaves from nine to at least 28 days post inoculation (dpi). For TaPHO2, the ability of BMVCP5 to simultaneously silence all three homoeologs was demonstrated. To investigate the feasibility of BMV VIGS in wheat roots, ectopically expressed enhanced GREEN FLUORESCENT PROTEIN (eGFP) in a transgenic wheat line was targeted for silencing. Silencing of eGFP fluorescence was observed in both the maturation and elongation zones of roots. BMVCP5 mediated significant silencing of eGFP and TaPHO2 mRNA expression in roots at 14 and 21 dpi, and TaPHO2 silencing led to the doubling of inorganic phosphate concentration in the 2nd through 4th systemic leaves. All 54 wheat cultivars screened were susceptible to BMV infection. BMVCP5-mediated TaPDS silencing resulted in the expected bleaching phenotype in all eight cultivars examined, and decreased TaPDS transcript was detected in all three cultivars examined. This BMVCP5 VIGS technology may serve as a rapid and effective functional genomics tool for high-throughput gene function studies in aerial and root tissues and in many wheat cultivars.

Tobacco System for Studying Protein Colocalization and Interactions

Transient protein expression in a heterologous system has been very useful in many research fields. As a plant expression system, tobacco has some unique advantages including big leaves, simple infiltration and transformation, high activity in expressing transgenes, and easy sampling for microscopy. Because of these advantages, tobacco system has been extensively used for many purposes, such as large-scale expression and purification of proteins of interest, protein colocalization, protein degradation, protein-protein interaction assays including co-immunoprecipitation (CoIP), fluorescence resonance energy transfer (FRET), and bimolecular fluorescence complementation (BiFC), transcription regulation, plant-pathogen interactions, and functional verification of small RNAs. A large number of publications have used this system and generated critical results to support their conclusions. The results obtained from tobacco system are highly reproducible and mostly consistent with those generated from traditional techniques, indicating its reliability. Here we describe a protocol for studying protein-protein interactions in tobacco system, which could be applied to multiple experimental purposes as the procedure of tobacco leaf infiltration is basically shared among them.