Plant species utilize a variety of regulatory mechanisms to ensure sustainable productivity. Within this intricate framework, numerous non-coding RNAs (ncRNAs) play a crucial regulatory role in plant biology, surpassing the essential functions of RNA molecules as messengers, ribosomal, and transfer RNAs. ncRNAs represent an emerging class of regulators, operating directly in the form of small interfering RNAs (siRNAs), microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). These ncRNAs exert control at various levels, including transcription, post-transcription, translation, and epigenetic. Furthermore, they interact with each other, contributing to a variety of biological processes and mechanisms associated with stress resilience. This review primarily concentrates on the recent advancements in plant ncRNAs, delineating their functions in growth and development across various organs such as root, leaf, seed/endosperm, and seed nutrient development. Additionally, this review broadens its scope by examining the role of ncRNAs in response to environmental stresses such as drought, salt, flood, heat, and cold in plants. This compilation offers updated information and insights to guide the characterization of the potential functions of ncRNAs in plant growth, development, and stress resilience in future research.

Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural characteristics, is typically regulated by numerous genes. This study aimed to dissect the genetic regulators underlying 14 plant architectural traits and 10 biomass yield traits in the Sorghum Association Panel across two growing seasons. We identified 321 associated loci through genome-wide association studies (GWAS), involving 234 264 single nucleotide polymorphisms (SNPs). These loci include genes with known associations to biomass traits, such as maturity, dwarfing (Dw), and leafbladeless1, as well as several uncharacterized loci not previously linked to these traits. We also identified 22 pleiotropic loci associated with variation in multiple phenotypes. Three of these loci, located on chromosomes 3 (S03_15463061), 6 (S06_42790178; Dw2), and 9 (S09_57005346; Dw1), exerted significant and consistent effects on multiple traits across both growing seasons. Additionally, we identified three genomic hotspots on chromosomes 6, 7, and 9, each containing multiple SNPs associated with variation in plant architecture and biomass yield traits. Chromosome-wise correlation analyses revealed multiple blocks of positively associated SNPs located near or within the same genomic regions. Finally, genome-wide correlation-based network analysis showed that loci associated with flowering, plant height, leaf traits, plant density, and tiller number per plant were highly interconnected with other genetic loci influencing plant architectural and biomass yield traits. The pyramiding of favorable alleles related to these traits holds promise for enhancing the future development of bioenergy sorghum crops.

The increasing frequency and intensity of droughts present significant challenges to global food security. In this study, we examined the genetic and physiological mechanisms underlying drought tolerance and resilience in sorghum (Sorghum bicolor L.) by phenotyping the Sorghum Association Panel (SAP; n = 397) for a broad suite of traits. These included leaf anatomical characteristics (stomatal density [SD], stomatal size, pore area, stomatal pore area per leaf area, and anatomical maximum stomatal gas conductance), physiological traits [net photosynthetic rate (An), stomatal gas conductance (gsw), and intrinsic water-use efficiency (iWUE)], and functional traits (leaf width, leaf thickness, leaf mass area, and chlorophyll content). Substantial natural variation was detected within the SAP, and correlation analyses indicated that leaf anatomical and functional characteristics play key roles in regulating physiological traits, including An, gsw, and iWUE. Genome-wide association studies identified a genomic hotspot on chromosome 1 (77.5–78.6 Mb) region associated with 3 key single-nucleotide polymorphisms (S01_77550396, S01_78561058, and S01_78619413). Haplotype analysis of these loci uncovered 8 distinct allele combinations influencing SD, An, gsw, and iWUE. Application of the Ball–Woodrow–Berry gsw model to these haplotypes demonstrated that accessions from haplotypes 1 to 5 exhibited greater stomatal plasticity, displaying more dynamic responses under well-watered conditions. In contrast, accessions from haplotypes 6 to 8 showed more conservative stomatal behavior under water-limited conditions. These results provide insights into the coordinated genetic control of leaf traits underlying drought resilience in sorghum and offer a predictive framework for breeding cultivars with stable performance across diverse water regimes.

Drought and leaf blight caused by the fungus Ascochyta rabiei often co-occur in chickpea ( Cicer arietinum )-producing areas. While the responses of chickpea to either drought or A. rabiei infection have been extensively studied, their combined effect on plant defense mechanisms is unknown. Fine modulation of stress-induced signaling pathways under combined stress is an important stress adaptation mechanism that warrants a better understanding. Here we show that drought facilitates resistance against A. rabiei infection in chickpea. The analysis of proline levels and gene expression profiling of its biosynthetic pathway under combined drought and A. rabiei infection revealed the gene encoding proline dehydrogenase (CaProDH2) as a strong candidate conferring resistance to A. rabiei infection. Transcript levels of CaProDH2 , pyrroline-5-carboxylate (P5C) quantification, and measurement of mitochondrial reactive oxygen species (ROS) production showed that fine modulation of the proline–P5C cycle determines the observed resistance. In addition, CaProDH2- silenced plants lost basal resistance to A. rabiei infection induced by drought, while overexpression of the gene conferred higher resistance to the fungus. We suggest that the drought-induced accumulation of proline in the cytosol helps maintain cell turgor and raises mitochondrial P5C contents by a CaProDH2 -mediated step, which results in ROS production that boosts plant defense responses and confers resistance to A. rabiei infection. Our findings indicate that manipulating the proline–P5C pathway may be a possible strategy for improving stress tolerance in plants suffering from combined drought and A. rabiei infection.

Sorghum is emerging as an ideal genetic model for designing high-biomass bioenergy crops. Biomass yield, a complex trait influenced by various plant architectural features, is typically regulated by numerous genes. This study aims to dissect the genetic mechanisms underlying fourteen plant architectural and ten biomass yield traits in a sorghum association panel (SAP) across two growing seasons. We identified 321 associated loci via genome-wide association studies involving 234,264 single nucleotide polymorphisms (SNPs). These loci encompass both genes with a priori links to biomass traits, such as ‘maturity’, ‘dwarfing (Dw)’, ‘leafbladeless1’, ‘cryptochrome’, and several loci not previously linked to roles in determining these traits. We identified 22 pleiotropic loci associated with variation in multiple phenotypes. Three of these loci, located on chromosomes 3 (S03_15463061), 6 (S06_42790178; Dw2), and 9 (S09_57005346; Dw1), exert significant and consistent effects on multiple traits. Additionally, we identified three genomic hotspots on chromosomes 6, 7, and 9, containing multiple SNPs associated with variation in plant architecture and biomass yield traits. Positive correlations were observed among linked SNPs close to or within the same genomic regions. Thirteen haplotypes were identified from these positively correlated SNPs on chr 6, with haplotypes 8 and 11 emerging as optimal combinations, exhibiting pronounced effects on the traits. Lastly, network analysis revealed that loci associated with flowering, plant heights, leaf characteristics, plant number, and tiller number per plant were highly interconnected with other genetic loci linked to plant architecture and biomass yield traits. The pyramiding of favorable alleles related to these traits holds promise for enhancing the future development of bioenergy sorghum crops.

Photosynthesis is the fundamental biological process underlying plant growth, crop productivity, and global food security. However, its efficiency is highly vulnerable to abiotic stresses, which disrupt chlorophyll biosynthesis, electron transport, carbon assimilation, stomatal regulation, and photoprotective mechanisms, ultimately reducing crop yield. Improving photosynthetic resilience under adverse environments has therefore become a major objective of modern crop improvement. Recent advances in phenomics and high-throughput phenotyping (HTP) have transformed the evaluation of photosynthesis-related traits by enabling rapid, non-destructive, and large-scale assessment across diverse environments, while facilitating quantitative characterization of structural, physiological, biochemical, and thermal responses to abiotic stress. Technologies including chlorophyll fluorescence, gas-exchange analysis, thermal imaging, hyperspectral imaging, LiDAR, and UAV-based sensing provide comprehensive insights into plant physiological responses and stress adaptation. Integration of these phenomic approaches with genomic information and artificial intelligence (AI)-driven analytical frameworks has strengthened genomic and phenomic prediction, enabling more accurate identification of candidate genes, selection of superior genotypes, and accelerated genetic gain. This review critically synthesizes recent advances in photosynthesis-related traits, phenomics, HTP technologies, and their integration with genomics and AI-assisted breeding, highlighting current challenges, knowledge gaps, and future opportunities for developing climate-resilient wheat and rice cultivars and promoting sustainable crop production.