Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world’s demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs’ phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.

Rice is a major food crop for more than half of the world’s population, while its production is seriously threatened by flooding, a common environmental stress worldwide. Flooding leads to oxygen deficiency, which is a major problem for submerged plants. Over the past three decades, significant progress has been made in understanding rice adaptation and molecular regulatory mechanisms in response to flooding. At the seed germination and seedling establishment stages, the CIPK15-SnRK1A-MYBS1 signaling cascade plays a central role in determining rice submergence tolerance. However, from seedlings to mature plants for harvesting, SUB1A- and SK1/SK2-regulated pathways represent two principal and opposite regulatory mechanisms in rice. In addition, phytohormones, especially gibberellins, induce adaptive responses to flooding throughout the rice growth period. This review summarizes the significant adaptive traits observed in flooded rice varieties and updates the molecular genetics and mechanisms of submergence tolerance in rice.

Hybrid sterility is the major obstacle to the utilization of inter-subspecific heterosis in hybrid rice breeding. The S5 locus, composed of three adjacent genes ORF3, ORF4, and ORF5, plays a crucial role in regulating indica/japonica hybrids’ female sterility. Through a series of crosses involving 38 parents, three alleles of S5, ORF3+ORF4−ORF5n, ORF3+ORF4+ORF5n, and ORF3−/ORF4−/ORF5n, all could be regarded as wide-compatibility alleles, and when crossed with indica or japonica rice, they all showed significantly high fertility. Then, in order to explore the genes’ function, we further knocked out genes by using CRISPR/Cas9-based genome editing. Our results demonstrate that the ORF3+ was not just the protector in the killer-protector system, and knocking out ORF3 of the indica allele seriously affected the rice’s normal development. We observed the concrete enhancing hybrid spikelet fertility from the crosses between the ORF4+ knockout japonica materials with indica varieties. By conducting the comparative RNA-Seq analysis of young spikelets, we found that the ORF4+/ORF4− could modulate the hybrid fertility by affecting the expressions of genes related to the function of the Golgi apparatus. This study indicated that knocking out the ORF4+ of the japonica allele or using the alleles carrying ORF5n would provide effective approaches to overcome indica/japonica hybrid female sterility in rice breeding.

The RING-Type E3 ubiquitin ligase GRAIN WIDTH 2 (GW2) is a key regulator of grain size and weight in rice (Oryza sativa). However, its substrates and broader roles, particularly in grain size and photosynthesis, remain largely unknown. Here, we applied EMS mutagenesis to the gw2 background and identified a mutant, ylr, exhibiting altered leaf color and reduced grain yield. We identified YLR as an allele of a divinyl reductase involved in converting chlorophyll-a to monovinyl chlorophyll-a during chlorophyll biosynthesis. Interestingly, non-frameshift mutations in the YLR α-helix structure resulted in lighter leaf coloration and fewer tillers, whereas frameshift mutations in YLR led to dwarf plant height. We confirmed that proper YLR function maintains chlorophyll content and chloroplast integrity, ultimately influencing photosynthesis and grain yield. Scanning electron microscopy and transcriptome analysis showed that YLR positively regulates grain length through the alteration of cell number. We further demonstrated that GW2 interacts with and ubiquitinates YLR, targeting it for degradation. Collectively, these findings establish a GW2-YLR regulatory module that integrates leaf color, photosynthesis, and grain yield, supporting coordination between source- and sink-related genes and offering potential targets for optimizing photosynthesis and crop productivity.