Developmental stage-dependent decoupling of molecular and phenotypic responses to heat in wheat grain

Heat-induced CHH methylation changes near an F-box protein gene in Arabidopsis mature-stage seeds

It is found that heat-induced CHH methylation targets specific genomic loci in a developmental stage-specific manner, with a differentially methylated window located within 6 kb of AT5G44410, an F-box protein-encoding gene.

Molecular insights and translational opportunities to enhance heat tolerance in rice

Abstract Heat stress is an increasingly serious threat to rice (Oryza sativa L.) productivity, yet the genetic and regulatory architecture underlying thermotolerance remain poorly resolved and fragmented across studies. Earlier research focused on individual pathways or specific developmental stages; however, recent advances now support an integrated understanding of heat stress adaptation in rice. This review synthesizes emerging insights into molecular physiology, regulatory signaling, epigenetic memory, and genome‐scale variation associated with thermotolerance. We highlight the interconnected roles of calcium reactive oxygen species signaling, heat shock transcription factor networks, translational regulation, and chromatin‐based stress memory in shaping reproductive‐stage tolerance and maintaining grain quality under elevated temperatures. The review also emphasizes the value of pangenome analyses and structural variant discovery for identifying heat‐responsive genes and regulatory elements absent from single‐reference genomes. In addition, genome‐wide association studies, haplotype‐based breeding, genomic selection, and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)‐based genome editing are discussed as promising approaches for functional validation and deployment of favorable alleles controlling polygenic heat resilience. Despite these advances, several challenges continue to hinder translation into breeding‐ready outcomes, including limited field‐based validation of candidate genes, poor integration of multi‐omics datasets into predictive breeding frameworks, and insufficient understanding of reproductive‐stage regulatory networks. Furthermore, genotype × environment interactions, together with trade‐offs among yield, grain quality, and stress resilience, strongly influence the stability and transferability of thermotolerance traits across diverse agroecological environments. By integrating mechanistic insights with genome‐scale diversity and predictive breeding tools, this review outlines a genomics‐enabled roadmap for developing heat‐resilient rice cultivars under intensifying global warming and supporting sustainable global rice production.

Decoding Heat Tolerance in Rice: Physiological Mechanisms, Genetic Architecture, and Breeding Innovations

Heat stress impact on rice reproductive processes: challenges and new approaches

Heat stress represents one of the most severe abiotic constraints to rice ( Oryza sativa L.) productivity and is expected to intensify under ongoing climate change, particularly affecting the reproductive phase and leading to substantial yield and grain quality losses. This review synthesizes current knowledge on the impacts of heat stress on rice reproduction, with a focus on both male and female reproductive structures and their interactions. Evidence from anatomical, physiological, transcriptomic, and metabolomic studies to describe how elevated temperatures disrupt key reproductive processes, including microsporogenesis, anther dehiscence, pollen viability, pollen-pistil interactions, fertilisation, and embryo sac development were integrated in this review. It further discusses the genotype-dependent differences in reproductive thermotolerance; and key genes, metabolites, and pathways associated with heat stress perception, signalling, and tolerance are highlighted. Finally, it is briefly discussed how recent advances in breeding strategies, functional genomics and genome-editing technologies, particularly CRISPR-based approaches, are providing new opportunities to enhance reproductive resilience to heat stress and how it is essential to close the existing molecular knowledge gaps in the development of heat-tolerant rice varieties capable of sustaining productivity in a warming climate.

Pre‐Flowering Heat Wave Sensitivity on Yield and Its Components in Two Spring Barley Near‐Isogenic Lines for PPD‐H1 Alleles

Rising temperatures associated with climate change increasingly threaten cereal yields. Most previous studies have focused on chronic high temperatures, which primarily affect yield indirectly through modifications of crop phenology. In contrast, the effects of short‐term heat waves on reproductive development and yield formation remain poorly understood. In barley ( Hordeum vulgare L.), development and reproduction are tightly regulated by photoperiod sensitivity, mainly controlled by the PPD‐H1 gene, which may modulate plant responses to thermal stress. Here, we quantified the impact of a pre‐flowering heat wave on yield formation and spike fertility in near‐isogenic lines of spring barley differing at the PPD‐H1 locus, across four contrasting environmental backgrounds combining sowing date and photoperiod conditions. Heat waves were imposed for 10 days at the flag leaf stage under field and outdoor conditions, increasing daily maximum temperatures with minimal effects on mean temperature and phenology. Across environments, the heat wave consistently reduced grain yield. Yield losses were primarily driven by reductions in grain number rather than grain weight and were markedly greater in the photoperiod‐insensitive ppd‐H1 line than in the photoperiod‐sensitive Ppd‐H1 line. Differences in flowering time between near‐isogenic lines were small or absent under most conditions, indicating that the contrasting heat wave responses were largely independent of phenological escape and instead reflected direct effects on reproductive development. The lower resilience of ppd‐H1 was associated with both reduced floret fertility at flowering and increased grain abortion, particularly in apical spikelets, whereas spike fertility in Ppd‐H1 plants was largely preserved. Our results demonstrate that the wild‐type Ppd‐H1 allele confers enhanced tolerance to short‐term heat stress immediately before flowering by stabilising spike fertility and grain set. This study highlights the importance of photoperiod genes not only in shaping phenology but also in conferring intrinsic resilience of reproductive processes to heat waves, providing valuable insights for breeding barley cultivars adapted to increasingly variable thermal environments.

Integrative physiology, transcriptomic, and metabolomic analysis reveals the response mechanism of melon seedlings to cold stress.

Early-spring cultivation enables melons to be marketed ahead of the regular season, yet cold stress during this critical growth stage severely suppresses seedling growth and development, ultimately causing substantial yield losses. To date, the physiological shifts, molecular regulatory cascades and metabolic reprogramming triggered by cold stress in melon seedlings have not been fully characterized. In this work, we combined physiological assays, transcriptome, and metabolome profiling to dissect cold-responsive regulatory networks at the seedling stage using two melon inbred lines with divergent cold tolerance: NM3 (cold-tolerant, Netted muskmelon) and M40-1 (cold-sensitive, Hami melon). Our phenotypic and physiological data revealed that cold treatment drastically retarded seedling growth and triggered leaf wilting, alongside elevated reactive oxygen species (ROS) and malondialdehyde (MDA) concentrations in both inbred lines. Relative to cold-sensitive M40-1, NM3 maintained superior growth performance, accompanied by greater accumulation of sensitive and stronger antioxidant enzymatic activities. Transcriptome comparison uncovered sets of differentially expressed genes (DEGs) enriched in phenylalanine metabolism, flavone/flavonol/isoflavonoid biosynthesis, glutathione (GSH) metabolism and fatty acid metabolic pathways. Metabolite quantification further indicated that flavonoids, soluble sugars, lipids and terpenoids accumulated to markedly higher abundances in NM3 after 6 h of cold treatment. Weighted gene co-expression network analysis (WGCNA) integrating transcriptomic and metabolomic datasets pinpointed hub genes and signature metabolites tightly linked to cold tolerance, such as MELO3C017481 (encoding xyloglucan endotransglucosylase-hydrolase 23, XTH23) and MELO3C021100 (encoding heat shock protein 70, HSP70), as well as numerous transcription factors (TFs) and functional genes participating in sugar and flavonoid metabolism. Integrated transcriptomic and metabolomic profiling further verified that genes and metabolites governing flavonoid synthesis and GSH metabolism serve as central modulators of melon cold tolerance. We also found that cold stress robustly activated GSH-related gene expression, and exogenous GSH supplementation effectively relieved cold-induced seedlings injury. Collectively, this study deepens our mechanistic understanding of cold tolerance in melon seedlings, confirms that flavonoids and GSH metabolites act as core components facilitating plant stress adaptation, and supplies valuable genetic and metabolic resources to accelerate the breeding of cold-tolerant melon varieties.