Overview of molecular mechanisms of plant leaf development: a systematic review

Evolution of plant cell-type-specific cis-regulatory elements

Cis-regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa, integrating data from 103,911 nuclei representing 126 discrete cell states across nine distinct organs. We used comparative genomics to compare cell-type resolved chromatin accessibility between O. sativa and 57,552 nuclei from four additional grass species (Zea mays, Sorghum bicolor, Panicum miliaceum, and Urochloa fusca). Accessible chromatin regions (ACRs) had different levels of conservation depending on the degree of cell-type specificity. We found a complex relationship between ACRs with conserved noncoding sequences, cell-type specificity, conservation, and tissue-specific switching. Additionally, we found that epidermal ACRs were less conserved compared to other cell types, potentially indicating that more rapid regulatory evolution has occurred in the L1-derived epidermal layer of these species. Finally, we identified and characterized a conserved subset of ACRs that overlapped the repressive histone modification H3K27me3, implicating them as potentially silencer-like CREs maintained by evolution. Collectively, this comparative genomics approach highlights the dynamics of plant cell-type-specific CRE evolution.

Physiological and Cellular Ultrastructural Responses of Isatis indigotica Fort. under Salt Stress

This study aimed to analyze the effects of salt stress on the growth physiology and plant-cell ultrastructure of Isatis indigotica Fort. (I. indigotica) to evaluate its adaptability under salt stress. The effects of different concentrations of salt (NaCl; 0, 25, and 300 mmol·L-1) on the agronomic traits, activities of related enzymes, ion balance, and mesophyll-cell ultrastructure of I. indigotica were studied in a controlled pot experiment. Results showed that compared with those of the control group, the aerial-part fresh weight, underground fresh weight, tiller number, root length, root diameter, plant height, and leaf area of salt-stressed I. indigotica increased at 25 mmol·L-1 and then decreased at 300 mmol·L-1. The changes in levels of superoxide dismutase, peroxidase, ascorbate peroxidase, and catalase showed a similar trend, with significant differences compared with control group. Salt stress altered the ion balance of I. indigotica, resulting in a significant increase in Na+ content and a significant decrease in K+ content. The contents of Ca2+ and Mg2+ changed to varying degrees. The analysis of the microstructure of the root showed that under salt treatment, the epidermal cells of the root significantly thickened and the diameter of the xylem decreased. The results of ultrastructural analysis of mesophylls showed that salt stress can cause cell-membrane contraction, cell-gap enlargement, disorder in the structures of chloroplasts and mitochondria, and an increase in the number of osmiophilic particles. These changes were aggravated by the increase in NaCl concentration. This study reveals the response of I. indigotica to salt stress and provides a basis for further study on the salt-tolerance mechanism of I. indigotica.

Spinach genomes reveal migration history and candidate genes for important crop traits

Spinach (Spinacia oleracea) is an important leafy crop possessing notable economic value and health benefits. Current genomic resources include reference genomes and genome-wide association studies. However, the worldwide genetic relationships and the migration history of the crop remained uncertain, and genome-wide association studies have produced extensive gene lists related to agronomic traits. Here, we re-analysed the sequenced genomes of 305 cultivated and wild spinach accessions to unveil the phylogeny and history of cultivated spinach and to explore genetic variation in relation to phenotypes. In contrast to previous studies, we employed machine learning methods (based on Extreme Gradient Boosting, XGBoost) to detect variants that are collectively associated with agronomic traits. Variant-based cluster analyses revealed three primary spinach groups in the Middle East, Asia and Europe/US. Combining admixture analysis and allele-sharing statistics, migration routes of spinach from the Middle East to Europe and Asia are presented. Using XGBoost machine learning models we predict genomic variants influencing bolting time, flowering time, petiole color, and leaf surface texture and propose candidate genes for each trait. This study enhances our understanding of the history and phylogeny of domesticated spinach and provides valuable information on candidate genes for future genetic improvement of the crop.

Better estimation of evapotranspiration and transpiration using an improved modified Priestly-Taylor model based on a new parameter of leaf senescence in a rice field

Evapotranspiration (ET) is at the heart of the global water, energy, and carbon cycles. As ET is difficult and expensive to measure, it is crucial to develop estimation models that can be widely applied. Currently, an improved Priestley-Taylor (PT) model considers soil moisture stress, temperature constraints, and leaf senescence; however, its parameter (fs) for simulating crop senescence is based on empirical values, making it difficult to apply to different varieties and complex external conditions and thus challenging to generalize. We improved the parameters fs in the original model based on the chlorophyll decomposition that accompanies crop senescence through easily observable SPAD values (Soil-Plant Analysis Development readings) in the field. We validated the improved model by obtaining ET of different rice varieties in 2022 and 2023 using the energy balance residual method at the Free Air Concentration Enrichment Experimental (FACE) Facility located in Yangzhou City, China. The results showed that the simulation of leaf senescence using SPAD values was feasible and could be extended to different varieties. The new model using improved leaf senescence parameter for estimating ET and transpiration (T) in three plots (2022 and 2023) exhibited slightly enhanced accuracy, particularly at the later stages of crop growth. Moreover, the higher the T/ET ratio of the cropland, the more significant the improvement. This new development enhances the ability of PT models to estimate ET and T using readily available field observations and provides some suggestions for wider application in the field for other crop species.

Advancements in Rice Leaf Development Research

Rice leaf morphology is a pivotal component of the ideal plant architecture, significantly impacting rice yield. The process of leaf development unfolds through three distinct stages: the initiation of leaf primordia, the establishment and maintenance of polarity, and leaf expansion. Genes regulating leaf morphology encompass transcription factors, hormones, and miRNAs. An in-depth synthesis and categorization of genes associated with leaf development, particularly those successfully cloned, hold paramount importance in unraveling the complexity of rice leaf development. Furthermore, it provides valuable insights into the potential for molecular-level manipulation of rice leaf types. This comprehensive review consolidates the stages of rice leaf development, the genes involved, molecular regulatory pathways, and the influence of plant hormones. Its objective is to establish a foundational understanding of the creation of ideal rice leaf forms and their practical application in molecular breeding.