Prospects for potato genome editing to engineer resistance against viruses and cold-induced sweetening

Advancements in genome editing tools for genetic studies and crop improvement

The rapid increase in global population poses a significant challenge to food security, compounded by the adverse effects of climate change, which limit crop productivity through both biotic and abiotic stressors. Despite decades of progress in plant breeding and genetic engineering, the development of new crop varieties with desirable agronomic traits remains a time-consuming process. Traditional breeding methods often fall short of addressing the urgent need for improved crop varieties. Genome editing technologies, which enable precise modifications at specific genomic loci, have emerged as powerful tools for enhancing crop traits. These technologies, including RNA interference, Meganucleases, ZFNs, TALENs, and CRISPR/Cas systems, allow for the targeted insertion, deletion, or alteration of DNA fragments, facilitating improvements in traits such as herbicide and insect resistance, nutritional quality, and stress tolerance. Among these, CRISPR/Cas9 stands out for its simplicity, efficiency, and ability to reduce off-target effects, making it a valuable tool in both agricultural biotechnology and plant functional genomics. This review examines the functional mechanisms and applications of various genome editing technologies for crop improvement, highlighting their advantages and limitations. It also explores the ethical considerations associated with genome editing in agriculture and discusses the potential of these technologies to contribute to sustainable food production in the face of growing global challenges.

Adoption of CRISPR-Cas for crop production: present status and future prospects

Background

Global food systems in recent years have been impacted by some harsh environmental challenges and excessive anthropogenic activities. The increasing levels of both biotic and abiotic stressors have led to a decline in food production, safety, and quality. This has also contributed to a low crop production rate and difficulty in meeting the requirements of the ever-growing population. Several biotic stresses have developed above natural resistance in crops coupled with alarming contamination rates. In particular, the multiple antibiotic resistance in bacteria and some other plant pathogens has been a hot topic over recent years since the food system is often exposed to contamination at each of the farm-to-fork stages. Therefore, a system that prioritizes the safety, quality, and availability of foods is needed to meet the health and dietary preferences of everyone at every time.

Methods

This review collected scattered information on food systems and proposes methods for plant disease management. Multiple databases were searched for relevant specialized literature in the field. Particular attention was placed on the genetic methods with special interest in the potentials of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and Cas (CRISPR associated) proteins technology in food systems and security.

Results

The review reveals the approaches that have been developed to salvage the problem of food insecurity in an attempt to achieve sustainable agriculture. On crop plants, some systems tend towards either enhancing the systemic resistance or engineering resistant varieties against known pathogens. The CRISPR-Cas technology has become a popular tool for engineering desired genes in living organisms. This review discusses its impact and why it should be considered in the sustainable management, availability, and quality of food systems. Some important roles of CRISPR-Cas have been established concerning conventional and earlier genome editing methods for simultaneous modification of different agronomic traits in crops.

Conclusion

Despite the controversies over the safety of the CRISPR-Cas system, its importance has been evident in the engineering of disease- and drought-resistant crop varieties, the improvement of crop yield, and enhancement of food quality.

Challenges for crop improvement

The genetic improvement of crops faces the significant challenge of feeding an ever-increasing population amidst a changing climate, and when governments are adopting a 'more with less' approach to reduce input use. Plant breeding has the potential to contribute to the United Nations Agenda 2030 by addressing various sustainable development goals (SDGs), with its most profound impact expected on SDG2 Zero Hunger. To expedite the time-consuming crossbreeding process, a genomic-led approach for predicting breeding values, targeted mutagenesis through gene editing, high-throughput phenomics for trait evaluation, enviromics for including characterization of the testing environments, machine learning for effective management of large datasets, and speed breeding techniques promoting early flowering and seed production are being incorporated into the plant breeding toolbox. These advancements are poised to enhance genetic gains through selection in the cultigen pools of various crops. Consequently, these knowledge-based breeding methods are pursued for trait introgression, population improvement, and cultivar development. This article uses the potato crop as an example to showcase the progress being made in both genomic-led approaches and gene editing for accelerating the delivery of genetic gains through the utilization of genetically enhanced elite germplasm. It also further underscores that access to technological advances in plant breeding may be influenced by regulations and intellectual property rights.

Development of homozygous tetraploid potato and whole genome doubling-induced the enrichment of H3K27ac and potentially enhanced resistance to cold-induced sweetening in tubers

Polyploid plants typically display advantages on some agronomically important traits over their diploid counterparts. Extensive studies have shown genetic, transcriptomic, and epigenetic dynamics upon polyploidization in multiple plant species. However, few studies have unveiled those alternations imposed only by ploidy level, without any interference from heterozygosity. Cultivated potato is highly heterozygous. Thus, in this study, we developed two homozygous autotetraploid lines and one homozygous diploid line in parallel from a homozygous diploid potato. We confirmed their ploidy levels using chloroplast counting and karyotyping. Oligo-FISH and genome re-sequencing validated that these potato lines are nearly homozygous. We investigated variations in phenotypes, transcription, and histone modifications between two ploidies. Both autotetraploid lines produced larger but fewer tubers than the diploid line. Interestingly, each autotetraploid line displayed ploidy-related differential expression for various genes. We also discovered a genome-wide enrichment of H3K27ac in genic regions upon whole-genome doubling (WGD). However, such enrichment was not associated with the differential gene expression between two ploidies. The tetraploid lines may exhibit better resistance to cold-induced sweetening (CIS) than the diploid line in tubers, potentially regulated through the expression of CIS-related key genes, which seems to be associated with the levels of H3K4me3 in cold-stored tubers. These findings will help to understand the impacts of autotetraploidization on dynamics of phenotypes, transcription, and histone modifications, as well as on CIS-related genes in response to cold storage.

Insight into aphid mediated Potato Virus Y transmission: A molecular to bioinformatics prospective

Potato, the world's most popular crop is reported to provide a food source for nearly a billion people. It is prone to a number of biotic stressors that affect yield and quality, out of which Potato Virus Y (PVY) occupies the top position. PVY can be transmitted mechanically and by sap-feeding aphid vectors. The application of insecticide causes an increase in the resistant vector population along with detrimental effects on the environment; genetic resistance and vector-virus control are the two core components for controlling the deadly PVY. Using transcriptomic tools together with differential gene expression and gene discovery, several loci and genes associated with PVY resistance have been widely identified. To combat this virus we must increase our understanding on the molecular response of the PVY-potato plant-aphid interaction and knowledge of genome organization, as well as the function of PVY encoded proteins, genetic diversity, the molecular aspects of PVY transmission by aphids, and transcriptome profiling of PVY infected potato cultivars. Techniques such as molecular and bioinformatics tools can identify and monitor virus transmission. Several studies have been conducted to understand the molecular basis of PVY resistance/susceptibility interactions and their impact on PVY epidemiology by studying the interrelationship between the virus, its vector, and the host plant. This review presents current knowledge of PVY transmission, epidemiology, genome organization, molecular to bioinformatics responses, and its effective management.

Metabolic changes associated with chilling injury tolerance in tomato fruit with hot water pretreatment

Hot water treatment (HWT) of tomato (Solanum lycopersicum L.) fruit reduces the symptoms of chilling injury (CI). The aim of this study was to identify metabolites associated with HWT-induced CI tolerance in tomato fruit cv. Imperial. Mature green tomatoes with HWT (42°C/5 min) and control were stored under chilling conditions (5°C/20 days) and then ripened (21°C/7 days). Methanol extracts from pericarp were analyzed for total phenolics (TP), antioxidant activity (AoxA), and metabolic profiling by UPLC-DAD-MS and GC-MS. After cold storage and ripening, HWT fruit showed less CI, higher TP, and AoxA than control. It also showed an increased accumulation of phenolics, sugars, and some alkaloids that may be mediated by azelaic acid, glutamine, and tryptophan. The levels of N-feruloyl putrescine, esculeoside AII, and hydroxy-α-tomatine II were reduced. The better metabolic performance of HWT fruit under cold storage was associated with a higher accumulation of several metabolites (e.g., antioxidants and osmolytes) in ripening fruit. PRACTICAL APPLICATION: The identification of metabolites associated with the reduction of chilling injury (CI) symptoms in HWT tomato fruit extends the understanding of the mechanisms involved in CI tolerance. This information provides targets that could be used to develop strategies for preventing CI (e.g., genetic improvement of tomato, direct application of key metabolites). The application of such strategies will increase the economic value and decrease postharvest losses.

Invertase inhibitors in potato: towards a biochemical and molecular understanding of cold-induced sweetening

Invertase inhibitors classified as cell wall/apoplastic and vacuolar belonging to the pectin methylesterase family, play a major role in cold-induced sweetening (CIS) process of potato tubers. The CIS process is controlled at the post-translational level via an interaction between invertase (cell wall/apoplastic and vacuolar) by their compartment-specific inhibitors (cell wall/apoplastic and vacuolar). Invertase inhibitors have been cloned, sequenced and functionally characterized from potato cultivars differing in their CIS ability. The secondary structure of the invertase inhibitors consisted of seven alpha-helices and four conserved cysteine residues. The well-conserved three amino acids i.e. Pro-Lys-Phe are known to interact with invertase. Location of the genes encoding cell wall/apoplastic and vacuolar invertase inhibitors on potato chromosome number twelve in a tandem orientation without any intervening genes suggest their divergence into the cell wall and vacuole forms following the event of gene duplication. Under cold storage conditions, the vacuolar invertase inhibitor gene showed developmentally regulated alternative splicing and produce hybrid mRNAs which were the result of mRNA splicing of an upstream region of vacuolar invertase inhibitor gene to a downstream region of the apoplastic invertase inhibitor gene. Transgenic potato tubers overexpressing invertase inhibitors resulted in decreased invertase activity, low reducing sugars and improved processing quality making invertase inhibitors highly potential candidate genes for overcoming CIS. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene-editing technology offers transgene-free breeding for developing CIS resistant potato cultivars. Moreover, the post-transcriptional regulation of invertase inhibitors during cold storage can be warranted. This review summarizes progress and current knowledge on biochemical and molecular approaches used for the understanding of invertase inhibitors with special reference to key findings in potato.