Challenges of climate change: omics-based biology of saffron plants and organic agricultural biotechnology for sustainable saffron production

Agrochemical-free genetically modified and genome-edited crops: Towards achieving the United Nations sustainable development goals and a 'greener' green revolution

Sustainable farming on ever-shrinking agricultural land and declining water resources for the growing human population is one of the greatest environmental and food security challenges of the 21st century. Conventional, age-old organic farming practices alone, and foods based on costly cellular agriculture, do not have the potential to be upscaled to meet the food supply challenges for feeding large populations. Additionally, agricultural practices relying on chemical inputs have a well-documented detrimental impact on human health and the environment. As the available farming methods have reached their productivity limits, new approaches to agriculture, combining friendly, age-old farming practices with modern technologies that exclude chemical interventions, are necessary to address the food production challenges. Growing genetically modified (GM) crops without chemical inputs can allow agricultural intensification with reduced adverse health and environmental impacts. Additionally, integrating high-value pleiotropic genes in their genetic improvement coupled with the use of modern agricultural technologies, like robotics and artificial intelligence (AI), will further improve productivity. Such 'organic-GM' crops will offer consumers healthy, agrochemical-free GM produce. We believe these agricultural practices will lead to the beginning of a potentially new chemical-free GM agricultural revolution in the era of Agriculture 4.0 and help meet the targets of the United Nations Sustainable Development Goals (SDGs). Furthermore, given the advancement in the genome editing (GE) toolbox, we ought to develop a new category of 'trait-reversible GM crops' to avert the fears of those who believe in ecological damage by GM crops. Thus, in this article, we advocate farming with no or minimal chemical use by combining chemical-free organic farming with the existing biofortified and multiple stress tolerant GM crops, while focusing on the development of novel 'biofertilizer-responsive GE crops' and 'trait-reversible GE crops' for the future.

Xylooligosaccharides Enhance Lettuce Root Morphogenesis and Growth Dynamics

Enhancing root development is pivotal for boosting crop yield and augmenting stress resilience. In this study, we explored the regulatory effects of xylooligosaccharides (XOSs) on lettuce root growth, comparing their impact with that of indole-3-butyric acid potassium salt (IBAP). Treatment with XOS led to a substantial increase in root dry weight (30.77%), total root length (29.40%), volume (21.58%), and surface area (25.44%) compared to the water-treated control. These enhancements were on par with those induced by IBAP. Comprehensive phytohormone profiling disclosed marked increases in indole-3-acetic acid (IAA), zeatin riboside (ZR), methyl jasmonate (JA-ME), and brassinosteroids (BRs) following XOS application. Through RNA sequencing, we identified 3807 differentially expressed genes (DEGs) in the roots of XOS-treated plants, which were significantly enriched in pathways associated with manganese ion homeostasis, microtubule motor activity, and carbohydrate metabolism. Intriguingly, approximately 62.7% of the DEGs responsive to XOS also responded to IBAP, underscoring common regulatory mechanisms. However, XOS uniquely influenced genes related to cutin, suberine, and wax biosynthesis, as well as plant hormone signal transduction, hinting at novel mechanisms of stress tolerance. Prominent up-regulation of genes encoding beta-glucosidase and beta-fructofuranosidase highlights enhanced carbohydrate metabolism as a key driver of XOS-induced root enhancement. Collectively, these results position XOS as a promising, sustainable option for agricultural biostimulation.

Ameliorating the effects of multiple stresses on agronomic traits in crops: modern biotechnological and omics approaches

While global climate change poses a significant environmental threat to agriculture, the increasing population is another big challenge to food security. To address this, developing crop varieties with increased productivity and tolerance to biotic and abiotic stresses is crucial. Breeders must identify traits to ensure higher and consistent yields under inconsistent environmental challenges, possess resilience against emerging biotic and abiotic stresses and satisfy customer demands for safer and more nutritious meals. With the advent of omics-based technologies, molecular tools are now integrated with breeding to understand the molecular genetics of genotype-based traits and develop better climate-smart crops. The rapid development of omics technologies offers an opportunity to generate novel datasets for crop species. Identifying genes and pathways responsible for significant agronomic traits has been made possible by integrating omics data with genetic and phenotypic information. This paper discusses the importance and use of omics-based strategies, including genomics, transcriptomics, proteomics and phenomics, for agricultural and horticultural crop improvement, which aligns with developing better adaptability in these crop species to the changing climate conditions.

Robotics-assisted, organic agricultural-biotechnology based environment-friendly healthy food option: Beyond the binary of GM versus Organic crops

Human society cannot afford the luxury of the business-as-usual approach when dealing with the emerging challenges of the 21st century. The challenges of food production to meet the pace of population growth in an environmentally-sustainable manner have increased considerably, emphasizing the need to explore newer approaches to agriculture. Agrochemical-based agricultural practices are known to have serious environmental and health implications. Even conventional organic farming is not sustainable in the long run. Although some "age-old" practices are useful, these will not help feed more people on the same or less land more sustainably. Sustainable intensification is the way forward. There is a need to incorporate a customer-centric outlook and make the organic system sustainable. Here, we bring forth the necessity to enhance the efficiency of organic agriculture by the inclusion of robotics and agrochemical-free GM seeds. Such an organic-GM hybrid agriculture system integrated with the use of artificial intelligence (AI) based technologies will have better energy efficiency. The produce from such a system will offer consumers a 'third' choice and create a new food label, 'organically-grown GM produce'.

The menace of saffron adulteration: Low-cost rapid identification of fake look-alike saffron using Foldscope and machine learning technology

Saffron authenticity is important for the saffron industry, consumers, food industry, and regulatory agencies. Herein we describe a combo of two novel methods to distinguish genuine saffron from fake in a user-friendly manner and without sophisticated instruments. A smartphone coupled with Foldscope was used to visualize characteristic features and distinguish "genuine" saffron from "fake." Furthermore, destaining and staining agents were used to study the staining patterns. Toluidine blue staining pattern was distinct and easier to use as it stained the papillae and the margins deep purple, while its stain is lighter yellowish green toward the central axis. Further to automate the process, we tested and compared different machine learning-based classification approaches for performing the automated saffron classification into genuine or fake. We demonstrated that the deep learning-based models are efficient in learning the morphological features and classifying samples as either fake or genuine, making it much easier for end-users. This approach performed much better than conventional machine learning approaches (random forest and SVM), and the model achieved an accuracy of 99.5% and a precision of 99.3% on the test dataset. The process has increased the robustness and reliability of authenticating saffron samples. This is the first study that describes a customer-centric frugal science-based approach to creating an automated app to detect adulteration. Furthermore, a survey was conducted to assess saffron adulteration and quality. It revealed that only 40% of samples belonged to ISO Category I, while the average adulteration percentage in the remaining samples was 36.25%. After discarding the adulterants from crude samples, their quality parameters improved significantly, elevating these from ISO category III to Category II. Conversely, it also means that Categories II and III saffron are more prone to and favored for adulteration by fraudsters.

Understanding saffron biology using omics- and bioinformatics tools: stepping towards a better Crocus phenome

Saffron is a unique plant in many aspects, and its cellular processes are regulated at multiple levels. The genetic makeup in the form of eight chromosome triplets (2n = 3x = 24) with a haploid genetic content (genome size) of 3.45 Gbp is decoded into different types of RNA by transcription. The RNA then translates into peptides and functional proteins, sometimes involving post-translational modifications too. The interactions of the genome, transcriptome, proteome and other regulatory molecules ultimately result in the complex set of primary and secondary metabolites of saffron metabolome. These complex interactions manifest in the form of a set of traits 'phenome' peculiar to saffron. The phenome responds to the environmental changes occurring in and around saffron and modify its response in respect of growth, development, disease response, stigma quality, apocarotenoid biosynthesis, and other processes. Understanding these complex relations between different yet interconnected biological activities is quite challenging in saffron where classical genetics has a very limited role owing to its sterility, and the absence of a whole-genome sequence. Omics-based technologies are immensely helpful in overcoming these limitations and developing a better understanding of saffron biology. In addition to creating a comprehensive picture of the molecular mechanisms involved in apocarotenoid synthesis, stigma biogenesis, corm activity, and flower development, omics-technologies will ultimately lead to the engineering of saffron plants with improved phenome.

High-value pleiotropic genes for developing multiple stress-tolerant biofortified crops for 21st-century challenges

The agriculture-based livelihood systems that are already vulnerable due to multiple challenges face immediate risk of increased crop failures due to weather vagaries. As breeders and biotechnologists, our strategy is to advance and innovate breeding for weather-proofing crops. Plant stress tolerance is a genetically complex trait. Additionally, crops rarely face a single type of stress in isolation, and it is difficult for plants to deal with multiple stresses simultaneously. One of the most helpful approaches to creating stress-resilient crops is genome editing and trans- or cis-genesis. Out of hundreds of stress-responsive genes, many have been used to impart tolerance against a particular stress factor, while a few used in combination for gene pyramiding against multiple stresses. However, a better approach would be to use multi-role pleiotropic genes that enable plants to adapt to numerous environmental stresses simultaneously. Herein we attempt to integrate and present the scattered information published in the past three decades about these pleiotropic genes for crop improvement and remodeling future cropping systems. Research articles validating functional roles of genes in transgenic plants were used to create groups of multi-role pleiotropic genes that could be candidate genes for developing weather-proof crop varieties. These biotech crop varieties will help create 'high-value farms' to meet the goal of a sustainable increase in global food productivity and stabilize food prices by ensuring a fluctuation-free assured food supply. It could also help create a gene repository through artificial gene synthesis for 'resilient high-value food production' for the 21st century.

Corm Rot of Saffron: Epidemiology and Management

Saffron, comprising of dried stigmas of the plant known as Crocus sativus, is one of the most important and scantly cultivated agricultural products. It has been used as a precious spice for the last at least 3500 years. Due to its numerous medicinal qualities and pharmacological applications, it is considered as a “golden condiment”, and its demand and consumptions has risen over a period of time. Although efforts are continuously being made to enhance the productivity in the traditional areas and promote the cultivation of saffron in the newer areas, there are several constraints hindering these efforts. Prevalence of corm rot is one such limiting factor which results in the reduction in saffron production and decline in the area under its cultivation. The disease not only reduces the yield substantially, but also adversely affects the production of daughter corms. Complete understanding and knowledge about the disease is still lacking due to the inadequate information about its etiology and epidemiology. Moreover, due to the non-availability of resistant genotypes and lack of improved cultural practices, presently no effective and sustainable management strategies are available. This review article gives an overall account of the history and impact of saffron corm rot, its present status, yield losses caused by it, dynamics of the pathogens associated with the disease, their survival and dispersal, factors influencing disease intensity, epidemiology and sustainable management strategies. As comprehensive information on the disease is presently not available, an attempt has been made to review the current knowledge regarding corm rot of saffron. The information about the disease discussed here can eventually be beneficial for the growers, students, researchers, plant protection organizations, development departments, extension workers, policy makers, government agencies and public organizations.

Plummeting anthropogenic environmental degradation by amending nutrient-N input method in saffron growing soils of north-west Himalayas

Nitrous-oxide emission and nitrate addition from agriculture to earth's environment are two main agriculture related anthropogenic causes of environmental degradation that needs greater attention. For addressing the aforesaid issue, new techniques/practices need to be developed and implemented. The present investigation, which was focused on this issue, resulted in developing a new mode of nitrogen (N) placement, i.e. 'mid rib placement upper to corms in two splits (MRPU-2S)', that could reduce nitrous oxide N emission by around 70.11% and, nitrate N leaching and runoff by around 68.26 and 67.09%, respectively, over conventional method, in saffron growing soils of northwest Himalayas. Besides plummeting environmental degradation, MRPU-2S further resulted in enhancing saffron yield by 33.33% over conventional method. The findings of the present investigation were used to develop new empirical models for predicting saffron yield, nitrate N leaching and nitrous-oxide N emission. The threshold limits of nitrate N leaching and nitrous oxide N emission have also been reported exclusively in the present study.

Role of Biocontrol Agents in Management of Corm Rot of Saffron Caused by Fusarium oxysporum

Saffron (Crocus sativus L.) is considered as one of the most expensive spices. Fusarium corm rot of saffron, caused by Fusarium oxysporum, is known to cause severe yield losses worldwide. In the present study, efficacy of biocontrol agents (Trichoderma asperellum, Pseudomonas fluorescens, Pseudomonas aeruginosa, Pseudomonas putida, Bacillus stratosphericus, Bacillus pumilus, and Bacillus subtilis) along with a chemical fungicide, carbendazim, was evaluated for managing the corm rot of saffron. Under in vitro conditions, using dual culture and poison food techniques on potato dextrose agar, T. asperellum and carbendazim significantly reduced the mycelial growth of the pathogen F. oxysporum, with the inhibition of 62.76 and 60.27%, respectively, compared with control. Under field conditions, dipping of saffron corms in carbendazim and T. asperellum exhibited maximum reduction of 82.77 and 77.84%, respectively, in the disease incidence, during the first year of experiment. However, during the second year, maximum reduction in the incidence of corm rot (68.63%) was recorded with the T. asperellum. Moreover, the population density of F. oxysporum was also significantly reduced by 60 and 80.19% while using T. asperellum after 75 and 260 days of sowing of saffron corms, compared to its population before planting of corms. In case of growth promotion traits, such as sprouting and flowering, biocontrol treatments reduced the number of days (average) of sprouting and flower emergence after sowing, compared to control.

Effect of ecological factors on the accumulation of phenolic compounds in Iris species from Latvia, Lithuania and Ukraine

INTRODUCTION

It is important to conduct studies on the influence of environmental factors on the accumulation of secondary metabolites in plants, as well as the cultivation of plants and harvesting of their raw material.

OBJECTIVE

In this study, we examined the influence of habitat types, soil composition, climatic factors and altitude on the content of phenolic compounds in Iris species from different populations in Latvia, Lithuania and Ukraine.

METHODOLOGY

According to high-performance liquid chromatography (HPLC) analysis, 25 compounds (flavonoids, isoflavonoids, isoflavonoid glucosides, xanthones, phenolcarboxylic acids) were identified in the methanol extracts of 16 samples of Iris rhizomes. The quantitative data were further analysed by principal component analysis (PCA) to reveal the impact of environmental factors on the accumulation of compounds in plants.

RESULTS

Iris pseudacorus from Latvia and Lithuania had a more diverse composition of phenolic compounds than samples from Ukraine. Sampled plants of the Iris subg. Iris had a higher content of the analysed compounds than those of Iris subg. Limniris. PCA results showed that the levels of phenolic compounds in Iris rhizomes were influenced by the content of soil nutrients. The phosphorus and potassium content had a significant impact on the levels of phenolic compounds, whereas the impact of nitrogen content was not significant. Meteorological factors had a small impact; however, sunshine duration had a significant positive effect and the amount of precipitation had a significant negative impact.

CONCLUSION

The results of this study suggest that rhizomes of Iris species may be an important source of pharmacologically active compounds such as flavonoids, isoflavonoids and xanthones. Studies on the effect of environmental factors on the production and accumulation of secondary metabolites in Iris species are important because they contribute to knowledge of quantitative parameters of secondary metabolites in medicinal plants and could be employed for the cultivation and harvesting of raw material for medicinal purposes.

Host-Pathogen Interaction in Fusarium oxysporum Infections: Where Do We Stand?

Fusarium oxysporum, a ubiquitous soilborne pathogen, causes devastating vascular wilt in more than 100 plant species and ranks 5th among the top 10 fungal plant pathogens. It has emerged as a human pathogen, too, causing infections in immune-compromised patients. Therefore, it is important to gain insight into the molecular processes involved in the pathogenesis of this transkingdom pathogen. A complex network comprising interconnected and overlapping signal pathways-mitogen-activated protein kinase signaling pathways, Ras proteins, G-protein signaling components and their downstream pathways, components of the velvet (LaeA/VeA/VelB) complex, and cAMP pathways-is involved in perceiving the host. This network regulates the expression of various pathogenicity genes. However, plants have evolved an elaborate protection system to combat this attack. They, too, possess intricate mechanisms at the molecular level which, once triggered by pathogen attack, transduce signals to activate defense response. This review focuses on understanding and presenting a wholistic picture of the molecular mechanisms of F. oxysporum-host interactions in plant immunity.

Multiplex Fluorescent, Activity-Based Protein Profiling Identifies Active α-Glycosidases and Other Hydrolases in Plants

With nearly 140 α-glycosidases in 14 different families, plants are well equipped with enzymes that can break the α-glucosidic bonds in a large diversity of molecules. Here, we introduce activity-based protein profiling (ABPP) of α-glycosidases in plants using α-configured cyclophellitol aziridine probes carrying various fluorophores or biotin. In Arabidopsis (Arabidopsis thaliana), these probes label members of the GH31 family of glycosyl hydrolases, including endoplasmic reticulum-resident α-glucosidase-II Radial Swelling3/Priority for Sweet Life5 (RSW3/PSL5) and Golgi-resident α-mannosidase-II Hybrid Glycosylation1 (HGL1), both of which trim N-glycans on glycoproteins. We detected the active state of extracellular α-glycosidases such as α-xylosidase XYL1, which acts on xyloglucans in the cell wall to promote cell expansion, and α-glucosidase AGLU1, which acts in starch hydrolysis and can suppress fungal invasion. Labeling of α-glycosidases generates pH-dependent signals that can be suppressed by α-glycosidase inhibitors in a broad range of plant species. To demonstrate its use on a nonmodel plant species, we applied ABPP on saffron crocus (Crocus sativus), a cash crop for the production of saffron spice. Using a combination of biotinylated glycosidase probes, we identified and quantified 67 active glycosidases in saffron crocus stigma, of which 10 are differentially active. We also uncovered massive changes in hydrolase activities in the corms upon infection with Fusarium oxysporum using multiplex fluorescence labeling in combination with probes for serine hydrolases and cysteine proteases. These experiments demonstrate the ease with which active α-glycosidases and other hydrolases can be analyzed through ABPP in model and nonmodel plants.

Time to Redefine Organic Agriculture: Can't GM Crops Be Certified as Organics?

The challenges of sustainable food production without damaging the environment for a growing human population have increased considerably. The current agricultural practices involving chemical fertilizers and even organic farming are not sustainable in the long run and can have deleterious effects on the environment. Thus, new, innovative solutions need to be identified and propagated for tackling this. Among such innovations, that can complement conventional as well as organic farming methods, are genetic modification (GM) and aquaculture. Yet, GM technologies often face resistance from civil groups owing to an 'unknown' fear, akin to Frankenstein's monster. How real is this fear? Our discussion rests on basic questions like, why can't 'organics' include GM crops that do not require chemical inputs for cultivation, and can GM crops like Golden rice qualify to be 'organic' if cultivated through organic practices? Do we need to rethink organic agriculture in the context of the present and future challenges of 21st century?

Saffron'omics': The challenges of integrating omic technologies

Saffron is one of the highly exotic spices known for traditional values and antiquity. It is used for home décor besides serving as a colorant flavor and is widely known for medicinal value. Over the last few years, saffron has garnered a lot of interest due to its anti-cancer, anti-mutagenic, anti-oxidant and immunomodulatory properties. Integration of systems biology approaches with wide applications of saffron remains a growing challenge as new techniques and methods advance. Keeping in view of the dearth of a review summarizing the omics and systems biology of saffron, we bring an outline on advancements in integrating omic technologies, the medicinal plant has seen in recent times.