GERDH: an interactive multi-omics database for cross-species data mining in horticultural crops.

Horticultural plants contribute immensely to the quality of human's life. The rapid development of omics studies on horticultural plants has resulted in large volumes of valuable growth- and development-related data. Genes that are essential for growth and development are highly conserved in evolution. Cross-species data mining reduces the impact of species heterogeneity and has been extensively used for conserved gene identification. Owing to the lack of a comprehensive database for cross-species data mining using multi-omics data from all horticultural plant species, the current resources in this field are far from satisfactory. Here, we introduce GERDH (https://dphdatabase.com), a database platform for cross-species data mining among horticultural plants, based on 12 961 uniformly processed publicly available omics libraries from more than 150 horticultural plant accessions, including fruits, vegetables and ornamental plants. Important and conserved genes that are essential for a specific biological process can be obtained by cross-species analysis module with interactive web-based data analysis and visualization. Moreover, GERDH is equipped with seven online analysis tools, including gene expression, in-species analysis, epigenetic regulation, gene co-expression, enrichment/pathway and phylogenetic analysis. By interactive cross-species analysis, we identified key genes contributing to postharvest storage. By gene expression analysis, we explored new functions of CmEIN3 in flower development, which was validated by transgenic chrysanthemum analysis. We believe that GERDH will be a useful resource for key gene identification and will allow for omics big data to be more available and accessible to horticultural plant community members.

Comparative assessment of environmental impacts and water scarcity footprint of horticultural crops in Iran.

Examining the pollution rates generated by horticultural crops and discerning their impact on water consumption are pivotal considerations for fostering sustainable production of these valuable crops. This study focuses on investigating the environmental consequences and water footprint associated with cultivating diverse horticultural crops in northern Iran. The research employs the life cycle assessment method to gauge environmental impacts by using IMPACT 2002+ and the Water Scarcity Indicator (WSI) to assess water footprints. Notably, the results indicate that walnuts exhibit the highest environmental index, surpassing other crops by sevenfold, and the greatest WSI at 2652.78 m3/ton. Nitrogen fertilizer and on-farm emissions emerged as the primary contributors to pollution among consumed inputs. The assessment underscores human health as a critical concern in the environmental impact of horticultural crop production, likely attributed to elevated chemical input consumption and associated emissions. The findings emphasize the substantial challenges faced by orchard management in Mazandaran province, the primary horticultural crop producer in Iran, grappling with chemical usage and water scarcity.

Comprehensive review: Effects of climate change and greenhouse gases emission relevance to environmental stress on horticultural crops and management.

Global climate change exerts a significant impact on sustainable horticultural crop production and quality. Rising Global temperatures have compelled the agricultural community to adjust planting and harvesting schedules, often necessitating earlier crop cultivation. Notably, climate change introduces a suite of ominous factors, such as greenhouse gas emissions (CGHs), including elevated temperature, increased carbon dioxide (CO2) concentrations, nitrous oxide (N2O) and methane (CH4) ozone depletion (O3), and deforestation, all of which intensify environmental stresses on crops. Consequently, climate change stands poised to adversely affect crop yields and livestock production. Therefore, the primary objective of the review article is to furnish a comprehensive overview of the multifaceted factors influencing horticulture production, encompassing fruits, vegetables, and plantation crops with a particular emphasis on greenhouse gas emissions and environmental stressors such as high temperature, drought, salinity, and emission of CO2. Additionally, this review will explore the implementation of novel horticultural crop varieties and greenhouse technology that can contribute to mitigating the adverse impact of climate change on agricultural crops.

Effect of microplastics used in agronomic practices on agricultural soil properties and plant functions: Potential contribution to the circular economy of rural areas.

The extensive use of plastic materials and their improper disposal results in high amounts of plastic waste in the environment. Aging of plastics leads to their breakdown into smaller particles, such as microplastics (MPs) and nanoplastics. This research investigates plastics used in agricultural practices as they contribute to MP pollution in agricultural soils. The distribution and characteristics of MPs in agricultural soils were evaluated. In addition, the effect of MPs on soil properties, the relationship between MPs and metals in soil, the effect of MPs on the fate of pesticides in agricultural soils and the influence of MPs on plant growth were analysed, discussing legume, cereal and vegetable crops. Finally, a brief description of the main methods of chemical analysis and identification of MPs is presented. This study will contribute to a better understanding of MPs in agricultural soils and their effect on the soil-plant system. The changes induced by MPs in soil parameters can lead to potential benefits as it is possible to increase the availability of micronutrients and reduce plant uptake of toxic elements. Furthermore, although plastic pollution remains an emerging threat to soil ecosystems, their presence may result in benefits to agricultural soils, highlighting the principles of the circular economy.

Combining novel technologies with interdisciplinary basic research to enhance horticultural crops.

Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.

Functions of Melatonin during Postharvest of Horticultural Crops.

Melatonin, a tryptophan-derived molecule, is endogenously generated in animal, plant, fungal and prokaryotic cells. Given its antioxidant properties, it is involved in a myriad of signaling functions associated with various aspects of plant growth and development. In higher plants, melatonin (Mel) interacts with plant regulators such as phytohormones, as well as reactive oxygen and nitrogen species including hydrogen peroxide (H2O2), nitric oxide (NO) and hydrogen sulfide (H2S). It shows great potential as a biotechnological tool to alleviate biotic and abiotic stress, to delay senescence and to conserve the sensory and nutritional quality of postharvest horticultural products which are of considerable economic importance worldwide. This review provides a comprehensive overview of the biochemistry of Mel, whose endogenous induction and exogenous application can play an important biotechnological role in enhancing the marketability and hence earnings from postharvest horticultural crops.

Hedgerows increase the diversity and modify the composition of arbuscular mycorrhizal fungi in Mediterranean agricultural landscapes.

Sustainable agriculture is essential to address global challenges such as climate change and biodiversity loss. Hedgerows enhance aboveground biodiversity and provide ecosystem services, but little is known about their impact on soil biota. Arbuscular mycorrhizal (AM) fungi are one of the key components of belowground biodiversity. We compared the diversity and composition of AM fungal communities at four farmland sites located in Central Spain, where 132 soil samples in total were collected to assess soil physical and chemical properties and the AM fungal communities. We compared the richness (number of AM fungal taxa), taxonomic, functional, and phylogenetic diversity, and structure of the AM fungal communities across three farmland habitat types, namely hedgerows, woody crops (olive groves and vineyard), and herbaceous crops (barley, sunflower, and wheat). Our results showed positive effects of hedgerows on most diversity metrics. Almost 60% of the AM fungal taxa were shared among the three farmland habitat types. Hedgerows increased AM fungal taxonomic richness (31%) and alpha diversity (25%), and especially so compared to herbaceous crops (45% and 28%, respectively). Hedgerows harbored elevated proportions of AM fungi with non-ruderal life-history strategies. AM fungal communities were more similar between hedgerows and woody crops than between hedgerows and adjacent herbaceous crops, possibly because of differences in tillage and fertilization. Unexpectedly, hedgerows reduced phylogenetic diversity, which might be related to more selective associations of AM fungi with woody plants than with herbaceous crops. Overall, the results suggest that planting hedgerows contributes to maintain belowground diversity. Thus, European farmers should plant more hedgerows to attain the goals of the EU Biodiversity Strategy for 2030.

Starch branching enzymes as putative determinants of postharvest quality in horticultural crops.

Starch branching enzymes (SBEs) are key determinants of the structure and amount of the starch in plant organs, and as such, they have the capacity to influence plant growth, developmental, and fitness processes, and in addition, the industrial end-use of starch. However, little is known about the role of SBEs in determining starch structure-function relations in economically important horticultural crops such as fruit and leafy greens, many of which accumulate starch transiently. Further, a full understanding of the biological function of these types of starches is lacking. Because of this gap in knowledge, this minireview aims to provide an overview of SBEs in horticultural crops, to investigate the potential role of starch in determining postharvest quality. A systematic examination of SBE sequences in 43 diverse horticultural species, identified SBE1, 2 and 3 isoforms in all species examined except apple, olive, and Brassicaceae, which lacked SBE1, but had a duplicated SBE2. Among our findings after a comprehensive and critical review of published data, was that as apple, banana, and tomato fruits ripens, the ratio of the highly digestible amylopectin component of starch increases relative to the more digestion-resistant amylose fraction, with parallel increases in SBE2 transcription, fruit sugar content, and decreases in starch. It is tempting to speculate that during the ripening of these fruit when starch degradation occurs, there are rearrangements made to the structure of starch possibly via branching enzymes to increase starch digestibility to sugars. We propose that based on the known action of SBEs, and these observations, SBEs may affect produce quality, and shelf-life directly through starch accumulation, and indirectly, by altering sugar availability. Further studies where SBE activity is fine-tuned in these crops, can enrich our understanding of the role of starch across species and may improve horticulture postharvest quality.

Toward Understanding the Molecular Recognition of Fungal Chitin and Activation of the Plant Defense Mechanism in Horticultural Crops.

Large volumes of fruit and vegetable production are lost during postharvest handling due to attacks by necrotrophic fungi. One of the promising alternatives proposed for the control of postharvest diseases is the induction of natural defense responses, which can be activated by recognizing molecules present in pathogens, such as chitin. Chitin is one of the most important components of the fungal cell wall and is recognized through plant membrane receptors. These receptors belong to the receptor-like kinase (RLK) family, which possesses a transmembrane domain and/or receptor-like protein (RLP) that requires binding to another RLK receptor to recognize chitin. In addition, these receptors have extracellular LysM motifs that participate in the perception of chitin oligosaccharides. These receptors have been widely studied in Arabidopsis thaliana (A. thaliana) and Oryza sativa (O. sativa); however, it is not clear how the molecular recognition and plant defense mechanisms of chitin oligosaccharides occur in other plant species or fruits. This review includes recent findings on the molecular recognition of chitin oligosaccharides and how they activate defense mechanisms in plants. In addition, we highlight some of the current advances in chitin perception in horticultural crops.

Overwintering of the Argentine strain of Neoseiulus californicus (Acari: Phytoseiidae).

Overwintering and diapause are variable among mite species and strains. The aims of this study were to determine whether certain crops constitute overwintering sites for the Argentine strain of the predator Neoseiulus californicus and whether females underwent reproductive diapause in winter. Neoseiulus californicus was recorded monthly on the vegetables tomato, sweet pepper, eggplant, and artichoke, and on strawberry, among other crops in Buenos Aires province, Argentina. This mite was found at a lower percentage of crops in the winter than in the other seasons. Since the predator was quite frequent on artichoke, this crop could constitute a refuge during adverse environmental conditions. The mite's frequency on several crops in other seasons and potential association with a strawberry pest is discussed. In the laboratory, individuals exposed to winter conditions throughout the life cycle exhibited a long pre-oviposition period and low oviposition rate, but did not diapause. After being kept under winter conditions from larva to adult, when individuals were transferred to the optimal spring temperatures and lighting, the pre-oviposition period was shorter and the fecundity higher than under winter conditions. When individuals remained under spring conditions from larva to adult and were then transferred to the winter parameters during the first 15 days of adulthood, the pre-oviposition period was long and the oviposition rate low. Once the optimal conditions were restored, the daily fecundity became similar to that of the individuals remaining under optimal conditions throughout the life cycle. Fecundity of N. californicus decreased significantly under winter conditions but reproductive diapause was not observed.

Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system.

"Masseiras" is an ancient Portuguese agriculture system, where soil was developed from sand dunes enriched with seaweeds over more than a century. Due to the importance for the local economy, this system evolved for greenhouse structures. In this study we compared the bacterial community composition and structure of "Masseiras" soil, aiming at assessing the potential impact of different agricultural practices. The bulk soil of two greenhouses (following or not the recommended agriculture good practices, FGP and NFGP, respectively) was compared based on their physicochemical properties and bacterial community. In both FGP and NFGP, Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Gemmatimonadetes were in a proportion of 5:1:1:1:1:1. However, the bacterial community of soil FGP was richer and more diverse than that of soil NFGP. Members of the classes Bacilli and Gemm-1, with higher relative abundance in NFGP and FGP, respectively, were those contributing most for distinguishing the bacterial communities of both soils. The differences in the structure of the bacterial communities correlated (Mantel test) with some soil physicochemical properties, such as electrical conductivity and nitrate and Zn contents, which were significantly higher in soil NFGP than in soil FGP.

Fortifying Horticultural Crops with Essential Amino Acids: A Review.

To feed the world's growing population, increasing the yield of crops is not the only important factor, improving crop quality is also important, and it presents a significant challenge. Among the important crops, horticultural crops (particularly fruits and vegetables) provide numerous health compounds, such as vitamins, antioxidants, and amino acids. Essential amino acids are those that cannot be produced by the organism and, therefore, must be obtained from diet, particularly from meat, eggs, and milk, as well as a variety of plants. Extensive efforts have been devoted to increasing the levels of essential amino acids in plants. Yet, these efforts have been met with very little success due to the limited genetic resources for plant breeding and because high essential amino acid content is generally accompanied by limited plant growth. With a deep understanding of the biosynthetic pathways of essential amino acids and their interactions with the regulatory networks in plants, it should be possible to use genetic engineering to improve the essential amino acid content of horticultural plants, rendering these plants more nutritionally favorable crops. In the present report, we describe the recent advances in the enhancement of essential amino acids in horticultural plants and possible future directions towards their bio-fortification.

Evaluation of vegetable-faba bean (Vicia faba L.) intercropping under Latvian agro-ecological conditions.

BACKGROUND: Monoculture is used mostly in conventional agriculture, where a single crop is cultivated on the same land for a period of at least 12 months. In an organic and integrated growing approach, more attention is paid to plant-environment interactions and, as a result, diverse growing systems applying intercropping, catch crops, and green manure are being implemented. Thus, field experiments for evaluation of vegetable/faba bean full intercropping efficiency, in terms of vegetable and faba bean yield and protein content, were set up during two consecutive growing seasons (2014 and 2015). RESULTS: Data obtained showed that the most efficient intercropping variants were cabbage/faba bean (cabbage yield 1.27-2.91 kg m-2 , immature faba bean pods 0.20-0.43 kg m-2 ) and carrot/faba bean (carrot yield 1.67-2.28 kg m-2 , immature faba bean pods 0.10-0.52 kg m-2 ), whilst onion and faba bean intercrop is not recommended for vegetable growing since it induces a very low onion yield (0.66-1.09 kg m-2 ), although the highest immature faba bean pod yield was found in the onion/faba bean intercropping scheme (up to 0.56 kg m-2 ). CONCLUSION: Vegetable/faba bean intercropping can be used in practical horticulture for carrot and cabbage growing in order to ensure sustainable farming and environmentally friendly horticultural production. © 2017 Society of Chemical Industry.

FERONIA homologs in stress responses of horticultural plants: current knowledge and missing links.

Owing to its versatile roles in almost all aspects of plants, FERONIA (FER), a receptor-like kinase of the Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) subfamily, has received extensive research interests during the past decades. Accumulating evidence has been emerged that FER homologs in horticultural crops also play crucial roles in reproductive biology and responses to environmental stimuli (abiotic and biotic stress factors). Here, we provide a review for the latest advances in the studies on FER homologs in modulating stress responses in horticultural crops, and further analyze the underlying mechanisms maintained by FER. Moreover, we also envisage the missing links in current work and provide a perspective for future studies on this star protein.

Machine learning based recommendation of agricultural and horticultural crop farming in India under the regime of NPK, soil pH and three climatic variables.

Machine learning (ML) can make use of agricultural data related to crop yield under varying soil nutrient levels, and climatic fluctuations to suggest appropriate crops or supplementary nutrients to achieve the highest possible production. The aim of this study was to evaluate the efficacy of five distinct ML models for a dataset sourced from the Kaggle repository to generate practical recommendations for crop selection or determination of required nutrient(s) in a given site. The datasets contain information on NPK, soil pH, and three climatic variables: temperature, rainfall, and humidity. The models namely Support vector machine, XGBoost, Random forest, KNN, and Decision Tree were trained using yields of individual data sets of 11 agricultural and 10 horticultural crops, as well as combined yield of both agri-horticultural crops. The results strongly suggest to evaluate individual data sets separately for each crop category rather than using combined the data sets of both categories for better predictions. Comparing the five ML models, the XGBoost demonstrated the highest level of accuracy. The precision rates of XGBoost for recommending agricultural crops, horticultural crops, and a combination of both were 99.09 % (AUC 1.0), 99.3 % (AUC 1.0), and 98.51 % (AUC 0.99), respectively. This non-intrusive method for generating crop recommendations in diverse environmental conditions holds the potential to provide valuable insights for the development of a user-friendly AI cloud-based interface. Such an interface would enable rapid decision-making for optimal fertilizer applications and the selection of suitable crops for cultivation at specific sites.

Post-harvest proteomics and food security.

To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.

Melatonin: Current status and future perspectives in horticultural plants.

Global warming in this century increases incidences of various abiotic stresses, restricting plant growth and productivity and posing a severe threat to global food production and security. Different phytohormones are produced by plants to mitigate the adverse effects of these stresses. One such phytohormone is melatonin (MEL), which, being a potential bio-stimulator, helps to govern a wide array of functions in horticultural crops. Recent advancements have determined the role of MEL in plants' responses to abiotic stresses. MEL enhances physiological functions such as seed germination, growth and development, seedling growth, root system architecture, and photosynthetic efficiency. The potential function of MEL in stressful environments is to regulate the enzymatic and non-enzymatic antioxidant activity, thus playing a role in the substantial scavenging of reactive oxygen species (ROS). Additionally, MEL, as a plant growth regulator and bio-stimulator, aids in promoting plant tolerance to abiotic stress, mainly through improvements in nutrient uptake, osmolyte production, and cellular membrane stability. This review, therefore, focuses on the possible functions of MEL in the induction of different abiotic stresses in horticultural crops. Therefore, this review would help readers learn more about MEL in altered environments and provide new suggestions on how this knowledge could be used to develop stress tolerance.

MicroRNAs: emerging regulators in horticultural crops.

Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.

Assessment of reclaimed agro-wastewater polluted with insecticide residues for irrigation of growing lettuce (Lactuca sativa L) using solar photocatalytic technology.

Scientific literature is full of works studying the removal of different pollutants from water through different Advanced Oxidation Processes (AOPs). Many of them only suggest it is reused for agricultural purposes or for small crops in pots. This study is based on the reuse of reclaimed agricultural wastewater contaminated with four insecticides (chlorantraniliprole, imidacloprid, pirimicarb and thiamethoxam) for growing lettuce in field conditions. First, solar photocatalysis with TiO2/Na2S2O8 was used on a pilot plant in a sunny area (Murcia, SE of Spain) as an environmentally friendly technology to remove insecticide residues and their main reaction intermediates from contaminated water. The necessary fluence (H, kJ m-2) to accomplish 90% removal (H90) ranged from 0.12 to 1212 kJ m-2 for pirimicarb and chlorantraniliprole, respectively. Only six (derived from imidacloprid, pirimicarb and thiametoxam) of 18 transformation intermediate products studied were detected in reclaimed water during the photoperiod (2000 kJ m-2 of accumulated UVA radiation) although all of them were totally photodegraded after a fluence of 1250 kJ m-2. Secondly, reclaimed agro-wastewater was used to irrigate two lettuce crops grown under greenhouse conditions and under agricultural field conditions. In no cases, insecticide residues nor their TIPs were noticed above their respective LOQs (limits of quantification) in soil and lettuce samples (between 0.03 and 0.04 µg kg-1 for pirimicarb and 2.49 and 2.23 µg kg-1 for thiamethoxam, respectively) when they were irrigated with reclaimed water, while residues of the four insecticides and some of their intermediates were found in soil and lettuce by the end of cultivation when they were irrigated with non-reclaimed contaminated water. According to the results, this technology can be applied in a sustainable way, mainly in areas with water scarcity and high solar radiation, contributing to water utilisation in drought areas and the use of renewable energy.

Effect of Relative Humidity on the Population Dynamics of the Predator Amblyseius swirskii and Its Prey Carpoglyphus lactis in the Context of Slow-Release Sachets for Use in Biological Control in Greenhouses.

Amblyseius swirskii is a predatory mite that is widely used for biological control in greenhouses. One way this predator is released is in a formulation in slow-release sachets. These sachets are prepared with the predatory mite, the factitious prey mite Carpoglyphus lactis, and a food substrate for the latter. The objective of the present study was to study the effects of microclimatic conditions in this type of formulation on the population dynamics of mites inside the sachets and on the release of predatory mites. These experiments were conducted under laboratory conditions in two trials. The ambient relative humidity affected the water content of the food substrate of the prey mite inside the sachets, with an initial value of 21.49 ± 0.42%, which was reduced to values of 4.7 ± 0.25%, 10.87 ± 1.03% and 17.27 ± 0.82% after 21 days of trials when they were exposed to low, medium and high ambient relative humidity levels, respectively. Relative humidity significantly altered the dynamics of the populations of both species inside the sachets and the exits of the predator from the sachets to the external environment.