Global crop productivity faces a significant threat from climate change-induced drought stress (DS), which is vital for sustainable agriculture and global food security. Uncovering DS adaptation and tolerance mechanisms in crops is necessary to alleviate climate challenges. Innovative plant breeding demands revolutionary approaches to develop stress-smart plants. Metabolomics, a promising field in plant breeding, offers a predictive tool to identify metabolic markers associated with plant performance under DS, enabling accelerated crop improvement. Central to DS adaptation is metabolomics-driven metabolic regulation, which is critical for maintaining cell osmotic potential in crops. Recent innovations allow rapid mapping of specific metabolites to their genetic pathways, providing a valuable resource for plant scientists. Metabolomics-driven molecular breeding, integrating techniques such as mQTL and mGWAS, enhances our ability to discover key genetic elements linked to stress-responsive metabolites. This integration offers a beneficial platform for plant scientists, yielding significant insights into the complex metabolic networks underlying DS tolerance. Therefore, this review discusses (1) insights into metabolic regulation for DS adaptation, (2) the multifaceted role of metabolites in DS tolerance and nutritional/yield trait improvement, (3) the potential of single-cell metabolomics and imaging, (4) metabolomics-driven molecular breeding, and (5) the application of metabolic and genetic engineering for DS-tolerant crops. We finally propose that the metabolomics-driven approach positions drought-smart crops as key contributors to future food production, supporting the vital goal of achieving “zero hunger”.

The pear (Pyrus spp.) is well known for diverse flavors, textures, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the pear pangenome of 1.15 Gb by combining these two genomes with five previously published pear genomes representing cultivated and wild germplasm. Using the constructed pangenome, we identified 21224 gene PAVs (Presence-absence variation) and 1158812 SNPs (Single Nucleotide Polymorphism) in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, PAV-based analysis provides additional insights into the pear population structure. In addition, some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhance sepal shedding in ‘Xuehuali’ which is vital for pear quality. PsbMGH3.1 may play a role in the IAA pathway, contributing to a distinct low-auxin phenotype observed in plants by heterologously overexpressing this gene. This research helps capture the genetic diversity of pear populations and provides genomic resources for accelerating breeding.

Trehalose (Tre) is a non-reducing disaccharide found in many species, including bacteria, fungi, invertebrates, yeast, and even plants, where it acts as an osmoprotectant, energy source, or protein/membrane protector. Despite relatively small amounts in plants, Tre concentrations increase following exposure to abiotic stressors. Trehalose-6-phosphate, a precursor of Tre, has regulatory functions in sugar metabolism, crop production, and stress tolerance. Among the various abiotic stresses, temperature extremes (heat or cold stress) are anticipated to impact crop production worldwide due to ongoing climate changes. Applying small amounts of Tre can mitigate negative physiological, metabolic, and molecular responses triggered by temperature stress. Trehalose also interacts with other sugars, osmoprotectants, amino acids, and phytohormones to regulate metabolic reprogramming that underpins temperature stress adaptation. Transformed plants expressing Tre-synthesis genes accumulate Tre and show improved stress tolerance. Genome-wide studies of Tre-encoding genes suggest roles in plant growth, development, and stress tolerance. This review discusses the functions of Tre in mitigating temperature stress—highlighting genetic engineering approaches to modify Tre metabolism, crosstalk, and interactions with other molecules—and in-silico approaches for identifying novel Tre-encoding genes in diverse plant species. We consider how this knowledge can be used to develop temperature-resilient crops essential for sustainable agriculture.