An efficient Agrobacterium-mediated genetic transformation method for foxtail millet (Setaria italica L.)

Genome-wide identification and functional analysis of the SiCIN gene family in foxtail millet (Setaria italica L.)

Cell wall invertase (CIN) is a vital member of plant invertase (INV) and plays a key role in the breakdown of sucrose. This enzyme facilitates the hydrolysis of sucrose into glucose and fructose, which is crucial for various aspects of plant growth and development. However, the function of CIN genes in foxtail millet (Setaria italica) is less studied. In this research, we used the blast-p of NCBI and TBtools for bidirectional comparison, and a total of 13 CIN genes (named SiCINs) were identified from foxtail millet by using Arabidopsis and rice CIN sequences as reference sequences. The phylogenetic tree analysis revealed that the CIN genes can be categorized into three subfamilies: group 1, group 2, and group 3. Furthermore, upon conducting chromosomal localization analysis, it was observed that the 13 SiCINs were distributed unevenly across five chromosomes. Cis-acting elements of SiCIN genes can be classified into three categories: plant growth and development, stress response, and hormone response. The largest number of cis-acting elements were those related to light response (G-box) and the cis-acting elements related to seed-specific regulation (RY-element). qRT-PCR analysis further confirmed that the expression of SiCIN7 and SiCIN8 in the grain was higher than that in any other tissues. The overexpression of SiCIN7 in Arabidopsis improved the grain size and thousand-grain weight, suggesting that SiCIN7 could positively regulate grain development. Our findings will help to further understand the grain-filling mechanism of SiCIN and elucidate the biological mechanism underlying the grain development of SiCIN.

C4 cereal and biofuel crop microbiomes

Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.

The role of phenomics and genomics in delineating the genetic basis of complex traits in millets

Millets, comprising a diverse group of small-seeded grains, have emerged as vital crops with immense nutritional, environmental, and economic significance. The comprehension of complex traits in millets, influenced by multifaceted genetic determinants, presents a compelling challenge and opportunity in agricultural research. This review delves into the transformative roles of phenomics and genomics in deciphering these intricate genetic architectures. On the phenomics front, high-throughput platforms generate rich datasets on plant morphology, physiology, and performance in diverse environments. This data, coupled with field trials and controlled conditions, helps to interpret how the environment interacts with genetics. Genomics provides the underlying blueprint for these complex traits. Genome sequencing and genotyping technologies have illuminated the millet genome landscape, revealing diverse gene pools and evolutionary relationships. Additionally, different omics approaches unveil the intricate information of gene expression, protein function, and metabolite accumulation driving phenotypic expression. This multi-omics approach is crucial for identifying candidate genes and unfolding the intricate pathways governing complex traits. The review highlights the synergy between phenomics and genomics. Genomically informed phenotyping targets specific traits, reducing the breeding size and cost. Conversely, phenomics identifies promising germplasm for genomic analysis, prioritizing variants with superior performance. This dynamic interplay accelerates breeding programs and facilitates the development of climate-smart, nutrient-rich millet varieties and hybrids. In conclusion, this review emphasizes the crucial roles of phenomics and genomics in unlocking the genetic enigma of millets.

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.

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.

A highly efficient genetic transformation system for broccoli and subcellular localization

INTRODUCTION

Agrobacterium-mediated genetic transformation has been widely used for the identification of functional genes and regulatory and developmental mechanisms in plants. However, there are still some problems of low genetic transformation efficiency and high genotype dependence in cruciferous crops.

METHODS

In this study, broccoli, a worldwide Brassica crop, was used to investigate the effects of genotype, explant type, concentration of hygromycin B used during seedling selection, overexpression vector type, RNAi and CRISPR/cas9 on the genetic transformation efficiency. At the same time, two vectors, PHG-031350 and PHG-CRa, were used for subcellular localization of the glucoraphanin synthesis-related gene FMOGS-OX5 and clubroot resistance gene by a PEG-Ca2+-mediated transient transformation system for broccoli protoplasts. Finally, the Agrobacterium-mediated genetic transformation system of broccoli was optimized and improved.

RESULTS AND DISCUSSION

This study showed that hypocotyl explants are more suitable for Agrobacterium-mediated transgene and CRISPR/Cas9 gene editing of broccoli. In contrast to previous studies, we found that 5 mg/L hygromycin B was more advantageous for the selection of resistant broccoli sprouts, and genotype 19B42 reached the highest transformation rate of 26.96%, which is higher than that in Brassica oleracea crops. In addition, the inbred line 19B42 successfully achieved high genetic transformation of overexpression, RNAi and CRISPR/Cas9 vectors; thus, it is powerful recipient material for the genetic transformation of broccoli. Subcellular localization proved that the glucoraphanin metabolism-related gene Bol031350 and clubroot resistance gene CRa were both expressed in the cytoplasm and nucleus, which provided a scientific basis for studying the regulation of glucosinolate metabolism and clubroot resistance in cruciferous crops. Therefore, these findings will provide new insight into the improvement of the genetic transformation and molecular breeding of Brassica oleracea crops.

Genetic enhancement of climate-resilient traits in small millets: A review

Agriculture is facing the challenge of feeding the ever-growing population that is projected to reach ten billion by 2050. While improving crop yield and productivity can address this challenge, the increasing effects of global warming and climate change seriously threaten agricultural productivity. Thus, genomics and genome modification technologies are crucial to improving climate-resilient traits to enable sustained yield and productivity; however, significant research focuses on staple crops such as rice, wheat, and maize. Crops that are naturally climate-resilient and nutritionally superior to staple cereals, such as small millets, remain neglected and underutilized by mainstream research. The ability of small millets to grow in marginal regions having limited irrigation and poor soil fertility makes these crops a better choice for cultivation in arid and semi-arid areas. Hence, mainstreaming small millets for cultivation and using omics technologies to dissect the climate-resilient traits to identify the molecular determinants underlying these traits are imperative for addressing food and nutritional security. In this context, the review discusses the genomics and genome modification approaches for dissecting key traits in small millets and their application for improving these traits in cultivated germplasm. The review also discusses biofortification for nutritional security and machine-learning approaches for trait improvement in small millets. Altogether, the review provides a roadmap for the effective use of next-generation approaches for trait improvement in small millets. This will lead to the development of improved varieties for addressing multiple insecurities prevailing in the present climate change scenario.

Assessing the genetic fidelity of somatic embryo-derived plantlets of finger millet by random amplified polymorphic DNA analysis

Finger millet [Eleusine coracana (L.) Gaertn.] is an important cereal because of its mineral-nutrition value. With the increasing demand, there is a pressing need to conserve it through biotechnological approaches. High-frequency somatic embryogenesis from seed-derived callus of E. coracana was developed on Murashige-Skoog (MS) medium supplemented with a combination of auxins [Indole-3-acetic acid (IAA), 2,4-Dichlorophenoxy acetic acid (2,4-D)] and cytokinins [6-Benzylaminopurine (BAP), kinetin (KN)] in different concentrations, ranging from 0.1 to 5.0 mg L^-1. Seeds cultured on this medium produced three different types of primary callus. Type I callus was very compact and dark brown, type II callus was light brownish and type III callus appeared whitish and light brown. All three types of calli had differential proliferation responses. Type II compact brown calli were obtained on the MS medium supplemented with 1.0 and 1.5 mg 2,4-Dichlorophenoxy acetic acid L^-1 and 0.5 mg kinetin L^-1. Friable yellowish embryogenic calli with a large number of somatic embryos were developed within 60 days after being transferred to auxins and cytokinin (1.0 and 1.5 mg 2,4-Dichlorophenoxy acetic acid L^-1 and 0.5 mg Kinetin L^-1) along with 200 mg casein hydrolysate L^-1. Germination of somatic embryos on a half-strength MS medium supplemented with 0.1% Kinetin led to the development of healthy plantlets within 30 days. Genetic fingerprinting using random amplified polymorphic DNA (RAPD) revealed high levels of genetic fidelity. The study provides methods and hormonal concentrations required to develop somatic embryos in E. coracana for its genetic improvement and conservation.

Multi-omics intervention in Setaria to dissect climate-resilient traits: Progress and prospects

Millets constitute a significant proportion of underutilized grasses and are well known for their climate resilience as well as excellent nutritional profiles. Among millets, foxtail millet (Setaria italica) and its wild relative green foxtail (S. viridis) are collectively regarded as models for studying broad-spectrum traits, including abiotic stress tolerance, C₄ photosynthesis, biofuel, and nutritional traits. Since the genome sequence release, the crop has seen an exponential increase in omics studies to dissect agronomic, nutritional, biofuel, and climate-resilience traits. These studies have provided first-hand information on the structure, organization, evolution, and expression of several genes; however, knowledge of the precise roles of such genes and their products remains elusive. Several open-access databases have also been instituted to enable advanced scientific research on these important crops. In this context, the current review enumerates the contemporary trend of research on understanding the climate resilience and other essential traits in Setaria, the knowledge gap, and how the information could be translated for the crop improvement of related millets, biofuel crops, and cereals. Also, the review provides a roadmap for studying other underutilized crop species using Setaria as a model.

Tissue Culture and Somatic Embryogenesis in Warm-Season Grasses—Current Status and Its Applications: A Review

Warm-season grasses are C4 plants and have a high capacity for biomass productivity. These grasses are utilized in many agricultural production systems with their greatest value as feeds for livestock, bioethanol, and turf. However, many important warm-season perennial grasses multiply either by vegetative propagation or form their seeds by an asexual mode of reproduction called apomixis. Therefore, the improvement of these grasses by conventional breeding is difficult and is dependent on the availability of natural genetic variation and its manipulation through breeding and selection. Recent studies have indicated that plant tissue culture system through somatic embryogenesis complements and could further develop conventional breeding programs by micropropagation, somaclonal variation, somatic hybridization, genetic transformation, and genome editing. This review summarizes the tissue culture and somatic embryogenesis in warm-season grasses and focus on current status and above applications including the author’s progress.

Efficient Genome Editing in Setaria italica Using CRISPR/Cas9 and Base Editors

The genome editing toolbox based on CRISPR/Cas9 has brought revolutionary changes to agricultural and plant scientific research. With the development of stable genetic transformation protocols, a highly efficient genome editing system for foxtail millet (Setaria italica) is required. In the present study, we use the CRISPR/Cas9 single- and multi-gene knockout system to target the SiFMBP, SiDof4, SiBADH2, SiGBSS1, and SiIPK1 genes in the foxtail millet protoplasts to screen out highly efficient targeted sgRNAs. Then, we recovered homozygous mutant plants with most of the targeted genes through an Agrobacterium-mediated genetic transformation of foxtail millet. The mutagenesis frequency in the T₀ generation was as high as 100%, and it was passed stably on to the next generation. After screening these targeted edited events, we did not detect off-target mutations at potential sites. Based on this system, we have achieved base editing successfully using two base editors (CBE and ABE) to target the SiALS and SiACC genes of foxtail millet. By utilizing CBE to target the SiALS gene, we created a homozygous herbicide-tolerant mutant plant. The current system could enhance the analysis of functional genomics and genetic improvement of foxtail millet.

Efficient Transformation of Catalpa bungei Shows Crystal Genes Conferring Resistance to the Shoot Borer Omphisa plagialis

Although Catalpa bungei is a forest plant with considerable economic and ornamental value in China, its wood and decorative qualities are constrained by insect pests such as the shoot borer Omphisa plagialis (Lepidoptera). Overexpressing insect resistance genes such as crystal genes to develop an insect-resistant variety of C. bungei is an environmental and ecological approach. However, genotype limitations and low regeneration rates of embryogenic calli (EC) inhibit the development of transformation and the insect-resistant gene expression system in C. bungei. Here, we first established embryogenic callus induction and regeneration systems of five genotypes using mature seed and stem segment explants; the highest induction and regeneration rates of EC were 39.89 and 100%, respectively. Next, an efficient and stable Agrobacterium-mediated genetic transformation system was developed from EC and its positive frequency was up to 92.31%. Finally, using the transformation system, 15 and 22 transgenic C. bungei lines that expressed Cry2A and Cry9Aa-like were generated, respectively. These transgenic lines that exhibited significantly higher resistance to O. plagialis in the laboratory and field have great promise for meeting the challenge of future pest management under changing climatic conditions. Additionally, this efficient, fast, and stable transformation system could be a potential tool for gene function analysis and forest tree genetic improvement.

Genome-editing in millets: current knowledge and future perspectives

Millets are small seeded cereal crops predominantly cultivated and consumed by resource-poor farmers in the semi-arid tropics of Asia and Africa. Millets possess rich nutrients and a climate resilience property when compared to the other cereals such as rice and wheat. Millet improvement using modern genetic and genomic tools is falling behind other cereal crops due to their cultivation being restricted to less developed countries. Genome editing tools have been successfully applied to major cereal crops and, as a result, many key traits have been introduced into rice, wheat and maize. However, genome editing tools have not yet been used for most millets although they possess rich nutrients. The foxtail millet is the only millet utilised up to now for genome editing works. Limited genomic resources and lack of efficient transformation systems may slow down genome editing in millets. As millets possess many important traits of agricultural importance, high resolution studies with genome editing tools will help to understand the specific mechanism and transfer such traits to major cereals in the future. This review covers the current status of genome editing studies in millets and discusses the future prospects of genome editing in millets to understand key traits of nutrient fortification and develop climate resilient crops in the future.

Genetics and Genomics Interventions for Promoting Millets as Functional Foods

Several crops, including millets with immense nutritional and therapeutic values, were once a part of our regular diet. However, due to domestication and selection pressures, many of them have become marginally cultivated crops confined to a particular region, race, or locality. Millets are a perfect example of neglected species that have the potential to address both food and nutritional insecurities prevalent among the ever-growing global population. Starvation and malnutrition contribute to a large number of health-related issues, being the main reason behind the occurrence of most of the severe diseases worldwide. These constraints are repeatedly disturbing both the social and economic health of global society. Naturally, millets are rich in minerals, nutrients, and bioactive compounds, and these crops are less dependent on synthetic fertilizers, systemic irrigation, and pest/weed control. Given this, the review emphasizes the nutritional values, health benefits, processing techniques, and genomic advancements of millets. In addition, it proposes a roadmap for enhancing the utility and commercialization of millets.

TRANSIENT EXPRESSION OF REPORTER GENES IN CULTIVARS OF Amaranthus caudatus L

Local cultivars of A. caudatus: Helios and Karmin were used as plant material. Amaranth is a new pseudocereal introduced in Ukraine. The plant biomass of amaranth is used in medicine, food industry and cosmetology industry. Aim. The purpose of the work was to identify the optimal conditions for the transient expression of reporter genes in Amaranthus caudatus cultivars. Methods. Biochemical and microscopy methods were used in the following work. Seedlings and adult plants of different age were infiltrated with agrobacterial suspensions separately (genetic vector pCBV19 with a uidA gene and genetic vector pNMD2501 with a gfp gene in Agrobacterium tumefaciens GV3101 strain). Results. Transient expression of the uidA and gfp genes was obtained in amaranth plants after conduction series of experiments. The most intensive transient expression of gfp and uidA genes was observed in seedlings infiltrated at the age of 1 day. The maximum fluorescence of the GFP protein was observed on 5th–6th days. Conclusions. It was shown that the cultivar Helios was more susceptible to agrobacterial infection than the cultivar Karmin. The effectiveness of Agrobacterium mediated transformation was from 16% to 95% for the Helios cultivar and from 12% to 93% for the Karmin cultivar. The obtained results indicate that the studied amaranth cultivars can potentially be used for obtaining transient expression of target genes and synthesizing target proteins in their tissues in the future.

Modeling Agrobacterium-Mediated Gene Transformation of Tobacco (Nicotiana tabacum)-A Model Plant for Gene Transformation Studies

The multilayer perceptron (MLP) topology of an artificial neural network (ANN) was applied to create two predictor models in Agrobacterium-mediated gene transformation of tobacco. Agrobacterium-mediated transformation parameters, including Agrobacterium strain, Agrobacterium cell density, acetosyringone concentration, and inoculation duration, were assigned as inputs for ANN-MLP, and their effects on the percentage of putative and PCR-verified transgenic plants were investigated. The best ANN models for predicting the percentage of putative and PCR-verified transgenic plants were selected based on basic network quality statistics. Ex-post error calculations of the relative approximation error (RAE), the mean absolute error (MAE), the root mean square error (RMS), and the mean absolute percentage error (MAPE) demonstrated the prediction quality of the developed models when compared to stepwise multiple regression. Moreover, significant correlations between the ANN-predicted and the actual values of the percentage of putative transgenes (R ² = 0.956) and the percentage of PCR-verified transgenic plants (R ² = 0.671) indicate the superiority of the established ANN models over the classical stepwise multiple regression in predicting the percentage of putative (R ² = 0.313) and PCR-verified (R ²= 0.213) transgenic plants. The best combination of the multiple inputs analyzed in this investigation, to achieve maximum actual and predicted transgenic plants, was at OD ₆₀₀ = 0.8 for the LB4404 strain of Agrobacterium × 300 μmol/L acetosyringone × 20 min immersion time. According to the sensitivity analysis of ANN models, the Agrobacterium strain was the most important influential parameter in Agrobacterium-mediated transformation of tobacco. The prediction efficiency of the developed model was confirmed by the data series of Agrobacterium-mediated transformation of an important medicinal plant with low transformation efficiency. The results of this study are pivotal to model and predict the transformation of other important Agrobacterium-recalcitrant plant genotypes and to increase the transformation efficiency by identifying critical parameters. This approach can substantially reduce the time and cost required to optimize multi-factorial Agrobacterium-mediated transformation strategies.

Breeding and biotechnological interventions for trait improvement: status and prospects

Present review describes the molecular tools and strategies deployed in the trait discovery and improvement of major crops. The prospects and challenges associated with these approaches are discussed. Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly. Direct approaches include overexpression, RNA interference, genome editing, etc., while breeding majorly constitutes the indirect approach. With the advent of latest tools and technologies, these strategies could hasten the improvement of crop species. Next-generation sequencing, high-throughput genotyping, precision editing, use of space technology for accelerated growth, etc. had provided a new dimension to crop improvement programmes that work towards delivering better varieties to cope up with the challenges. Also, studies have widened from understanding the response of plants to single stress to combined stress, which provides insights into the molecular mechanisms regulating tolerance to more than one stress at a given point of time. Altogether, next-generation genetics and genomics had made tremendous progress in delivering improved varieties; however, the scope still exists to expand its horizon to other species that remain underutilized. In this context, the present review systematically analyses the different genomics approaches that are deployed for trait discovery and improvement in major species that could serve as a roadmap for executing similar strategies in other crop species. The application, pros, and cons, and scope for improvement of each approach have been discussed with examples, and altogether, the review provides comprehensive coverage on the advances in genomics to meet the ever-growing demands for agricultural produce.