Search

Miniature inverted-repeat transposable elements (MITEs) constitute a class of class II transposable elements (TEs) that are abundant in plant genomes, playing a crucial role in their evolution and diversity. Barley (Hordeum vulgare), the fourth-most important cereal crop globally, is widely used for brewing, animal feed, and human consumption. However, despite their significance, the mechanisms underlying the insertion or amplification of MITEs and their contributions to barley genome evolution and diversity remain poorly understood. Through our comprehensive analysis, we identified 32,258 full-length MITEs belonging to 2,992 distinct families, accounting for approximately 0.17% of the barley genome. These MITE families can be grouped into four well-known superfamilies (Tc1/Mariner-like , PIF/Harbinger-like , hAT-like , and Mutator-like) and one unidentified superfamily. Notably, we observed two major expansion events in the barley MITE population, occurring approximately 12-13 million years ago (Mya) and 2-3 Mya. Our investigation revealed a strong preference of MITEs for gene-related regions, particularly in promoters, suggesting their potential involvement in regulating host gene expression. Additionally, we discovered that 7.73% miRNAs are derived from MITEs, thereby influencing the origin of certain miRNAs and potentially exerting a significant impact on post-transcriptional gene expression control. Evolutionary analysis demonstrated that MITEs exhibit lower conservation compared to genes, consistent with their dynamic mobility. We also identified a series of MITE insertions or deletions associated with domestication, highlighting these regions as promising targets for crop improvement strategies. These findings significantly advance our understanding of the fundamental characteristics and evolutionary patterns of MITEs in the barley genome. Moreover, they contribute to our knowledge of gene regulatory networks and provide valuable insights for crop improvement endeavors. [ABSTRACT FROM AUTHOR]

ABSTRACT Septoria nodorum blotch (SNB) is a fungal disease of wheat caused by the necrotrophic fungus Parastagonospora nodorum (Berk.), considered as one of the most devastating fungal diseases affecting winter wheat (Triticum aestivum L.). The complex inheritance of resistance to SNB poses significant challenges to breeding programmes. Improving selection precision and identifying novel resistance QTLs are crucial for enhancing SNB resistance. This study investigated strategies for crop genetic improvement, including genome‐wide association mapping (GWAS) and genomic prediction (GP), within a practical breeding programme. A population of 1500 winter wheat breeding lines was phenotyped for SNB resistance over 5 years across 19 geographical locations under natural infection conditions. Despite highly unbalanced breeder's data, medium to high heritabilities for SNB resistance were achieved. GWAS identified 11 significant marker‐trait associations for SNB resistance across Chromosomes 2A, 2B, 4B, 4D, 5D and 7B. GP fivefold cross‐validation analysis revealed a predictive ability of 0.52 for SNB resistance. The resistant wheat genotypes and SNP markers identified in this study will be valuable assets for future breeding efforts to enhance SNB resistance in wheat. [ABSTRACT FROM AUTHOR]

Inter-specific hybridization is a key strategy in modern crop improvement, aiming to integrate desirable traits from wild species into cultivated backgrounds. This study delves into the evaluation and identification of advanced inter-specific derivatives (IDs) derived from crosses of cultivated chickpea with Cicer reticulatum and C. echinospermum. The primary aim was to incorporate desirable yield enhancement traits, disease resistance, and nutritional quality traits into cultivated chickpea. The IDs were assessed during rabi 2021-22 and 2022-23 in the northern plains zone of India. Significant amount of genetic variability was observed for key agro-morphological traits having high heritability and genetic advance. Superior derivatives were identified for early flowering, high seed yield, and resistance to Ascochyta blight, Botrytis grey mould, and Fusarium wilt. Significant variability for crude protein and total soluble sugar content was also observed among the derivatives. The findings highlight the potential of utilizing wild Cicer species to broaden the genetic base of cultivated chickpea for the development of robust, high-yielding, disease-resistant varieties with improved nutritional traits suitable for diverse environmental conditions. The superior derivatives identified in this study hold promise for future breeding programmes for improving productivity, disease resistance and nutritional quality. [ABSTRACT FROM AUTHOR]

Summary Tomato is one of the most economically important vegetable crops in the world and has been seriously affected by the devastating agricultural pest root‐knot nematodes (RKNs). Current understanding of tomato resistance to RKNs is quite limited. VQ motif‐containing family proteins are plant‐specific regulators; however, whether and how tomato VQs regulate resistance to RKNs is unknown. Here, we found that SlVQ15 recruited SlWRKY30IIc to coordinately control tomato defence against the RKN Meloidogyne incognita without affecting plant growth and productivity. The jasmonate (JA)‐ZIM domain (JAZ) repressors of the phytohormone JAs signalling associated and interfered with the interaction of SlVQ15 and SlWRKY30IIc. In turn, SlWRKY30IIc bound to SlJAZs promoters and cooperated with SlVQ15 to repress their expression, whereas this inhibitory effect was antagonized by SlJAZ5, forming a feedback regulatory mechanism. Moreover, SlWRKY30IIc expression was directly regulated by SlMYC2, a SlJAZ‐interacting negative regulator of resistance to RKNs. In conclusion, our findings revealed that a regulatory circuit of SlVQ15‐SlWRKY30IIc and the JA pathway fine‐tunes tomato defence against the RKN M. incognita, and provided candidate genes and clues with great potential for crop improvement. [ABSTRACT FROM AUTHOR]

Oxygenic photosynthesis is characterised by the cooperation of two photo-driven complexes, Photosystem II (PSII) and Photosystem I (PSI), sequentially linked through a series of redox-coupled intermediates. Divergent evolution has resulted in photosystems exhibiting complementary redox potentials, spanning the range necessary to oxidise water and reduce CO2 within a single system. Catalysing nature's most oxidising reaction to extract electrons from water is a highly specialised task that limits PSII's metabolic function. In contrast, potential electron donors in PSI span a range of redox potentials, enabling it to accept electrons from various metabolic processes. This metabolic flexibility of PSI underpins the capacity of photosynthetic organisms to balance energy supply with metabolic demands, which is key for adaptation to environmental changes. Here, we review the phenomenon of 'PSII-less photosynthesis' where PSI functions independently of PSII by operating cyclic electron flow using electrons derived from non-photochemical reactions. PSII-less photosynthesis enables supercharged ATP production and is employed, for example, by cyanobacteria's heterocysts to host nitrogen fixation and by bundle sheath cells of C4 plants to boost CO2 assimilation. We discuss the energetic benefits of this arrangement and the prospects of utilising it to improve the productivity and stress resilience of photosynthetic organisms. Oxygenic photosynthesis typically relies on two photo-driven complexes, Photosystem II (PSII) and Photosystem I (PSI). However, PSI can operate independently to boost energy production and amplify nitrogen fixation and CO2 capture in specialised cells. In this review, we propose that 'PSII-less photosynthesis' allows photosynthetic organisms to better balance energy needs and adapt to changing environments. We explore the potential of harnessing this process to improve crop productivity and stress resilience. [ABSTRACT FROM AUTHOR]

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for "Line8," a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii , a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy. [ABSTRACT FROM AUTHOR]

CRISPR/Cas9 is a powerful genome editing tool for trait improvement in various crops; however, enhancing mutation efficiency using CRISPR/Cas9 in watermelon and melon remains challenging. We designed four CRISPR systems with different sgRNA expression cassettes to target the phytoene desaturase (PDS) gene in melon. The constructed vectors were delivered to host plants using Agrobacterium-mediated transformation. Phenotypic and genotypic analyses of the edited melon seedlings revealed that the CRISPR systems with tRNA and Csy4 spacers driven by the Pol II-type promoter significantly improved mutation efficiency, reaching 25.20% and 42.82%, respectively. Notably, 78.95% of the mutations generated by the Csy4 system involved large-fragment deletions (LDs) between the two target sites. In watermelon, the Csy4 system achieved a PDS editing efficiency of 41.48%, with 71.43% of the edited seedlings showing LD between the two target sites. Sequencing analysis indicated that the edited melon seedlings exhibited heterozygous, three-allele mutation and chimeric events; the edited watermelon seedlings included 2/14 homozygous mutations. Compared to the commonly used Pol III promoter, using the Pol II promoter to drive sgRNA expression cassettes containing Csy4 showed the best improvement in CRISPR/Cas9 editing efficiency in melon; this system was also effective in watermelon. [ABSTRACT FROM AUTHOR]

• Using 20 validated, MYMV-linked cross-species transferable, polymorphic markers, a comprehensive genetic linkage map was constructed. • Spanning a total of 958.13 cM across the genome, these markers were precisely allocated to nine distinct linkage groups. • SMA analysis revealed two associations on LG4 that exhibited strong and significant associations with MYMV resistance and yield. • Identifying and characterizing marker CEDG127 presents a valuable opportunity for the targeted selection of superior recombinants. • By harnessing these genomic regions, crop improvement for robust MYMV resistance and enhanced yield can be achived. Black gram (Vigna mungo (L.) Hepper, the summer rice fallow pulse of India, also known as urad dal, is a highly nutritious pulse widely used in vegetarian protein diets. Single marker analysis assesses the association between a marker genotype and phenotype segregation, identifying potential quantitative trait loci (QTLs) in a population. SMA for resistance to mungbean yellow mosaic virus and yield-contributing traits were carried out in a set of 90 recombinant inbred lines derived from crossing the high-yielding black-gram variety KKM 1 and the MYMV-resistant variety VBN 6. Analysis revealed eight significant associations with black gram and the resulting map encompasses a total span of 958.13 cM and features 20 SSR regions. By performing single-marker analysis, we successfully identified four SSR markers responsible for MYMV resistance and four SSR markers associated with traits contributing to yield. Notably, four of these MYMV resistance-linked markers were distributed across four linkage groups, LG3, LG4, LG8 and LG9, and the phenotypic variance explained by these associations was 8.12, 8.57, 10.09, and 7.65 %, respectively. Furthermore, four SSRs linked to yield-related traits were identified: the number of primary branches per plant in LG11, the number of clusters per plant in LG10, the number of days to 50 % flowering in LG11 and the number of pods per plant in LG4, with PVEs ranging from 12.26 % to 12.32 %. SMA analysis revealed two remarkable peaks located on LG4 that were significantly associated with the crucial MYMV and the number of pods per plant (74.26 cM). Conversely, LG4 exhibited a strong and robust connection with MYMV resistance, a pivotal trait for preserving crop health and yield. Our research identified five major and three minor associations with MYMV resistance and yield traits, enabling precise marker-assisted breeding for developing MYMV-resistant black gram genotypes with improved yield. [ABSTRACT FROM AUTHOR]

At the cellular level, plant immunity is orchestrated by a complex network of proteins, among which the 14-3-3 proteins have emerged as pivotal players. Both microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) and effector-triggered immunity (ETI) are critical for plant survival against microbial threats, and the 14-3-3 proteins have been identified as central regulators of these processes. Due to their multifunctionality in many plant pathways and conserved nature, 14-3-3 proteins often serve as targets for viral, bacterial, and fungal elicitors/effectors. This highlights their significance as crucial targets to enhance crop resilience and disease resistance. 14-3-3 proteins, ubiquitously present in eukaryotic cells, are regulatory proteins involved in a plethora of cellular processes. In plants, they have been studied in the context of metabolism, development, and stress responses. Recent studies have highlighted the pivotal role of 14-3-3 proteins in regulating plant immunity. The ability of 14-3-3 proteins to modulate immune responses is primarily attributed to their function as interaction hubs, mediating protein–protein interactions and thereby regulating the activity and overall function of their binding partners. Here, we shed light on how 14-3-3 proteins contribute to plant defense mechanisms, the implications of their interactions with components of plant immunity cascades, and the potential for leveraging this knowledge for crop improvement strategies. [ABSTRACT FROM AUTHOR]

SUMMARY Manipulating plant height is an essential component of crop improvement. Plant height was generally reduced through breeding in wheat, rice, and sorghum to resist lodging and increase grain yield but kept high for bioenergy crops. Here, we positionally cloned a plant height quantitative trait locus (QTL) qHT7.1 as a MYB transcription factor controlling internode elongation, cell proliferation, and cell morphology in sorghum. A 740 bp transposable element insertion in the intronic region caused a partial mis‐splicing event, generating a novel transcript that included an additional exon and a premature stop codon, leading to short plant height. The dominant allele had an overall higher expression than the recessive allele across development and internode position, while both alleles' expressions peaked at 46 days after planting and progressively decreased from the top to lower internodes. The orthologue of qHT7.1 was identified to underlie the brachytic1 (br1) locus in maize. A large insertion in exon 3 and a 160 bp insertion at the promoter region were identified in the br1 mutant, while an 18 bp promoter insertion was found to be associated with reduced plant height in a natural recessive allele. CRISPR/Cas9–induced gene knockout of br1 in two maize inbred lines showed significant plant height reduction. These findings revealed functional connections across natural, mutant, and edited alleles of this MYB transcription factor in sorghum and maize. This enriched our understanding of plant height regulation and enhanced our toolbox for fine‐tuning plant height for crop improvement. [ABSTRACT FROM AUTHOR]

As a major staple food crop for the global human population, climate-resilient wheat is the key to global food security. In this context, there is an urgent need to combine advances in genomic technologies and cutting-edge tools in the crop breeding pipelines. The genetic improvement of wheat starts with a clear understanding of genes and genomic components. The past 4–5 years have seen unprecedented growth in wheat genomes, pangenomes, and functional genomics studies. More than 50 reference-level genome assemblies are available for wheat and its wild and related species. Wheat's wild and related species provide a rich source of new genes and alleles to improve wheat. Reference genome assemblies of wheat's wild and related progenitor species have provided a new, helpful resource for targeted gene discovery for wheat improvement. This review explores the journey of wheat genomics starting in 2003. There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years. [ABSTRACT FROM AUTHOR]

Summary: Plant survival to a potential plethora of diverse environmental insults is underpinned by coordinated communication amongst organs to help shape effective responses to these environmental challenges at the whole plant level. This interorgan communication is supported by a complex signal network that regulates growth, development and environmental responses. Nitric oxide (NO) has emerged as a key signalling molecule in plants. However, its potential role in interorgan communication has only recently started to come into view. Direct and indirect evidence has emerged supporting that NO and related species (S‐nitrosoglutathione, nitro‐linolenic acid) are mobile interorgan signals transmitting responses to stresses such as hypoxia and heat. Beyond their role as mobile signals, NO and related species are involved in mediating xylem development, thus contributing to efficient root–shoot communication. Moreover, NO and related species are regulators in intraorgan systemic defence responses aiming an effective, coordinated defence against pathogens. Beyond its in planta signalling role, NO and related species may act as ex planta signals coordinating external leaf‐to‐leaf, root‐to‐leaf but also plant‐to‐plant communication. Here, we discuss these exciting developments and emphasise how their manipulation may provide novel strategies for crop improvement. [ABSTRACT FROM AUTHOR]

The soybean (Glycine max) is a globally important crop due to its high protein and oil content, which serves as a key resource for human and animal nutrition, as well as bioenergy production. This review assesses recent advancements in soybean genetic improvement by conducting an extensive literature analysis focusing on enhancing resistance to biotic and abiotic stresses, improving nutritional profiles, and optimizing yield. We also describe the progress in breeding techniques, including traditional approaches, marker-assisted selection, and biotechnological innovations such as genetic engineering and genome editing. The development of transgenic soybean cultivars through Agrobacterium-mediated transformation and biolistic methods aims to introduce traits such as herbicide resistance, pest tolerance, and improved oil composition. However, challenges remain, particularly with respect to genotype recalcitrance to transformation, plant regeneration, and regulatory hurdles. In addition, we examined how wild soybean germplasm and polyploidy contribute to expanding genetic diversity as well as the influence of epigenetic processes and microbiome on stress tolerance. These genetic innovations are crucial for addressing the increasing global demand for soybeans, while mitigating the effects of climate change and environmental stressors. The integration of molecular breeding strategies with sustainable agricultural practices offers a pathway for developing more resilient and productive soybean varieties, thereby contributing to global food security and agricultural sustainability. [ABSTRACT FROM AUTHOR]

The plant‐based protein industry is rapidly growing and is projected to grow to over $27 billion by 2030. In addition to monetary benefits, plant‐based protein crops, particularly pulse crops (i.e., legume species with dry edible seed), can supplement the existing crop biodiversity and break the disease and insect pest cycle in drastically changing climatic conditions. Most commercially available plant‐based protein ingredients come from only 2% of the 150 plant species on which our food supply depends. Therefore, it is imperative to diversify the cropping system with pulse crops that provide a more nutritious, climate‐resilient, sustainable food value chain. At present, a large portion of US pulse crop production is exported, yet the shifting demographics, dietary preferences, and a rise in domestic consumption present enormous potential for existing and emerging pulse crops, as well as their breeding. Despite a rise in demand from consumers and industries, farmers are yet to fully reap the benefits of these crops due to a shortage of improved varieties. These new varieties could lead to a diverse, sustainable protein supply that satisfies the growing domestic and global demand for plant‐based foods. This review intends to comprehensively explore the geographical and cultural acceptance of plant‐based proteins, manufacturing techniques, protein products, anti‐nutritional factors, techniques and tools for protein estimation, high‐throughput estimation of seed protein, protein composition requirements in food, breeding strategies, crop improvement, and resources to improve plant‐based protein pulse crops. [ABSTRACT FROM AUTHOR]

ABSTRACT Legumes, characterized by their ability to form symbiotic relationships with nitrogen‐fixing bacteria, play crucial roles in agriculture, ecology and human nutrition. Phosphatidylethanolamine‐binding proteins (PEBPs) are the key genetic players that contribute to the diverse biological functions of legumes. In this review, we summarize the current understanding of important roles of PEBP genes in legumes, including flowering, inflorescence architecture, seed development and nodulation. We also delve into PEBP regulatory mechanisms and effects on plant growth, development, and adaptation to the environment. Furthermore, we highlight their potential biotechnological applications for crop improvement and promoting sustainable agriculture. This review emphasizes the multifaceted roles of PEBP genes, shedding light on their significance in legume biology and their potential for sustainable productive farming. [ABSTRACT FROM AUTHOR]

The article discusses strategies for applying RNA m6A modification in crop improvement, emphasizing the importance of precise gene expression manipulation for enhancing crop traits. It highlights the role of m6A modification in regulating gene expression in plants and presents examples of how manipulating m6A levels can enhance agronomic traits in crops like rice, potato, and strawberries. The article also outlines three proposed strategies for enhancing crop traits through m6A modification and provides steps for m6A editing to improve crop agronomic traits. [Extracted from the article]

N6‐methyladenosine (m6A) is the most prevalent internal modification of mRNA and plays an important role in regulating plant growth. However, there is still a lack of effective tools to precisely modify m6A sites of individual transcripts in plants. Here, programmable m6A editing tools are developed by combining CRISPR/dCas13(Rx) with the methyltransferase GhMTA (Targeted RNA Methylation Editor, TME) or the demethyltransferase GhALKBH10 (Targeted RNA Demethylation Editor, TDE). These editors enable efficient deposition or removal of m6A modifications at targeted sites of endo‐transcripts GhECA1 and GhDi19 within a broad editing window ranging from 0 to 46 nt. TDE editor significantly decreases m6A levels by 24%–76%, while the TME editor increases m6A enrichment, ranging from 1.37‐ to 2.51‐fold. Furthermore, installation and removal of m6A modifications play opposing roles in regulating GhECA1 and GhDi19 mRNA transcripts, which may be attributed to the fact that their m6A sites are located in different regions of the genes. Most importantly, targeting the GhDi19 transcript with TME editor plants results in a significant increase in root length and enhanced drought resistance. Collectively, these m6A editors can be applied to study the function of specific m6A modifications and have the potential for future applications in crop improvement. [ABSTRACT FROM AUTHOR]

Phytopathogens represent an ongoing threat to crop production and a significant impediment to global food security. During the infection process, these pathogens spatiotemporally deploy a large array of effectors to sabotage host defense machinery and/or manipulate cellular pathways, thereby facilitating colonization and infection. However, besides their pivotal roles in pathogenesis, certain effectors, known as avirulence (AVR) effectors, can be directly or indirectly perceived by plant resistance (R) proteins, leading to race-specific resistance. An in-depth understanding of the intricate AVR-R interactions is instrumental for genetic improvement of crops and safeguarding them from diseases. Magnaporthe oryzae (M. oryzae), the causative agent of rice blast disease, is an exceptionally virulent and devastating fungal pathogen that induces blast disease on over 50 monocot plant species, including economically important crops. Rice-M. oryzae pathosystem serves as a prime model for functional dissection of AVR effectors and their interactions with R proteins and other target proteins in rice due to its scientific advantages and economic importance. Significant progress has been made in elucidating the potential roles of AVR effectors in the interaction between rice and M. oryzae over the past two decades. This review comprehensively discusses recent advancements in the field of M. oryzae AVR effectors, with a specific focus on their multifaceted roles through interactions with corresponding R/target proteins in rice during infection. Furthermore, we deliberated on the emerging strategies for engineering R proteins by leveraging the structural insights gained from M. oryzae AVR effectors. [ABSTRACT FROM AUTHOR]

Recurring use of chemical fertilizers (CFs) in agriculture has resulted the remarkable improvement in crop productivity but their ruinous effects on environment have made a serious issue. Biological entities (e.g., several microorganisms) showing fertilizer‐like activities have gained attention in this regard. Several soil resident microorganisms interact strongly with neighboring plants and promote the growth and development of those plants through various means. In exchange of this, microbes utilize different compounds released from plant roots for their own nutrition. This mutualistic mode of interrelation predominantly relies on the transmission of signals from microbes to plants and vice versa. However, climatic factors (e.g., CO2 level, temperature, and water availability) are also important for this association. These bacterial strains are literally known as plant growth promoting rhizobacteria (PGPR) which facilitate plant growth through nitrogen fixation, mineral solubilization, phytostimulation, stress resistance, etc. Responding to the external environmental stimuli, they often modulate the expression of genes responsible for the transport of nutrients. Reduction of the use of CFs through the application of PGPR strains in the cultivation of some economically important plants has been reported by several authors. Significant yield improvement compared to the control groups was found in all experimental studies. Commercial development of the PGPR inoculants with remarkable biostimulating activities and their successive application should be expanded through collaborative association with different sectors after the removal of existing lacunae. Reading more than 100 articles on various aspects of rhizobacteria, the plan of writing this article has been executed. In this review, we have discussed about the colonization and potency of PGPR strains and how their well‐planned application in agriculture could evidently reinforce the global economy. The main structure of this text is designed as an outline from the development of interrelation between plants and PGPR to the commercialization of PGPR based on their potential role in the field of agriculture. [ABSTRACT FROM AUTHOR]

SUMMARY: DNA rearrangements, including inversions, translocations, and large insertions/deletions (indels), are crucial for crop evolution, domestication, and improvement. The rearrangements are frequently induced by ion beams via the mis‐repair of DNA double‐strand breaks (DSBs). Unfortunately, how ion beam‐induced DSBs are repaired has not been comprehensively analyzed and the mechanisms underlying DNA rearrangements remain unclear. In this study, clonal sectors originating from single mutated cells in carbon ion‐irradiated plants were used for whole‐genome sequencing analyses after Arabidopsis seeds and seedlings were irradiated. Comparative analyses of the induced mutations (e.g., size and frequency of indels and microhomology at the junctions of the rearrangements) in the irradiated materials suggested that the broken/rejoined DSB ends were more extensively processed in seedlings than in seeds. A mutation to canonical non‐homologous end‐joining (c‐NHEJ), which is a DSB repair pathway with minimal processing of DSB ends, increased the sensitivity to ion beams more in the seeds than in the seedlings, which was consistent with the junction analysis results, indicative of the minor contribution of c‐NHEJ to the carbon ion‐induced DSB repair in seedlings. Considering the characteristics of the large templated insertions in irradiated seedlings, ion‐beam‐induced DSBs in seedlings are likely repaired primarily by a polymerase theta‐mediated pathway. Polymerase theta‐deficient seedlings were more sensitive to ion beams than the c‐NHEJ‐deficient seedlings, consistent with this hypothesis. This study revealed the key characteristics of ion beam‐induced DSBs and the associated repair mechanisms related to the physiological status of the irradiated materials, with implications for elucidating the occurrence and induction of rearrangements. Significance Statement: DNA rearrangements, which are critical for crop improvement, can be randomly induced in genomes by ion beams. Our genomic analysis of irradiated plants revealed significant differences in the characteristics of the DNA rearrangements in seeds and seedlings, providing important insights into double‐strand break repair mechanisms and the associated rearrangement formation related to the physiological status of the irradiated materials. [ABSTRACT FROM AUTHOR]

Geophytic plants synchronize growth and quiescence with the external environment to survive and thrive under changing seasons. Together with seasonal growth adaptation, dormancy and sprouting are critical factors determining crop yield and market supply, as various geophytes also serve as major food, floriculture, and ornamental crops. Dormancy in such crops determines crop availability in the market, as most of them are consumed during the dormant stage. On the other hand, uniform/maximal sprouting is crucial for maximum yield. Thus, dormancy and sprouting regulation have great economic importance. Dormancy–sprouting cycles in geophytes are regulated by genetic, exogenous (environmental), and endogenous (genetic, metabolic, hormonal, etc.) factors. Comparatively, the temperature is more dominant in regulating dormancy and sprouting in geophytes, unlike above-ground tissues, where both photoperiod and temperature control are involved. Despite huge economic importance, studies concerning the regulation of dormancy and sprouting are scarce in the majority of geophytes. To date, only a few molecular factors involved in the process have been suggested. Recently, omics studies on molecular and metabolic factors involved in dormancy and growth regulation of underground vegetative tissues have provided more insight into the mechanism. Here, we discuss current knowledge of the environmental and molecular regulation and control of dormancy and sprouting in geophytes, and discuss challenges/questions that need to be addressed in the future for crop improvement. [ABSTRACT FROM AUTHOR]

Drought stress poses a critical threat to global crop yields and sustainable agriculture. The GASA genes are recognized for their pivotal role in stress tolerance and plant growth, but little is known about how they function in sunflowers. The investigation aimed to identify and elucidate the role of HaGASA genes in conferring sunflowers with drought tolerance. Twenty-seven different HaGASA gene family members were found in this study that were inconsistently located across eleven sunflower chromosomes. Phylogeny analysis revealed that the sunflower HaGASA genes were divided into five subgroups by comparing GASA genes with those from Arabidopsis, peanut, and soybean, with members within each subgroup displaying similar conserved motifs and gene structures. In-silico evaluation of cis-regulatory elements indicated the existence of specific elements associated with stress-responsiveness being the most abundant, followed by hormone, light, and growth-responsive elements. Transcriptomic data from the NCBI database was utilized to assess the HaGASA genes expression profile in different sunflower varieties under drought conditions. The HaGASA genes expression across ten sunflower genotypes under drought stress, revealed 14 differentially expressed HaGASA genes, implying their active role in the plant's stress response. The expression in different organs revealed that HaGASA2, HaGASA11, HaGASA17, HaGASA19, HaGASA21 and HaGASA26 displayed maximum expression in the stem. Our findings implicate HaGASA genes in mediating sunflower growth maintenance and adaptation to abiotic stress, particularly drought. The findings, taken together, provided a basic understanding of the structure and potential functions of HaGASA genes, setting the framework for further functional investigations into their roles in drought stress mitigation and crop improvement strategies. [ABSTRACT FROM AUTHOR]

Enhancing the genetic transformation efficiency of major crops remains a significant challenge, primarily due to their suboptimal regeneration efficiency. Developmental regulators, known as key regulatory genes, involved in plant meristem and somatic embryo formation, play a crucial role in improving plant meristem induction and regeneration. This review provides a detailed summary of the molecular mechanisms and regulatory networks of many developmental regulators, in the context of enhancing the genetic transformation efficiency in major crops. We also propose strategies for exploring and utilizing additional developmental regulators. Further investigation into the mechanisms of these regulators will deepen our understanding of the regenerative capacity and genetic transformation processes of plants, offering valuable support for future crop improvement efforts. The discovery of novel developmental regulators is expected to further advance crop transformation and the effective manipulation of various developmental regulators could provide a promising approach in order to enhance genetic transformation efficiency. [ABSTRACT FROM AUTHOR]

The field of plant breeding has witnessed significant transformations over millennia evolving from rudimentary selection strategies (Breeding 1.0) in ancient times to sophisticated techniques in the modern era (Breeding 4.0) which can identify the desirable alleles and engineer the plant to contain them all in a short amount of time, in essence, creating ‘designer plants’. This evolution aims to enhance crop variety and improve food security. However, challenges, such as climate change, population growth and limited arable land, necessitate more precise and efficient breeding methods. Here, artificial intelligence (AI) emerges as a promising solution. By mimicking human intelligence, AI can process vast datasets efficiently, addressing the complexities of modern plant breeding. In this context, AI facilitates high-throughput phenotyping, gene functional analysis and the processing of extensive environmental data. It revolutionises decision-making by transforming fragmented market information into systematic breeding strategies. This review explores the historical journey of plant breeding, emphasising the shift from traditional methods to AI-driven approaches. It highlights AI's critical role in developing climate-resilient and pest-resistant crops, ensuring that key staples like maize, wheat, rice, tomato, potato and cotton can meet global food security challenges effectively. [ABSTRACT FROM AUTHOR]

The present investigation was convened during kharif, 2022 (July-October), rabi-summer, 2023 (January-May) and kharif, 2023 (July-October) at J.N.K.V.V., Jabalpur, Madhya Pradesh, India to characterize 165 diverse soybean germplasm lines in pursuance of DUS (Distinctness, Uniformity, and Stability) guidelines focusing on integrating optimal morphological traits to pre-fine soybean crop improvement. The study revealed significant variation among soybean genotypes. The hypocotyl color, controlled by a monogenic trait, was found in 77 genotypes, closely associated with violet flower color, whereas non-pigmented hypocotyls present in 88 genotypes were linked to white flowers. Growth habits were categorized as determinate (59), semideterminate (103), and indeterminate (3), demonstrating that semi-determinate genotypes offer balanced resource allocation and reduced lodging. Most genotypes displayed medium flowering time (159) and medium plant height (134). Leaf shape was predominantly pointed ovate (121), with lanceolate leaves associated with higher number of seeds-1 pod. The presence of dark green leaves in 108 genotypes indicated higher chlorophyll content and enhanced photosynthetic efficiency to strengthen plant type. Semi-erect growth habit was prevalent in 152 genotypes, providing better soil coverage and moisture retention, while 13 genotypes showed erect growth. Pod pubescence was observed in 106 genotypes, offering protection against pests. These traits are found stable across the environment and may be used as an identification key for different varieties and donor germplasm lines. [ABSTRACT FROM AUTHOR]

Rice spikelet size, spikelet length and spikelet width, are very important traits directly related to a rice crop's yield. The accurate measurement of these parameters is quite significant in research such as breeding, yield evaluation and variety improvement for rice crops. Traditional measurement methods still mainly rely on manual labor, which is time-consuming, labor-intensive and error-prone. In this study, a novel method, dubbed the "SSM-Method", based on convolutional neural network and traditional image processing technology has been developed for the efficient and precise measurement of rice spikelet size parameters on rice panicle structures. Firstly, primary branch images of rice panicles were collected at the same height to build an image database. The spikelet detection model using convolutional neural network was then established for spikelet recognition and localization. Subsequently, the calibration value was obtained through traditional image processing technology. Finally, the "SSM-Method" integrated with a spikelet detection model and calibration value was developed for the automatic measurement of spikelet sizes. The performance of the developed SSM-Method was evaluated through testing 60 primary branch images. The test results showed that the root mean square error (RMSE) of spikelet length for two rice varieties (Huahang15 and Qingyang) were 0.26 mm and 0.30 mm, respectively, while the corresponding RMSE of spikelet width was 0.27 mm and 0.31 mm, respectively. The proposed algorithm can provide an effective, convenient and low-cost tool for yield evaluation and breeding research. [ABSTRACT FROM AUTHOR]

Rising food demands require new techniques to achieve higher genetic gains for crop production, especially in regions where climate can negatively affect agriculture. Wheat is a staple crop that often encounters this challenge, and ideotype breeding with optimized canopy traits for grain yield, such as determinate tillering, synchronized flowering, and stay-green (SG), can potentially improve yield under terminal drought conditions. Among these traits, SG has emerged as a key factor for improving grain quality and yield by prolonging photosynthetic activity during reproductive stages. This study aims to highlight the importance of growth dynamics in a wheat mapping population by using multispectral images obtained from uncrewed aerial vehicles as a high-throughput phenotyping technique to assess the effectiveness of using such images for determining correlations between vegetation indices and grain yield, particularly regarding the SG trait. Results show that the determinate group exhibited a positive correlation between NDVI and grain yield, indicating the effectiveness of these traits in yield improvement. In contrast, the indeterminate group, characterized by excessive vegetative growth, showed no significant NDVI–grain yield relationship, suggesting that NDVI values in this group were influenced by sterile tillers rather than contributing to yield. These findings provide valuable insights for crop breeders by offering a non-destructive approach to enhancing genetic gains through the improved selection of resilient wheat genotypes. [ABSTRACT FROM AUTHOR]

Soybean is an economically important oilseed crop with diverse uses as food, feed, biofuel and so forth. Although the demand for soybean is growing rapidly worldwide, the narrow genetic base of released cultivars due to meagre utilisation of available wild and untapped genetic resources is a major factor contributing to stagnant production and productivity levels of soybean. Considering the continuously increasing global population, changing dietary habits, ongoing climatic fluctuations, rapidly evolving biotic stresses and shrinking land and water resources, utilisation of novel and diverse sources of variation is required for the genetic enhancement of soybean. To widen the genetic base of commercial soybean cultivars and to improve the genetic gain of the crop focused and systematic pre‐breeding efforts can play a game‐changing role by supplying novel genes in crop improvement programs. This article discusses the rationale of tapping wild and untapped genetic resources of soybean, gene pools, soybean genetic resources conserved ex‐situ and its utilisation status, genetic base of commercial soybean cultivars, identified novel genes and genomic regions in wild genetic resources, pre‐breeding efforts in India and strategies for incorporating desirable traits in the elite cultivated gene pool for fulfilling the requirements of farmers and other end‐users. [ABSTRACT FROM AUTHOR]

Cell-penetrating peptides (CPPs), typically comprising 5–30 amino acids, can deliver impermeable cargo molecules across membranes into the cytosol of eukaryotic cells. CPPs can transport a broad spectrum of molecules, including peptides, proteins, nucleic acids, and small molecules. Delivery can be accomplished by covalently attaching a CPP to the target cargo or by the formation of a noncovalent complex between the CPP and cargo. CPPs penetrate cells via two distinct mechanisms: energy-dependent endocytic pathways or energy-independent direct translocation across the plasma membrane. CPPs could potentially reduce dependence on chemical fertilizers and pesticides, boost crop yields and resilience to extreme weather conditions, improve nutrient uptake from the soil, and enhance nutrient contents in plants. Cell-penetrating peptides (CPPs) are short (typically 5–30 amino acids), cationic, amphipathic, or hydrophobic peptides that facilitate the cellular uptake of diverse cargo molecules by eukaryotic cells via direct translocation or endocytosis across the plasma membrane. CPPs can deliver a variety of bioactive cargos, including proteins, peptides, nucleic acids, and small molecules into the cell. Once inside, the delivered cargo may function in the cytosol, nucleus, or other subcellular compartments. Numerous CPPs have been used for studies and drug delivery in mammalian systems. Although CPPs have many potential uses in plant research and agriculture, the application of CPPs in plants remains limited. Here we review the structures and mechanisms of CPPs and highlight their potential applications for sustainable agriculture. [ABSTRACT FROM AUTHOR]

Broad-spectrum disease resistance is more often conferred by atypical R genes than typical R genes. Atypical R genes are important for a holistic understanding of plant immunity. New resources and technologies facilitate the cloning, characterization, and engineering of atypical R genes. Atypical R proteins are promising candidates for trans-crop applications. Genetic resistance to plant diseases is essential for global food security. Significant progress has been achieved for plant disease-resistance (R) genes comprising nucleotide-binding domain, leucine-rich repeat-containing receptors (NLRs), and membrane-localized receptor-like kinases or proteins (RLKs/RLPs), which we refer to as typical R genes. However, there is a knowledge gap in how non-receptor-type or atypical R genes contribute to plant immunity. Here, we summarize resources and technologies facilitating the study of atypical R genes, examine diverse atypical R proteins for broad-spectrum resistance, and outline potential approaches for trans-crop applications of atypical R genes. Studies of atypical R genes are important for a holistic understanding of plant immunity and the development of novel strategies in disease control and crop improvement. [ABSTRACT FROM AUTHOR]

The reduction of photosynthetically active radiation impacts the growth and productivity of soybean in agroforestry and intercropping systems. Thus, this report explored the responses of 16 soybean cultivars submitted to shade levels in field conditions. Multi‐faceted and relative importance analyses revealed that the steam diameter and plant height are fundamental morphological markers for selecting shade‐resilient cultivars, both were high and positively correlated to yield components. Moreover, the responses to shade varied among soybean cultivars, with certain genotypes demonstrating distinct tolerance levels, which allowed also the estimative of genetic variance that revealed strong participation of genetic components in responses to shade. Multivariate and clustering analysis using steam diameter and plant height in combination with two yield components resulted in the identification of four soybean cultivars more tolerant to shade environments and two sensible. Therefore, this report provides insights into soybean cultivation under varying light conditions, provides a robust foundation for the integration of morphological and yield markers in breeding programmes focused on shade tolerance and guides future endeavours in crop improvement for optimal and sustainable yield and resilience in the climate change context. [ABSTRACT FROM AUTHOR]

[Objective] The aims of this study are to explore the effects of fertilization and biochar addition on soil respiration (Rs), environmental factors and vegetation index, and the effects of biotic factors and abiotic factors on soil respiration, and to provide the reference for the assessment of crop growth and carbon emission in farmland ecosystem. [Methods] In a sorghum-corn rotation agroecosystem of Taiyuan basin after a continuous 5-year (2011-2015) fertilization and biochar additon with 4 treatments (control: CK, biochar: B: inorganic fertilizer: INF and inorganic fertilizer + biochar: INF+B), based on periodic observations of Rs biological and abiotic factors for 2 consecutive years (2015-2016), we analyzed the effects of the 4 treatments on Rs and its relationship with biological and abiotic factors. [Results] (1) Compared with CK, B, INF and INF+B reduced soil temperature (2.8%~4.2%), and increased temperature sensitivity (Q10) of soil respiration (4.5%~20.2%) and soil respiration rate (0.5%~8.8%), increased the enhanced vegetation index (EVI) by 1.5%~6.2%, difference vegetation index (DVI) by 0.7%~6.0%, normalized vegetation index (NDVI) by 1.2%~5.4%, respectively; but the influence on these factors did not reach a significant level (p>0.05). (2) The effects of B, INF and INF+B on Rs differed in different growth stages. B, INF and INF+B increased the Rs in the early growth stage, while the Rs of CK treatment was higher than that in other treatments (except B treatment in the grouting stage) (p<0.05) in the later growth stage, resulting in no significant difference in Rs among all treatments in the whole growing stage. (3) Among the three vegetation indices, the seasonal variation of DVI showed the highest interpretation of the seasonal variation in Rs at 75.5%. Soil temperature in 10 cm depth (T10) and soil moisture over 0-10 cm depth (W.) explained 30.8% and 20.1% of the seasonal variation of Rs, respectively. From the R² and AIC values, the three-factor model with T10, Ws and DVI as independent variables predicted the seasonal change of Rs well. [Conclusion] There was no significant difference in Rs between the four treatments in whole sorghum, and Rs did not increase by fertilization and biochar addition. The results provided the basis for the relationship between inorganic fertilizer and biochar application on soil carbon emission, soil improvement and crop growth. [ABSTRACT FROM AUTHOR]

The use of slow and controlled release fertilizers (S/CRFs) has been beneficial in enhancing fertilizer utilization and crop yields, improving food security. However, the massive use of conventional S/CRFs has also polluted soil, water, and air, which poses a challenge to the sustainability of modern agriculture. To address this, a more efficient and environmentally-friendly material for crop nutrition is needed. Chitosan gels have proven to be an ideal carrier for nutrient transport given their biodegradability and high adsorption characteristics. This paper reviews the cross-linking of chitosan gels, preparation methods, nutrient transport, and performance, and how they contribute to sustainable agriculture. In addition, we detail the contribution of chitosan gels fertilizers to greenhouse gas reduction, soil conditioning, and crop yield improvement. In conclusion, although further research is needed on chitosan gels fertilizers as S/CRFs, it is expected that their use could lead to improved nutrient efficiency and reduced environmental pollution from a long-term development perspective. [ABSTRACT FROM AUTHOR]

Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes. [ABSTRACT FROM AUTHOR]

The African continent is vulnerable to food insecurity. Increased food costs, job losses, and climate change force Africans to chronic hunger. Biotechnology can be used to mitigate this by using techniques such as CRISPR/Cas9 systems, TALENs, and ZFNs. Biotechnology can utilize geminiviruses to deliver the necessary reagents for precise genome alteration. Additionally, plants infected with geminiviruses can withstand harsher weather conditions such as drought. Therefore, this article discusses geminivirus replication and its use as beneficial plant DNA viruses. It focuses explicitly on genome editing to increase plant resistance by manipulating plants' salicylic acid and jasmonic acid pathways. [ABSTRACT FROM AUTHOR]

Amaranth is a promising staple food that produces seeds with excellent nutritional quality. Although cultivated species intended for grain production have interesting agronomic traits, relatively little is known about wild species, which can prosper in diverse environments and could be a rich genetic source for crop improvement. This work focuses on the proteomic comparison between the seeds of wild and cultivated amaranth species using polarity-based protein extraction and two-dimensional gel electrophoresis. Differentially accumulated proteins (DAPs) showed changes in granule-bound starch synthases and a wide range of 11S globulin isoforms. The electrophoretic profile of these proteins suggests that they may contain significant phosphorylation as post-translational modifications (PTMs), which were confirmed via immunodetection. These PTMs may impact the physicochemical functionality of storage proteins, with potential implications for seed agronomic traits and food system applications. Low-abundant DAPs with highly variable accumulation patterns are also discussed; these were involved in diverse molecular processes, such as genic regulation, lipid storage, and stress response. [ABSTRACT FROM AUTHOR]

Introduction: For nearly two centuries, cranberry (Vaccinium macrocarpon Ait.) breeders have improved fruit quality and yield by selecting traits on fruiting stems, termed "reproductive uprights." Crop improvement is accelerating rapidly in contemporary breeding programs due to modern genetic tools and highthroughput phenotyping methods, improving selection efficiency and accuracy. Methods: We conducted genotypic evaluation on 29 primary traits encompassing fruit quality, yield, and chemical composition in two full-sib cranberry breeding populations--CNJ02 (n = 168) and CNJ04 (n = 67)--over 3 years. Genetic characterization was further performed on 11 secondary traits derived from these primary traits. Results: For CNJ02, 170 major quantitative trait loci (QTL; R²= 0.10) were found with interval mapping, 150 major QTL were found with model mapping, and 9 QTL were found to be stable across multiple years. In CNJ04, 69 major QTL were found with interval mapping, 81 major QTL were found with model mapping, and 4 QTL were found to be stable across multiple years. Meta-QTL represent stable genomic regions consistent across multiple years, populations, studies, or traits. Seven multi-trait meta-QTL were found in CNJ02, one in CNJ04, and one in the combined analysis of both populations. A total of 22 meta-QTL were identified in cross-study, cross-population analysis using digital traits for berry shape and size (8 meta-QTL), digital images for berry color (2 meta-QTL), and three-study cross-analysis (12 meta-QTL). Discussion: Together, these meta-QTL anchor high-throughput fruit quality phenotyping techniques to traditional phenotyping methods, validating state-of-the-art methods in cranberry phenotyping that will improve breeding accuracy, efficiency, and genetic gain in this globally significant fruit crop. [ABSTRACT FROM AUTHOR]

Drought stress is a major constraint on plant growth and agricultural productivity. Caffeic acid O-methyltransferase (COMT), an enzyme involved in the methylation of various substrates, plays a pivotal role in plant responses to abiotic stress. The involvement of COMTs in drought response, particularly through the enhancement of lignin and melatonin biosynthesis, remains poorly understood. In this study, LcCOMT was firstly proposed to be associated with the biosynthesis of both lignin and melatonin, as demonstrated through sequence comparison, phylogenetic analysis, and conserved motif identification. In vitro enzymatic assays revealed that LcCOMT effectively methylates N-acetylserotonin to melatonin, albeit with a higher Km value compared to caffeic acid. Sitedirected mutagenesis of residues Phe171 and Asp269 resulted in a significant reduction in catalytic activity for caffeic acid, with minimal impact on Nacetylserotonin, underscoring the specificity of these residues in substrate binding and catalysis. Under drought conditions, LcCOMT expression was significantly upregulated. Overexpression of LcCOMT gene in Arabidopsis plants conferred enhanced drought tolerance, characterized by elevated lignin and melatonin levels, increased chlorophyll and carotenoid content, heightened activities of antioxidant enzymes peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD), and reduced malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation. This study is among the few to demonstrate that COMT-mediated drought tolerance is achieved through the simultaneous promotion of lignin and melatonin biosynthesis. LcCOMT represents the first functionally characterized COMT in Apiaceae family, and it holds potential as a target for genetic enhancement of drought tolerance in future crop improvement strategies. [ABSTRACT FROM AUTHOR]

Realizing the full potential of genome editing for crop improvement has been slow due to inefficient methods for reagent delivery and the reliance on tissue culture for creating gene-edited plants. RNA viral vectors offer an alternative approach for delivering gene engineering reagents and bypassing the tissue culture requirement. Viruses, however, are often excluded from the shoot apical meristem, making virus-mediated gene editing inefficient in some species. Here, we developed effective approaches for generating gene-edited shoots in Cas9-expressing transgenic tomato plants using RNA virus-mediated delivery of single-guide RNAs (sgRNAs). RNA viral vectors expressing sgRNAs were either delivered to leaves or sites near axillary meristems. Trimming of the apical and axillary meristems induced new shoots to form from edited somatic cells. To further encourage the induction of shoots, we used RNA viral vectors to deliver sgRNAs along with the cytokinin biosynthesis gene, isopentenyl transferase. Abundant, phenotypically normal, gene-edited shoots were induced per infected plant with single and multiplexed gene edits fixed in the germline. The use of viruses to deliver both gene editing reagents and developmental regulators overcomes the bottleneck in applying virus-induced gene editing to dicotyledonous crops such as tomato and reduces the dependency on tissue culture. [ABSTRACT FROM AUTHOR]

High-throughput plant phenotype collection is of great significance for crop improvement breeding and cultivation management. As a place that can control the growth environment of plants, indoor is an important place for studying plant phenotypes. There are many platforms based on the greenhouse environment for the collection and analysis of phenotypic information. This paper describes the construction of four indoor plant phenotype collection platform, summarizes the data analysis and management methods, introduces the practical application of the indoor plant phenotype collection platform in plant research, and puts forward the prospect of the future development of the indoor plant phenotype collection platform. [ABSTRACT FROM AUTHOR]

Summary: Mesophyll conductance (gm) is a crucial plant trait that can significantly limit photosynthesis. Measurement of photosynthetic C18O16O discrimination (Δ18O) has proved to be the only viable means of resolving gm in both C3 and C4 plants. However, the currently available methods to exploit Δ18O for gm estimation are error prone due to their inadequacy in constraining the degree of oxygen isotope exchange (θ) during mesophyll CO2 hydration.Here, we capitalized on experimental manipulation of leaf water isotopic dynamics to establish a novel, nonsteady state, regression‐based approach for simultaneous determination of gm and θ from online Δ18O measurements.We demonstrated the methodological and theoretical robustness of this new Δ18O‐gm estimation approach and showed through measurements on several C3 and C4 species that this approach can serve as a benchmark method against which to identify previously‐unrecognized biases of the existing Δ18O‐gm methods.Our results highlight the unique value of this nonsteady state‐based approach for contributing to ongoing efforts toward quantitative understanding of mesophyll conductance for crop yield improvement and carbon cycle modeling. See also the Commentary on this article by Ogée, 243: 2045–2047. [ABSTRACT FROM AUTHOR]

Crop improvement and production domains encounter large amounts of expanding data with multi-layer complexity that forces researchers to use machine-learning approaches to establish predictive and informative models to understand the sophisticated mechanisms underlying these processes. All machine-learning approaches aim to fit models to target data; nevertheless, it should be noted that a wide range of specialized methods might initially appear confusing. The principal objective of this study is to offer researchers an explicit introduction to some of the essential machine-learning approaches and their applications, comprising the most modern and utilized methods that have gained widespread adoption in crop improvement or similar domains. This article explicitly explains how different machine-learning methods could be applied for given agricultural data, highlights newly emerging techniques for machinelearning users, and lays out technical strategies for agri/crop research practitioners and researchers. [ABSTRACT FROM AUTHOR]

Improving crop traits requires genetic diversity, which allows breeders to select advantageous alleles of key genes. In species or loci that lack sufficient genetic diversity, synthetic directed evolution (SDE) can supplement natural variation, thus expanding the possibilities for trait engineering. In this review, we explore recent advances and applications of SDE for crop improvement, highlighting potential targets (coding sequences and cis-regulatory elements) and computational tools to enhance crop resilience and performance across diverse environments. Recent advancements in SDE approaches have streamlined the generation of variants and the selection processes; by leveraging these advanced technologies and principles, we can minimize concerns about host fitness and unintended effects, thus opening promising avenues for effectively enhancing crop traits. [ABSTRACT FROM AUTHOR]

ABSTRACT The Mediator complex is a multisubunit transcription coregulator that transfers regulatory signals from different transcription factors to RNA polymerase II (Pol II) to control Pol II‐dependent transcription in eukaryotes. Studies on Arabidopsis Mediator subunits have revealed their unique or overlapping functions in various aspects of plant growth, stress adaptation and metabolite homeostasis. Therefore, the utilization of the plant Mediator complex for crop improvement has been of great interest. Advances in genome editing and sequencing techniques have expedited the characterization of Mediator subunits in economically important crops such as tomato, rice, wheat, soybean, sugarcane, pea, chickpea, rapeseed and hop. In this review, we summarize recent progress in understanding the molecular mechanisms of how the Mediator complex regulates crop growth, development and adaptation to environmental stress. We also discuss the conserved and diverse functions of the Mediator complex in different plant species. In addition, we propose several future research directions to deepen our understanding of the important roles of Mediator subunits and their interacting proteins, which would provide promising targets for genetic modification to develop new cultivars with desirable agronomic traits. [ABSTRACT FROM AUTHOR]

ABSTRACT Drought is one of the most severe environmental factors limiting plant growth and crop yield, necessitating the identification of genes that enhance drought resistance for crop improvement. Through screening an ethyl methyl sulfonate‐mutagenized rice mutant library, we isolated the PEG tolerance mutant 97‐1 (ptm97‐1), which displays enhanced resistance to osmotic and drought stress, and increased yield under drought conditions. A point mutation in OsMATE6 was identified as being associated with the drought‐resistant phenotype of ptm97‐1. The role of OsMATE6 in conferring drought resistance was confirmed by additional OsMATE6 knockout mutants. OsMATE6 is expressed in guard cells, shoots and roots and the OsMATE6‐GFP fusion protein predominantly localizes to the plasma membrane. Our ABA efflux assays suggest that OsMATE6 functions as an ABA efflux transporter; mutant protoplasts exhibited a slower ABA release rate compared to the wild type. We hypothesize that OsMATE6 regulates ABA levels in guard cells, influencing stomatal closure and enhancing drought resistance. Notably, OsMATE6 knockout mutants demonstrated greater yields under field drought conditions compared to wild‐type plants, highlighting OsMATE6 as a promising candidate for improving crop drought resistance. [ABSTRACT FROM AUTHOR]

Climate change creates a leverage point in plant breeding. We must rethink the way we employ plant breeding, utilize genetic diversity, and prioritize edible plant production across the landscape. A long-term strategy to 'redirect' the process of crop domestication that prioritizes the generation of abiotic and biotic stresstolerant cultivars is needed. A proposed neo-domestication strategy is presented as a case study. It entails the re-domestication of chile by retro-crossing of modern plant cultivars with landraces and a desert-adapted wild relative. An organized, collaborative effort could reintroduce stress tolerance genes that will render new cultivars more tolerant to challenges imposed by climate change. Purposeful populations generated using a broad spectrum of genetic diversity could also provide the basis for an evolutionary-participatory plant breeding process. The process must recognize the need for a paradigm shift in our resource allocation and breeding strategies. To succeed, a shared vision for neo-domestication of chile must recognize the importance of human cultural values and the need for sustained cooperation among stakeholders. [ABSTRACT FROM AUTHOR]

In plants, sugar metabolism involves a complex interplay of genetic, molecular and environmental factors. To better understand the molecular mechanisms underlying these processes, we utilized a multi-layered approach that integrated transcriptomic and metabolomic datasets generated from multiple different varieties of sweet corn. Through this analysis, we found 2533 genes that were differentially expressed in the immature kernel tissues of sweet corn, including genes involved in transcriptional regulation, sugar metabolism, primary metabolism, and other processes associated with adaptability of sweet corn. We also detected 31 differential metabolites among the three types of sweet corn. Utilizing an integrated approach encompassing transcriptomics and eGWAS, we elucidated the transcriptional regulatory patterns governing these differential metabolites. Specifically, we delved into the transcriptional modulation of malate- and ubiquitin-associated genes across a range of sweet corn varieties, shedding new light on the molecular mechanisms underlying their regulation. This study provides a framework for future research aimed at improving the current understanding of sugar metabolism and regulatory gene networks in sweet corn, which could ultimately lead to the development of novel strategies for crop improvement. [ABSTRACT FROM AUTHOR]

Scientists aim to improve crop response under stress conditions and gain better yields in continuously changing environmental conditions. They rely on plant phenotyping to quantify crop response under adverse conditions to achieve this goal and select the most tolerant genotypes. Recent advances in phenotyping platforms allow dissecting of complex traits such as abiotic stress. For example, the phenotyping platform is integrated with artificial intelligence (AI) and remote sensing tools to provide more robust, high throughput data collections in real-time changing environments. This review will give a deep understanding of the requirement of phenomics in crop improvement under stress conditions. We have discussed different phenotyping platforms, suitable traits for phenotyping, and machine learning and AI integration with the high throughput phenotypic platform for collecting a large data set of crops under stress conditions. Overall our review will dissect the phenomics aspects of complex traits, such as biotic and abiotic stress-related traits requiring sensor advancement, high-quality imagery combined with machine learning methods, and efforts in transdisciplinary science to foster integration across disciplines and better our understanding of plant stress biology. [ABSTRACT FROM AUTHOR]

Induced mutation by Ethyl Methane Sulphonate (EMS) has been found to be a very useful technique for crop improvement. Chemical mutagens, such as EMS, have been widely used to induce a variety of practical variations in several fruit crops. Therefore, a study was undertaken to determine the LD50 and the effects of mutagens on growth-related, yield-related, and quality-related observations, as well as the mortality percentage of runners derived from the Winter Dawn variety of strawberry using EMS to create variability for desirable traits. The runners were treated with EMS. The treated runners, along with a control group, were planted for growth in pots under a polytunnel. Based on the probit curve derived from the survival of the treated plant, the LD50 dose for EMS was found to be 3%. The 0.1% and 0.2% EMS doses showed good results in terms of growth, yield, and quality. An increase in the concentration of EMS resulted in a decrease in plant survival rate. [ABSTRACT FROM AUTHOR]