Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

Enhancing Abiotic Stress Resilience in Mediterranean Woody Perennial Fruit Crops: Genetic, Epigenetic, and Microbial Molecular Perspectives in the Face of Climate Change

Enhanced abiotic stresses such as increased drought, elevated temperatures, salinity, and extreme weather phenomena severely affect major crops in the Mediterranean area, a 'hot spot' of climate change. Plants have evolved mechanisms to face stressful conditions and adapt to increased environmental pressures. Intricate molecular processes involving genetic and epigenetic factors and plant-microbe interactions have been implicated in the response and tolerance to abiotic stress. Deciphering the molecular mechanisms whereby plants perceive and respond to stress is crucial for developing strategies to counteract climate challenges. Progress in determining genes, complex gene networks, and biochemical pathways, as well as plant-microbiota crosstalk, involved in abiotic stress tolerance has been achieved through the application of molecular tools in diverse genetic resources. This knowledge could be particularly useful for accelerating plant improvement and generating resilient varieties, especially concerning woody perennial crops, where classical breeding is a lengthy and labor-intensive process. Similarly, understanding the mechanisms of plant-microbe interactions could provide insights into innovative approaches to facing stressful conditions. In this review, we provide a comprehensive overview and discuss the recent findings concerning the genetic, epigenetic, and microbial aspects shaping abiotic stress responses, in the context of enhancing resilience in important Mediterranean woody perennial fruit 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.

Comprehensive insights on association mapping in perennial fruit crops breeding - Its implications, current status and future perspectives

In order to provide food and nutritional security for the world's rapidly expanding population, fruit crop researchers have identified two critical priorities: increasing production and preserving fruit quality during the pre- and post-harvest periods. The genetic basis of these complex, commercially important fruit traits which are uniquely regulated by polygenes or multi-allelic genes that interact with one another and the environment can be analyzed with the aid of trait mapping tools. The most interesting trait mapping approach that offers the genetic level investigation for marker-trait associations (MTAs) for these complex fruit traits, without the development of mapping population, is association mapping. This approach was used during the genetic improvement program, emphasizing the obstacles (breeding strategies adopted, generation interval, and their genomic status) pertaining to perennial fruit crops. This method of studying population diversity and linkage disequilibrium in perennial fruit crops has been made possible by recent developments in genotyping, phenotyping, and statistical analysis. Thus, the purpose of this review is to provide an overview of different trait mapping techniques, with a focus on association mapping (method, essential components, viability, constraints, and future perspective) and its advantages, disadvantages, and possibilities for breeding perennial fruit crops.

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

NGS transcriptomic analysis uncovers the possible resistance mechanisms of olive to Spilocea oleagina leaf spot infection

Spilocea oleagina is a dangerous obligate fungal pathogen of olive, feared in the Mediterranean countries, causing Peacock's eye or leaf spot infection, which can lead to a serious yield loss of approximately 20% or higher depending on climatic conditions. Coping with this disease is much more problematic for organic farms. To date, knowledge on the genetic control of possible mechanisms of resistance/low susceptibility is quite limited. In this work, comparative transcriptomic analysis (RNA-seq) was conducted in leaf tissues of a low susceptible cultivar Koroneiki and a high susceptible cultivar Nocellara del Belice, both tested in the field using the NaOH test, considering two stages-"zero sign of disease" and "evident sign of infection". Cultivars showed a very large number of differentially expressed genes (DEGs) in both stages. 'Koroneiki' showed an extensive hormonal crosstalk, involving Abscisic acid (ABA) and ethylene synergistically acting with Jasmonate, with early signaling of the disease and remarkable defense responses against Spilocea through the over-expression of many resistance gene analogs or pathogenesis-related (PR) genes: non-specific lipid-transfer genes (nsLTPs), LRR receptor-like serine/threonine-protein kinase genes, GDSL esterase lipase, defensin Ec-AMP-D2-like, pathogenesis-related leaf protein 6-like, Thaumatin-like gene, Mildew resistance Locus O (MLO) gene, glycine-rich protein (GRP), MADS-box genes, STH-21-like, endochitinases, glucan endo-1,3-beta-glucosidases, and finally, many proteinases. Numerous genes involved in cell wall biogenesis, remodeling, and cell wall-based defense, including lignin synthesis, were also upregulated in the resistant cultivar, indicating the possible role of wall composition in disease resistance. It was remarkable that many transcription factors (TS), some of which involved in Induced Systemic Resistance (ISR), as well as some also involved in abiotic stress response, were found to be uniquely expressed in 'Koroneiki', while 'Nocellara del Belice' was lacking an effective system of defense, expressing genes that overlap with wounding responses, and, to a minor extent, genes related to phenylpropanoid and terpenoid pathways. Only a Thaumatin-like gene was found in both cultivars showing a similar expression. In this work, the genetic factors and mechanism underlying the putative resistance trait against this fungal pathogen were unraveled for the first time and possible target genes for breeding resistant olive genotypes were found.

Identifying conserved genes involved in crop tolerance to cold stress

Low temperature is a limiting factor for crop productivity in tropical and subtropical climates. Cold stress response in plants involves perceiving and relaying the signal through a transcriptional cascade composed of different transduction components, resulting in altered gene activity. We performed a meta-analysis of four previously published datasets of cold-tolerant and cold-sensitive crops to better understand the gene regulatory networks and identify key genes involved in cold stress tolerance conserved across phylogenetically distant species. Re-analysing the raw data with the same bioinformatics pipeline, we identified common cold tolerance-related genes. We found 236 and 242 commonly regulated genes in sensitive and tolerant genotypes, respectively. Gene enrichment analysis showed that protein modifications, hormone metabolism, cell wall, and secondary metabolism are the most conserved pathways involved in cold tolerance. Upregulation of the abiotic stress (heat and drought/salt) related genes [heat shock N -terminal domain-containing protein, 15.7kDa class I-related small heat shock protein-like, DNAJ heat shock N -terminal domain-containing protein, and HYP1 (HYPOTHETICAL PROTEIN 1)] in sensitive genotypes and downregulation of the abiotic stress (heat and drought/salt) related genes (zinc ion binding and pollen Ole e 1 allergen and extensin family protein) in tolerant genotypes was observed across the species. Almost all development-related genes were upregulated in tolerant and downregulated in sensitive genotypes. Moreover, protein-protein network analysis identified highly interacting proteins linked to cold tolerance. Mapping of abiotic stress-related genes on analysed species genomes provided information that could be essential to developing molecular markers for breeding and building up genetic improvement strategies using CRISPR/Cas9 technologies.

Morphological, physiological, biochemical, and transcriptome studies reveal the importance of transporters and stress signaling pathways during salinity stress in Prunus

The almond crop has high economic importance on a global scale, but its sensitivity to salinity stress can cause severe yield losses. Salt-tolerant rootstocks are vital for crop economic feasibility under saline conditions. Two commercial rootstocks submitted to salinity, and evaluated through different parameters, had contrasting results with the survival rates of 90.6% for 'Rootpac 40' (tolerant) and 38.9% for 'Nemaguard' (sensitive) under salinity (Electrical conductivity of water = 3 dS m^-1). Under salinity, 'Rootpac 40' accumulated less Na and Cl and more K in leaves than 'Nemaguard'. Increased proline accumulation in 'Nemaguard' indicated that it was highly stressed by salinity compared to 'Rootpac 40'. RNA-Seq analysis revealed that a higher degree of differential gene expression was controlled by genotype rather than by treatment. Differentially expressed genes (DEGs) provided insight into the regulation of salinity tolerance in Prunus. DEGs associated with stress signaling pathways and transporters may play essential roles in the salinity tolerance of Prunus. Some additional vital players involved in salinity stress in Prunus include CBL10, AKT1, KUP8, Prupe.3G053200 (chloride channel), and Prupe.7G202700 (mechanosensitive ion channel). Genetic components of salinity stress identified in this study may be explored to develop new rootstocks suitable for salinity-affected regions.

Morphological, physiological, biochemical, and transcriptome studies reveal the importance of transporters and stress signaling pathways during salinity stress in Prunus

The almond crop has high economic importance on a global scale, but its sensitivity to salinity stress can cause severe yield losses. Salt-tolerant rootstocks are vital for crop economic feasibility under saline conditions. Two commercial rootstocks submitted to salinity, and evaluated through different parameters, had contrasting results with the survival rates of 90.6% for ‘Rootpac 40’ (tolerant) and 38.9% for ‘Nemaguard’ (sensitive) under salinity (Electrical conductivity of water = 3 dS m⁻¹). Under salinity, ‘Rootpac 40’ accumulated less Na and Cl and more K in leaves than ‘Nemaguard’. Increased proline accumulation in ‘Nemaguard’ indicated that it was highly stressed by salinity compared to ‘Rootpac 40’. RNA-Seq analysis revealed that a higher degree of differential gene expression was controlled by genotype rather than by treatment. Differentially expressed genes (DEGs) provided insight into the regulation of salinity tolerance in Prunus. DEGs associated with stress signaling pathways and transporters may play essential roles in the salinity tolerance of Prunus. Some additional vital players involved in salinity stress in Prunus include CBL10, AKT1, KUP8, Prupe.3G053200 (chloride channel), and Prupe.7G202700 (mechanosensitive ion channel). Genetic components of salinity stress identified in this study may be explored to develop new rootstocks suitable for salinity-affected regions.

Molecular mechanism of mulberry response to drought stress revealed by complementary transcriptomic and iTRAQ analyses

BACKGROUND

The use of mulberry leaves has long been limited to raising silkworms, but with the continuous improvement of mulberry (Morus alba) resource development and utilization, various mulberry leaf extension products have emerged. However, the fresh leaves of mulberry trees have a specific window of time for picking and are susceptible to adverse factors, such as drought stress. Therefore, exploring the molecular mechanism by which mulberry trees resist drought stress and clarifying the regulatory network of the mulberry drought response is the focus of the current work.

RESULTS

In this study, natural and drought-treated mulberry grafted seedlings were used for transcriptomic and proteomic analyses (CK vs. DS9), aiming to clarify the molecular mechanism of the mulberry drought stress response. Through transcriptome and proteome sequencing, we identified 9889 DEGs and 1893 DEPs enriched in stress-responsive GO functional categories, such as signal transducer activity, antioxidant activity, and transcription regulator activity. KEGG enrichment analysis showed that a large number of codifferentially expressed genes were enriched in flavonoid biosynthesis pathways, hormone signalling pathways, lignin metabolism and other pathways. Through subsequent cooperation analysis, we identified 818 codifferentially expressed genes in the CK vs. DS9 comparison group, including peroxidase (POD), superoxide dismutase (SOD), aldehyde dehydrogenase (ALDHs), glutathione s-transferase (GST) and other genes closely related to the stress response. In addition, we determined that the mulberry gene MaWRKYIII8 (XP_010104968.1) underwent drought- and abscisic acid (ABA)-induced expression, indicating that it may play an important role in the mulberry response to drought stress.

CONCLUSIONS

Our research shows that mulberry can activate proline and ABA biosynthesis pathways and produce a large amount of proline and ABA, which improves the drought resistance of mulberry. MaWRKYIII8 was up-regulated and induced by drought and exogenous ABA, indicating that MaWRKYIII8 may be involved in the mulberry response to drought stress. These studies will help us to analyse the molecular mechanism underlying mulberry drought tolerance and provide important gene information and a theoretical basis for improving mulberry drought tolerance through molecular breeding in the future.

Transcriptomic Analysis of the Pistacia vera (L.) Fruits Enable the Identification of Genes and Hormone-Related Gene Linked to Inflorescence Bud Abscission

Pistacia vera (L.) is an alternate bearing species. The tree produces axillary inflorescence buds every year. Still, they abscise in “ON” overloaded shoots, causing a limited production in the following “OFF” year, causing a significant and unfavorable production fluctuation. In this work, we carried out de novo discovery and transcriptomic analysis in fruits of “ON” and “OFF” shoots of the cultivar Bianca. We also investigated whether the fruit signaling pathway and hormone biosynthesis directly or indirectly linked to the premature fall of the inflorescence buds causing alternate bearing. We identified 1536 differentially expressed genes (DEGs) in fruits of “ON” vs. “OFF” shoots, which are involved primarily in sugar metabolism, plant hormone pathways and transcription factors. The premature bud abscission linked to the phenomenon is attributable to a lack of nutrients (primarily sugar) and the possible competition between the same branches’ sinks (fruits vs. inflorescence buds). Hormone pathways are involved as a response to signals degradation and remobilization of carbon and nutrients due to the strengthening of the developing embryos. Genes of the secondary metabolism and transcription factors are also involved in tailoring the individual branches response to the nutritional stress and sink competition. Crosstalk among sugar and various hormone-related genes, e.g., ethylene, auxin, ABA and cytokinin, were determined. The discovery of putative biomarkers like callose synthase 5, trehalose-6-phosphate synthase, NAD(P)-linked oxidoreductase and MIOX2, Jasmonate, and salicylic acid-related genes can help to design precision farming practices to mitigate the alternate bearing phenomenon to increase farming profitability. The aim of the analysis is to provide insight into the gene expression profiling of the fate of “ON” and “OFF” fruits associated with the alternate bearing in the pistachio.

Advances in genomics and genome editing for breeding next generation of fruit and nut crops

Fruit tree crops are an essential part of the food production systems and are key to achieve food and nutrition security. Genetic improvement of fruit trees by conventional breeding has been slow due to the long juvenile phase. Advancements in genomics and molecular biology have paved the way for devising novel genetic improvement tools like genome editing, which can accelerate the breeding of these perennial crops to a great extent. In this article, advancements in genomics of fruit trees covering genome sequencing, transcriptome sequencing, genome editing technologies (GET), CRISPR-Cas system based genome editing, potential applications of CRISPR-Cas9 in fruit tree crops improvement, the factors influencing the CRISPR-Cas editing efficiency and the challenges for CRISPR-Cas9 applications in fruit tree crops improvement are reviewed. Besides, base editing, a recently emerging more precise editing system, and the future perspectives of genome editing in the improvement of fruit and nut crops are covered.