Indian Agricultural Research Institute

Drought stress has been known to adversely affect growth, development, and productivity of plants to varying extent. Being a multifaceted trait, drought tolerance involves interaction of an array of genes, pathways, and mechanisms. A unique regulatory scheme is adopted by different plants, which provides tolerance to drought stress in association with biochemical and physiological mechanisms. Transcriptome analysis of a drought tolerant [Nagina 22 (N-22)] and drought sensitive (IR-64) cultivars provides insights into the genes/pathways/mechanisms involved in terminal drought stress tolerance. In the present study, comparative physio-biochemical analyses of the rice cultivars under terminal drought stress substantiated their performance. Whole transcriptome analysis of leaf and root from the rice cultivars exposed to terminal drought stress revealed 6077 and 10050 differentially expressed genes (DEGs) in leaf of N-22 and IR-64, respectively, under drought stress. A maximum of 2682 genes were up-regulated exclusively in N-22 while 7198 genes were down-regulated exclusively in leaf of IR-64. Interestingly, the highest number (2594) of genes was down-regulated exclusively in roots of IR-64, while only 1497 gene were up-regulated exclusively in root of N-22. Differential expression of OsNAC10, OsbZIP23, OsABA8ox1, OsCPK4, OsLEA3, and OsNCED4 along with the GO terms enriched with up-regulated genes for transcription factors (TFs), redox homeostasis, and ABA signaling in N-22 under terminal drought stress play crucial roles in stress tolerance. The stress-responsive genes for transcription factors, redox homeostasis, and ABA signaling up-regulated in N-22 were mainly responsible for terminal drought tolerance. These stress-associated genes can be utilized for genetic improvement of rice for drought tolerance.

In nature, melatonin is widely distributed, and not only does it play a vital role for animals and humans, but also for plants. Plants use melatonin for a wide range of purposes, including preventing senescence, acting as an antioxidant, regulating growth and development, and adjusting to stressful conditions. Fruits and vegetables contain it naturally, and its presence greatly influences the ripening and post-harvest processes. As a result of increasing the activity of antioxidant enzymes, non-enzymatic antioxidants, and enzymes involved in repairing oxidized proteins, melatonin is effective in reducing reactive oxygen species levels in post-harvest fruits and vegetables. Exogenous melatonin can also increase endogenous melatonin levels, enhancing its effects on a variety of physiological processes. Exogenous melatonin has been shown to improve the post-harvest preservation of fruits and vegetables in several studies. While transgenic methods could potentially be used to overproduce melatonin in plants and improve post-harvest preservation, current attempts are limited to increasing endogenous melatonin in plants. Recent advances in understanding melatonin’s role and mechanisms in post-harvest fruits and vegetables are summarized in this review. Additionally, it provides insights into future approaches to maximizing fruit and vegetable preservation post-harvest. Research in this area could lead to innovative strategies for reducing food losses and improving the quality of fruits and vegetables after harvest.

Abiotic stresses are among the potent threats to plant production and growth. The abiotic stresses are accountable for the obstruction of biological redox homeostasis, oxidative stress, and formation of reactive oxygen species (ROS) in the plants. From sprouting and growth to the reproductive stage, plants are routinely opened to several abiotic challenges, including temperature, heavy metal, salt, and drought pressures. Certain defense mechanisms exist in plants that provide definite and precise signaling in the metabolic pathways to combat and survive. Among these signaling molecules, hydrogen sulfide (H2S) is recognized as a useful ‘gasotransmitter’ which has been emerged as a vital gaseous signal in regulating gene expression under various abiotic stresses. Though, the defensive role of this gasotransmitter is almost established, yet its precise role in plants remains a point to discuss more and more considering recent advancements related to plant and environment interactions. Hence, this chapter attempts to provide an insight into the various roles of H2S as a gasotransmitter to assist plant adaptations under challenging abiotic conditions.

Nitric oxide (NO) is a gasotransmitter molecule involved in a variety of physiological functions related to acclimation responses in plants for biotic and abiotic stresses. Thus, NO holds great promise in extending the shelf life of freshly harvested fruits and vegetables. Various investigations have identified the signalling function of NO in respiration, ripening, senescence, chilling injury alleviation and membrane damage to biological tissues by maintaining a greater antioxidant system. This chapter describes the relevance and role of nitric oxide to improve postharvest storage life and the quality of freshly harvested fruits and vegetables.

Hydrogen sulfide (H2S) is a naturally occurring gaseous molecule in plants and a potential signalling molecule that regulates many physiological processes in the plant system. Various studies have reported the beneficial effect of H2S in delaying the fruit ripening, senescence, and better fruit quality during storage. It reduces oxidative damage, membrane permeability, and lipid peroxidation by boosting the antioxidant defence mechanism in many fruits and vegetables. It has a greater potential for use in the postharvest industry for reducing postharvest decay and improving fruit quality with extended storage life. This chapter is mainly focused on the role of H2S in postharvest physiology, its signalling action, and cross-talk with other hormones viz. ethylene, abscisic acid, and nitric oxide during fruit ripening.

A new biomolecule called melatonin (N-acetyl-5-methoxytryptamine) affects the growth of horticultural crops both before and after harvest. The most important role of melatonin in higher plants is an indoleamine neurotransmitter and antioxidant that can regulate reactive oxygen and nitrogen species. It is a signalling agent that induces various specific physiological activities in plants that might serve to increase growth, photosynthesis, root initiation, fixation of carbon, defence, and germination of seed against various abiotic and biotic stressors. However, its role in postharvest biology bears significant potential in improving quality, fruit ripening, shelf life, postharvest preservation, and stress protection (biotic as well as abiotic stress) during storage. Recent studies on postharvest biology of horticultural crops revealed the role of melatonin in preventing senescence, antioxidant action, etc. which are very important with respect to economic value of horticultural commodities. The positive influence of melatonin on postharvest biology is utilised in shelf life extension and quality retention in terms of sensorial and nutritional quality. It is now well evident that the addition of melatonin enhances the postharvest biology of various horticultural crops. Additionally, many new aspects have been identified where melatonin may have possible roles in reduction in the pesticide residues accumulation and heavy metals in foods. The detailed information on the diverse functional role of melatonin in postharvest biology, viz. its importance in postharvest management, signalling, regulation, application in horticultural crops, etc. are discussed in detail in this chapter.

Vegetables are usually herbaceous and succulent plants. This succulent nature of vegetable crops makes them susceptible to attack by a wide variety of pests. Traditionally insect resistance has not been as widely investigated as disease resistance due to relatively smaller economic losses caused by insects as compared to pathogens in earlier times. But owing to indiscriminate use of pesticides, population of natural enemies has declined which in turn has increased the frequency of insect epidemics. Outbreak of Tuta absoluta in tomato is a recent example. Intense selection of crops has reduced the genetic variability and has increased their genetic vulnerability to insects. Some pests like Meloidogyne spp., Helicoverpa and aphids are polyphagous and cannot be managed by chemical sprays. In such cases resorting to insect resistance is the best option for a breeder. But development of insect resistant variety takes considerable time and efforts. Recent advancements in omics approaches has accelerated the resistance breeding. Genetic markers permit effective indirect selection for insect resistant plants. They are effective tools for identifying genomic regions controlling pest resistance. Molecular markers permit transfer of precise DNA segments from disease resistant species to susceptible cultivars thus preventing the problem of linkage drag. This review highlights the achievements in recent years in vegetable resistance breeding via various omics-based approaches viz. genomics, transcriptomics, proteomics and metabolomics.

Vegetables are the richest source of vitamins, essential elements, and minerals like calcium and iron. Most of the human population are vegetarians; they fulfil their daily nutrient requirements by consuming vegetables. However, the production of vegetables is seriously hampered by several biotic stresses, viz., bacteria, fungi, nematodes, and viruses, which pose a considerable challenge to meeting future demands for such a large population. Among several biotic stresses, root-knot nematodes (RKNs) (Meloidogyne spp.) are the major threat to vegetable production. RKNs are obligate and sedentary root endoparasites of almost all vegetable crops and are considered the most damaging pests in agriculture. Since RKNs target the root vascular system, they provoke host nutrient deprivation and defective food and water transport by forming galls in the roots. They also cause aboveground symptoms of growth stunting, wilting, chlorosis in patches, and reduced crop yields. Besides the direct damage, RKNs act as a predisposing agent to other soil-borne bacterial and fungal pathogens and aggravate the problem, further leading to development of disease complexes. Considering the difficulties, researchers worldwide find eco-friendly approaches to protect vegetable production from such tiny and more damaging soil-borne pathogens.

Root-knot nematodes (Meloidogyne spp.) are the most widespread, have a vast host range, vascular feeder endoparasites, and, therefore, are considered the most damaging among the plant-parasitic nematodes globally. This chapter describes the systematics of the major species of Meloidogyne based on morphological, morphometrical, enzyme phenotypes, and molecular parameters. The existence of host races and cytological races in general and the occurrence of economically important Meloidogyne species in India are tabulated along with estimations on recent crop losses. A brief account of the general biology, life cycle, and host-parasite relationship of Meloidogyne sp. is included. The damage symptoms of Meloidogyne spp. on different vegetable crops is depicted through images. The management of nematode vegetable cropping systems has been dealt in detail. This includes cultural/agronomic practices, biological control through fungal and bacterial bioagents, host plant resistance, newer chemical nematicides, and their integration. A dedicated section is included on managing root-knot nematodes in protected cultivation systems. Root-knot nematode dissemination through horticultural nurseries has been highlighted, along with practical methods to check it. Lastly, some emerging problems of root-knot nematodes have been reported.

Genome or gene editing (GE) involves a repertoire of innovative molecular techniques that make use of sequence-specific nucleases (SSNs), for the precise modification of an organism's genome sequences. The CRISPR/Cas-based GE system, associated with Clustered Regularly Interspaced Short Palindromic Repeats, has emerged as a potent addition to the expanding genomics toolkit. It enables precise mutagenesis, gene knockouts, multiplex gene editing, and the manipulation of gene expression in plants. Undoubtedly, the application of CRISPR/Cas-based GE in plants has brought about a revolution in basic research, aiding in our understanding of gene functions and significantly advancing applied crop research. This, in turn, underscores its immense potential for crop improvement. Against this backdrop, the current Special Issue on "Genome Editing in Plants: A Tool for Precision Breeding and Functional Genomics" represents a timely effort to assemble a group of leading experts in the field of plant genome editing. This compilation includes a commentary article, two original research papers, and eleven review articles and is expected to bring about substantial progress in the field of plant science, particularly in the domain of genome editing.

The infective juveniles (IJs) of entomopathogenic nematode (EPN) Heterorhabditis bacteriophora find and infect their host insects in heterogeneous soil ecosystems by sensing a universal host cue (CO 2 ) or insect/plant-derived odorants, which bind to various sensory receptors, including G protein-coupled receptors (GPCRs). Nematode chemosensory GPCRs (NemChRs) bind to a diverse set of ligands, including odor molecules. However, there is a lack of information on the NemChRs in EPNs. Here we identified 21 GPCRs in the H. bacteriophora genome sequence in a triphasic manner, combining various transmembrane detectors and GPCR predictors based on different algorithms, and considering inherent properties of GPCRs. The pipeline was validated by reciprocal BLAST, InterProscan, GPCR-CA, and NCBI CDD search. Functional classification of predicted GPCRs using Pfam revealed the presence of four NemChRs. Additionally, GPCRs were classified into various families based on the reciprocal BLAST approach into a frizzled type, a secretin type, and 19 rhodopsin types of GPCRs. Gi/o is the most abundant kind of G-protein, having a coupling specificity to all the fetched GPCRs. As the 21 GPCRs identified are expected to play a crucial role in the host-seeking behavior, these might be targeted to develop novel insect-pest management strategies by tweaking EPN IJ behavior, or to design novel anthelminthic drugs. Our new and stringent GPCR detection pipeline may also be used to identify GPCRs from the genome sequence of other organisms.

Main conclusion Roots play an important role in adaptive plasticity of rice under dry/direct-sown conditions. However, hypomethylation of genes in leaves (resulting in up-regulated expression) complements the adaptive plasticity of Nagina-22 under DSR conditions. Abstract Rice is generally cultivated by transplanting which requires plenty of water for irrigation. Such a practice makes rice cultivation a challenging task under global climate change and reducing water availability. However, dry-seeded/direct-sown rice (DSR) has emerged as a resource-saving alternative to transplanted rice (TPR). Though some of the well-adapted local cultivars are used for DSR, only limited success has been achieved in developing DSR varieties mainly because of a limited knowledge of adaptability of rice under fluctuating environmental conditions. Based on better morpho-physiological and agronomic performance of Nagina-22 (N-22) under DSR conditions, N-22 and IR-64 were grown by transplanting and direct-sowing and used for whole genome methylome analysis to unravel the epigenetic basis of adaptive plasticity of rice. Comparative methylome and transcriptome analyses indicated a large number (4078) of genes regulated through DNA methylation/demethylation in N-22 under DSR conditions. Gene × environment interactions play important roles in adaptive plasticity of rice under direct-sown conditions. While genes for pectinesterase, LRK10, C2H2 zinc-finger protein, splicing factor, transposable elements, and some of the unannotated proteins were hypermethylated, the genes for regulation of transcription, protein phosphorylation, etc. were hypomethylated in CG context in the root of N-22, which played important roles in providing adaptive plasticity to N-22 under DSR conditions. Hypomethylation leading to up-regulation of gene expression in the leaf complements the adaptive plasticity of N-22 under DSR conditions. Moreover, differential post-translational modification of proteins and chromatin assembly/disassembly through DNA methylation in CHG context modulate adaptive plasticity of N-22. These findings would help developing DSR cultivars for increased water-productivity and ecological efficiency.

Fungicides, one important class of crop protection products, are important to protect the crops from fungal attacks to meet the challenge of increased food production in the present era of increasing global population and food demand. A large amount of the applied fungicides are lost in the different environmental compartments, either directly through intentional use (such as agronomic practices) or unintentionally (e.g., spray drift, surface runoff, leaching). Moreover, the injudicious and indiscriminate use of chemical fungicides results in various human and environmental health hazards. The presence of unwanted fungicide residues and their persistence behavior in environmental matrices may not only contaminate the soil, water, and air but also possess toxicity of both acute and chronic nature towards nontarget organisms. Bioremediation is a potent decontamination technique of different xenobiotics including pesticides with the use of biological resources such as plants and microbes. Among different bioremediation techniques, biodegradation, particularly microbial degradation using bacteria and fungi, is considered as an important decontamination tool due to its cost-effective and sustainable nature. Biodegradation of xenobiotics including fungicides by using bacteria is important in this regard. Therefore, a spotlight in the form of this chapter has been shone upon the role of bacteria in the degradation of fungicides from soil, along with an address to the present limitations and future opportunities hidden underneath them.

Tea, the major beverage worldwide, is one of the oldest commercial commodities traded from ancient times. Apart from many of its advantages, including health, socio-economic, climatic, and agro-ecological values, FAO has recognized that the tea value chain covering its growth in the field, processing and marketing, and finally, the hot cup at the user’s hand needs to be made sustainable during all these stages. Tea generates a lot of waste in different forms in different stages of its growth and processing, and these wastes, if not managed properly, may cause environmental pollution. A planned utilization of these wastes as feedstocks for various processes can generate more income, create rural livelihood opportunities, help grow tea environmentally sustainable, avoid GHG emissions, and make a real contribution to SDGs. Thermochemical and biological conversion of tea wastes generates value-added products. This review provides an overview on the impacts of the tea wastes on the environment, tea waste valorization processes, and applications of value-added products. The application of value-added products for energy generation, wastewater treatment, soil conditioners, adsorbents, biofertilizers, food additives, dietary supplements, animal feed bioactive chemicals, dye, colourant, and phytochemicals has been reviewed. Further, the challenges in sustainable utilization of tea wastes and opportunities for commercial exploitation of value-added products from tea wastes have been reviewed.

The purpose of this study is to explore the utilization of nanomaterials in the agricultural engineering sector and to understand their potential to contribute to sustainable growth in agriculture. This comprehensive review paper synthesizes existing research and examines the integration of nanomaterials in various aspects of agricultural engineering. It delves into how nanomaterials can enhance the efficiency and performance of agricultural machinery, prime movers, tire technology, lubrication systems, coolant formulations, irrigation methods, plant protection strategies, fertilizer application mechanisms, and food processing techniques. The study also considers potential health and safety risks associated with nanotechnology in agriculture. The results of this review paper highlight the extensive potential of nanomaterials in revolutionizing agricultural practices. Nanotechnology has the capacity to significantly improve agricultural processes, making them more efficient and sustainable. The integration of nanomaterials in various agricultural components and processes has shown promising outcomes. However, it also underscores the need for ongoing research to address potential health and safety risks. Incorporation of nanomaterials in agriculture holds great promise for sustainable growth and efficiency. It offers innovative solutions to enhance various aspects of agricultural engineering. While nanomaterials have the potential to revolutionize agriculture, it is crucial to proceed with caution and conduct continued research to mitigate potential health and safety risks. As agriculture seeks more efficient and sustainable practices, the integration of nanomaterials remains a frontier that necessitates ongoing exploration and vigilance in its implementation.

Root rot is a damaging disease caused by various pathogenic fungi including, Fusarium spp., Rhizoctonia spp., and especially oomycetes. This disease poses significant challenges to food crop production worldwide. Pythium and Phytophthora, most species of these genera, are fungus-like pathogens that can grow and expand in diverse agroecosystems, inflicting severe damage to the root systems of numerous food crops, including cereals, vegetables, and legumes. Multiple factors contribute to the proliferation of root rot, including temperature, soil moisture levels, and the existence of vulnerable host plants. Based on a wide range of scientific literature, this paper examines the impact of the disease on plant safety, emphasizing the substantial yield losses and economic harm faced by farmers worldwide. The paper provides also a comprehensive overview of the global prevalence, impact, and management strategies associated with root rot infections. A special highlight is directed at symptoms, infection process, and pathogenicity mechanisms employed by Pythium and Phytophthora species, with a particular case of olive root rot caused by these two pathogens. Additionally, detection strategies of pathogenic oomycetes are discussed as well, from conventional to recent tools that are employed now in the plant pathology field. Finally, various preventive and management strategies are provided in this work. These include cultural practices, chemical control measures, and biological control agents, from bacteria to antagonistic fungi with a special focus on the use of Trichoderma spp. strains, and host resistance breeding. The limitations and challenges associated with these strategies, such as the emergence of resistant strains and environmental concerns, are also addressed. In conclusion, this review helps to understand the biology, pathogenicity, and management options for these pathogens, which is crucial for developing sustainable solutions to mitigate the impact of root rot, ensuring food security, and raising sustainable agriculture in the face of this significant challenge.

Modern agriculture has a major impact on natural resources in terms of exploitation and use. Land and water resources are being exploited by ever-increasing population pressures. High nutritional inputs such as mineral nitrogen (N) fertilization are required to achieve higher and sustainable yields. Although crop production depends on N fertilizers, the excessive and inefficient use of N inputs is a worldwide issue that increases production costs and pollutes the environment. Strategies to increase N use efficiency (NUE) would be the key to reducing these negative impacts by improved agronomic practices. To develop effective management approaches, it would be helpful to understand the effect of N on various aspects of crop growth, development, and physiological processes in crops. In this review, we highlighted recent agronomic progress made to improve NUE by adopting primarily agronomic practices that may be more environmentally and economically beneficial, including site-specific-nitrogen management , enhanced use efficiency of fertilizer resources, conservation approaches, drip fertigation, crop modeling, and precision agriculture. The first section discusses the morphological and physiological effects of N on crops while in the second section, agronomic strategies for growing crops with higher NUE are discussed.

Anguina tritici is the first plant-parasitic nematode described in literature, dating back to the year 1743. It is responsible for causing earcockle (seed gall) and tundu diseases in wheat and rye. Notably, this nematode has been observed to survive in an anhydrobiotic state for up to 32 years within wheat seed galls. These exceptional characteristics have inspired the sequencing of the A. tritici genome. In this study, we present the initial draft genome of A. tritici , obtained using the Illumina MiSeq platform with coverage of 60-fold. The genome is estimated to have a size of 164 Mb and comprises 39,965 protein-coding genes, exhibiting a GC content of 39.1%. The availability of this genome data will serve as a foundation for future functional biological investigations, particularly for genes whose functions remain unknown to this day.

In survey sampling, auxiliary information is used to precisely estimate the finite population parameters. There are several approaches available in the literature that provide a practical method for incorporating auxiliary information during the estimation stage. In order to effectively utilize the auxiliary information, a geographically weighted regression (GWR) model-assisted integrated estimator of finite population total under a two-phase sampling design has been proposed in this article. Spatial simulation studies have been conducted to empirically assess the statistical properties of the proposed estimator. In the presence of spatial non-stationarity, empirical findings reveal that the proposed estimator outperforms all existing estimators such as two-phase HT, ratio, and regression estimators, demonstrating the importance of spatial information in survey sampling.