Engineering For Crop Improvement Research Articles

A Review on Molecular Mechanism of Plant Immunity against Fungal Pathogens

The molecular mechanisms of plant immunity, with a particular focus on how plants defend themselves against fungal pathogens. Plant immunity is a complex, multi-layered system involving pattern-triggered immunity (PTI) and effector-triggered immunity (ETI), which together form a robust defense against a wide array of pathogens. Advances in genomics and transcriptomics have significantly enhanced our understanding of these immune mechanisms by identifying key resistance (R) genes and uncovering the transcriptional networks that regulate immune responses. Proteomics and metabolomics further elucidate the functional aspects of immunity, revealing how proteins and metabolites are mobilized during pathogen attack. The advent of gene editing technologies, particularly CRISPR-Cas9, has opened new avenues for enhancing plant immunity by enabling precise modifications of genes associated with disease resistance. The ever-evolving nature of fungal pathogens, driven by genetic diversity and environmental changes, poses ongoing challenges. Emerging pathogens and the breakdown of existing resistance in crops underscore the need for durable resistance strategies, which can be achieved through the pyramiding of multiple R genes, susceptibility gene knockouts, and the harnessing of beneficial plant microbiomes. As climate change exacerbates the spread and virulence of fungal pathogens, developing climate-resilient crops that can withstand both abiotic stresses and pathogen pressures is becoming increasingly important. Future research should prioritize understanding the molecular dynamics of plant-pathogen interactions, leveraging new technologies for crop improvement, and fostering interdisciplinary collaboration to address these challenges. Ultimately, translating these scientific advances into practical applications will be crucial for ensuring global food security and sustainable agricultural systems in the face of mounting environmental and biological threats.

Application of genome editing in plant reproductive biology: recent advances and challenges.

This comprehensive review underscores the application of genome editing in plant reproductive biology, including recent advances and challenges associated with it. Genome editing (GE) is a powerful technology that has the potential to accelerate crop improvement by enabling efficient, precise, and rapid engineering of plant genomes. Over the last decade, this technology has rapidly evolved from the use of meganucleases (homing endonucleases), zinc-finger nucleases, transcription activator-like effector nucleases to the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (CRISPR/Cas), which has emerged as a popular GE tool in recent times and has been extensively used in several organisms, including plants. GE has been successfully employed in several crops to improve plant reproductive traits. Improving crop reproductive traits is essential for crop yields and securing the world's food supplies. In this review, we discuss the application of GE in various aspects of plant reproductive biology, including its potential application in haploid induction, apomixis, parthenocarpy, development of male sterile lines, and the regulation of self-incompatibility. We also discuss current challenges and future prospects of this technology for crop improvement, focusing on plant reproduction.

Molecular insights on the origin and development of waxy genotypes in major crop plants.

Starch is a significant ingredient of the seed endosperm with commercial importance in food and industry. Crop varieties with glutinous (waxy) grain characteristics, i.e. starch with high amylopectin and low amylose, hold longstanding cultural importance in some world regions and unique properties for industrial manufacture. The waxy character in many crop species is regulated by a single gene known as GBSSI (or waxy), which encodes the enzyme Granule Bound Starch Synthase1 with null or reduced activity. Several allelic variants of the waxy gene that contribute to varying levels of amylose content have been reported in different crop plants. Phylogenetic analysis of protein sequences and the genomic DNA encoding GBSSI of major cereals and recently sequenced millets and pseudo-cereals have shown that GBSSI orthologs form distinct clusters, each representing a separate crop lineage. With the rapidly increasing demand for waxy starch in food and non-food applications, conventional crop breeding techniques and modern crop improvement technologies such as gene silencing and genome editing have been deployed to develop new waxy crop cultivars. The advances in research on waxy alleles across different crops have unveiled new possibilities for modifying the synthesis of amylose and amylopectin starch, leading to the potential creation of customized crops in the future. This article presents molecular lines of evidence on the emergence of waxy genes in various crops, including their genesis and evolution, molecular structure, comparative analysis and breeding innovations.

A Review on Revolutionary Strategy for Crop Improvement: Genome Editing

Genome editing technology revolutionized crop improvement technology through sequence-specific, precise, site-directed, safe genetic manipulation and combat the major 21st century challenge such as achieving world food security meeting rising global food demand and improving food nutrition in the face of rapidly changing climate conditions. Crop improvement using conventional and molecular breeding approaches takes time, causing biosafety concerns and cannot equipoise with raising demand. Genome editing system like zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats (CRISPR) made a desirable targeted modification in crops for improving crop yield, nutraceutical quality and also enhance tolerance to environmental stress (biotic or abiotic) through add the desirable trait(s) and remove the undesirable. Genome manipulation tools progression creates new breakthroughs and speeds up crop improvement through site-directed mutagenesis efficiently for crop improvements to meet the ever-increasing global demand for food and produce more resilient crop with great flexibility to combat climate change.

Determinants of consumer acceptance of gene‐edited foods and its implications for innovators and policymakers

AbstractGene‐editing is a breakthrough technology for crop improvement that addresses many concerns associated with its predecessor and distinctly different technology, genetically modified crops. The commercial success of gene‐editing technology depends on the public's acceptance of its foods. This study used data from a national survey of United States consumers to identify the determinants of consumer acceptance of gene‐edited foods and compared them with those of genetically modified foods. Our study shows that consumer awareness and knowledge of gene‐edited foods are almost half those of genetically modified foods. In the study, we classified survey respondents in three clusters based on their attitudes toward food technologies and corporate distrust: technology‐loving, neutral, and technology‐averse. The technology‐averse cluster has the greatest share of individuals who indicated being aware of and knowledgeable about gene‐edited foods, and the largest share of respondents who stated having negative views toward agricultural biotechnology. Technology‐loving individuals have more positive perceptions about agricultural biotechnology and are more likely to consume genetically modified and gene‐edited foods in the future than neutral and technology‐averse individuals. Findings indicate that providing information on the technology and its health and environmental benefits did not affect consumers' willingness to consume genetically modified and gene‐edited foods. Prior perceptions of agricultural biotechnology, beliefs about safety, benefits, labeling, and the type of technology developer are important determinants of anticipated future consumption of genetically modified and gene‐edited foods. [EconLit Citations: Q13, Q16].

Integration of multi-omics technologies for crop improvement: Status and prospects.

With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.

Smart breeding approaches in post-genomics era for developing climate-resilient food crops.

Improving the crop traits is highly required for the development of superior crop varieties to deal with climate change and the associated abiotic and biotic stress challenges. Climate change-driven global warming can trigger higher insect pest pressures and plant diseases thus affecting crop production sternly. The traits controlling genes for stress or disease tolerance are economically imperative in crop plants. In this scenario, the extensive exploration of available wild, resistant or susceptible germplasms and unraveling the genetic diversity remains vital for breeding programs. The dawn of next-generation sequencing technologies and omics approaches has accelerated plant breeding by providing the genome sequences and transcriptomes of several plants. The availability of decoded plant genomes offers an opportunity at a glance to identify candidate genes, quantitative trait loci (QTLs), molecular markers, and genome-wide association studies that can potentially aid in high throughput marker-assisted breeding. In recent years genomics is coupled with marker-assisted breeding to unravel the mechanisms to harness better better crop yield and quality. In this review, we discuss the aspects of marker-assisted breeding and recent perspectives of breeding approaches in the era of genomics, bioinformatics, high-tech phonemics, genome editing, and new plant breeding technologies for crop improvement. In nutshell, the smart breeding toolkit in the post-genomics era can steadily help in developing climate-smart future food crops.

CRISPR/Cas9 Technology and Its Utility for Crop Improvement.

The rapid growth of the global population has resulted in a considerable increase in the demand for food crops. However, traditional crop breeding methods will not be able to satisfy the worldwide demand for food in the future. New gene-editing technologies, the most widely used of which is CRISPR/Cas9, may enable the rapid improvement of crop traits. Specifically, CRISPR/Cas9 genome-editing technology involves the use of a guide RNA and a Cas9 protein that can cleave the genome at specific loci. Due to its simplicity and efficiency, the CRISPR/Cas9 system has rapidly become the most widely used tool for editing animal and plant genomes. It is ideal for modifying the traits of many plants, including food crops, and for creating new germplasm materials. In this review, the development of the CRISPR/Cas9 system, the underlying mechanism, and examples of its use for editing genes in important crops are discussed. Furthermore, certain limitations of the CRISPR/Cas9 system and potential solutions are described. This article will provide researchers with important information regarding the use of CRISPR/Cas9 gene-editing technology for crop improvement, plant breeding, and gene functional analyses.

Multiplexed promoter and gene editing in wheat using a virus-based guide RNA delivery system.

The low efficiency of genetic transformation and gene editing across diverse cultivars hinder the broad application of CRISPR technology for crop improvement. The development of virus-based methods of CRISPR-Cas system delivery into the plant cells holds great promise to overcome these limitations. Here, we perform direct inoculation of wheat leaves with the barley stripe mosaic virus (BSMV) transcripts to deliver guide RNAs (sgRNA) into the Cas9-expressing wheat. We demonstrate that wheat inoculation with the pool of BSMV-sgRNAs could be used to generate heritable precise deletions in the promoter region of a transcription factor and to perform multiplexed editing of agronomic genes. We transfer the high-expressing locus of Cas9 into adapted spring and winter cultivars by marker-assisted introgression and use of the BSMV-sgRNAs to edit two agronomic genes. A strategy presented in our study could be applied to any adapted cultivar for creating new cis-regulatory diversity or large-scale editing of multiple genes in biological pathways or QTL regions, opening possibilities for the effective engineering of crop genomes, and accelerating gene discovery and trait improvement efforts.

Comprehending the evolution of gene editing platforms for crop trait improvement.

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), to address the problem of associated off-targets. The adaptation of this platform led to the development of concepts such as epigenome editing, base editing, and prime editing. Epigenome editing employed epi-effectors to manipulate chromatin structure, while base editing uses base editors to engineer precise changes for trait improvement. Newer technologies such as prime editing have now been developed as a “search-and-replace” tool to engineer all possible single-base changes. Owing to the availability of these, the field of genome editing has evolved rapidly to develop crop plants with improved traits. In this review, we present the evolution of the CRISPR/Cas system into new-age methods of genome engineering across various plant species and the impact they have had on tweaking plant genomes and associated outcomes on crop improvement initiatives.

Integrating speed breeding with artificial intelligence for developing climate-smart crops.

IntroductionIn climate change, breeding crop plants with improved productivity, sustainability, and adaptability has become a daunting challenge to ensure global food security for the ever-growing global population. Correspondingly, climate-smart crops are also the need to regulate biomass production, which is imperative for the maintenance of ecosystem services worldwide. Since conventional breeding technologies for crop improvement are limited, time-consuming, and involve laborious selection processes to foster new and improved crop varieties. An urgent need is to accelerate the plant breeding cycle using artificial intelligence (AI) to depict plant responses to environmental perturbations in real-time.Materials and methodsThe review is a collection of authorized information from various sources such as journals, books, book chapters, technical bulletins, conference papers, and verified online contents.ConclusionsSpeed breeding has emerged as an essential strategy for accelerating the breeding cycles of crop plants by growing them under artificial light and temperature conditions. Furthermore, speed breeding can also integrate marker-assisted selection and cutting-edged gene-editing tools for early selection and manipulation of essential crops with superior agronomic traits. Scientists have recently applied next-generation AI to delve deeper into the complex biological and molecular mechanisms that govern plant functions under environmental cues. In addition, AIs can integrate, assimilate, and analyze complex OMICS data sets, an essential prerequisite for successful speed breeding protocol implementation to breed crop plants with superior yield and adaptability.

Current Insights into the Molecular Mode of Action of Seaweed-Based Biostimulants and the Sustainability of Seaweeds as Raw Material Resources.

Natural biostimulants, such as seaweed extracts, can stimulate plant growth and development in both model and crop plants. Due to the increasing demands for their use in agriculture, it is crucial to ensure the sustainability of the sources from which they are produced. Furthermore, some seaweed extracts were recently shown to prime and protect from adverse environmental factors such as drought, salinity and extreme temperatures, as well as from oxidative stress. The molecular mode of action of these biostimulants has still not been fully elucidated, but there has been significant progress in this direction in the last years. Firstly, this review examines the sustainability aspects of harvesting seaweed resources as raw materials for manufacturing biostimulants and provides an overview of the regulatory landscape pertaining to seaweed-based biostimulants. The review then summarises the recent advances in determining the genetic and molecular mechanisms activated by seaweed-based biostimulants, their influence on transcriptome reconfiguration, metabolite adjustment, and ultimately stress protection, improved nutrient uptake, and plant growth and performance. This knowledge is important for deciphering the intricate stress signalling network modulated by seaweed-based biostimulants and can aid in designing molecular priming technologies for crop improvement.

Genomic prediction of cotton fibre quality and yield traits using Bayesian regression methods

Genomic selection or genomic prediction (GP) has increasingly become an important molecular breeding technology for crop improvement. GP aims to utilise genome-wide marker data to predict genomic breeding value for traits of economic importance. Though GP studies have been widely conducted in various crop species such as wheat and maize, its application in cotton, an essential renewable textile fibre crop, is still significantly underdeveloped. We aim to develop a new GP-based breeding system that can improve the efficiency of our cotton breeding program. This article presents a GP study on cotton fibre quality and yield traits using 1385 breeding lines from the Commonwealth Scientific and Industrial Research Organisation (CSIRO, Australia) cotton breeding program which were genotyped using a high-density SNP chip that generated 12,296 informative SNPs. The aim of this study was twofold: (1) to identify the models and data sources (i.e. genomic and pedigree) that produce the highest prediction accuracies; and (2) to assess the effectiveness of GP as a selection tool in the CSIRO cotton breeding program. The prediction analyses were conducted under various scenarios using different Bayesian predictive models. Results highlighted that the model combining genomic and pedigree information resulted in the best cross validated prediction accuracies: 0.76 for fibre length, 0.65 for fibre strength, and 0.64 for lint yield. Overall, this work represents the largest scale genomic selection studies based on cotton breeding trial data. Prediction accuracies reported in our study indicate the potential of GP as a breeding tool for cotton. The study highlighted the importance of incorporating pedigree and environmental factors in GP models to optimise the prediction performance.

Combining speed breeding with traditional and genomics‐assisted breeding for crop improvement

AbstractAccelerated crop growth strategy innovations are required as we reach saturation peaks regarding the productivity of major food crops. Speed breeding (SB) is one of the most promising technologies adopted for this purpose. SB hastens crop production by reducing plant growth and development, breeding time and swift generation advancement. Prolonged daily light exposure shortens the life cycle in some long‐day or day‐neutral plants leading to early seed harvest. This approach is best suited for controlled environment prebreeding/breeding activities and analysed for several crop species. SB can be integrated with different traditional and advanced genomics‐assisted breeding technologies like marker‐assisted selection (MAS), genomic selection (GS), pollen‐based selection (PBS), overexpression/knock‐down transgenics and genome editing to achieve more precise and faster results on translational genetic enhancement. This review will discuss the approaches and strategies adopted for the SB and its potential to integrate existing crop improvement technologies to attain more efficient outcomes on major food crops' varietal improvement.

CRISPR guides induce gene silencing in plants in the absence of Cas

BackgroundRNA-targeting CRISPR-Cas can provide potential advantages over DNA editing, such as avoiding pleiotropic effects of genome editing, providing precise spatiotemporal regulation, and expanded function including antiviral immunity.ResultsHere, we report the use of CRISPR-Cas13 in plants to reduce both viral and endogenous RNA. Unexpectedly, we observe that crRNA designed to guide Cas13 could, in the absence of the Cas13 protein, cause substantial reduction in RNA levels as well. We demonstrate Cas13-independent guide-induced gene silencing (GIGS) in three plant species, including stable transgenic Arabidopsis. Small RNA sequencing during GIGS identifies the production of small RNA that extend beyond the crRNA expressed sequence in samples expressing multi-guide crRNA. Additionally, we demonstrate that mismatches in guide sequences at position 10 and 11 abolish GIGS. Finally, we show that GIGS is elicited by guides that lack the Cas13 direct repeat and can extend to Cas9 designed crRNA of at least 28 base pairs, indicating that GIGS can be elicited through a variety of guide designs and is not dependent on Cas13 crRNA sequences or design.ConclusionsCollectively, our results suggest that GIGS utilizes endogenous RNAi machinery despite the fact that crRNA are unlike canonical triggers of RNAi such as miRNA, hairpins, or long double-stranded RNA. Given similar evidence of Cas13-independent silencing in an insect system, it is likely GIGS is active across many eukaryotes. Our results show that GIGS offers a novel and flexible approach to RNA reduction with potential benefits over existing technologies for crop improvement and functional genomics.

Genome Editing Technologies for Efficient Use of Plant Genetic Resources

Plant genetic resources (PGRs) are the basis for food and nutritional security, and enhanced utilization of these resources is of paramount importance for genetic improvement of crops. Till date the use of PGRs has been limited in conventional breeding programmes for developing widely adapted crop varieties. In the recent past, genome-wide association studies, genomics and functional genomics approaches using diverse germplasm accessions have facilitated discovery of novel quantitative trait loci (QTLs), genes and alleles associated with useful agronomic traits for use in crop improvement through molecular breeding and genetic engineering. More recently, genome editing has emerged as a new plant breeding technology with great potential for enhancing the use of PGRs, for addressing the challenges of climate change, malnutrition, environmental security, achieving SDGs by 2030, and to sustainably feed 10 billion people by 2050. In this article, an attempt has been made to highlight the use of CRISPR-based genome editing technologies for crop improvement through the use of PGRs.

Global Patent Trends in New Breeding Technology for Crop Improvement

Global Patent Trends in New Breeding Technology for Crop Improvement

A Strategy for the Production and Molecular Validation of Agrobacterium-Mediated Intragenic Octoploid Strawberry.

Intragenesis is an all-native engineering technology for crop improvement. Using an intragenic strategy to bring genes from wild species to cultivated strawberry could expand the genetic variability. A robust regeneration protocol was developed for the strawberry cv. ‘Shanghai Angel’ by optimizing the dose of Thidiazuron and identifying the most suitable explants. The expression cassette was assembled with all DNA fragments from F. vesca, harboring a sugar transporter gene FvSTP8 driven by a fruit-specific FvKnox promoter. Transformed strawberry was developed through an Agrobacterium-mediated strategy without any selectable markers. Other than PCR selection, probe-based duplex droplet digital PCR (ddPCR) was performed to determine the T-DNA insert. Four independent transformed shoots were obtained with a maximum of 5.3% efficiency. Two lines were confirmed to be chimeras, while the other two were complete transformants with six and 11 copies of the intragene, respectively. The presence of a vector backbone beyond the T-DNA in these transformants indicated that intragenic strawberries were not obtained. The current work optimized the procedures for producing transformed strawberry without antibiotic selection, and accurately determined the insertion copies by ddPCR in the strawberry genome for the first time. These strategies might be promising for the engineering of ‘Shanghai Angel’ and other cultivars to improve agronomic traits.

Why Insect Pollinators Important in Crop Improvement?

Three out of four plants provide fruits or seeds for human consumption as crops rely on insect pollinators across the world. Many fruit and vegetable crops such as almonds, apples, cranberries, melons, broccoli, cherries and blueberries are dependent upon insect pollinator services Thus, healthy and nutritious diet to humans is offered by the bee pollinators. These natural servants help in the fertilization and seed setting of 87 major food plants. Crop pollinators are in danger, and modern agronomic practices can minimize the threat to flower foragers by changing the landscape and redesigning the ecological procedures. Safeguarding over 20000 wild bee pollinators will be of great importance as these have enhanced the economic value of crops up to $235- 577 billion. Herein, emphasized are the questions, why insect pollinators are significant in crop improvement technology? and how this is improving the quality and quantity in food production.

MicroRNA Techniques: Valuable Tools for Agronomic Trait Analyses and Breeding in Rice

MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression at the post-transcriptional level. Extensive studies have revealed that miRNAs have critical functions in plant growth, development, and stress responses and may provide valuable genetic resources for plant breeding research. We herein reviewed the development, mechanisms, and characteristics of miRNA techniques while highlighting widely used approaches, namely, the short tandem target mimic (STTM) approach. We described STTM-based advances in plant science, especially in the model crop rice, and introduced the CRISPR-based transgene-free crop breeding. Finally, we discussed the challenges and unique opportunities related to combining STTM and CRISPR technology for crop improvement and agriculture.