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At least 19 recordsLinked to original sources

PubMed2026

Bioinformatics in crop research: using genomic data for crop improvement.

Sustainable crop development aims to maintain or increase yields while reducing environmental impact and managing the challenges imposed by climate change. As the global population grows and arable land becomes scarcer, the integration of molecular breeding with bioinformatics has emerged as an effective strategy for long-term crop improvement. Bioinformatics enables researchers to analyze and interpret the vast quantities of genetic data generated by high-throughput sequencing, making it possible to identify molecular markers, candidate genes, and regulatory networks linked to specific agronomic traits, which breeders then translate into focused, ecologically sustainable breeding programs. This approach has enabled major progress across several fronts: the identification of genes conferring resistance to biotic stressors (pests, pathogens) and abiotic stressors (drought, salinity, heat); the development of nutrient-efficient, low-input crop varieties; the improvement of agronomic performance and nutritional quality through identification of yield- and quality-related genes; and the conservation and deployment of genetic diversity to safeguard long-term breeding sustainability. By combining genomic data with precision breeding techniques, researchers are developing crops that are better adapted to a growing population and a changing climate, positioning the integration of molecular breeding and bioinformatics as a central pillar of future global food security.

bioinformatics↗

PubMedDate not supplied

[Characteristics of the microflora of soddy-podzol soil during single-crop cultivation of agricultural plants and during crop rotation].

Structural organization of microbial populations in soddy-podzolic soil was studied during growth of agricultural plants in monoculture and in crop rotation. The content of bacteria and their biomass decreased when plants were grown in monoculture. The content of actinomycetes, bacilli and oligonitrophilic microorganisms increased in soil during crop rotation as compared with monocultures, suggesting a higher rate of mobilization processes. The content of microscopic fingi in soil increased when lupine was grown in monoculture. Growth of plants in monoculture affects the cenotic structure of soil microflora. The composition of active soil microflora was characterized by a wider spectrum of microbial forms during crop rotation of monocultures.

Agriculture↗

PubMed1977

Intensive fattening of beef cattle by stall feeding on the Lilongwe Plain, Malawi. II. Utilisation of crop residues, crop by-products and leucaena.

Experiments were conducted over three dry seasons to investigate the value for fattening beef cattle, of crop residues (maize stover, groundnut haulm) and madeya (maize bran) with varying levels of dried leucaena leaf or cottonseed cake. The inclusion of groundnut haulm in the roughage increased animal performance when madeya was restricted. Increasing the protein content of the madeya supplement but restricting the quantity of madeya fed did not influence liveweight gain although the efficiency of concentrate conversion was enhanced. Restricting the amount of maize stover and feeding madeya to appetite had no significant effect on liveweight gain, but the inclusion of leucaena up to a level of 12 per cent crude protein improved animal performance. There were no differences between cottonseed cake or leucaena when fed with madeya at the same levels of crude protein.

Animal Feed↗

PubMed1975

Prolactin binding activity on the crop sacs of juvenile, mature, parent and prolactin-injected pigeons.

Specific prolactin (PRL) binding activity of lactoperoxidase catalyzed 125I-labeled ovine-PRL was determined in a membrane-rich particulate fraction of pigeon crop sacs. Levels of TSH, LH or FSH as high as 1000 ng each were unable to displace the 125I-o-PRL bound to 600 mug of crop sac microsomal protein, whereas competitive displacement was achieved with as little as 0.5 ng unlabeled PRL. Ovine GH exhibited some cross reactivity when incubated in amounts greater than 500 ng, but this could be accounted for by its stated PRL contamination. Specific PRL binding activities were determined in juvenile and mature pigeons with unstimulated crop sacs, and parent pigeons with 'crop milk' and mature birds injected with PRL for 4 days. Crop sacs from juvenile birds contained approximately twice as much binding activity as crop sacs from mature pigeons. Parent and PRL injected pigeons, each with proliferated crop sac epithelium, exhibited 4-5 times as much specific PRL binding as the non-proliferated crops from juvenile or mature birds. These results show that the pigeon crop sac contains specific binding sites for PRL, and that the crop sac response to PRL is associated with an increase in PRL binding activity.

Age Factors↗

PubMed1978

[Effect of plant residues on the parasitic activity of soilborne pathogens and the saprophytic microflora of the soil. III. Influence of rye and rape grown as winter catch crop on the incidence of Cercosporella herpotrichoides Fron (author's transl)].

In a five-years field trial, the influence of two winter catchcrops, rye and rape, upon the incidence of Cercosporella herpotrichoides has been studied. The winter catch-crops had been repeated three times, followed either by stubble-crop or without in fall of the fourth year. The variants (blocks) had been completed by two variants without catch-crop, either carefully cultivated or overgrown with weeds. Each of the four blocks had been divided three times to be grown with three different crop sequences containing 80%, 60% (with the insusceptible corn), or 40% haulm fruit, respectively. Each of the 12 variants had been divided into two parts by continuous fallow stripe, one part being artificially infested with the pathogen in the beginning (1st winter wheat). In the 2nd, 3rd, and 4th year, only spring crops were grown, followed by winter wheat in the 5th year. The final exploration resulted in a medium to heavy degree of infection, being significantly higher in the 80% cereal crop sequence than in the 60% and 40% sequences. Concerning the catch-crops, infection in the rye variants was equal or significantly lower than in the carefully cultivated variants without catch-crop. On the other hand, infection of the rape variants had become significantly higher than that of the catch-crop-free ones, about as heavily as in the weed-infested variants. From fall 1966 to summer 1969, the development of the saprophytic soil microflora and several other edaphic parameters had been investigated. Remarkable differences in intensity of disintegration have been observed under the influence of the main crops, cereals or potatoes, respectively, but no differences could be stated resulting from the matter of disintegration--residues of rye or rape--, which might interpret the contrasting effects on the pathogen. Too, no indication for antagonistic activity of bacteria or actinomycetes has been noted. The results are compared with known facts of Cercosporella and of other soil borne pathogens. The difference in biology of Cercosporella on the one hand, and of root infecting fungi on the other hand seems to be most important to explain the results obtained.

Actinomycetales↗

PubMed2025

Synergic impact mechanisms of cover crop residue on Cd and As availability and native organic carbon mineralization in Cd and As co-contaminated paddy soil.

The synergic impacts of cover crop residue on heavy metal and metalloid availability and soil organic carbon (SOC) mineralization in contaminated paddy soil and the underlying microbial mechanism remain unclear. This study investigated the availability of cadmium (Cd) and arsenic (As) and mineralization of native SOC in paddy soil treated with 0, 0.4 %, 0.8 % and 1.2 % of δ13C-labeled cover crop residue (Astragalus sinicus L.) via 90-day incubation experiments, the related functional genes and functional microbial communities were analyzed using metagenomic binning assembly. Cover crop residue with addition rate from 0.4 % to 1.2 % significantly decreased available Cd by 56 %-85 % but increased available As by 39 %-66 % compared to the control treatment. Cover crop residue resulted in a positive priming effect on native SOC mineralization but benefited SOC sequestration. Cover crop residue increased the abundance of genes encoding iron reductase (mtrABC, pilA, omcB), sulfate reductase (sir, fpr), As(V) reductase (ArsC), organic carbon hydrolases, methanogenesis, and methylotrophy. Genomes associated with Chloroflexota and Bacteroidota encoded all these key pathways, and their abundance increased with cover crop residue application. Cover crop residue decreased soil Eh, dissolved crystalline iron oxides, enriched specific microorganisms, including Chloroflexota and Bacteroidota, and then synergistically promoted the decrease in Cd availability and the increase in As availability and native SOC mineralization in the examined paddy soil. These findings provided practical and feasible guidance for achieving both safe production and carbon sequestration in contaminated paddy fields, highlighting the requirement to cautious utilization of cover crop residue in As-contaminated paddy fileds.

Soil Pollutants↗

PubMed2026

Adaptive evolution of polyploid crops.

Crop evolution represents a fundamental biological process through which plants respond to selection in different environments. This encompasses mechanisms operating at multiple scales of biological organization, including genetic and epigenetic regulation and higher-order interactions among molecular complexes. This Review synthesizes how polyploidy shapes crop evolution by generating duplicated genes, driving genome reorganization, altering dosage relationships and promoting regulatory divergence, which together influence crop metabolism, physiology, development and environmental responses. We focus mainly on the mechanisms underlying adaptation in polyploid crops, including the consequences of gene and genome duplication, genome reorganization and subfunctionalization. We also examine how hybridization, phenotypic plasticity and crop-microbiome interactions intersect with polyploidy to expand or constrain adaptive potential. Together, these processes affect crop survival, fitness and breeding value under changing environments. We suggest that future research connect polyploid genome architecture with experimentally validated signatures of selection and field performance to make better use of polyploidy-derived variation in crop improvement.

Polyploidy↗

PubMed2026

Herbicide Resistance Genes in Crops: Mechanisms, Progress, and Future Perspectives.

While previous reviews have largely focused on individual crops or single target-site mechanisms, the full-chain comparative landscape across major cereal crops remains unexplored. Here, we fill this critical gap by providing the first systematic, cross-crop comparative review that spans herbicide targets, resistance mechanisms, and breeding applications across four major cereals-rice, maize, wheat, and sorghum. Weed infestation is a serious constraint on crop production. Chemical weed control faces challenges such as herbicide resistance evolution and ecological risks. Developing herbicide-resistant varieties is a fundamental approach to achieve green and sustainable weed management. This review systematically summarizes research progress on herbicide resistance genes from three aspects: herbicide classification, resistance mechanisms, and crop breeding applications. It highlights key differences among four major cereal crops (rice, maize, wheat, and sorghum) in resistance-gene discovery and translational progress. Rice has the richest target-site resistance-gene resources. Maize leads in commercialization of transgenic herbicide resistance. Wheat focuses on endogenous precise editing due to genome complexity and regulatory constraints. Sorghum relies on specific mutations to serve cereal-legume intercropping systems. Based on this comparison, this review identifies the core trends in resistance breeding: from single-gene to multi-gene stacking, and from exogenous gene introduction to endogenous gene editing. It also points out common bottlenecks, including insufficient systematic mining of resistance-gene resources, lagging elucidation of non-target-site resistance regulatory networks, and strong genotype dependence in genetic transformation. Future efforts should focus on exploring broad-spectrum resistance genes, optimizing precise editing technologies, and developing sustainable resistance management strategies. This review provides a theoretical framework and practical references for molecular breeding of herbicide-resistant crops.

crop breeding↗

PubMed2026

CROP: a feature-independent context-aware method for CRISPR-Cas9 frameshift prediction.

MOTIVATION: The CRISPR-Cas9 complex has revolutionized genome-editing technologies. By designing a 20 nt-long guide RNA, a Cas9 nuclease can be guided to cleave almost any genomic target site (followed by NGG). The cleavage induces double-stranded DNA breaks, which are then repaired by cellular pathways. Accurate CRISPR-Cas9 repair-outcome prediction is essential for designing guide RNAs with desired genomic effects, such as gene knockout. A central challenge is quantifying the rate of frameshifts, i.e. repair-outcomes that lead to a change in the local length that is not a multiple of three. Previous methods for frameshift-rate prediction were trained on only a few experimental or cellular contexts, mostly relied on manually defined microhomology features, and were limited by sparse features and class labels. RESULTS: We developed CROP, a feature-independent context-aware repair-outcome prediction method. By aggregating specific repair outcomes as Δlength classes, CROP overcomes class sparsity. We designed CROP to work with variable input sequence lengths and output classes to utilize multiple datasets simultaneously. We benchmarked CROP against state-of-the-art repair-outcome prediction methods over 18 datasets, which we curated and standardized from various studies. Across all datasets, CROP outperformed all competing methods in frameshift-rate prediction. We performed cross-experiment and cross-cellular frameshift-rate predictions to investigate the generalizability of repair mechanisms. Finally, we show that CROP learned microhomology principles from raw sequences without explicit feature engineering, establishing an end-to-end architecture for CRISPR-Cas9 repair-outcome prediction that learns from multiple datasets. AVAILABILITY AND IMPLEMENTATION: CROP is available at https://github.com/OrensteinLab/CROP.

CRISPR-Cas Systems↗

PubMed1979

The nutritional significance of root and tuber crop development as staples in the Caribbean community.

The competition between cereals and root crops as CARICOM staples is described. The move to substitute locally grown food for imported wheat is shown to favor root crop development in the region. Against this background, traditional nutrition-prompted objections to wheat substitution by root crops are examined. Evidence is cited to show the essential adequacy of protein in root crops, except plantain and cassava and for all humans except perhaps some infants. The low protein in cassava and plantain, it is proposed, can be easily overcome in the process of local root crop development. Finally, it is argued that there exists the potential to obtain cheap calories from root crops. This and the generation of economic activity among small farmers, concomitant with root crop development, are seen as possible indicators of good nutrition for the region in the future.

Diet↗

PubMed1976

Composition of crop and gizzard contents in the laying hen.

Crop and gizzard contents were analysed at six stages of egg formation. 2. The crop was empty during the day and full during the night while the gizzard contained a constant amount of dry matter. The water content of the crop did not change but that of the gizzard was at a minimum just after the ovulation and at a maximum 18 h later. 3. The osmotic pressure of the gizzard contents remained constant and close to that of the blood; that of the crop contents was almost isotonic at oviposition but hypertonic 18 h later. In both organs the pH of the liquid phase varied cyclicly with the egg formation and was lowest during egg shell deposition. 4. The Na+, K+ and Cl- contents of the crop liquid phase did not vary but Ca2+ increased with decreasing pH.Na+ and K+ were also constant in the gizzard liquid phase but Cl- and Ca2+ increased during shell formation. 5. It is concluded that the amount of HCl secreted by the proventiculus is related to egg shell deposition and that calcium solubilisation depends on microbial fermentation in crop and HCl secretion by proventriculus.

Animals↗

PubMed2025

Genomics control of biostimulant-induced stress tolerance and crop yield enhancement.

Biostimulants are changing modern agriculture, as they have the potential to secure healthy and sustainable food production while preserving the environment. They have two main biological effects: growth promotion and stress protection. Both effects can lead to enhancement of the yield and improvement of the marketable grade of the produce in crops, without compromising crop quality. Their use increased exponentially in the past decade, as they are highly efficient, ecologically friendly (non-toxic, biodegradable), and applicable to all major crops. While exponential data on the physiological mechanisms of stress protection is accumulating in recent years, the information as to how biostimulants act at the molecular level is still rather limited. Here we review the growing evidence of the biostimulants role in stress protection and yield enhancement of crops, as well as the recent transcriptomic and metabolomic data, which indicate biostimulants' molecular mode of action. In particular, we outline the role of genes encoding signaling components, plant hormones (abscisic acid, brassinosteroids, and ethylene), genes encoding transcription factors from ERF, WRKY, NAC, and MYB families, and genes related to growth, photosynthesis, and stress response. Finally, we describe strategies to study the genetic and genomics control of biostimulants mode of action, with foci on stress tolerance and yield enhancement. In Arabidopsis, established systems for biostimulants-induced protection against drought and oxidative stress will allow both forward and reverse genetics approaches to identify key genes from the biostimulants network. Mutations in such genes compromise the stress-protective effect of biostimulants. In major crops such as pepper and tomato, large Genome Wide Association Studies (GWAS) panels can be utilized to study crops responses to biostimulants in terms of drought tolerance, fruit qualities, and yield in order to pinpoint genes controlling biostimulants-induced stress protection and yield enhancement. The combination of these approaches allows identification and verification of important genes involved in the pathways of biostimulant-induced stress protection and yield enhancement, as well as deciphering parts of the intricate biostimulant-signaling network.

Crops, Agricultural↗

PubMed2025

Genome editing research initiatives and regulatory landscape of genome edited crops in India.

Food and nutritional security are the top priorities in Indian agriculture. Exponential population growth coupled with climate change effects has become a serious challenge for sustainable agriculture. Genome editing has revolutionized the agricultural sector because of its ability to create precise, stable and predictable modifications in the genome and therefore, offers great opportunities for crop improvement in India. However, for harvesting the real benefits of this technology in agriculture sector, there is a strong need of creating awareness among the end users and development of suitable policies for regularization of genome edited products. Many regulatory agencies around the world have been modernizing their regulatory approaches to be more risk proportionate and to reflect a more science-based approach. In this article, recent research initiatives and developments undertaken by different Indian institutes/organizations for the genetic improvement of agricultural and horticultural crops via genome editing technologies are summarized. Furthermore, to benefit from this potential technology in our country, regulatory policies must be clear, science-based and proportionate. Therefore, in the present review, the regulatory policies related to the genome editing of crop products in India are discussed in detail. This review will sensitize researchers and stakeholders to the application of genome editing techniques in crop improvement and various biosafety committees involved in the development and regulation of genome edited crops.

Crops, Agricultural↗

PubMed1979

Bioavailability of Cd to Food crops in relation to heavy metal content of sludge-amended soil.

Results of greenhouse and laboratory experiments on factors influencing uptake and accumulation of Cd by economic crops are summarized.Tolerance to Cd is highly crop-specific. For example, 21 different economic crops were grown in pots filled with a calcareous soil treated with increasing amounts of Cd. Yields versus Cd addition rate relations showed yield reductions to occur with Cd sensitive plants (spinach, soybean, curlycress, and lettuce) at addition rates varying from 5 to 15 mug Cd/g soil, whereas tolerant crops (tomato, squash, cabbage, and rice) did not suffer a yield reduction when treated at rates less than 150 mug Cd/g soil. Nutrient solution experiments likewise revealed marked differences in growth of crops. Corn, turnip, beets, bean, and tomato plants grown in solution cultures containing 0.1 mug Cd/ml accumulated different amounts of Cd in leaf tissue depending upon crop species; leaf Cd concentrations ranged from a low of 9 mug Cd/g leaf for beans to 200 mug Cd/g leaf for beets. Large differences also occur with regard to distribution of Cd within the plant. Fruit and seed tissue contain less Cd than leaves. Experiments comparing the toxicity of Cd to Cu, Ni, and Zn in an acid soil +/- lime showed Cd to be the most phytotoxic. While interactive effects occur with regard to metal uptake and accumulation by plants, Cd uptake is essentially dependent upon the Cd concentration of the soil. Studies of chemical speciation of Cd in relation to Cd availability indicate that the free Cd(2+) concentration correlates better with Cd uptake than Cd total of the soil solution.

Agriculture↗

PubMed1977

[Effect of plant residues on the parasitic activity of soil-borne pathogens and the saprophytic microflora of the soil. II. Influence of a second crop cultivation one the incidence of Rhizoctonia solani (author's transl].

In a more years-lasting field trial the influence of a second crop cultivation of rye and rape in winter time on the incidence of Rhizoctonia solani Kühn on potato or mustard as indicator plants was studied. The second crops were ploughed in during spring time. On part of the trial was artificially infested by this causal agent. Three crop rotations with different proportions of host plants (potato) were compared. The results obtained demonstrate the following: 1. On the part of experimental area arficially infested the incidence rate was higher for 3 till 4 years than on the control plots, but later it became equally to the control one, which also was very high (approximately 50). 2. In the last very dry year (1969) the disease developed only a little. 3. The second crop cultivation decreased the incidence of R. solani in 7 (rye) or 8 (rape) of 10 cases, but mostly the rate of decreasing was low. 4. A high weed density induced by a diminished mechanical cultivation increased the incidence of R. solani at the end of the experiment (1969), specially in the rotation with 80% host plants. 5. The number of soil bacteria, the respiration rate, and partly also the activity of dehydrogenase and the soil acidity were increased by green manuring of the second crop, however, the number of the actinomycetes, and the cellulolytic activity didn't be influenced remarkably. 6. The second crop cultivation ist nounced as a measure stimulating the soil fertiligy and discussed in connection with the microbial processes taking place in soil.

Agriculture↗

PubMed2026

Scaling up orphan crop research: genebank genetics highlight geographic structure in cultivated cowpea from 10 617 global accessions.

Vigna unguiculata (L.) Walp. is a dryland legume crop, providing essential food and nutritional security for millions of people across the semi-arid tropics, in Africa, Asia and Latin America. However, as a typical 'orphan crop', cowpea has long remained underrepresented in global genomic research to support crop improvement. Here, we conducted the largest genetic diversity analysis of cowpea to date, comprising 10 617 accessions sourced from seven international collections. Using genotyping-by-sequencing, we characterised the global patterns of genetic diversity, assessed redundancy within and across collections, and examined the geographic structure of the cowpea global allele pool. Our results revealed nine distinct genetic groups with clear geographic associations and fine-scale population differentiation, reflecting dispersal history, regional adaptation and the influence of modern breeding. Duplication across collections was detected, highlighting the need for improved curation and integration of germplasm resources. Landraces from sub-Saharan Africa do not fully capture the genetic diversity present in several other geographic regions, indicating the existence of abundant and untapped genetic resources worldwide. These findings not only provide insights into the genetic structure and evolutionary history of cowpea but also offer a valuable foundation for harnessing global germplasm diversity to enhance breeding potential and accelerate crop improvement.

Vigna↗

PubMed1977

[A long-term experiment on the complex influence of cultivating, fertilizing, and crop rotation measures on humic substances in soil and development of yield (author's transl)].

In a 10-year field experiment, the influence of fertilizing, cultivating, and crop rotation measures on the C-content of the soil, humus quality of the organic soil substance, and the yield was investigated. With cultivation of fodder plants only, the C-content of the soil can be improved by increased mineral and increased organo-mineral fertilization at any depth of cultivation. When in the same location there was a turn between cereals and green crops, a decrease of C-rate can only be prevented by increased organo-mineral fertilization. Continuous cultivation of root crops resulted in a decrease of the C-content. Deeper tillage of the soil generally decreased C-content. Within the years, a variability of the pure humin substances could be detected, depending on the rotation of crops and C-content. The composition of the fulvic acids is differentiated in dependence on the factors "time" and "cultivation". The effect of fertilization variants on the yield was different. Fertilization in that location with manure only, compared with mineral fertilization, caused in most cases depression in yield. Decrease on yield by deeper ploughing had the least influence with root crops.

Agriculture↗

PubMed2026

The emerging impact of CRISPR and gene editing on global crop improvement.

The advent of CRISPR-based genome editing has revolutionized crop improvement, offering unprecedented precision and efficiency in modifying key agronomic traits. This review comprehensively examines the mechanisms, applications, and future potential of CRISPR technology in enhancing global crop production. CRISPR-Cas systems, originally identified as adaptive immune mechanisms in bacteria and archaea, have been repurposed for targeted genome editing in plants. The CRISPR-Cas9 system, in particular, has emerged as a powerful tool for introducing site-specific double-strand breaks, enabling precise genetic modifications. The three-stage process of adaptation, expression, and interference underlies the CRISPR mechanism, with guide RNAs directing Cas endonucleases to specific genomic loci. Advances in CRISPR technology have expanded its applications beyond gene knockouts, encompassing base editing, prime editing, and epigenome editing. These innovations have facilitated the development of crops with enhanced yield, stress tolerance, disease resistance, nutritional content, and post-harvest quality. However, challenges related to off-target effects, regulatory hurdles, ethical concerns, and public acceptance must be addressed to fully harness the potential of CRISPR in agriculture. Integration of CRISPR with other cutting-edge technologies, such as synthetic biology, artificial intelligence, and high-throughput phenotyping, holds immense promise for accelerating crop improvement efforts. As research continues to refine CRISPR tools and expand their applicability across diverse plant species, this transformative technology is poised to play a pivotal role in shaping a sustainable, resilient, and productive global food system for future generations.

Gene Editing↗