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Although finger millet is considered the future food, there are currently very few reports on how it reacts to salinity stress. This study aimed to compare the responses of twenty-seven native finger millet landraces under salt stress (0 mM to 250 mM NaCl in Hoagland solution). The degree of germination, seedling growth, biomass output, carotenoid content, membrane damage, and mineral accumulation were used to assess stress tolerance. With an increase in NaCl concentration, all landraces saw a drop in biomass production, shoot length, root length, and germination percentage. The decline was greater in ST-JA-SM and less in ST-JA-WA among landraces. All of the landraces showed a decrease in carotenoid content (108.76 ± 7.56 to 1.96 ± 0.83 µg mg−1 FW) with increasing salt concentration, whereas malondialdehyde (MDA) content (0.17 ± 0.05 to 8.36 ± 0.53 µM g−1 FW) was found to be increasing due to the stress imposed by salinity. The salt stress-sensitive landraces ST-JA-SM had greater MDA than the salt stress-tolerant ST-JA-WA. NaCl stress increased sodium and potassium levels in the seedlings of all the landraces. The magnitude of Na+ and K+ ions accumulation was higher in ST-JA-WA and less in ST-JA-SM. The salt tolerance indices for K+ ranged from 0.94 to 1.19, and that of Na+ ranged from 0.71 to 1.51. Combined these findings suggest that ST-JA-SM is stress-sensitive and ST-JA-WA is a stress-tolerant landrace that can be exploited in crop improvement programs. Additionally, it can be used as a participant in research on stress tolerance alleviation with noble elements like silicon or selenium. [ABSTRACT FROM AUTHOR]

Rice, serving as a crucial staple food for more than half of the global population, confronts significant challenges from insect pests, particularly the rice leaf folder (Cnaphalocrocis medinalis), which leads to substantial yield losses. This study meticulously evaluates 94 rice landraces for leaffolder resistance under diverse environmental conditions usisng genotype × environment (G × E) interaction analysis. The additive main effects and multiplicative interaction model and genotype and genotype × environment interaction (GGE) biplot are employed to assess stability and resistance traits. The findings reveal that 44 genotypes demonstrate stable resistance across three test environments (Kharif, 2021, Rabi, 2021–2022 and Kharif, 2022). Resistance is primarily governed by genotypic factors (89.93%), with minimal influence from the environment (5.22%). The GGE biplot highlights distinct mega-environments, identifying Kharif, 2021, followed by Kharif, 2022, as the ideal test environments. This study identifies specific stable resistant genotypes that could prove valuable for sustainable pest management and contribute to further crop improvement programs. [ABSTRACT FROM AUTHOR]

Millet, a vital and nutritionally dense cereal extensively cultivated in Sub-Saharan Africa, plays a key role in ensuring food security. This study investigates the starch synthase (SS) gene family, which is crucial for starch biosynthesis and influences various plant functions and stress responses. While the specific roles of SS genes in millet under drought conditions are not fully elucidated, this research provides a thorough analysis of the SS gene family in millet. A total of twelve millet SS genes (SiSSs) were identified and classified into four subfamilies (I–IV) through gene structure and phylogenetic analysis. The SiSS genes were unevenly distributed across millet chromosomes, with cis-acting elements associated with plant growth and stress defense being identified. Quantitative PCR (qPCR) revealed dynamic and varied expression patterns of SiSSs in different tissues under drought stress. Millet plants subjected to drought conditions showed higher tissue starch content and increased starch synthase activity compared to controls. Importantly, the expression levels of the twelve SiSSs were positively correlated with both starch content and synthase activity, suggesting their significant role in drought tolerance. This study enhances our understanding of the millet SS gene family and highlights the potential of these genes in breeding programs aimed at developing drought-resistant millet varieties. Further research is recommended to validate these findings and delve deeper into the mechanisms underlying drought tolerance.

The issue of food security continues to be a prominent global concern, affecting a significant number of individuals who experience the adverse effects of hunger and malnutrition. The finding of a solution of this intricate issue necessitates the implementation of novel and paradigm-shifting methodologies in agriculture and food sector. In recent times, the domain of artificial intelligence (AI) has emerged as a potent tool capable of instigating a profound influence on the agriculture and food sectors. AI technologies provide significant advantages by optimizing crop cultivation practices, enabling the use of predictive modelling and precision agriculture techniques, and aiding efficient crop monitoring and disease identification. Additionally, AI has the potential to optimize supply chain operations, storage management, transportation systems, and quality assurance processes. It also tackles the problem of food loss and waste through post-harvest loss reduction, predictive analytics, and smart inventory management. This study highlights that how by utilizing the power of AI, we could transform the way we produce, distribute, and manage food, ultimately creating a more secure and sustainable future for all.

Wheat is a crop of great food importance for food production in Brazil. However, the improvement of this crop is still concentrated in isolated areas, which hinders advances in new cultivation regions due to the extensive demand for existing information. In this investigation, four wheat genotypes analysed to study associations and interrelationships between wheat traits across nine environments during the agricultural years of 2016, 2017 and 2018. The experiment was conducted using a randomised block design with four repetitions, and the analysis was divided into two groups: morphological and productive traits of wheat, comprising three and eleven characteristics, respectively. Canonical correlations between the morphological and productive groups were found to be dependent in most environments. Taller plants with longer main spikes and longer tiller spikes can be indirectly selected to increase grain yield under different sowing conditions. The information generated in this study indicate that some care must be taken when using the interrelations between trait groups to select or recommend genotypes for broader regions, as these relationships are influenced by the specific conditions of each region and sub-region. [ABSTRACT FROM AUTHOR]

ABSTRACT Eleocharis vivipara, an amphibious sedge in the Cyperaceae family, has several remarkable properties, most notably its alternate use of C3 photosynthesis underwater and C4 photosynthesis on land. However, the absence of genomic data has hindered its utility for evolutionary and genetic research. Here, we present a high‐quality genome for E. vivipara, representing the first chromosome‐level genome for the Eleocharis genus, with an approximate size of 965.22 Mb mainly distributed across 10 chromosomes. Its Hi–C pattern, chromosome clustering results, and one‐to‐one genome synteny across two subgroups indicates a tetraploid structure with chromosome count 2n = 4x = 20. Phylogenetic analysis suggests that E. vivipara diverged from Cyperus esculentus approximately 32.96 million years ago (Mya), and underwent a whole‐genome duplication (WGD) about 3.5 Mya. Numerous fusion and fission events were identified between the chromosomes of E. vivipara and its close relatives. We demonstrate that E. vivipara has holocentromeres, a chromosomal feature which can maintain the stability of such chromosomal rearrangements. Experimental transplantation and cross‐section studies showed its terrestrial culms developed C4 Kranz anatomy with increased number of chloroplasts in the bundle sheath (BS) cells. Gene expression and weighted gene co‐expression network analysis (WGCNA) showed overall elevated expression of core genes associated with the C4 pathway, and significant enrichment of genes related to modified culm anatomy and photosynthesis efficiency. We found evidence of mixed nicotinamide adenine dinucleotide ‐ malic enzyme and phosphoenolpyruvate carboxykinase type C4 photosynthesis in E. vivipara, and hypothesize that the evolution of C4 photosynthesis predates the WGD event. The mixed type is dominated by subgenome A and supplemented by subgenome B. Collectively, our findings not only shed light on the evolution of E. vivipara and karyotype within the Cyperaceae family, but also provide valuable insights into the transition between C3 and C4 photosynthesis, offering promising avenues for crop improvement and breeding. [ABSTRACT FROM AUTHOR]

Kuttanad in India is known as ‘the rice bowl of Kerala’ and renowned for its unique rice cultivation system that is below sea level. However, rice production in this wetland ecosystem is seriously threatened by sheath blight disease caused by the fungus Rhizoctonia solani, which has resulted in a significant decline in grain quality and a 50% loss in yield. In the present study, we isolated two endophytic Bacillus subtilis strains, NIIST B616 and NIIST B627, from the roots of rice plants growing in the Kuttanad region and tested their efficacy in controlling sheath blight disease. We found that rice plants inoculated with a combination of both Bacillus strains and R. solani had a 64.71% lower disease incidence and a 31.02% higher harvest index than plants treated with R. solani alone. An analysis of defence-related enzymes and chemicals revealed that treatment with both isolates together greatly enhanced levels of l-phenylalanine ammonia-lyase (PAL; 2.8 fold), peroxidase (POX; 7.4 fold), polyphenol oxidase (PPO; 4.5 fold), and total phenol (8.5 fold) compared with plants treated solely with R. solani, indicating that these isolates significantly increased plant defence responses through induced systemic resistance (ISR), and this finding was validated through a split-root experiment. More detailed analysis using gas chromatography–tandem mass spectrometry (GC-MS/MS) and liquid chromatography–tandem mass spectrometry (LC-MS/MS) techniques revealed that cyclo-(Pro-Leu) and cyclo-(Pro-Phe) were the major components responsible for the antifungal properties of the two isolates and their capacity to trigger ISR in plants. Thus, the Bacillus strains and their metabolites may be deemed viable alternatives for controlling the prevalence of sheath blight disease in rice plants and augmenting rice production at unique locations such as Kuttanad. [ABSTRACT FROM AUTHOR]

Background: The tropical legume Mucuna pruriens (L.) DC. can meet three agricultural needs: low-cost protein, high-value medicines, and green manure or cover crops. But like other underutilized crops, it needs more modern breeding resources. Identifying marker-trait associations (MTAs) can facilitate marker-assisted breeding and crop improvement. Recent studies have demonstrated the feasibility of identifying MTAs using a small number of accessions (< 100). We have characterized a panel of 70 M. pruriens accessions across two consecutive years and performed association analysis for 16 phenotypic traits related to seed (seed length, seed width, seed thickness, seed yield per plant, hundred seed weight); pod (pod length, pod width, number of pods per cluster, number of pods per plant); inflorescence (inflorescence length, flower buds per inflorescence, flower length, pedicel length), and biochemical attributes (L-DOPA, total protein, total carbohydrate), using 66 genic-microsatellite markers following mixed linear model. Results: The results showed significant phenotypic (P < 0.05) and genetic diversity (Shannon's information index, I = 0.62) in our germplasm collection. Many tested traits were highly heritable (broad-sense heritability ranging from 42.86 to 99.93%). A total of 15 MTAs was detected at an adjusted significance level of P < 5.55 × 10− 3 for nine traits (seed length, seed thickness, seed width, hundred seed weight, seed yield per plant, inflorescence length, flower buds per inflorescence, flower length, and petiole length), contributed by 10 SSR markers (MPU_19, MPU_42, MPU_54, MPU_57, MPU_58, MPU_83, MPU_89, MPU_108, MPU_111, and MPU_122.) with phenotypic variance explained (PVE) ranging from 14.7 to 31.1%. Out of the ten trait-associated markers, the BLAST analysis revealed putative functions of seven markers, except MPU_57, MPU_58, and MPU_83. Conclusion: Fifteen MTAs identified for important traits with phenotypic variance explained > 10% from mixed linear model offer a solid resource base for improving this crop. This is the first report on association mapping in M. pruriens and our results are expected to assist with marker-assisted breeding and identifying candidate genes in this promising legume. [ABSTRACT FROM AUTHOR]

Understanding the complex interactions between genotype-environment dynamics is fundamental for optimizing crop improvement. However, traditional phenotyping methods limit assessments to the end of the growing season, restricting continuous crop monitoring. To address this limitation, we developed a methodology for spatiotemporal registration of time-series 3D point cloud data, enabling field phenotyping over time for accurate crop growth tracking. Leveraging multi-scan terrestrial laser scanning (TLS), we captured high-resolution 3D LiDAR data in a cotton breeding field across various stages of the growing season to generate fourdimensional (4D) crop models, seamlessly integrating spatial and temporal dimensions. Our registration procedure involved an initial pairwise terrain-based matching for rough alignment, followed by a bird's-eye view adjustment for fine registration. Point clouds collected throughout nine sessions across the growing season were successfully registered both spatially and temporally, with average registration errors of approximately 3 cm. We used the generated 4D models to monitor canopy height (CH) and volume (CV) for eleven cotton genotypes over two months. The consistent height reference established via our spatiotemporal registration process enabled precise estimations of CH (R² = 0.95, RMSE = 7.6 cm). Additionally, we analyzed the relationship between CV and the interception of photosynthetically active radiation (IPARf), finding that it followed a curve with exponential saturation, consistent with theoretical models, with a standard error of regression (SER) of 11%. In addition, we compared mathematical models from the Richards family of sigmoid curves for crop growth modeling, finding that the logistic model effectively captured CH and CV evolution, aiding in identifying significant genotype differences. Our novel TLS-based digital phenotyping methodology enhances precision and efficiency in field phenotyping over time, advancing plant phenomics and empowering efficient decision-making for crop improvement efforts. [ABSTRACT FROM AUTHOR]

Soybean represents a vital source of premium plant-based proteins for human nutrition. Importantly, the level of water-soluble protein (WSP) is crucial for determining the overall quality and nutritional value of such crops. Enhancing WSP levels in soybean plants is a high-priority goal in crop improvement. This study aimed to elucidate the genetic basis of WSP content in soybean seeds by identifying quantitative trait loci (QTLs) and set the foundation for subsequent gene cloning and functional analysis. Using 180 F10 recombinant inbred lines generated by crossing the high-protein soybean cultivar JiDou 12 with the wild variety Ye 9, our researcher team mapped the QTLs influencing protein levels, integrating Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene expression profiling to identify candidate genes. During the 2020 and 2022 growing seasons, a standard bell-shaped distribution of protein content trait data was observed in these soybean lines. Eight QTLs affecting protein content were found across eight chromosomes, with LOD scores ranging from 2.59 to 7.30, explaining 4.15–11.74% of the phenotypic variance. Notably, two QTLs were newly discovered, one with a elite allele at qWSPC-15 from Ye 9. The major QTL, qWSPC-19, on chromosome 19 was stable across conditions and contained genes involved in nitrogen metabolism, amino acid biosynthesis, and signaling. Two genes from this QTL, Glyma.19G185700 and Glyma.19G186000, exhibited distinct expression patterns at maturity, highlighting the influence of these genes on protein content. This research revealed eight QTLs for WSP content in soybean seeds and proposed a gene for the key QTL qWSPC-19, laying groundwork for gene isolation and enhanced soybean breeding through the use of molecular markers. These insights are instrumental for developing protein-rich soybean cultivars. [ABSTRACT FROM AUTHOR]

One of the critical growth and development stages that is vulnerable to drought and heat stress even in hardy staple crops is germination. Sorghum is a critically essential, resilient, and diverse crop that displays genotypic variations in its ability to withstand such harsh conditions, limiting crop stand and ultimately leading to yield losses. Therefore, the goal of this study was to evaluate the performance of 50 high potential genotypes of African sorghum, including landraces, breeding lines and check varieties to simulated drought and heat stress at germination stage. The study used a split plot arrangement for temperature treatments, laid in a completely randomized design with three replications. Final germination percentage, mean germination time, germination index and coefficient variation of germination time (CVt) were determined. Data was subjected to generalized linear model, principal component analysis, hierarchical agglomerative cluster analysis and principal coordinate analysis to determine statistical differences in genotypes and visualize groups of genotypes according to their overall performance in assessed germination parameters. Drought stress and supra-optimal temperatures suppressed and delayed germination. The genotypes were grouped into six distinct clusters based on their performance. Genotypes NPGRC1593, NPGRC1782, NPGRC1476 and IS224426 performed exceptionally well under both stressors and outperformed check varieties in almost all parameters assessed. To improve crop establishment and increase agricultural yields, breeding and crop improvement programs should focus on genotypes that can withstand both stresses. [ABSTRACT FROM AUTHOR]

Summary: The afila (af) mutation causes the replacement of leaflets by a branched mass of tendrils in the compound leaves of pea – Pisum sativum L. This mutation was first described in 1953, and several reports of spontaneous af mutations and induced mutants with a similar phenotype exist. Despite widespread introgression into breeding material, the nature of af and the origin of the alleles used remain unknown.Here, we combine comparative genomics with reverse genetic approaches to elucidate the genetic determinants of af. We also investigate haplotype diversity using a set of AfAf and afaf cultivars and breeding lines and molecular markers linked to seven consecutive genes.Our results show that deletion of two tandemly arranged genes encoding Q‐type Cys(2)His(2) zinc finger transcription factors, PsPALM1a and PsPALM1b, is responsible for the af phenotype in pea. Eight haplotypes were identified in the af‐harbouring genomic region on chromosome 2. These haplotypes differ in the size of the deletion, covering more or less genes.Diversity at the af locus is valuable for crop improvement and sheds light on the history of pea breeding for improved standing ability. The results will be used to understand the function of PsPALM1a/b and to transfer the knowledge for innovation in related crops. [ABSTRACT FROM AUTHOR]

• Modern varieties are derived from wild progenitors through crop domestication. • Limited genetic diversity is a constraint of crop improvement programs to keep pace with the challenges of climate change. • Crop wild relatives and their rich reservoir of gene pool provide the armor against crop stresses. • Genome editing tools are used to explore the germplasm of popular crops for domestication and climate-resilient genes. • Crop domestication is accelerated by Cis-regulating mutation, CRISPR-Cas-, and multiplex editing. Crop domestication is one of the oldest crop improvement methods, significantly impacting socioeconomic conditions globally. Modern varieties are derived from wild progenitors through crop domestication. These varieties are generated by crossing compatible genotypes to obtain the desired phenotype-containing progenies. The uncertainties and stress conditions caused by climate change deeply impact the current agricultural scenario. However, limited genetic diversity is the major constraint of the present crop improvement programs in keeping pace with climate change and several resulting biotic and abiotic stresses. Therefore, using crop wild relative and their rich reservoir of resistant genes to biotic and abiotic stressors must provide the armors against the crop stresses. However, crop wild relatives are unsuitable for direct intensive cropping because of many undesirable agronomic traits and are incompatible for gene transfer with conventional breeding. With the dawn of new-generation sequencing techniques and genome editing tools, scientists are trying to explore the germplasm of popular crops for domestication and climate-resilient genes. Considering the above context, the present review discusses the genetics of crop domestication, different strategies for a targeted mutation to accelerate crop domestication, and the current status of various crops. Further, it will discuss current challenges and the future fate of crop domestication using advanced biotechnological tools. [ABSTRACT FROM AUTHOR]

The storage substances of rice are critical factors that simultaneously affect grain yield and quality. Starch is the major component in the endosperm, directly affecting the seed yield as well as the cooking and eating quality of grains. Growing evidence suggests that some transcription factors are involved in regulating seed traits and starch biosynthesis. Here, we reveal the role of an NF-Y transcription factor gene, OsNF-YA8 , in regulation of seed traits and starch accumulation. OsNF-YA8 encodes a rice NF-YA protein containing the 166-amino acid. The RT-qPCR showed that OsNF-YA8 is expressed in roots, stems, leaves, flag leaves, and panicles, and dramatically increased in panicle during rice filling. Intracellular localization analysis showed that OsNF-YA8 is a nucleus-localized protein. In the OsNF-YA8 overexpression lines, rice grain length increased by 13.80–14.21 %, rice grain thickness decreased by 3.22–6.65 %, and the total starch content increased by 14.70–33.14 %. The overexpression of the OsNF-YA8 also decreased average starch granule size, and changed starch properties. Moreover, OsNF-YA8-overexpression up-regulated the expressions of genes involved in sucrose synthesis/transport and starch synthesis. By contrast, RNAi of OsNF-YA8 decreased the grain length, grain width, 1000 grain weight and starch content of rice seeds, and down-regulated the expressions of genes involved in sucrose synthesis/transport and starch synthesis. These results suggest that OsNF-YA8 enhances starch accumulation and confers seed traits by positively regulating starch biosynthesis in rice. The findings provide a new perspective on genetic improvement of crop agronomic traits and seed quality. [Display omitted] • OsNF-YA8 encodes a nucleus-localized protein with 166-amino acid. • The overexpression of the OsNF-YA8 confers seed improvement traits. • OsNF-YA8 promotes starch accumulation by positively regulates starch biosynthesis. • OsNF-YA8 impacts on rice grain size and physicochemical properties of starch grains. • OsNF-YA8 upregulates the expression of sucrose and starch synthesis-related genes. [ABSTRACT FROM AUTHOR]

The upsurge of stemphylium blight disease noticed during recent cropping years is the prime global threat for lentil (Lens culinaris Medik.) production. Identification of factors that influence lentil yield with the help of an advanced regression model will speed up the progress of lentil crop improvement for biotic stress tolerance. In this context, an experiment was undertaken to identify the key control factors of lentil yield under stemphylium blight stress. The field experiment was laid out under alpha lattice design using fifty lentil genotypes with two replications. An advanced dimension reduction cum regression approach Partial Least Square Regression (PLSR) was employed to mitigate the effect of multi-collinearity among 23 yield-influencing traits along with traditional Stepwise Multiple Linear Regression (SMLR). The results of SMLR analysis indicated that pods per plant, number of seeds per pod, hundred seed weight, superoxide dismutase and pod yield per plant had considerable effects on seed yield per plant with the R-squared value of 0.940. The first four PLSR components were considered to be optimum which were cumulatively explained 93.10% of the total variance towards lentil seed yield. The trait pods per plant was recorded with the highest PLSR regression coefficient devoid of multi-collinearity effects among the independent yield attributing variables under stemphylium blight environment and hence concluded to be the most influencing trait towards lentil seed yield followed by seeds per pod, hundred seed weight, pod yield per plant and superoxide dismutase. [ABSTRACT FROM AUTHOR]

Base editing represents a cutting-edge genome editing technique that utilizes the CRISPR system to guide base deaminases with high precision to specific genomic sites, facilitating the targeted alteration of individual nucleotides. Unlike traditional gene editing approaches, base editing does not require DNA double-strand breaks or donor templates. It functions independently of the cellular DNA repair machinery, offering significant advantages in terms of both efficiency and accuracy. In this review, we summarize the core design principles of various DNA base editors, their distinctive editing characteristics, and tactics to refine their efficacy. We also summarize their applications in crop genetic improvement and explore their potential contributions to forest genetic engineering. [ABSTRACT FROM AUTHOR]

Soybean is an important agricultural crop known for its high protein and oil content, contributing to essential nutritional and health benefits for humans. Domesticated in China over 5,000 years ago, soybean has since adapted to diverse environments and spread worldwide. This study aimed to investigate the genomic characteristics and population structures of 2,317 publicly available soybean whole-genome sequences from diverse geographical regions, including China, Korea, Japan, Europe, North America, and South America. We used large-scale whole-genome sequencing data to perform high-resolution analyses to reveal the genetic characteristics of soybean accessions. Soybean accessions from China and Korea exhibited landrace characteristics, indicating higher genetic diversity and adaptation to local environments. On the other hand, soybean accessions from Japan, the European Union, and South America were found to have low genetic diversity due to artificial selection and breeding for agronomic traits. We also identified key variants and genes associated with the ability to adapt to different environments. In Korean soybean accessions, we observed strong selection signals for isoflavone synthesis, an adaptive trait critical for improving soybean adaptability, survival, and reproductive success by mitigating environmental stress. Identifying specific genomic regions showing unique patterns of selective sweeps for genes such as HIDH, CYP73A11, IFS1, and CYP81E11 associated with isoflavone synthesis provided valuable insights into potential adaptation mechanisms. Our research has significantly improved our understanding of soybean diversity at the genetic level. We have identified key genetic variants and genes influencing adaptability, laying the foundation for future advances in genomics-based breeding programs and crop improvement efforts. [ABSTRACT FROM AUTHOR]

The SEVEN IN ABSENTIA (SINA) E3 ubiquitin ligase is widely involved in drought and salt stress in plants. However, the biological function of the SINA proteins in cotton is still unknown. This study aimed to reveal the function of GhSINAT5 through biochemical, genetic and molecular approaches. GhSINAT5 is expressed in several tissues of cotton plants, including roots, stems, leaves and cotyledons, and its expression levels are significantly affected by polyethylene glycol, abscisic acid and sodium chloride. When GhSINAT5 was silenced in cotton plants, drought and salinity stress occurred, and the length, area and volume of the roots significantly decreased. Under drought stress, the levels of proline, superoxide dismutase, peroxidase and catalase in the GhSINAT5-silenced cotton plants were significantly lower than those in the non-silenced control plants, whereas the levels of hydrogen peroxide and malondialdehyde were greater. Moreover, the expression of stress-related genes in silenced plants under drought stress suggested that GhSINAT5 may play a positive role in the plant response to drought and salt stress by regulating these stress response-related genes. These findings not only deepen our understanding of the mechanisms of drought resistance in cotton but also provide potential targets for future improvements in crop stress resistance through genetic engineering. [ABSTRACT FROM AUTHOR]

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have revolutionized genome editing, significantly advancing the improvement of cultivated crop species. This review provides an overview of genome-edited crops that have either reached the market or received the necessary approvals but are not yet available to consumers. We analyze various genome-editing studies to understand the distribution of different genome-editing systems, the types of site-directed nucleases employed, and the geographical spread of these studies, with a specific focus on global and European contexts. Additionally, we examine the target crops involved. The review also outlines the multiple steps required for the legal acceptance of genome-edited crops within European jurisdictions. We conclude with suggestions for the future prospects of genome-editing research in Europe, aiming to streamline the approval process and enhance the development and adoption of genome-edited crops. [ABSTRACT FROM AUTHOR]

In this study, we assessed the effects of biochar prepared from an invasive tree, Broussonetia papyrifera on the growth of selected pulse (Cajanus cajan and Vigna radiata) and cereal (Oryza sativa and Zea mays) crops under laboratory conditions. Two experiments were designed, one with biochar powder and another with biochar water extract to mimic the environmental conditions of the growing season of the crops. The findings of the study revealed that the seeds of pulse crops responded slower during the initial days (3 to 7 days) of exposure to the biochar powder whereas a marked increase in root and shoot growth parameters was observed with increasing doses of biochar at 15th day, compared with the control. With an initial increase in growth behaviour of pulses (at 3rd day), a stable growth response was observed at 7th and 15th days under control treatments. Both cereal and pulse crops showed better growth responses with increasing dose of biochar, and maximum growth was observed at 1-2% (for powder) and 2-4% (for extract) biochar doses. Application of powdered biochar showed better growth responses than the extract, as it facilitated gradual-release of nutrients, thus allowed the plants to stay healthy for a longer period of time. The results underscore the importance of using biochar based on the specific crop types, seed sizes, and growth stages to fully utilize its potential in sustainable agriculture. Harnessing the beneficial attributes of biochar not only enhances soil quality and crop yields but also presents a promising avenue for environmentally friendly weed control and resource utilization, aligning with broader objectives of agricultural sustainability and food security. Further investigations focused on optimizing biochar formulations and conducting field-scale trials will be essential in realizing its transformative impact on global agricultural practices. [ABSTRACT FROM AUTHOR]

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

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for ~15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits. The authors present a comprehensive regulome atlas for rice by mapping chromatin accessibility across 23 tissues from three rice varieties. By integrating matched RNA-seq data, they accurately predict numerous associations between non-coding regulatory elements and target genes. This study provides a foundational resource for gene editing and breeding strategies targeting non-coding regions in rice, potentially advancing crop improvement efforts. [ABSTRACT FROM AUTHOR]

This study focuses on semantic segmentation in crop Opuntia spp. orthomosaics; this is a significant challenge due to the inherent variability in the captured images. Manual measurement of Opuntia spp. vegetation areas can be slow and inefficient, highlighting the need for more advanced and accurate methods. For this reason, we propose to use deep learning techniques to provide a more precise and efficient measurement of the vegetation area. Our research focuses on the unique difficulties posed by segmenting high-resolution images exceeding 2000 pixels, a common problem in generating orthomosaics for agricultural monitoring. The research was carried out on a Opuntia spp. cultivation located in the agricultural region of Tulancingo, Hidalgo, Mexico. The images used in this study were obtained by drones and processed using advanced semantic segmentation architectures, including DeepLabV3+, UNet, and UNet Style Xception. The results offer a comparative analysis of the performance of these architectures in the semantic segmentation of Opuntia spp., thus contributing to the development and improvement of crop analysis techniques based on deep learning. This work sets a precedent for future research applying deep learning techniques in agriculture. [ABSTRACT FROM AUTHOR]

Despite hybrid dominance contributing to the genetic improvement of crops, little is known about heterosis and inheritance patterns of endogenous substances in sorghum (Sorghum bicolor (L.) Moench) root bleeding sap. In this study, six sterile and six restorer lines of sorghum and 36 hybrid sorghum combinations formulated as incomplete double-row crosses were selected as test materials, and heterosis, combining ability, heritability, and their interrelationships of root bleeding sap endogenous substances in different hybrid sorghum combinations and their parents were investigated. The results showed that the root bleeding sap of the F1 generation of hybrid sorghum had a high heterosis in both soluble sugar content and amino acid content at the flowering stage, and the average high-parent heterosis was 129.34% and 74.57%, respectively. Indole-3-acetic acid (IAA), cytokinins (CTK), gibberellic acid (GA3), abscisic acid (ABA), soluble sugar, amino acid, and root bleeding intensity were mainly affected by non-additive genetic effects of the genes. Soluble protein was affected by additive genetic effects of the genes and had a high narrow heritability (75.50%), which could be selected at low generations in breeding. The combining ability analyses showed that the sterile lines 521A and 170A, and the restorer lines Ji318R and 0–30 were promising parents with high general combining ability. Correlation analysis showed that all endogenous substances of root bleeding sap were positively correlated with the sum of parental general combining ability (GCA) at highly significant levels, and IAA, CTK, GA3, ABA, soluble sugar, amino acid, and root bleeding intensity were positively correlated with male GCA at significant or highly significant levels. Therefore, the GCA of the restorer lines root bleeding sap endogenous material or the sum of both parents' GCA can be used to predict the performance of wounding endogenous material in the F1 generation of hybrid sorghum. Overall, this study results can help elucidate heterosis mechanisms of root bleeding sap endogenous material and improve sorghum quality. [ABSTRACT FROM AUTHOR]

Integrated nutrient management and crop rotation are important farming practices, which enhance the nutrient use efficiency of crops and reduce the incidence of diseases and insect pests. The study was carried out to address the gap in using integrated nutrient management in crop rotation systems for soil qualities and crop yield improvement. That was done by adjusting the balance ratio of dry bio-slurry and nitrogen fertilizers. The experiment was containing ten levels; Control (0,0), recommended nitrogen, 50% dry-bio slurry, 100% dry-bio slurry, 75% dry-bio slurry, 75% dry-bio slurry+25% recommended nitrogen, 50% dry-bio slurry+50% recommended nitrogen, 25% dry-bio slurry+75% recommended nitrogen, 100% dry-bio slurry + 25% recommended nitrogen and 100% dry-bio slurry + 50% recommended nitrogen that was laid out in randomized complete block design with three replications for three years. The data on soil properties and yield components of potatoes and wheat were collected and analyzed using statistical analysis system software 9.4. An application of dry bio-slurry with nitrogen fertilizer was significantly affected both crop yield and soil properties in the rotation system. The application of 25% dry bio-slurry with 75% recommended nitrogen gave the highest tuber yield of potato (27.6 tha-1) as compared to control. Similarly, using 100% and 75% sole dry bio-slurry resulted in the highest grain yield (3.85 tha-1) and above-ground biomass (9.59 tha-1) of wheat. The combination of 25% dry bio-slurry with 75% recommended nitrogen scored the highest net benefit (2889.2 US$) with an acceptable marginal return (4463.3%) via by improving crops yield in the system. So, an application of 25% dry bio-slurry with 75% recommended nitrogen could be promoted for yield-soil improvement in the study area and similar agroecology. [ABSTRACT FROM AUTHOR]

Background: Boron (B) is an essential micronutrient for plants. Inappropriate B supply detrimentally affects the productivity of numerous crops. Understanding of the molecular responses of plants to different B supply levels would be of significance in crop improvement and cultivation practices to deal with the problem. Results: We conducted a comprehensive analysis of the transcriptome and proteome of tobacco seedlings to investigate the expression changes of genes/proteins in response to different B supply levels, with a particular focus on B deficiency. The global gene and protein expression profiles revealed the potential mechanisms involved in the responses of tobacco to B deficiency, including up-regulation of the NIP5;1-BORs module, complex regulation of genes/proteins related to cell wall metabolism, and up-regulation of the antioxidant machinery. Conclusion: Our results demonstrated that B deficiency caused severe morphological and physiological disorders in tobacco seedlings, and revealed dynamic expression changes of tobacco genes/proteins in response to different B supply levels, especially to B deficiency, thus offering valuable insights into the molecular responses of tobacco to B deficiency. [ABSTRACT FROM AUTHOR]

ABSTRACT Thaumatin‐like proteins (TLPs) are part of the pathogenesis‐related (PR) proteins that are important in host plant defense. TLPs have multiple defense functions against pathogens (bacteria, viruses, and fungi) and are involved in other biological processes of several living organisms. However, the biological role of TLPs must be elucidated for other species, such as Phaseolus lunatus, popularly known as lima bean. In this study, we propose to investigate the biological activity of TLPs in P. lunatus, which can help develop a detailed functional characterization of the TLP gene in other crop cultures. As a result, a total of 31 PlTPLs genes and 16 highly conserved cysteine residues for each family member were identified in the lima bean genome. Regarding phylogenetic analysis, 128 TLPs from different plant species, including P. lunatus, were used, and the phenetic tree revealed that the TLPs could be divided into six groups. The leading group was Group 4, containing 34 TLPs; the smallest was Group 7, containing only a single TLP. The analysis of antimicrobial and antiviral activity revealed that 27 PlTLPs have antimicrobial activity and 7 PlTLPs have potential antiviral activity. For chromosomal distribution of the PlTLPs, 8 of 11 chromosomes presented at least one PlTLs on one of the chromosomes. Finally, molecular modeling was carried out between two TLPs (PlTLP5 and PlTLP14), which presented antimicrobial and antiviral activity and did not have allergenic activity. The results showed that the two candidates presented ≥90% of their residues in the favorable regions and ∼10% in the permitted regions, demonstrating that the two PlTLPs are considered promising targets for biotechnological applications, especially those related to the genetic improvement of agricultural crops and the development of antimicrobial agents. [ABSTRACT FROM AUTHOR]

Background: This research explores the efficacy of mutagenesis, specifically using sodium azide (SA) and hydrazine hydrate (HZ) treatments, to introduce genetic diversity and enhance traits in three wheat (Triticum aestivum L.) genotypes. The experiment entails subjecting the seeds to different doses of SA and HZ and cultivating them in the field for two consecutive generations: M1 (first generation) and M2 (second generation). We then employed selective breeding techniques with Start Codon Targeted (SCoT) markers to select traits within the wheat gene pool. Also, the correlation between SCoT markers and specific agronomic traits provides insights into the genetic mechanisms underlying mutagenesis-induced changes in wheat. Results: In the study, eleven genotypes were derived from parent varieties Sids1, Sids12, and Giza 168, and eight mutant genotypes were selected from the M1 generation and further cultivated to establish the M2 generation. The results revealed that various morphological and agronomical characteristics, such as plant height, spikes per plant, spike length, spikelet per spike, grains per spikelet, and 100-grain weight, showed increases in different genotypes from M1 to M2. SCoT markers were employed to assess genetic diversity among the eleven genotypes. The bioinformatics analysis identified a correlation between SCoT markers and the transcription factors ABSCISIC ACID INSENSITIVE3 (ABI3) and VIVIPAROUS1 (VP1), crucial for plant development, growth, and stress adaptation. A comprehensive examination of genetic distance and the function identification of gene-associated SCoT markers may provide valuable insights into the mechanisms by which SA and HZ act as mutagens, enhancing wheat agronomic qualities. Conclusions: This study demonstrates the effective use of SA and HZ treatments to induce gene diversity through mutagenesis in the wheat gene pool, resulting in the enhancement of agronomic traits, as revealed by SCoT markers. The significant improvements in morphological and agronomical characteristics highlight the potential of mutagenesis techniques for crop improvement. These findings offer valuable information for breeders to develop effective breeding programs to enhance wheat quality and resilience through increased genetic diversity. [ABSTRACT FROM AUTHOR]

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

Lodging has posed a serious threat to the yield and quality of rice. This study aims to explore the effect of mechanical and physicochemical properties on the lodging resistance of hybrid japonica rice. The test subjects were selected as the curved panicle hybrid japonica rice Liaoyou 2006 (LY2006), Liaoyou 5218 (LY5218), and Liaoyou 5273 (LY5273) in northern China. The control object was selected as the conventional japonica rice Nonglin 313 (NL313(CK)) easy to fall. Then the agronomic characters and microstructure of the plant were measured to establish the mechanical evaluation index for the lodging resistance of japonica hybrid rice, including the maximum bending force, breaking moment, bending section coefficient, single stem weight mass moment, bending strength, Young's elastic modulus and inertia moment, according to the bending and tensile test. Finally, the correlation between the physicochemical and mechanical properties and lodging index was also studied to investigate the effects of mechanical and physicochemical properties on the lodging resistance of hybrid japonica rice under natural cultivation conditions in the field. Four results were obtained. 1) The type of plant was used to improve the structure of rice plants. Thus, ventilation and light transmission were provided for the plants to create a microclimate, thereby strengthening the individual stems and their lodging resistance. The plant height and panicle weight of hybrid japonica rice LY2006, LY5218, and LY5273 were significantly higher than those of conventional japonica rice NL313, whereas, their lodging resistance was greater than that of NL313. Therefore, the shorter the plant height was, and the lighter the panicle was, the stronger the lodging resistance was under suitable cultivation conditions. The structure of the rice plant type was optimized for the unity of high-stem and high-yield. 2) The length of the basal internodes and leaf sheaths of hybrid japonica rice shared a significant impact on the lodging resistance. The lengths of the second and third internodes of hybrid japonica rice LY2006, LY5218, and LY5273 were significantly lower than those of conventional japonica rice NL313, while the lengths of the second and third leaf sheaths were significantly higher. Therefore, the short basal internodes and the long leaf sheaths effectively enhanced the lodging resistance of rice plants. 3) The lodging resistance depended on the thickness of cells and tissues, the area of vascular bundles, as well as the content of cellulose, lignin, and potassium in the stems of hybrid japonica rice. The hybrid japonica rice LY2006, LY5218, and LY5273 presented the strong lodging resistance, indicating the relatively larger cell and tissue thickness, vascular bundle area, as well as the higher content of cellulose, lignin, and potassium. The cultivation and genetic regulation were optimized during rice growth. 4) The mechanical properties of hybrid japonica rice stems also played a decisive role in the lodging resistance of rice plants. The breaking resistance, bending moment, bending section coefficient, single stem weight mass moment, bending strength, Young's modulus, and inertia moment were used as the evaluation indexes for the lodging resistance of hybrid japonica rice. It was found that there was a significant positive correlation between lodging resistance and the maximum breaking resistance, bending moment, bending section coefficient, bending strength, and Young's modulus (P<0.01). There was a significant negative correlation between single stem weight mass moment and inertia moment (P<0.01). The finding can provide comprehensive data support and theoretical support to improve the lodging resistance varieties and agronomic traits in northern japonica hybrid rice. [ABSTRACT FROM AUTHOR]

Genetic engineering has become an essential element in developing climate-resilient crops and environmentally sustainable solutions to respond to the increasing need for global food security. Genome editing using CRISPR/Cas [Clustered regulatory interspaced short palindromic repeat (CRISPR)-associated protein (Cas)] technology is being applied to a variety of organisms, including plants. This technique has become popular because of its high specificity, effectiveness, and low production cost. Therefore, this technology has the potential to revolutionize agriculture and contribute to global food security. Over the past few years, increasing efforts have been seen in its application in developing higher-yielding, nutrition-rich, disease-resistant, and stress-tolerant "crops", fruits, and vegetables. Cas proteins such as Cas9, Cas12, Cas13, and Cas14, among others, have distinct architectures and have been used to create new genetic tools that improve features that are important for agriculture. The versatility of Cas has accelerated genomic analysis and facilitated the use of CRISPR/Cas to manipulate and alter nucleic acid sequences in cells of different organisms. This review provides the evolution of CRISPR technology exploring its mechanisms and contrasting it with traditional breeding and transgenic approaches to improve different aspects of stress tolerance. We have also discussed the CRISPR/Cas system and explored three Cas proteins that are currently known to exist: Cas12, Cas13, and Cas14 and their potential to generate foreign-DNA-free or non-transgenic crops that could be easily regulated for commercialization in most countries. [ABSTRACT FROM AUTHOR]

Background: Hulless barley (Hordeum vulgare L. var. nudum Hook. f.) is a significant cereal crop and a substantial source of forage for livestock. Long non-coding RNAs (lncRNAs) and metabolites play crucial roles in the nutrient accumulation and regeneration of hulless barley plants following mowing. The study aimed to identify differentially expressed lncRNAs and metabolites in hulless barley plants by analyzing transcriptomic and metabolomic datasets at 2 h, 24 h, and 72 h following mowing. Results: The study revealed that 190, 90, and 438 lncRNA genes were differentially expressed at the 2 h, 24 h, and 72 h time points compared to the non-mowing control. We identified 14 lncRNA genes—11 downregulated and 3 upregulated—showing consistently significant differential expression across all time points after mowing. These differentially expressed lncRNAs target genes involved in critical processes such as cytokinin signaling, cell wall degradation, storage protein accumulation, and biomass increase. In addition, we identified ten differentially expressed metabolites targeting diverse metabolic pathways, including plant hormones, alkaloids, and flavonoids, before and after mowing at various time points. Endogenous hormone analysis revealed that cytokinin most likely played a crucial role in the regeneration of hulless barley after mowing. Conclusions: This study created a comprehensive dataset of lncRNAs, metabolites, and hormones in hulless barley after mowing, revealing valuable insights into the functional characteristics of lncRNAs, metabolites, and hormones in regulating plant regeneration. The results indicated that cytokinin plays a significant role in facilitating the regeneration process of hulless barley after mowing. This comprehensive dataset is an invaluable resource for better understanding the complex mechanisms that underlie plant regeneration, with significant implications for crop improvement. [ABSTRACT FROM AUTHOR]

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

【Objective】Purple leaf mustard is a new variety of mustard with high anthocyanin bred by crossing green leaf Shuidong mustard (A national product of geographical indication in China), and its fertilization technology needs to be further studied. Replacing part of chemical fertilizer by organic fertilizer is considered to be a more effective fertilization measure for soil improvement and increase of crop yield and quality. It is of great significance to provide guidance for the scientific production of mustard by studying the effects of different fertilization treatments on soil properties, yield and quality of mustard. 【Method】In the study, the Ganoderma lucidum residue compost was used as the tested organic fertilizer, the green leaf Shuidong mustard and purple leaf mustard were used as the tested crops for pot experiment. Taking the single application of chemical fertilizer (conventional application of compound fertilizer only) as control (CK), under the condition of 3/4 reduction of chemical fertilizer, three treatments of low (7.90 g), medium (15.80 g) and high (31.60 g) mushroom residue compost were set: T1, T2 and T3, the indexes of soil pH value, physical clay (PC, <0.01 mm), OM, AN, AP, AK, PH, FW, RL, Chl, Ant, SS and Vc contents of mustard after harvest were measured, and the differences of soil properties and yield and quality of mustard under different treatments were analyzed. 【Result】The results showed that, with the increase of the amount of G. lucidum residue compost, except for soil pH value and PC content, the other 11 indexes showed an increasing trend. The soil OM, RL, SS and Vc content of T1, T2 and T3 were higher than those of CK, while the AN content was lower than that of CK; the contents of soil AP, AK, FW, Chl and Ant of mustard of T3 were higher than those of CK, and the PH of T3 and CK were equivalent, but higher than that of T2 and T1. Compared with CK, the soil OM, AP and AK contents of green leaf Shuidong mustard and purple leaf mustard under T3 increased by 13.24%/14.28%, 6.74%/6.06% and 6.43%/6.04%, AN content decreased by 0.81%/1.45%, respectively; FW, RL, the contents of Chl, SS and Vc of two kinds of mustards increased by 0.33%/6.64%, 34.65%/43.29%, 11.03%/6.53%, 53.36%/44.45% and 16.66%/15.44%, respectively. Under the same treatment, the PH, RL, FW, Chl, Ant, SS, and Vc content of purple leaf mustard were significantly higher than those of green leaf Shuidong mustard.【Conclusion】It shows that the G. lucidum residue compost replacing part of chemical fertilizer can improve the soil and the production and quality of mustard, with T3 showing the best fertilizer effect. Under the same fertility, purple leaf mustard has better growth, pigment content and quality tcompared with green leaf Shuidong mustard [ABSTRACT FROM AUTHOR]

Throughout the growth and development of higher plants, the shoot apical meristem（SAM）and root apical meristem（RAM） continually differentiate to generate roots, stems, leaves and flowers, then forming above-ground and below-ground organs, respectively. As one of important intercellular signal transduction molecule, small peptides are involved in regulation of many physiological processes in plant development and resistance to biotic and abiotic stress. Particularly, they play crucial role in regulating the activity of SAM and RAM, which ultimately affect the origin and development of plant organs. In recent years, emerging evidences reveal the importance roles of small peptides in maintaining meristems homeostasis and regulating crop agronomic traits. This review highlights the biological functions and molecular mechanisms of small peptides and their receptors in maintaining the homeostasis of meristems in Arabidopsis and crop species. It also discusses the role of small peptides in regulating crop yield traits and their application in crop improvement. Additionally, the review proposes and prospects the potential interesting research direction of small peptides. [ABSTRACT FROM AUTHOR]

Plant breeders leverage mutagenesis using chemical, biological, and physical mutagens to create novel trait variations. Many widely used sorghum genotypes have a narrow genetic base, which hinders improvements using classical breeding. Enhancing the diversity of the sorghum genome thus remains a key priority for sorghum breeders. To accelerate the genetic enhancement of sorghum, an extensive library comprised of seeds from 150,000 individual mutant plants of the Sorghum bicolor inbred line BTx623 was established using ethyl methanesulphonate (EMS) as a mutagen. The sorghum mutant library was bulked into 1498 pools (~100 seed heads per pool). In each pool, DNA was extracted from a subset of the seed and screened using the FIND‐IT technology based on droplet digital PCR. All 43 nucleotide substitutions that were screened using FIND‐IT were identified, demonstrating the potential to identify any EMS‐derived mutation in an elite line of sorghum within days. This diverse library represents the largest collection of sorghum mutants ever conceived, estimated to cover 240% of all possible EMS‐induced mutation points within the Sorghum genome. Using FIND‐IT, the speed at which a specific desired EMS‐derived mutation can be identified is a major upgrade to conventional reverse genetic techniques. Additionally, the ease at which valuable variants can be integrated into elite commercial lines is a far simpler and less expensive process compared to genome editing. Genomic variations in the library will have direct utility as a breeding resource for commercial sorghum applications, allowing enhanced adaptation to climate change and enhanced yield potential in marginal environments. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance (AMR) represents a significant global health problem which challenges Sustainable Development Goal 3 of the United Nations, with growing concerns about the possibility of AMR transmission through the food chain. The indiscriminate use of antimicrobials for the treatment of food production animals and for agricultural crop improvement, in addition to the direct discharge of livestock farm residues to sewage and the use of animal manure in agriculture, are among the factors that can facilitate the selection and transmission of AMR throughout the food chain. The study of food microbiomes has been boosted by the advent of next‐generation sequencing techniques, which have enabled gaining in‐depth understanding of the diversity of antimicrobial resistance genes present in food and associated environments (the so‐called resistome). The aim of this review is to provide an accurate and comprehensive overview of the knowledge currently available on the resistome of the most frequently consumed foods worldwide, from a One Health perspective. To this end, the different metagenomic studies which have been conducted to characterize the resistome of foods are compiled and critically discussed. [ABSTRACT FROM AUTHOR]

Stem elongation has a major influence on plant height and has been a key trait targeted in crop improvement, as illustrated by the green revolution. Particularly in cereal crops, there is a growing awareness of how genetic variation for elongation may be applied to specific challenges in production and may interact with other aspects of development. In comparison, this understanding is less developed in legume crops despite their significance in global agriculture and may have additional implications considering their distinct differences in growth habit and inflorescence structure. This review outlines the relevance of stem elongation in legume crops, provides an overview of its genetic control, and concludes with a discussion of potential interactions with other production traits, including stress tolerance and symbioses. [ABSTRACT FROM AUTHOR]

Wild crop germplasm and landrace varieties have long been considered as a source of novel genetic variation for improving domesticated crops. Due to genetic bottlenecks that occurred during domestication, dissemination, and subsequent crop improvement, many beneficial genes are absent from commercial varieties and elite breeding germplasm, yet are still present in wild populations. To catalog potential novel disease resistance genes useful for breeding more resilient dry beans, we screened wild and landrace Phaseolus vulgaris L. accessions archived in the USDA GRIN seed bank for untapped resistance to anthracnose (Colletotrichum lindemuthianum) and bean common mosaic necrosis virus (BCMNV). A population of 194 wild and 55 landrace accessions were screened for resistance to two highly virulent races of anthracnose (race 2047 and race 3481) and for resistance to the BCMNV strain NL‐3. Thirteen accessions, all wild, were resistant to both anthracnose races, with MX‐QT‐3 and PI 661812 displaying complete resistance with no disease symptoms across all replications. Surprisingly, no natural resistance to BCMNV strain NL‐3 was detected in the wild germplasm. PI 442541, PI 661891, and W6 10164 were the only three accessions that expressed the I‐gene phenotype and all three have some history of cultivation. This study provides a resource for introgression of genetic diversity for anthracnose resistance into cultivated beans and reveals that innate resistance to BCMNV may not exist in wild populations of P. vulgaris. Core Ideas: Wild Phaseolus vulgaris germplasm has genetic and phenotypic diversity not present in cultivated varieties.Resistance to two races of anthracnose exists in wild bean germplasm.Resistance to BCMNV NL‐3 was not found in wild bean germplasm, but in three landraces. [ABSTRACT FROM AUTHOR]

Improvements in crop growth and productivity have been partly ascribed to the effect of plant population on spacing and the number of plants stand-1 in a field. In a field experiment conducted at the Teaching and Research Farm of Ekiti State University in Ado-Ekiti, Nigeria, the growth and yield of muskmelon were determined using four different spacings (1x1, 1x1.33, 1x2, and 2x2 m), and 1 or 2 plants stand-1 to attain 2,500 - 20,000 plants ha-1 population. Using a Randomized Complete Block Design with three replicates, the experiment's 4x2 factorial was established. The number of leaves, leaf area, vine length, branches, branch length, flowering, number of fruits hectare-1, fruit weight, fruit yield, and fruit pulp width were all measured. The 2,500 plants ha-1 produced the longest vine (131.50 cm) and branches (111.78 cm), while the 5,000 plants ha-1 (2 plants stand-1) generated the most significant number of leaves (81.83) and largest leaf area (156.33 cm²). The 1 plant stand-1 group produced more leaves, more significant leaf areas, and longer vines and branches. At larger plant densities, fruit yield and number per hectare per year increased. However, fruit size decreased. 20,000 plants ha-1 (2 plants stand-1) of muskmelons produced the most significant number of fruits (20,803.30) and fruit output (10.29 t ha-1); hence it is recommended that this setting be utilized for muskmelons production. [ABSTRACT FROM AUTHOR]

Late blight (LB) caused by Phytophthora infestans (Mont.) de Bary, is one of the most destructive diseases of potato and tomato worldwide. Globally, application of fungicide is an effective approach for potato LB management. Isolates of P. infestans were collected from different fields in Egypt and characterized using microsatellite markers and mitcondrial DNA. Twelve fungicides were applied in vitro to test their control P. infestans isolates. Nine potato cultivars were evaluated under artificial inoculation. Field trials were conducted to evaluate the efficacy of applied fungicides to LB management and potato productivity at El-Behera governorate in two seasons. Our results revealed that collected isolates of P. infestans were A1 mating type, 23_A1 clonal lineage and Ia/IR1 mitcondrial DNA. Furthermore, potato cultivar Burren was highly resistant and recorded the lowest area under disease progress curve (AUDPC). On the other hand, cultivars Alaska, Spunta, Lady Rosita and Mondial were highly susceptible and revealed the highest AUDPC values. In vitro, all fungicide applications inhibited linear growth of P. infestans isolates (EG-Pi1 and EG-Pi2). For field trial, Equation-Pro, and Consonto were the most effective fungicides in respect of LB management where lowest disease severity and AUDPC were recorded in both prophylactically and curatively during two seasons. Moreover, potato tuber production significantly increased with Equation -- Pro application. The results of this study provided crucial information for potato breeding programs and crop improvement as well as successful management strategy for late blight challenge. [ABSTRACT FROM AUTHOR]

Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing diversity in crops. This study was carried out at Lovely Professional University's agricultural research farm in Punjab, India, during the year 2023. The experimental design followed a randomized complete block design (RCBD) with three replications. The experiment aimed to assess the effect of three chemical mutagens, sodium azide (SA), ethyl methyl sulphonates (EMSs), and methyl methane sulfonate (MMS), at three different concentrations (0.2%, 0.4%, and 0.6%), in SL958 and SL744 soybean varieties to select the mutant exhibiting the highest yield. The data were collected and analysed using a two-way ANOVA test through SPSS software (version 22), and the means were separated using Duncan's multiple range test (DMRT) at the 5% level of significance. Between the two varieties, the highest seed germination percentage (76.0% seedlings/plot) was recorded in SL958 (0.4% SA), while the lowest (30.33% seedlings/plot) was observed in 0.6% MMS as compared to the control (53% and 76% in SL744 and SL958 at 10 days after sowing, respectively). Several weeks after sowing, the average plant height was observed to be higher (37.84 ± 1.32 cm) in SL958 (0.4% SA) and lower (20.58 ± 0.30 cm) in SL744 (0.6% SA), as compared to the controls (SL958: 26.09 ± 0.62 cm and SL744: 27.48 ± 0.74 cm). The average leaf count was the highest (234.33 ± 3.09 tetrafoliate leaves/plant) in SL958 (0.4% SA) while it was the lowest (87 leaves/plant) in 0.6% MMS as compared to the control (SL744 180.00 ± 1.63 and SL958 160.73 ± 1.05). The highest total leaf areas recorded in the SL958 and SL744 M1plants were 3625.8 ± 1.43 cm2 and 2311.03 ± 3.65 cm2, respectively. Seeds of the SL958 variety treated with 0.4% SA resulted in the development of tetrafoliate leaves with a broad leaf base and the maximum yield (277.55 ± 1.37 pods/plant) compared to the narrow pentafoliate leaves obtained through the treatment with EMS. Meanwhile, in the SL744 variety, the same treatment led to tetrafoliate leaves with a comparatively lower yield of 206.54 ± 23.47 pods/plant as compared to the control (SL744 164.33 ± 8.58 and SL958 229.86 ± 0.96). The highest protein content (47.04 ± 0.87% TSP) was recorded in the SL958 (0.4% SA) M2 seeds followed by a content of 46.14 ± 0.64% TSP in the SL744 (0.4% SA) M2 seeds, whereas the lowest content (38.13 ± 0.81% TSP) was found in SL958 (0.6% MMS). Similar observations were recorded for the lipid and fibre content. The 0.4% SA treatment in SL958 proved to be efficient in generating the highest leaf area (tetrafoliate leaves) and a reasonable yield of M1 (the first generation after mutation) plants. [ABSTRACT FROM AUTHOR]

Simple Summary: Peanut vines are abundant and cheap, and are a key forage source for ruminants; however, knowledge of the bacterial species that colonize peanut vines over time during rumen incubation remains limited. In this study, in situ nylon bag degradation, scanning electron microscopy, and 16S rRNA gene sequencing and metagenomics technology were used to study the attachment characteristics and function of microorganisms involved in peanut vine degradation, with the aim of providing basic knowledge regarding the utilization of peanut vine and other roughage. Our results demonstrate that the colonization of peanut vine by microorganisms is dynamic in the rumen. The dominant phyla and genera, as well as the structure and function, of the microbial communities varied over time. This experiment identified the key microorganisms and CAZymes were important for plant fiber degradation. Therefore, our data proved new insights into biomass conversion, reveal that numerous bacteria and enzymes are involved in forage degradation in the rumen, and lay the foundation for targeted improvement of crop residue utilization for ruminants. The aim of this study was to improve the utilization of peanut vines as forage material for ruminants by investigating the degradation pattern of peanut vines in the dairy cow rumen. Samples of peanut vine incubated in cow rumens were collected at various time points. Bacterial diversity was investigated by scanning electron microscopy (SEM) and 16S rRNA gene sequencing. Carbohydrate-active enzymes (CAZymes) were analyzed by metagenomics. The peanut vines degraded rapidly from 2 to 24 h, before slowing from 24 to 72 h. SEM images confirmed dynamic peanut vine colonization. Firmicutes and Bacteroidetes were the two most dominant bacterial phyla throughout. Principal coordinates analysis indicated significant microbial composition changes at 6 and 24 h. This may be because, in the early stage, soluble carbohydrates that are easily degradable were degraded, while in the later stage, fibrous substances that are difficult to degrade were mainly degraded. Glycoside hydrolases (GHs) were the most abundant CAZymes, with peak relative abundance at 6 h (56.7 trans per million, TPM), and reducing at 24 (55.9 TPM) and 72 h (55.3 TPM). Spearman correlation analysis showed that Alistipes_sp._CAG:435, Alistipes_sp._CAG:514, Bacteroides_sp._CAG:1060, Bacteroides_sp._CAG:545, Bacteroides_sp._CAG:709, Bacteroides_sp._CAG:770, bacterium_F082, bacterium_F083, GH29, GH78, and GH92 were important for plant fiber degradation. These findings provide fundamental knowledge about forage degradation in the cow rumen, and will be important for the targeted improvement of ruminant plant biomass utilization efficiency. [ABSTRACT FROM AUTHOR]

Summary: Although forward‐genetics‐metabolomics methods such as mGWAS and mQTL have proven effective in providing myriad loci affecting metabolite contents, they are somehow constrained by their respective constitutional flaws such as the hidden population structure for GWAS and insufficient recombinant rate for QTL. Here, the combination of mGWAS and mQTL was performed, conveying an improved statistical power to investigate the flavonoid pathways in common wheat. A total of 941 and 289 loci were, respectively, generated from mGWAS and mQTL, within which 13 of them were co‐mapped using both approaches. Subsequently, the mGWAS or mQTL outputs alone and their combination were, respectively, utilized to delineate the metabolic routes. Using this approach, we identified two MYB transcription factor encoding genes and five structural genes, and the flavonoid pathway in wheat was accordingly updated. Moreover, we have discovered some rare‐activity‐exhibiting flavonoid glycosyl‐ and methyl‐transferases, which may possess unique biological significance, and harnessing these novel catalytic capabilities provides potentially new breeding directions. Collectively, we propose our survey illustrates that the forward‐genetics‐metabolomics approaches including multiple populations with high density markers could be more frequently applied for delineating metabolic pathways in common wheat, which will ultimately contribute to metabolomics‐assisted wheat crop improvement. [ABSTRACT FROM AUTHOR]

Aims: Reactive oxygen species (ROS) are key regulators of plant growth, development, and stress tolerance. Stress-induced changes in ROS levels trigger multilevel signaling. However, the precise mechanisms by which ROS signals are translated into changes in gene expression remain poorly defined. Focusing on six key antioxidant enzymes, we performed a meta-analysis of transcriptome data available in public databases to analyze ROS-mediated control of nuclear gene expression. Results: An information-guided pipeline was developed, which identified 19 putative transcription factors (TFs), as components in a "common alarm signal cascade" pathway following perception of changes in ROS levels. Crucially, 30%–35% of the abiotic stress transcriptome signatures had binding sites for common alarm signal-transcription factors (CAS-TFs) in their promoter regions. Furthermore, Phloem Early Dof 2 (PEAR2), DNA binding with one finger 5.8 (DOF5.8), and Obf-Binding Protein 3 (OBP3) were identified as top-ranked TFs on the basis of a cumulative DAPseq (DNA-affinity purification sequencing) score on the promoters of selected genes regulating core pathways of salt, drought, heat, and cold stress tolerance. Innovation: This study identifies a set of CAS-TFs that may play a major role in shaping the transcriptome of abiotic stress-induced ROS signaling. Ranking analysis identified PEAR2, DOF5.8, and OBP3 as the top-ranked CAS-TFs that regulated known markers of abiotic stress tolerance. Conclusion: The current findings suggest a major role of ROS in the abiotic stress signaling and also identify a set of TFs that take part in the signaling. Taken together, these findings suggested that the common alarm signal cascade underpins broad-range tolerance against multistress conditions. The identification of associated ROS-responsive CAS-TFs may provide novel targets for crop improvement. [ABSTRACT FROM AUTHOR]

Coffee is one of Brazil's main commodities. Among the goals of crop improvement, the search for drought-tolerant materials has stood out, mainly due to the water scarcity of the producing regions. The knowledge of genetic diversity and the morphophysiological analysis of plants allow the identification of genotypes with potential use in genetic improvement. Thus, this study aimed to evaluate the diversity, by morphophysiological characteristics, in 173 genotypes of Coffea canephora, from populations of contrasting crosses regarding the drought tolerance of the breeding program of Incaper, and to identify the relative importance of traits, subsidizing the selection for drought tolerance, based on the factor analysis index (FAI). The experiment was conducted in three evaluation periods, under field conditions without irrigation at the Incaper Experimental Farm of Marilândia, in the state of Espírito Santo. There was great variability between and within populations, which was affected by the evaluation season. Based on the traits of greater relative importance identified in this work (LL, LW, SLA, LAR, LT, TLA, PBL, CHL, NO3−, TSP, PRO, A, and iWUE), the FAI identified the genotypes 76 × 48 − 1, 76 × 48 − 10, 76 × 48 − 16, 76 × 48 − 76, 76 × 48 − 77, 76 × 48 − 83, 76 × 48 − 90, 76 × 48 − 128, 76 × 04 − 1, and 76 × 04 − 32 as more promising, from the ideotype of lower LL, LW, SLA, and LAR, and higher LT, TLA, PBL, CHL, NO3−, TSP, PRO, A, and iWUE. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a common staple food widely cultivated and consumed globally. The increase in world population and slow genetic gain in rice production in the face of a rapidly evolving climate could cause food scarcity and decreased crop productivity. It is crucial to expedite the development and release of climate-resilient crop varieties through selective breeding and improvement to mitigate the impact of climate change. Speed breeding has emerged as a promising tool for rice breeding, offering the potential to accelerate the generation time. By streamlining the breeding process and reducing the time taken for each generation, speed breeding empowers breeders to screen for desired traits rapidly and efficiently, enhancing the selection and development of improved rice varieties to meet the growing global demand for food. This review focuses on the applications of speed breeding technology to accelerate rice breeding and further highlights the critical factors for speed breeding development in rice production, such as temperature, humidity, light, and genetic diversity. Understanding and optimizing these factors is vital in successfully implementing speed breeding technology in developing robust, high-yielding, and climate-resilient rice varieties for feeding the future. [ABSTRACT FROM AUTHOR]

Drought stress has negative effects on crop growth and production. Characterization of transcription factors that regulate the expression of drought‐responsive genes is critical for understanding the transcriptional regulatory networks in response to drought, which facilitates the improvement of crop drought tolerance. Here, we identified an Alfin‐like (AL) family gene ZmAL14 that negatively regulates drought resistance. Overexpression of ZmAL14 exhibits susceptibility to drought while mutation of ZmAL14 enhances drought resistance. An abscisic acid (ABA)‐activated protein kinase ZmSnRK2.2 interacts and phosphorylates ZmAL14 at T38 residue. Knockout of ZmSnRK2.2 gene decreases drought resistance of maize. A dehydration‐induced Rho‐like small guanosine triphosphatase gene ZmROP8 is directly targeted and repressed by ZmAL14. Phosphorylation of ZmAL14 by ZmSnRK2.2 prevents its binding to the ZmROP8 promoter, thereby releasing the repression of ZmROP8 transcription. Overexpression of ZmROP8 stimulates peroxidase activity and reduces hydrogen peroxide accumulation after drought treatment. Collectively, our study indicates that ZmAL14 is a negative regulator of drought resistance, which can be phosphorylated by ZmSnRK2.2 through the ABA signaling pathway, thus preventing its suppression on ZmROP8 transcription during drought stress response. [ABSTRACT FROM AUTHOR]

SUMMARY: Wild species are an invaluable source of new traits for crop improvement. Over the years, the tomato community bred cultivated lines that carry introgressions from different species of the tomato tribe to facilitate trait discovery and mapping. The next phase in such projects is to find the genes that drive the identified phenotypes. This can be achieved by genotyping a few thousand individuals resulting in fine mapping that can potentially identify the causative gene. To couple trait discovery and fine mapping, we are presenting large, recombination‐rich, Backcross Inbred Line (BIL) populations involving an unexplored accession of the wild, green‐fruited species Solanum pennellii (LA5240; the 'Lost' Accession) with two modern tomato inbreds: LEA, determinate, and TOP, indeterminate. The LEA and TOP BILs are in BC2F6–8 generation and include 1400 and 500 lines, respectively. The BILs were genotyped with 5000 SPET markers, showing that in the euchromatic regions there was one recombinant every 17–18 Kb while in the heterochromatin a recombinant every 600–700 Kb (TOP and LEA respectively). To gain perspective on the topography of recombination we compared five independent members of the Self‐pruning gene family with their respective neighboring genes; based on PCR markers, in all cases we found recombinants. Further mapping analysis of two known morphological mutations that segregated in the BILs (self‐pruning and hairless) showed that the maximal delimited intervals were 73 Kb and 210 Kb, respectively, and included the known causative genes. The 'Lost'_BILs provide a solid framework to study traits derived from a drought‐tolerant wild tomato. Significance Statement: We are presenting a very large Introgression population from drought‐tolerant wild tomato species for fine mapping and epistasis analyses. [ABSTRACT FROM AUTHOR]

Improvements in self-pollinated crops rely on crosses between different genotypes. It has been suggested that the repeated use of "the best" genotypes may lead to the restriction of the genetic diversity of the crop. In wheat, the analysis of gliadin (storage protein) polymorphism has provided evidence that genetic diversity was high and stable throughout the 20th century. Moreover, a worldwide analysis of gliadin polymorphism shows that genetic diversity is structured spatially across countries and their regions. Therefore, the analysis of gliadin genotypes in a given grain sample can provide reliable information about the origin of grains in this sample. An unexpected finding is that many registered common wheat cultivars are genetically non-uniform and composed of authentic biotypes (genotypically related lines originated from the initial cross) in spite of current crop-registration rules that include a strict demand for each new cultivar to be genetically uniform (DUS rules). In summary, the results suggest that each cultivar is the fruit of joint effects of a breeder and of a region's environmental factors. We believe this finding will not be restricted to wheat and suggest there may be a need to re-evaluate relevant rules of cultivar registration for crop species in general. [ABSTRACT FROM AUTHOR]