Recent trends and advances of RNA interference (RNAi) to improve agricultural crops and enhance their resilience to biotic and abiotic stresses

HTS analysis of resistance induction against PPV by four hairpin constructs in Nicotiana benthamiana Domin

Plum pox virus (PPV) is the most devastating viral disease of the stone fruits worldwide. Inefficiency of the traditional control measures against PPV along with its globally widespread distribution and the economic importance of stone fruits, signify the necessity and importance of PPV resistance programs. In the present study, Agrobacterium-mediated transformation of Nicotiana benthamiana Domin was performed using four inverted repeat constructs derived from UTR/P1, HCPro, HCPro/P3, and CP regions of PPV-T isolate KyEsAp301. The efficacy of the constructs for inducing virus resistance in transgenic plants was evaluated by inoculation with PPV-D, -M, and -T strains. The potential of hairpin structures in the production of siRNAs and miRNAs in both wild-type and transgenic plants was compared by small RNA high-throughput sequencing. Although the four PPV genomic regions were used for transgenic resistance in previous experiments, small RNA high-throughput sequencing was first time used in this study to demonstrate the efficacy of the PPV constructs and to determine expression profiles of siRNAs and miRNAs. The results revealed that the potentials of hairpin constructs in producing siRNAs and their accumulation in target regions were significantly different. Expression profiles of several known and novel miRNAs were dramatically changed in response to PPV infection in both wild-type and transgenic plants, demonstrating plausible involvement of these miRNAs in plant-virus interactions. Based on the abundance of siRNAs and lack of PPV virus accumulation in transgenic plants harboring UTR/P1 and CP hairpin construct, we have concluded that UTR/P1 and CP are likely the best viral regions for induction of resistance against PPV.

Can the molecular and transgenic breeding of crops be an alternative and sustainable technology to meet food demand?

The gradual increase in the worldwide population represents various challenges, and one of the most alarming being the food demand. Historically technological advances led to the development of crops that meets the requirements and demands. Currently, molecular breeding unlocks the genetic potential of crops for their improvement, positioning it as a key technology for the development of new crops. The implementation of OMICs sciences, such spatial and single cell transcriptomics is providing a large and precise information, which can be exploited for crop improvement related to increasing yield, improving the nutritional value; designing new strategies for diseases resistance and management and for conserving biodiversity. Furthermore, the use of new technologies such CRISPR/CAS9 brought us the ability to modify the selected regions of the genome to select the superior's genotypes at a short time and the use of artificial intelligence aid in the analysis of big data generated by OMICS sciences. On the other hand, the application of molecular improvement technologies open up discussion on global regulatory measures, the socio-economic and socio-ethics, as the frameworks on its global regulation and its impact on the society create the public perception on its acceptance. In this review, the use and impact of OMICs sciences and genetic engineering in crops development, the regulatory measures, the socio-economic impact and as well as the mediatic information on genetically modified crops worldwide is discussed along with comprehensive insights on the potential of molecular plant breeding as an alternative and sustainable technology to meet global food demand.

Selenium Treatment Alleviates the Inhibition Caused by Nep-L Gene Knockdown in Silkworm (Bombyx mori)

Recent studies have emphasized the beneficial effects of 50 μM selenium (Se) on the growth and development of the silkworm, Bombyx mori; however, less is known about its underlying mechanism. To unravel the effect of 50 μM Se on the silkworms with neutral endopeptidase 24.11-like gene (NEP-L) knockdown, we injected small interfering RNA (siRNA) into the body cavity of silkworms. Phenotypic characteristics, mRNA expression of the Nep-L gene, and enriched Se content were evaluated in silkworms from each treatment group. After injecting Nep-L siRNA, the body weight, cocoon quality (cocoon weight, cocoon shell weight, and cocoon shell ratio), and egg production of silkworms were significantly reduced, without any significant effect on egg laying number. However, Se treatment could significantly alleviate the inhibition of body weight, and cocoon quality, without significant effects on egg laying number and production. In addition, the gene knockdown increased Se content in the B. mori. On the molecular level, the targeted Nep-L gene was inhibited significantly by siRNA interference, essentially with the strongest effect at 24 h after RNAi, followed by steady recovery. Among the three fragments, the siRNA of Nep-L-3 was the most effective in interfering with target gene expression. Nep-L gene showed the highest expression in Malpighian tubules (MTs). Both at the phenotypic and genotypic levels, our results show that Nep-L knockdown can exert a significant inhibitory effect on silkworms, and 50 μM Se can reverse the negative effect, which provides a practical prospect for strengthening the silkworm food industry.

Carbon-based nanocarriers for plant growth promotion: fuelling when needed

Climate change (i.e., rising temperature and precipitation) due to global warming is affecting soil fertility, thereby significantly causing a decrease in agriculture production worldwide. At the same time, increasing demands for food supplies with the growing global population puts extra pressure to improve agricultural production. Indeed, chemical fertilizers and pesticides are a great help in fuelling agro-production, but their excess use could deteriorate the environment and human health. Nevertheless, nanomaterials, especially carbon-based nanostructured materials (CB-NMs), have revolutionized the agricultural sector in various ways including the on-demand supply of essential nutrients, biomolecules, and growth factors to plants. Carbon nanofibers (CNFs) are one such example that can be tuned to carry essential nutrients (i.e., Fe, Cu, Zn, and Mo) and deliver to plants when and what is in need. As a result, it not only improves the crop yield but also maintains the nutritional quality (protein, carbohydrate, and mineral contents) of plant products. This review discusses the most innovative development in CB-NM-based carriers (CNFs, carbon nanotubes (CNTs), and graphene as well as its derivatives) for plant growth applications including the approaches being used for their lab-scale synthesis. In addition, their application as the carrier of micronutrients and biomolecules and the successful delivery (and the underlying mechanism) of genes, nucleic acids, microbes, and their components in plants are discussed.

Leveraging RNA interference technology for selective and sustainable crop protection

Double-stranded RNA (dsRNA) has emerged as key player in gene silencing for the past two decades. Tailor-made dsRNA is now recognized a versatile raw material, suitable for a wide range of applications in biopesticide formulations, including insect control to pesticide resistance management. The mechanism of RNA interference (RNAi) acts at the messenger RNA (mRNA) level, utilizing a sequence-dependent approach that makes it unique in term of effectiveness and specificity compared to conventional agrochemicals. Two primary categories of small RNAs, known as short interfering RNAs (siRNAs) and microRNAs (miRNAs), function in both somatic and germline lineages in a broad range of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. Furthermore, the application of RNAi in crop protection can be achieved by employing plant-incorporated protectants through plant transformation, but also by non-transformative strategies such as the use of formulations of sprayable RNAs as direct control agents, resistance factor repressors or developmental disruptors. This review explores the agricultural applications of RNAi, delving into its successes in pest-insect control and considering its broader potential for managing plant pathogens, nematodes, and pests. Additionally, the use of RNAi as a tool for addressing pesticide-resistant weeds and insects is reviewed, along with an evaluation of production costs and environmental implications.

RNAi-biofungicides: a quantum leap for tree fungal pathogen management

Fungal diseases threaten the forest ecosystem, impacting tree health, productivity, and biodiversity. Conventional approaches to combating diseases, such as biological control or fungicides, often reach limits regarding efficacy, resistance, non-target organisms, and environmental impact, enforcing alternative approaches. From an environmental and ecological standpoint, an RNA interference (RNAi) mediated double-stranded RNA (dsRNA)-based strategy can effectively manage forest fungal pathogens. The RNAi approach explicitly targets and suppresses gene expression through a conserved regulatory mechanism. Recently, it has evolved to be an effective tool in combating fungal diseases and promoting sustainable forest management approaches. RNAi bio-fungicides provide efficient and eco-friendly disease control alternatives using species-specific gene targeting, minimizing the off-target effects. With accessible data on fungal disease outbreaks, genomic resources, and effective delivery systems, RNAi-based biofungicides can be a promising tool for managing fungal pathogens in forests. However, concerns regarding the environmental fate of RNAi molecules and their potential impact on non-target organisms require an extensive investigation on a case-to-case basis. The current review critically evaluates the feasibility of RNAi bio-fungicides against forest pathogens by delving into the accessible delivery methods, environmental persistence, regulatory aspects, cost-effectiveness, community acceptance, and plausible future of RNAi-based forest protection products.

Genome-wide selection of potential target candidates for RNAi against Nilaparvata lugens

BACKGROUND

Nilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study.

RESULTS

Here, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates.

CONCLUSION

The combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates.

RNA interference: a promising biotechnological approach to combat plant pathogens, mechanism and future prospects

Plant pathogens and other biological pests represent significant obstacles to crop Protection worldwide. Even though there are many effective conventional methods for controlling plant diseases, new methods that are also effective, environmentally safe, and cost-effective are required. While plant breeding has traditionally been used to manipulate the plant genome to develop resistant cultivars for controlling plant diseases, the emergence of genetic engineering has introduced a completely new approach to render plants resistant to bacteria, nematodes, fungi, and viruses. The RNA interference (RNAi) approach has recently emerged as a potentially useful tool for mitigating the inherent risks associated with the development of conventional transgenics. These risks include the use of specific transgenes, gene control sequences, or marker genes. Utilizing RNAi to silence certain genes is a promising solution to this dilemma as disease-resistant transgenic plants can be generated within a legislative structure. Recent investigations have shown that using target double stranded RNAs via an effective vector system can produce significant silencing effects. Both dsRNA-containing crop sprays and transgenic plants carrying RNAi vectors have proven effective in controlling plant diseases that threaten commercially significant crop species. This article discusses the methods and applications of the most recent RNAi technology for reducing plant diseases to ensure sustainable agricultural yields.

Strategies and bibliometric analysis of legumes biofortification to address malnutrition

MAIN CONCLUSION

Biofortification of legumes using diverse techniques such as plant breeding, agronomic practices, genetic modification, and nano-technological approaches presents a sustainable strategy to address micronutrient deficiencies of underprivileged populations. The widespread issue of chronic malnutrition, commonly referred to as "hidden hunger," arises from the consumption of poor-quality food, leading to various health and cognitive impairments. Biofortified food crops have been a sustainable solution to address micronutrient deficiencies. This review highlights multiple biofortification techniques, such as plant breeding, agronomic practices, genetic modification, and nano-technological approaches, aimed at enhancing the nutrient content of commonly consumed crops. Emphasizing the biofortification of legumes, this review employs bibliometric analysis to examine research trends from 2000 to 2023. It identifies key authors, influential journals, contributing countries, publication trends, and prevalent keywords in this field. The review highlights the progress in developing biofortified crops and their potential to improve global nutrition and help underprivileged populations.

Selenium Treatment Ameliorates the Adverse Effects Caused by Dynamin Gene Knockdown in Bombyx mori

Our previous research reported the influence of 50 μM selenium (Se) on the cytosolization (endocytosis) pathway, which in turn stimulates the growth and development of Bombyx mori. Lately, dynamin is recognized as one of the key proteins in endocytosis. To explore the underlying mechanisms of Se impact, the dynamin gene was knocked down by injecting siRNAs (Dynamin-1, Dynamin-2, and Dynamin-3). This was followed by an analysis of the target gene and levels of silk protein genes, as well as growth and developmental indices, Se-enrichment capacity, degree of oxidative damage, and antioxidant capacity of B. mori. Our findings showed a considerable decrease in the relative expression of the dynamin gene in all tissues 24 h after the interference and a dramatic decrease in the silkworm body after 48 h. RNAi dynamin gene decreased the silkworm body weight, cocoon shell weight, and the ratio of cocoon. In the meantime, malondialdehyde level increased and glutathione level and superoxide dismutase/catalase activities decreased. 50 μM Se markedly ameliorated these growth and physiological deficits as well as decreases in dynamin gene expression. On the other hand, there were no significant effects on fertility (including produced eggs and laid eggs) between the interference and Se treatments. Additionally, the Se content in the B. mori increased after the dynamin gene interference. The dynamin gene was highly expressed in the silk gland and declined significantly after interference. Among the three siRNAs (Dynamin-1, Dynamin-2, and Dynamin-3), the dynamin-2 displayed the highest interference effects to target gene expression. Our results demonstrated that 50 μM Se was effective to prevent any adverse effects caused by dynamin knockdown in silkworms. This provides practical implications for B. mori breeding industry.

Manifestation of agronomically valuable traits in the progeny of a sorghum mutant carrying the genetic construct for RNA silencing of the γ-kafirin gene

Improving the nutritional value of grain sorghum, a drought- and heat-tolerant grain crop, is an important task in the context of global warming. One of the reasons for the low nutritional value of sorghum grain is the resistance of its storage proteins (kafirins) to proteolytic digestion, which is due, among other things, to the structural organization of protein bodies, in which γ-kafirin, the most resistant to proteases, is located on the periphery, encapsulating more easily digested α-kafirins. The introduction of genetic constructs capable of inducing RNA silencing of the γ-kafirin (gKAF1) gene opens up prospects for solving this problem. Using Agrobacterium-mediated genetic transformation of immature embryos of the grain sorghum cv. Avans we have obtained a mutant with improved digestibility of endosperm proteins (up to 92 %) carrying a genetic construct for RNA silencing of the gKAF1 gene. The goal of this work was to study the stability of inheritance of the introduced genetic construct in T2-T4 generations, to identify the number of its copies, as well as to trace the manifestation of agronomically valuable traits in the offspring of the mutant. The mutant lines were grown in experimental plots in three randomized blocks. The studied lines were characterized by improved digestibility of kafirins, a modified type of endosperm, completely or partially devoid of the vitreous layer, an increased percentage of lysine (by 75 %), reduced plant height, peduncle length, 1000-grains weight, and grain yield from the panicle. In T2, a line with monogenic control of GA resistance was selected. qPCR analysis showed that in different T3 and T4 plants, the genetic construct was present in 2-4 copies. In T3, a line with a high digestibility of endosperm proteins (81 %) and a minimal decrease in agronomically valuable traits (by 5-7 %) was selected.

Genome-Wide Identification and Characterization of Major RNAi Genes Highlighting Their Associated Factors in Cowpea (Vigna unguiculata (L.) Walp.)

In different regions of the world, cowpea (Vigna unguiculata (L.) Walp.) is an important vegetable and an excellent source of protein. It lessens the malnutrition of the underprivileged in developing nations and has some positive effects on health, such as a reduction in the prevalence of cancer and cardiovascular disease. However, occasionally, certain biotic and abiotic stresses caused a sharp fall in cowpea yield. Major RNA interference (RNAi) genes like Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are essential for the synthesis of their associated factors like domain, small RNAs (sRNAs), transcription factors, micro-RNAs, and cis-acting factors that shield plants from biotic and abiotic stresses. In this study, applying BLASTP search and phylogenetic tree analysis with reference to the Arabidopsis RNAi (AtRNAi) genes, we discovered 28 VuRNAi genes, including 7 VuDCL, 14 VuAGO, and 7 VuRDR genes in cowpea. We looked at the domains, motifs, gene structures, chromosomal locations, subcellular locations, gene ontology (GO) terms, and regulatory factors (transcription factors, micro-RNAs, and cis-acting elements (CAEs)) to characterize the VuRNAi genes and proteins in cowpea in response to stresses. Predicted VuDCL1, VuDCL2(a, b), VuAGO7, VuAGO10, and VuRDR6 genes might have an impact on cowpea growth, development of the vegetative and flowering stages, and antiviral defense. The VuRNAi gene regulatory features miR395 and miR396 might contribute to grain quality improvement, immunity boosting, and pathogen infection resistance under salinity and drought conditions. Predicted CAEs from the VuRNAi genes might play a role in plant growth and development, improving grain quality and production and protecting plants from biotic and abiotic stresses. Therefore, our study provides crucial information about the functional roles of VuRNAi genes and their associated components, which would aid in the development of future cowpeas that are more resilient to biotic and abiotic stress. The manuscript is available as a preprint at this link: doi:10.1101/2023.02.15.528631v1.

Deciphering the roles of unknown/uncharacterized genes in plant development and stress responses

In recent years, numerous genes that encode proteins with specific domains that participate in different biological processes or have different molecular functions have been identified. A class of genes with typical domains whose function has rarely been identified and another type of genes with no typical domains have attracted increasing attentions. As many of these so-called as unknown/uncharacterized (U/U) genes are involved in important processes, such as plant growth and plant stress resistance, there is much interest in deciphering their molecular roles. Here, we summarize our current understanding of these genes, including their structures, classifications, and roles in plant growth and stress resistance, summarize progress in the methods used to decipher the roles of these genes, and provide new research perspectives. Unveiling the molecular functions of unknown/uncharacterized genes may suggest strategies to fine-tune important physiological processes in plants, which will enrich the functional network system of plants and provide more possibilities for adaptive improvement of plants.