Transcriptomic and Metabolomic Analyses Reveal the Key Genes Related to Shade Tolerance in Soybean

The Combination of Physiological and Transcriptomic Approaches Reveals New Insights into the Molecular Mechanisms of Leymus chinensis Growth Under Different Shading Intensities

Leymus chinensis is a grass species in the family Triticeae that is found in the Eurasian grassland region and is known for its outstanding ecological advantages and economic value. However, the increasing adoption of photovoltaic agriculture has modified the light environment for the grass, markedly inhibiting its photosynthesis, growth, and yield. This study used physiological and transcriptomic analyses to investigate the complex response mechanisms of two L. chinensis genotypes (Zhongke No. 3 [Lc3] and Zhongke No. 5 [Lc5]) under shading stress. Growth phenotype analysis revealed the superior growth performance of Lc3 under shading stress, evidenced by enhanced plant height and photosynthetic parameters. Additionally, differentially expressed genes (DEGs) were predominantly enriched in starch and sucrose metabolism and glycolysis/gluconeogenesis pathways, which were the most consistently enriched in both L. chinensis genotypes. However, the flavonoid biosynthesis and galactose metabolism pathways were more enriched in Lc3. Weighted gene co-expression network analysis identified the LcGolS2 gene, which encodes galactinol synthase, as a potential hub gene for resistance to shade stress in comparisons across different cultivars and shading treatments. The use of qRT-PCR analysis further validated the genes involved in these pathways, suggesting that they may play critical roles in regulating the growth and development of L. chinensis under shading conditions. These findings provide new insights into the molecular mechanisms underlying the growth and development of L. chinensis under different shading stress conditions.

Shade tolerance in wheat is related to photosynthetic limitation and morphological and physiological acclimations

Low solar irradiance reaching the canopy due to fog and heavy haze is a significant yield-limiting factor worldwide. However, how plants adapt to shade stress and the mechanisms underlying the reduction in leaf photosynthetic capacity and grain yield remain unclear. In this study (conducted during 2018-2021), we investigated the impact of light deprivation (60%) at the pre-anthesis and post-anthesis stages on leaf carboxylation efficiency, source-to-sink relationships, sucrose metabolism, and grain yield of wheat cultivars with contrasting shade tolerance. Shade stress decreased stomatal conductance, stomatal limitation value, intrinsic water use efficiency, rubisco activity, and carboxylation efficiency of flag leaves during grain-filling, whereas intercellular CO2 concentration increased. These findings indicate that non-stomatal limitation reduces the net photosynthesis rate in a weak-light environment. Shade-tolerant cultivars (MM-51 and CM-39) adapted to low-light conditions via a higher leaf area of flag leaves, light interception rate, and chlorophyll a and b contents; this increased non-structural carbohydrates and sucrose contents in developing grains, ultimately decreasing yield loss by shade stress. Pre-anthesis shading resulted in a greater yield loss than post-anthesis shading because of decreased plant biomass, grain number per spike and 1,000-kernel weight. This study indicates that Rubisco-mediated non-stomatal limitation reduces P N and sucrose content in plants exposed to low-light stress, contributing to decreased grain yield. Our study provides information on the mechanism underlying shade stress tolerance, which will help design future strategies for reducing yield loss in the context of global dimming.

Plant membrane transporters function under abiotic stresses: a review

MAIN CONCLUSION

In the present review, we discussed the detailed signaling cascades via membrane transporters that confer plant tolerance to abiotic stresses and possible significant use in plant development for climate-resilient crops. Plant transporters play significant roles in nutrient uptake, cellular balance, and stress responses. They facilitate the exchange of chemicals and signals across the plant's membrane by signal transduction, osmotic adjustment, and ion homeostasis. Therefore, research into plant transporters is crucial for understanding the mechanics of plant stress tolerance. Transporters have potential applications in crop breeding for increased stress resistance. We discuss new results about various transporter families (ABC, MATE, NRAMP, NRT, PHT, ZIP), including their functions in abiotic stress tolerance and plant development. Furthermore, we emphasize the importance of transporters in plant responses to abiotic stresses such as drought, cold, salt, and heavy metal toxicity, low light, flooding, and nutrient deficiencies. We discuss the transporter pathways and processes involved in diverse plant stress responses. This review discusses recent advances in the role of membrane transporters in abiotic stress tolerance in Arabidopsis and other crops. The review contains the genes discovered in recent years and associated molecular mechanisms that improve plants' ability to survive abiotic stress and their possible future applications by integrating membrane transporters with other technologies.

Identification of candidate genes and development of KASP markers for soybean shade-tolerance using GWAS

Shade has a direct impact on photosynthesis and production of plants. Exposure to shade significantly reduces crops yields. Identifying shade-tolerant genomic loci and soybean varieties is crucial for improving soybean yields. In this study, we applied a shade treatment (30% light reduction) to a natural soybean population consisting of 264 accessions, and measured several traits, including the first pod height, plant height, pod number per plant, grain weight per plant, branch number, and main stem node number. Additionally, we performed GWAS on these six traits with and without shade treatment, as well as on the shade tolerance coefficients (STCs) of the six traits. As a result, we identified five shade-tolerance varieties, 733 SNPs and four candidate genes over two years. Furthermore, we developed four kompetitive allele-specific PCR (KASP) makers for the STC of S18_1766721, S09_48870909, S19_49517336, S18_3429732. This study provides valuable genetic resources for breeding soybean shade tolerance and offers new insights into the theoretical research on soybean shade tolerance.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Multi-Omics Approach Reveals OsPIL1 as a Regulator Promotes Rice Growth, Grain Development, and Blast Resistance

Rice (Oryza sativa) is a crucial crop, achieving high yield concurrent pathogen resistance remains a challenge. Transcription factors play roles in growth and abiotic tolerance. However, rice phytochrome-interacting factor-like 1 (OsPIL1) in pathogen resistance and agronomic traits remains unexplored. We generated OsPIL1 overexpressing (OsPIL1 OE) rice lines and evaluated their impact on growth, grain development, and resistance to Magnaporthe oryzae. Multiomics analysis (RNA-seq, metabolomics, and CUT&Tag) and RT-qPCR validated OsPIL1 target genes and key metabolites. In the results, OsPIL1 OE rice lines exhibited robust growth, longer grains, and enhanced resistance to M. oryzae without compromising growth. Integrative multiomics analysis revealed a coordinated regulatory network centered on OsPIL1, explaining these desirable traits. OsPIL1 likely acts as a positive regulator, targeting transcriptional elements or specific genes with direct functions in several biological programs. In particular, a range of key signaling genes (phosphatases, kinases, plant hormone genes, transcription factors), and metabolites (linolenic acid, vitamin E, trigonelline, d-glucose, serotonin, choline, genistein, riboflavin) contributed to enhanced rice growth, grain size, pathogen resistance, or a combination of these traits. These findings highlight OsPIL1's regulatory role in promoting important traits and provide insights into potential strategies for rice breeding.