The role of omics in improving the orphan crop tef.

Tef or teff [Eragrostis tef (Zucc.) Trotter] is a cereal crop indigenous to the Horn of Africa, where it is a staple food for a large population. The popularity of tef arises from its resilience to environmental stresses and its nutritional value. For many years, tef has been considered an orphan crop, but recent research initiatives from across the globe are helping to unravel its undisclosed potential. Advanced omics tools and techniques have been directed toward the exploration of tef's diversity with the aim of increasing its productivity. In this review, we report on the most recent advances in tef omics that brought the crop into the spotlight of international research.

The Calvin-Benson-Bassham cycle in C4 and Crassulacean acid metabolism species.

The Calvin-Benson-Bassham (CBB) cycle is the ancestral CO2 assimilation pathway and is found in all photosynthetic organisms. Biochemical extensions to the CBB cycle have evolved that allow the resulting pathways to act as CO2 concentrating mechanisms, either spatially in the case of C4 photosynthesis or temporally in the case of Crassulacean acid metabolism (CAM). While the biochemical steps in the C4 and CAM pathways are known, questions remain on their integration and regulation with CBB cycle activity. The application of omic and transgenic technologies is providing a more complete understanding of the biochemistry of C4 and CAM species and will also provide insight into the CBB cycle in these plants. As the global population increases, new solutions are required to increase crop yields and meet demands for food and other bioproducts. Previous work in C3 species has shown that increasing carbon assimilation through genetic manipulation of the CBB cycle can increase biomass and yield. There may also be options to improve photosynthesis in species using C4 photosynthesis and CAM through manipulation of the CBB cycle in these plants. This is an underexplored strategy and requires more basic knowledge of CBB cycle operation in these species to enable approaches for increased productivity.

CRISPR enables heritable genome editing in planta.

Recent exciting developments in clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing showcase its potential to rapidly and efficiently edit genomes in planta, eliminating long processes of tissue culture and extensive breeding for crop improvement. These new methods offer heritable transgene-free edits in one generation, making them an attractive option for improving commercially important crops.

Principles, functions, and biological implications of m6A in plants.

Over the past decade, N 6-methyladenosine (m6A) has emerged as a prevalent and dynamically regulated modification across the transcriptome; it has been reversibly installed, removed, and interpreted by specific binding proteins, and has played crucial roles in molecular and biological processes. Within this scope, we consolidate recent advancements of m6A research in plants regarding gene expression regulation, diverse physiologic and pathogenic processes, as well as crop trial implications, to guide discussions on challenges associated with and leveraging epitranscriptome editing for crop improvement.

A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB).

Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome-scale genome assembly of B. carinata accession HC20 using long-read Oxford Nanopore sequencing and Bionano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the long-read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early-generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species.

A Solanum lycopersicum polyamine oxidase contributes to the control of plant growth, xylem differentiation, and drought stress tolerance.

Polyamines are involved in several plant physiological processes. In Arabidopsis thaliana, five FAD-dependent polyamine oxidases (AtPAO1 to AtPAO5) contribute to polyamine homeostasis. AtPAO5 catalyzes the back-conversion of thermospermine (T-Spm) to spermidine and plays a role in plant development, xylem differentiation, and abiotic stress tolerance. In the present study, to verify whether T-Spm metabolism can be exploited as a new route to improve stress tolerance in crops and to investigate the underlying mechanisms, tomato (Solanum lycopersicum) AtPAO5 homologs were identified (SlPAO2, SlPAO3, and SlPAO4) and CRISPR/Cas9-mediated loss-of-function slpao3 mutants were obtained. Morphological, molecular, and physiological analyses showed that slpao3 mutants display increased T-Spm levels and exhibit changes in growth parameters, number and size of xylem elements, and expression levels of auxin- and gibberellin-related genes compared to wild-type plants. The slpao3 mutants are also characterized by improved tolerance to drought stress, which can be attributed to a diminished xylem hydraulic conductivity that limits water loss, as well as to a reduced vulnerability to embolism. Altogether, this study evidences conservation, though with some significant variations, of the T-Spm-mediated regulatory mechanisms controlling plant growth and differentiation across different plant species and highlights the T-Spm role in improving stress tolerance while not constraining growth.

Unraveling the Mechanisms of Efficient Phosphorus Utilization in Popcorn (Zea mays L. var. everta): Insights from Proteomic and Metabolite Analysis.

The expansion of agriculture and the need for sustainable practices drives breeders to develop plant varieties better adapted to abiotic stress such as nutrient deficiency, which negatively impacts yields. Phosphorus (P) is crucial for photosynthesis and plant growth, but its availability in the soil is often limited, hampering crop development. In this study, we examined the response of two popcorn inbred lines, L80 and P7, which have been characterized previously as P-use inefficient and P-use efficient, respectively, under low (stress) and high P (control) availability. Physiological measurements, proteomic analysis, and metabolite assays were performed to unravel the physiological and molecular responses associated with the efficient use of P in popcorn. We observed significant differences in protein abundances in response to the P supply between the two inbred lines. A total of 421 differentially expressed proteins (DEPs) were observed in L80 and 436 DEPs in P7. These proteins were involved in photosynthesis, protein biosynthesis, biosynthesis of secondary metabolites, and energy metabolism. In addition, flavonoids accumulated in higher abundance in P7. Our results help us understand the major components of P utilization in popcorn, providing new insights for popcorn molecular breeding programs.

Chromosome translocation affects multiple phenotypes, causes genome-wide dysregulation of gene expression, and remodels metabolome in hexaploid wheat.

Chromosomal rearrangements (CRs) may occur in newly formed polyploids due to compromised meiotic fidelity. Moreover, CRs can be more readily tolerated in polyploids allowing their longer-term retention and hence potential spreading/fixation within a lineage. The direct functional consequences of CRs in plant polyploids remain unexplored. Here, we identified a heterozygous individual from a synthetic allohexaploid wheat in which the terminal parts of the long-arms of chromosomes 2D (approximately 193 Mb) and 4A (approximately 167 Mb) were reciprocally translocated. Five homogeneous translocation lines including both unbalanced and balanced types were developed by selfing fertilization of the founder mutant (RT [2DL; 4AL]-ter/1, reciprocal translocation). We investigated impacts of these translocations on phenotype, genome-wide gene expression and metabolome. We find that, compared with sibling wild-type, CRs in the form of both unbalanced and balanced translocations induced substantial changes of gene expression primarily via trans-regulation in the nascent allopolyploid wheat. The CRs also manifested clear phenotypic and metabolic consequences. In particular, the genetically balanced, stable reciprocal translocations lines showed immediate enhanced reproductive fitness relative to wild type. Our results underscore the profound impact of CRs on gene expression in nascent allopolyploids with wide-ranging phenotypic and metabolic consequences, suggesting CRs are an important source of genetic variation that can be exploited for crop breeding.

Fast-forward breeding for a food-secure world.

Crop production systems need to expand their outputs sustainably to feed a burgeoning human population. Advances in genome sequencing technologies combined with efficient trait mapping procedures accelerate the availability of beneficial alleles for breeding and research. Enhanced interoperability between different omics and phenotyping platforms, leveraged by evolving machine learning tools, will help provide mechanistic explanations for complex plant traits. Targeted and rapid assembly of beneficial alleles using optimized breeding strategies and precise genome editing techniques could deliver ideal crops for the future. Realizing desired productivity gains in the field is imperative for securing an adequate future food supply for 10 billion people.

Harnessing the potential of mutation breeding, CRISPR genome editing, and beyond for sustainable agriculture.

By 2050, the global population is projected to exceed 9.5 billion, posing a formidable challenge to ensure food security worldwide. To address this pressing issue, mutation breeding in horticultural crops, utilizing physical or chemical methods, has emerged as a promising biotechnological strategy. However, the efficacy of these mutagens can be influenced by various factors, including biological and environmental variables, as well as targeted plant materials. This review highlights the global challenges related to food security and explores the potential of mutation breeding as an indispensable biotechnological tool in overcoming food insecurity. This review also covers the emergence of CRISPR-Cas9, a breakthrough technology offering precise genome editing for the development of high-yield, stress-tolerant crops. Together, mutation breeding and CRISPR can potentially address future food demands. This review focuses into these biotechnological advancements, emphasizing their combined potential to fortify global food security in the face of a booming population.

Morphological and genetic characterization of jackfruit (Artocarpus heterophyllus) in the Kayunga and Luwero districts of Uganda.

BACKGROUND: Jackfruit (Artocarpus heterophyllus) is an economically valuable fruit tree in Uganda. However, the production of jackfruit in Uganda is low. Additionally, because of deforestation, genetic erosion of the resource is predicted before its exploitation for crop improvement and conservation. As a prerequisite for crop improvement and conservation, 100 A. heterophyllus tree isolates from the Kayunga and Luwero districts in Uganda were characterized using 16 morphological and 10 microsatellite markers. RESULTS: The results from the morphological analysis revealed variations in tree height, diameter at breast height (DBH), and crown diameter, with coefficient of variation (CV) values of 20%, 41%, and 33%, respectively. Apart from the pulp taste, variation was also observed in qualitative traits, including tree vigor, trunk surface, branching density, tree growth habit, crown shape, leaf blade shape, fruit shape, fruit surface, flake shape, flake color, flake flavor and pulp consistency/texture. Genotyping revealed that the number of alleles amplified per microsatellite locus ranged from 2 to 5, with an average of 2.90 and a total of 29. The mean observed (Ho) and expected (He) heterozygosity were 0.71 and 0.57, respectively. Analysis of molecular variance (AMOVA) indicated that 81% of the variation occurred within individual trees, 19% among trees within populations and 0% between the two populations. The gene flow (Nm) in the two populations was 88.72. The results from the 'partitioning around medoids' (PAM), principal coordinate analysis (PCoA) and genetic cluster analysis further revealed no differentiation of the jackfruit populations. The Mantel test revealed a negligible correlation between the morphological and genetic distances. CONCLUSIONS: Both morphological and genetic analyses revealed variation in jackfruit within a single interbreeding population. This diversity can be exploited to establish breeding and conservation strategies to increase the production of jackfruit and hence boost farmers' incomes. However, selecting germplasm based on morphology alone may be misleading.

Application of genome editing techniques to regulate gene expression in crops.

BACKGROUND: Enhanced agricultural production is urgently required to meet the food demands of the increasing global population. Abundant genetic diversity is expected to accelerate crop development. In particular, the development of the CRISPR/Cas genome editing technology has greatly enhanced our ability to improve crop's genetic diversity through direct artificial gene modification. However, recent studies have shown that most crop improvement efforts using CRISPR/Cas techniques have mainly focused on the coding regions, and there is a relatively lack of studies on the regulatory regions of gene expression. RESULTS: This review briefly summarizes the development of CRISPR/Cas system in the beginning. Subsequently, the importance of gene regulatory regions in plants is discussed. The review focuses on recent developments and applications of mutations in regulatory regions via CRISPR/Cas techniques in crop breeding. CONCLUSION: Finally, an outline of perspectives for future crop breeding using genome editing technologies is provided. This review provides new research insights for crop improvement using genome editing techniques.

Finger millet (Eleusine coracana L.): from staple to superfood-a comprehensive review on nutritional, bioactive, industrial, and climate resilience potential.

MAIN CONCLUSION: This review discusses the Finger millet's rich nutritional profile, bioactive potential, and industrial applications, combined with its climate resilience, which make it a promising crop for enhancing food security and promoting sustainable agriculture. This review also highlights its significant potential to address malnutrition and mitigate climate change impacts. The emergence of Finger millet from "poor man's staple food" to "a nutrient rich cereal" has encouraged the need to explore this crop at a wider scale. It is a highly significant crop due to its rich nutritional and bioactive profile, diverse biological activities, and promising industrial applications, along with the high climate resilience. This comprehensive review evaluates its nutritional composition by comparing favorably with other cereals and millets and emphasizing its potential to address malnutrition and enhance food security. Furthermore, it explores the phytochemical/bioactive potential and strategies to enhance their bioavailability followed biological activities of Finger millet by highlighting its various health-promoting properties. The review also discusses industrial potential of finger millet including its role in nutraceutical and functional food production, as well as bioenergy generation. In addition, role of Finger millet as a climate-resilient crop; specifically, the available genetic resources and identification of genes and quantitative trait loci (QTLs) associated with major stress tolerance traits have also been discussed. By providing a comprehensive synthesis of existing knowledge, this study offers valuable insights for researchers, policymakers, and stakeholders engaged in efforts to promote sustainable agriculture, enhance food and nutrition security, and mitigate the impacts of climate change.

The long and tortuous path towards improving photosynthesis by engineering elevated mesophyll conductance.

The growing demand for global food production is likely to be a defining issue facing humanity over the next 50 years. To tackle this challenge, there is a desire to bioengineer crops with higher photosynthetic efficiencies, to increase yields. Recently, there has been a growing interest in engineering leaves with higher mesophyll conductance (gm), which would allow CO2 to move more efficiently from the substomatal cavities to the chloroplast stroma. However, if crop yield gains are to be realised through this approach, it is essential that the methodological limitations associated with estimating gm are fully appreciated. In this review, we summarise these limitations, and outline the uncertainties and assumptions that can affect the final estimation of gm. Furthermore, we critically assess the predicted quantitative effect that elevating gm will have on assimilation rates in crop species. We highlight the need for more theoretical modelling to determine whether altering gm is truly a viable route to improve crop performance. Finally, we offer suggestions to guide future research on gm, which will help mitigate the uncertainty inherently associated with estimating this parameter.

Metalloid transporters in plants: bridging the gap in molecular structure and physiological exaptation.

The rhizosphere contains both essential nutrients and potentially harmful substances for plant growth. Plants, as sessile organisms, must efficiently absorb the necessary nutrients while actively avoiding the uptake of toxic compounds. Metalloids, which are elements that exhibit properties of both metals and nonmetals, can have different effects on plant growth, ranging from being essential and beneficial to being toxic. The toxicity of metalloids in plants arises due to either the dosage of exposure or the specific elemental type. To utilize or detoxify these elements, plants have developed various transporters that regulate their uptake and distribution in plants. Arguably, genomic sequence analysis suggests the presence of such transporter families throughout the plant kingdom, from chlorophytes to higher plants. These transporters form defined families with related transport preferences. The isoforms within these families have evolved with specialized functions regulated by defined selectivity. Hence, understanding transporters' chemistry to atomic detail is important to achieve desired genetic modifications for crop improvement. Here, we outline various adaptations in plant transport systems to deal with metalloids, including their uptake, distribution, detoxification, and homeostasis in plant tissues. Structural parallels are drawn to other nutrient transporter systems to support emerging themes of functional diversity of active sites of transporters, elucidating adaptations of plants to utilize and extrude metalloid concentrations. Considering the observed physiological importance of metalloids, this review intends to highlight the shared and disparate features in metalloid transport systems and their corresponding nutrient transporters.

Up-regulation of non-photochemical quenching improves water use efficiency and reduces whole-plant water consumption under drought in Nicotiana tabacum.

Water supply limitations will likely impose increasing restrictions on future crop production, underlining a need for crops that use less water per mass of yield. Water use efficiency (WUE) therefore becomes a key consideration in developing resilient and productive crops. In this study, we hypothesized that it is possible to improve WUE under drought conditions via modulation of chloroplast signals for stomatal opening by up-regulation of non-photochemical quenching (NPQ). Nicotiana tabacum plants with strong overexpression of the PsbS gene encoding PHOTOSYSTEM II SUBUNIT S, a key protein in NPQ, were grown under differing levels of drought. The PsbS-overexpressing lines lost 11% less water per unit CO2 fixed under drought and this did not have a significant effect on plant size. Depending on growth conditions, the PsbS-overexpressing lines consumed from 4-30% less water at the whole-plant level than the corresponding wild type. Leaf water and chlorophyll contents showed a positive relation with the level of NPQ. This study therefore provides proof of concept that up-regulation of NPQ can increase WUE, and as such is an important step towards future engineering of crops with improved performance under drought.

The role of microRNAs in NBS-LRR gene expression and its implications for plant immunity and crop development.

Plants evolved, over millions of years, complex defense systems against pathogens. Once infected, the interaction between pathogen effector molecules and host receptors triggers plant immune responses, which include apoptosis, systemic immune response, among others. An important protein family responsible for pathogen effector recognition is the nucleotide binding site-leucine repeat rich (NBS-LRR) proteins. The NBS-LRR gene family is the largest disease resistance gene class in plants. These proteins are widely distributed in vascular plants and have a complex multigenic cluster distribution in plant genomes. To counteract the genetic load of such a large gene family on fitness cost, plants evolved a mechanism using post transcriptional gene silencing induced by small RNAs, particularly microRNAs. For the NBS-LRR gene family, the small RNAs involved in this silencing mechanism are mainly the microRNA482/2118 superfamily. This suppression mechanism is relieved upon pathogen infection, thus allowing increased NBS-LRR expression and triggering plant immunity. In this review, we will discuss the biogenesis of microRNAs and secondary RNAs involved in this silencing mechanism, biochemical and structural features of NBS-LRR proteins in response to pathogen effectors and the evolution of microRNA-based silencing mechanism with a focus on the miR482/2118 family. Furthermore, the biotechnological manipulation of microRNA expression, using both transgenic or genome editing approaches to improve cultivated plants will be discussed, with a focus on the miR482/2118 family in soybean.

Metal nanoparticles to improve the heat resilience in wheat (Triticum aestivumL.).

This study evaluated the efficacy of phytogenic silver and zinc nanoparticles in improving heat resilience in various wheat varieties. The silver and zinc nanoparticles were synthesized using plant leaf extract and characterized using various techniques. Four wheat varieties (DBW187, Black Wheat, DBW 50, and PBW 621) were subjected to field trials. The random block design was used, and nanoparticles in different concentrations were applied at various growth stages and morphologically, and yield parameters were recorded. UV-vis spectroscopy spectral analysis showed peaks for Ag nanoparticles at 420 nm wavelength and Zn nanoparticles at 240 and 350 nm wavelength, depicting the preliminary confirmation of nanoparticle synthesis. Electron microscopic analysis (TEM and SEM) provided morphological insights and confirmed synthesis of fine-sized particle mostly in a range between 10 and 60 nm. Energy dispersive x-ray analysis confirmed the elemental composition of the synthesized nanoparticles, with Ag and Zn elements detected in their respective samples. It also confirmed the oxide nature of synthesized ZnNPs. Dynamic light scattering analysis provided size distribution profiles, indicating average sizes of approximately 61.8 nm for Ag nanoparticles and 46.5 nm for Zn nanoparticles. The concentrations of Ag and Zn nanoparticles in the samples were found to be 196.3 ppm and 115.14 ppm, respectively, through atomic absorption spectroscopic analysis. Fourier transform infrared spectroscopy analysis revealed characteristic functional groups present in the nanoparticles. The results of field experiments established that Ag nanoparticles at 75 ppm concentration exhibited the most significant enhancements in plant growth. Conversely, Zn nanoparticles at a 100 ppm concentration demonstrated the most substantial improvements in the growth and yield of heat-stressed wheat varieties. The study concludes that optimized concentrations of silver and zinc nanoparticles can effectively improve heat stress resilience in wheat. These findings are promising to enhance abiotic stress resilience in crops.

Attaining the promise of plant gene editing at scale.

Crop improvement relies heavily on genetic variation that arises spontaneously through mutation. Modern breeding methods are very adept at combining this genetic variation in ways that achieve remarkable improvements in plant performance. Novel traits have also been created through mutation breeding and transgenesis. The advent of gene editing, however, marks a turning point: With gene editing, synthetic variation will increasingly supplement and, in some cases, supplant the genetic variation that occurs naturally. We are still in the very early stages of realizing the opportunity provided by plant gene editing. At present, typically only one or a few genes are targeted for mutation at a time, and most mutations result in loss of gene function. New technological developments, however, promise to make it possible to perform gene editing at scale. RNA virus vectors, for example, can deliver gene-editing reagents to the germ line through infection and create hundreds to thousands of diverse mutations in the progeny of infected plants. With developmental regulators, edited somatic cells can be induced to form meristems that yield seed-producing shoots, thereby increasing throughput and shrinking timescales for creating edited plants. As these approaches are refined and others developed, they will allow for accelerated breeding, the domestication of orphan crops and the reengineering of metabolism in a more directed manner than has ever previously been possible.

A synthetic C4 shuttle via the ß-hydroxyaspartate cycle in C3 plants.

Plants depend on the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) for CO2 fixation. However, especially in C3 plants, photosynthetic yield is reduced by formation of 2-phosphoglycolate, a toxic oxygenation product of Rubisco, which needs to be recycled in a high-flux-demanding metabolic process called photorespiration. Canonical photorespiration dissipates energy and causes carbon and nitrogen losses. Reducing photorespiration through carbon-concentrating mechanisms, such as C4 photosynthesis, or bypassing photorespiration through metabolic engineering is expected to improve plant growth and yield. The ß-hydroxyaspartate cycle (BHAC) is a recently described microbial pathway that converts glyoxylate, a metabolite of plant photorespiration, into oxaloacetate in a highly efficient carbon-, nitrogen-, and energy-conserving manner. Here, we engineered a functional BHAC in plant peroxisomes to create a photorespiratory bypass that is independent of 3-phosphoglycerate regeneration or decarboxylation of photorespiratory precursors. While efficient oxaloacetate conversion in Arabidopsis thaliana still masks the full potential of the BHAC, nitrogen conservation and accumulation of signature C4 metabolites demonstrate the proof of principle, opening the door to engineering a photorespiration-dependent synthetic carbon-concentrating mechanism in C3 plants.