Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

Although epigenetic modifications have been intensely investigated over the last decade due to their role in crop adaptation to rapid climate change, it is unclear which epigenetic changes are heritable and therefore transmitted to their progeny. The identification of epigenetic marks that are transmitted to the next generations is of primary importance for their use in breeding and for the development of new cultivars with a broad-spectrum of tolerance/resistance to abiotic and biotic stresses. In this review, we discuss general aspects of plant responses to environmental stresses and provide an overview of recent findings on the role of transgenerational epigenetic modifications in crops. In addition, we take the opportunity to describe the aims of EPI-CATCH, an international COST action consortium composed by researchers from 28 countries. The aim of this COST action launched in 2020 is: (1) to define standardized pipelines and methods used in the study of epigenetic mechanisms in plants, (2) update, share, and exchange findings in epigenetic responses to environmental stresses in plants, (3) develop new concepts and frontiers in plant epigenetics and epigenomics, (4) enhance dissemination, communication, and transfer of knowledge in plant epigenetics and epigenomics.

This review discusses the potential of artificial intelligence (AI), particularly machine learning (ML) and its subset, deep learning (DL), in advancing the genetic improvement of Solanaceous crops. AI has emerged as a powerful solution to overcome the limitations of traditional breeding techniques, which often involve time-consuming, resource-intensive processes with limited predictive accuracy. Through advanced algorithms and predictive models, ML and DL facilitate the identification and optimization of key traits, including higher yield, improved quality, pest resistance, and tolerance to extreme climatic conditions. By integrating big data analytics and omics, these methods enhance genomic selection (GS), support gene-editing technologies like CRISPR-Cas9, and accelerate crop breeding, thus enabling the development of resilient and adaptable crops. This review highlights the role of ML and DL in improving Solanaceae crops, such as tomato, potato, eggplant, and pepper, with the aim of developing novel varieties with superior agronomic and quality traits. Additionally, this study examines the advantages and limitations of AI-driven breeding compared to traditional methods in Solanaceae, emphasizing its contribution to agricultural resilience, food security, and environmental sustainability.

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.

Salinity stress is a major abiotic factor limiting tomato (Solanum lycopersicum) production, particularly in arid and semi-arid regions. Utilizing genetic resources from wild tomato relatives, such as Solanum pennellii, through the exploitation of introgression lines (ILs) provides a promising strategy to enhance salt tolerance. This study evaluates the performance of nine tomato genotypes, including one commercial tomato hybrid (Formula F₁) and eight ILs under three different soil salinity levels (1.88, 6.44, and 8.63 mS/cm), trying to identify salt-tolerant lines that maintain yield and fruit quality. Morphological characteristics, gas exchange parameters, yield traits, fruit quality characteristics, and antioxidant activity were assessed. High-performance liquid chromatography (HPLC) was employed to quantify the levels of carotenoids, namely lycopene and β-carotene, of fruits in selected genotypes. Additionally, total antioxidant capacity was measured in leaves, using DPPH, FRAP and FOLIN assays. The results indicate that out of all the evaluated characteristics, four plant-related traits, four fruit-related traits, one gas exchange parameter, and three productivity-related traits presented strong correlations to total yield (g/plant). These 12 traits could be considered as potential indexes for genotype salinity tolerance discrimination and could be utilized as an efficient marker tool for distinguishing tolerant genotypes to salinity stress, allowing breeders to reduce the time-consuming process of developing new salinity-tolerant varieties. Regarding genotypes’ ranking based on the relative performance of agronomic traits under a salinity regime of 8.63 mS/cm compared to a salinity regime of 1.88 mS/cm, IL6-6 exhibited significant tolerance to high-salinity conditions compared to the commercial hybrid and other ILs, like IL8-9. This tolerant IL maintained higher plant growth, yield, and fruit quality traits, including elevated levels in its fruits’ carotenoids and leaves’ antioxidant capacity, under severe salinity conditions, highlighting its potential for breeding programs targeting saline environments. ILs can help maintain productivity and fruit quality under salinity stress, making them a promising solution for sustainable tomato cultivation in salinity-affected regions. These findings, combined with previous results, suggest that tomato introgression lines offer a valuable genetic resource for developing tomato varieties suitable for harsh environments.