Combining novel technologies with interdisciplinary basic research to enhance horticultural crops

Multi-Omic Advances in Olive Tree (Olea europaea subsp. europaea L.) Under Salinity: Stepping Towards 'Smart Oliviculture'

Soil salinisation is threatening crop sustainability worldwide, mainly due to anthropogenic climate change. Molecular mechanisms developed to counteract salinity have been intensely studied in model plants. Nevertheless, the economically relevant olive tree (Olea europaea subsp. europaea L.), being highly exposed to soil salinisation, deserves a specific review to extract the recent genomic advances that support the known morphological and biochemical mechanisms that make it a relative salt-tolerant crop. A comprehensive list of 98 olive cultivars classified by salt tolerance is provided, together with the list of available olive tree genomes and genes known to be involved in salt response. Na+ and Cl- exclusion in leaves and retention in roots seem to be the most prominent adaptations, but cell wall thickening and antioxidant changes are also required for a tolerant response. Several post-translational modifications of proteins are emerging as key factors, together with microbiota amendments, making treatments with biostimulants and chemical compounds a promising approach to enable cultivation in already salinised soils. Low and high-throughput transcriptomics and metagenomics results obtained from salt-sensitive and -tolerant cultivars, and the future advantages of engineering specific metacaspases involved in programmed cell death and autophagy pathways to rapidly raise salt-tolerant cultivars or rootstocks are also discussed. The overview of bioinformatic tools focused on olive tree, combined with machine learning approaches for studying plant stress from a multi-omics perspective, indicates that the development of salt-tolerant cultivars or rootstocks adapted to soil salinisation is progressing. This could pave the way for 'smart oliviculture', promoting more productive and sustainable practices under salt stress.

A novel transcription factor CsSNACA2 plays a pivotal role within nitrogen assimilation in tea plants

Tea (Camellia sinensis) is a globally renowned economic crop, with organs such as leaves and buds utilized for consumption. As a perennial foliage crop, tea plants have high-nitrogen consumption and demand but exhibit relatively low nitrogen use efficiency. Exploring the genetic factors involved in nitrogen assimilation in tea plants could lead to improvements in both tea yield and quality. Here, we first conducted transcriptome sequencing on two tissues (roots and young leaves) under two different nitrate levels (0.2 and 2.5 mm KNO3) and at six time points (0, 15, and 45 min; 2 and 6 h and 2 days). Differential gene expression patterns were observed for several genes that exhibited altered expression at 2 h. Clustering and enrichment analyses, along with co-expression network construction, provided evidence for the crucial involvement of CsSNACA2 in nitrogen assimilation. CsSNACA2 overexpression elicited pronounced phenotypic changes in nitrogen-deficient plants. Furthermore, CsSNACA2 suppressed the expression of CsNR (encoding nitrate reductase) and CsCLCa (encoding aNO 3 - /H+ exchanger). Moreover, CsSNACA2 served as a downstream target of CsSPL6.1. In addition, we characterized Csi-miR156e and Csi-miR156k, which directly cleave CsSPL6.1. This study identified a transcription factor module participating in nitrogen assimilation in tea plants, providing a genetic foundation for future innovations in tea cultivar improvement. These results broaden our understanding of the genetic mechanisms governing nitrogen assimilation in dicotyledonous plants.

A systematic review of the role of integrated farming and the participation of universities in ensuring food security: Malaysia's effort

Food security is critical for promoting health and well-being and achieving sustainable development, especially in developing countries. Despite the recent efforts to improve it, food security is still a concern due to the rapid increase in populations, conflicts, and natural disasters worldwide. Universities, particularly agricultural universities, play an essential role in addressing food security issues by researching, developing new technologies, and providing education and training to farmers and other stakeholders. The main objective of this review is to discuss the role of universities and integrated farming in ensuring food security, specifically in Malaysia. It includes a brief overview of the different types of integrated farming methods that can be used to improve food security and finally discusses the Student Farmer Entrepreneur program, which can be crucial for promoting food security by increasing agricultural productivity, promoting local food production, encouraging sustainable agriculture practices, and supporting rural development. This review also considers the significant impact of the Malaysian government and universities on food security. With integrated farming and the Student Farmer Entrepreneur program, food security can be further improved.

Depicting the genetic and metabolic panorama of chemical diversity in the tea plant

As a frequently consumed beverage worldwide, tea is rich in naturally important bioactive metabolites. Combining genetic, metabolomic and biochemical methodologies, here, we present a comprehensive study to dissect the chemical diversity in tea plant. A total of 2837 metabolites were identified at high-resolution with 1098 of them being structurally annotated and 63 of them were structurally identified. Metabolite-based genome-wide association mapping identified 6199 and 7823 metabolic quantitative trait loci (mQTL) for 971 and 1254 compounds in young leaves (YL) and the third leaves (TL), respectively. The major mQTL (i.e., P < 1.05 × 10-5, and phenotypic variation explained (PVE) > 25%) were further interrogated. Through extensive annotation of the tea metabolome as well as network-based analysis, this study broadens the understanding of tea metabolism and lays a solid foundation for revealing the natural variations in the chemical composition of the tea plant. Interestingly, we found that galloylations, rather than hydroxylations or glycosylations, were the largest class of conversions within the tea metabolome. The prevalence of galloylations in tea is unusual, as hydroxylations and glycosylations are typically the most prominent conversions of plant specialized metabolism. The biosynthetic pathway of flavonoids, which are one of the most featured metabolites in tea plant, was further refined with the identified metabolites. And we demonstrated the further mining and interpretation of our GWAS results by verifying two identified mQTL (including functional candidate genes CsUGTa, CsUGTb, and CsCCoAOMT) and completing the flavonoid biosynthetic pathway of the tea plant.

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.

An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture

This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.

Integrated approaches for increasing plant yield under salt stress

Salt stress affects large cultivated areas worldwide, thus causing remarkable reductions in plant growth and yield. To reduce the negative effects of salt stress on plant growth and yield, plant hormones, nutrient absorption, and utilization, as well as developing salt-tolerant varieties and enhancing their morpho-physiological activities, are some integrative approaches to coping with the increasing incidence of salt stress. Numerous studies have been conducted to investigate the critical impacts of these integrative approaches on plant growth and yield. However, a comprehensive review of these integrative approaches, that regulate plant growth and yield under salt stress, is still in its early stages. The review focused on the major issues of nutrient absorption and utilization by plants, as well as the development of salt tolerance varieties under salt stress. In addition, we explained the effects of these integrative approaches on the crop's growth and yield, illustrated the roles that phytohormones play in improving morpho-physiological activities, and identified some relevant genes involve in these integrative approaches when the plant is subjected to salt stress. The current review demonstrated that HA with K enhance plant morpho-physiological activities and soil properties. In addition, NRT and NPF genes family enhance nutrients uptake, NHX1, SOS1, TaNHX, AtNHX1, KDML, RD6, and SKC1, maintain ion homeostasis and membrane integrity to cope with the adverse effects of salt stress, and sd1/Rht1, AtNHX1, BnaMAX1s, ipal-1D, and sft improve the plant growth and yield in different plants. The primary purpose of this investigation is to provide a comprehensive review of the performance of various strategies under salt stress, which might assist in further interpreting the mechanisms that plants use to regulate plant growth and yield under salt stress.

Deoxynivalenol accumulation and detoxification in cereals and its potential role in wheat-Fusarium graminearum interactions

Deoxynivalenol (DON) is a prominent mycotoxin showing significant accumulation in cereal plants during infection by the phytopathogen Fusarium graminearum. It is a virulence factor that is important in the spread of F. graminearum within cereal heads, and it causes serious yield losses and significant contamination of cereal grains. In recent decades, genetic and genomic studies have facilitated the characterization of the molecular pathways of DON biosynthesis in F. graminearum and the environmental factors that influence DON accumulation. In addition, diverse scab resistance traits related to the repression of DON accumulation in plants have been identified, and experimental studies of wheat-pathogen interactions have contributed to understanding detoxification mechanisms in host plants. The present review illustrates and summarizes the molecular networks of DON mycotoxin production in F. graminearum and the methods of DON detoxification in plants based on the current literature, which provides molecular targets for crop improvement programs. This review also comprehensively discusses recent advances and challenges related to genetic engineering-mediated cultivar improvements to strengthen scab resistance. Furthermore, ongoing advancements in genetic engineering will enable the application of these molecular targets to develop more scab-resistant wheat cultivars with DON detoxification traits.

Magnesium promotes tea plant growth via enhanced glutamine synthetase-mediated nitrogen assimilation

Acidic tea (Camellia sinensis) plantation soil usually suffers from magnesium (Mg) deficiency, and as such, application of fertilizer containing Mg can substantially increase tea quality by enhancing the accumulation of nitrogen (N)-containing chemicals such as amino acids in young tea shoots. However, the molecular mechanisms underlying the promoting effects of Mg on N assimilation in tea plants remain unclear. Here, both hydroponic and field experiments were conducted to analyze N, Mg, metabolite contents, and gene expression patterns in tea plants. We found that N and amino acids accumulated in tea plant roots under Mg deficiency, while metabolism of N was enhanced by Mg supplementation, especially under a low N fertilizer regime. 15N tracing experiments demonstrated that assimilation of N was induced in tea roots following Mg application. Furthermore, weighted gene correlation network analysis (WGCNA) analysis of RNA-seq data suggested that genes encoding glutamine synthetase isozymes (CsGSs), key enzymes regulating N assimilation, were markedly regulated by Mg treatment. Overexpression of CsGS1.1 in Arabidopsis (Arabidopsis thaliana) resulted in a more tolerant phenotype under Mg deficiency and increased N assimilation. These results validate our suggestion that Mg transcriptionally regulates CsGS1.1 during the enhanced assimilation of N in tea plant. Moreover, results of a field experiment demonstrated that high Mg and low N had positive effects on tea quality. This study deepens our understanding of the molecular mechanisms underlying the interactive effects of Mg and N in tea plants while also providing both genetic and agronomic tools for future improvement of tea production.

Integrated transcriptomic and metabolomic analyses reveal key genes controlling flavonoid biosynthesis in Citrus grandis 'Tomentosa' fruits

As a well-recognized traditional Chinese medicine (TCM), immature fruits of Citrus grandis 'Tomentosa' (CGT) serve to cure chronic cough in humans. Specialized metabolites including flavonoids may have contribute to this curing effect. Knowledge about the molecular mechanisms underlying flavonoid biosynthesis in 'Tomentosa' fruits will, therefore, support the breeding of varieties with improved medicinal properties. Hence, we profiled the transcriptomes and metabolites of the fruits of two contrasting C. grandis varieties, namely 'Zheng-Mao' ('ZM') used in TCM production, and a locally cultivated pomelo, namely 'Guang-Qing' ('GQ'), at four developmental stages. A total of 39 flavonoids, including 14 flavanone/flavone, 5 isoflavonoids, 12 flavonols, and 6 anthocyanins, were identified, and 16 of which were quantitatively determined in the fruits of the two varieties. We found that 'ZM' fruits contain more flavonoids than 'GQ'. Specifically, rhoifolin levels were significantly higher in 'ZM' than in 'GQ'. We annotated 31,510 genes, including 1,387 previously unknown ones, via transcriptome sequencing of 'ZM' and 'GQ.' A total of 646 genes were found to be differentially expressed between 'ZM' and 'GQ' throughout at all four fruit developmental stages, indicating that they are robust expression markers for future breeding programs. Weighted gene co-expression network analysis identified 18 modules. Combined transcriptional and metabolic analysis revealed 25 genes related to flavonoid biosynthesis and 16 transcriptional regulators (MYBs, bHLHs, WD40) that may be involved in the flavonoids biosynthesis in C. grandis 'Tomentosa' fruits.

Dynamic Changes in the Antioxidative Defense System in the Tea Plant Reveal the Photoprotection-Mediated Temporal Accumulation of Flavonoids under Full Sunlight Exposure

To reveal the mechanisms underlying how light affects flavonoid metabolism and the potential role of flavonoids in protecting against photooxidative stress in tea leaves, tea plants adapted to low-light conditions were exposed to full sunlight over 48 h. There was an increase in the activities of catalase (CAT) and superoxide dismutase (SOD) as well as greater accumulation of reactive oxygen species, lutein, tocopherols, ascorbate and malondialdehyde, suggestive of a time-dependent response to photooxidative stress in tea leaves. Analysis of the time dependency of each element of the antioxidant system indicated that carotenoids and tocopherols exhibited the fastest response to light stress (within 3 h), followed by SOD, CAT and catechin, which peaked at 24 h. Meanwhile, flavonols, vitamin C and glutathione showed the slowest response. Subsequent identification of the main phytochemicals involved in protecting against oxidative stress using untargeted metabolomics revealed a fast and initial accumulation of nonesterified catechins that preceded the increase in flavonol glycosides and catechin esters. Gene expression analysis suggested that the light-induced accumulation of flavonoids was highly associated with the gene encoding flavonol synthase. Ultraviolet B (UV-B) irradiation further validated the time-dependent and collaborative effects of flavonoids in photoprotection in tea plants. Intriguingly, the dynamics of the metabolic response are highly distinct from those reported for Arabidopsis, suggesting that the response to light stress is not conserved across plants. This study additionally provides new insights into the functional role of flavonoids in preventing photooxidative stress and may contribute to further improving tea quality through the control of light intensity.