Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.)

Arbuscular mycorrhizal symbiosis reshapes the drought adaptation strategies of a dominant sand-fixation shrub species in northern China

Drylands are home to over 38 % of the world's population and are among the areas most sensitive to climate change and human activity. Most xerophytes rely on arbuscular mycorrhizal fungi (AMF) for improved drought tolerance. Although research has focused on crops and economically significant plants, the response of sand-fixation shrubs to AMF under drought conditions remains underexplored. This study aims to investigate how AMF affects the drought adaptation strategies of the sand-fixation shrub Artemisia ordosica. A culture system for A. ordosica and the main symbiotic partner Funneliformis mosseae was established, and phenotypic, metabolomic, and transcriptomic analyses were conducted to assess physiological changes induced by arbuscular mycorrhizal symbiosis (AMS) under varying drought stress conditions. AMS influenced A. ordosica's metabolic pathways and its drought adaptation strategies, promoted the redistribution of sugars and flavonoids, and shaped different metabolic patterns of seedlings and adult A. ordosica. AMS had an important shaping ability in the accumulation of proline at A. ordosica seedlings, but had a significant influence on the accumulation of sugars of A. ordosica at the adult growth stage. AMS enhanced the ability of the host to adapt to extreme drought by modulating metabolites at the adult growth stage of A. ordosica. AMS also facilitated an accumulation of key metabolites under well-watered conditions but also intensified interactions with pathogens, leading to a trade-off between drought adaptation and immune capacity under extreme drought of A. ordosica during the adult growth stage. This study uses metabolome and transcriptome methods to explore AMS effects on A. ordosica's drought adaptation strategies, revealing a significant trade-off between drought adaptation and immune capacity. The findings highlight AMS's role in modifying the drought adaptation strategies of A. ordosica in desert ecosystems, and enhance our understanding of key species for sand fixation and ecological restoration, and maintain ecological security.

Transcriptomics combined with physiological analysis and metabolomics revealed the response of potato tuber formation to nitrogen

The absorption of the essential element nitrogen by plants affects various aspects of plant physiological activity, including gene expression, metabolite content and growth. However, the molecular mechanism underlying the potato tuberization response to nitrogen remains unclear. Potato plants were subjected to pot experiments under nitrogen deficiency, normal nitrogen levels and nitrogen sufficiency. A comprehensive analysis of the physiological responses, transcriptomic profiles, and metabolic pathways of potato stolons subjected to nitrogen stress was conducted. Transcriptomic analysis revealed 2756 differentially expressed genes (DEGs) associated with nitrogen stress. Metabolomic analysis identified a total of 600 differentially accumulated metabolites (DAMs). Further correlation analysis of the major DEGs and DAMs revealed that 9 key DEGs were associated with alpha-linolenic acid metabolism, 16 key DEGs with starch and sucrose metabolism, 7 key DEGs with nitrogen metabolism, and 16 key DEGs with ABC transporters. Nitrogen deficiency significantly increased the sucrose, GDP-glucose and L-glutamic acid levels and promoted stolon growth by increasing the expression of AMY (alpha-amylase), BE (1,4-alpha-glucan branching enzyme), SS (starch synthase), SPS (sucrose‒phosphate synthase) and AGPS (glucose‒1-phosphate adenylyltransferase). However, high nitrogen levels had the opposite effect. In addition, high nitrogen levels upregulated EG (endoglucanase), SUS (sucrose synthase) and GDH (glutamate dehydrogenase) and led to significant accumulation of 9-Hydroperoxy-10,12,15-octadecatrienoate (9(S)-HpOTrE), (13 S)-Hydroperoxyoctadeca-9,11,15-trienoate (13 (S)-HpOTrE) and L-glutamine, ultimately affecting the balance between plant growth and defense. Overall, our comprehensive study revealed the co-expressed genes and potential pathways related to potato tuber formation under different nitrogen conditions. These data provide a better understanding needed for improving potato tuber traits at the molecular and metabolic levels.

Exploring CDF gene family in wild potato under salinity stress unveils promising candidates for developing climate-resilient crops

The DNA-binding with one finger (Dof) gene family is a class of plant-specific transcription factors involved in diverse biological processes, including response to biotic and abiotic stresses. Members of this family have been reported in the cultivated potato Solanum tuberosum, but clues to the roles of several Dof genes are still lacking. Potato wild relatives represent a genetic reservoir for breeding as they could provide useful alleles for adaptation to the environment and tolerance to biotic and abiotic stresses. We performed an in silico analysis to identify genes belonging to the Dof family in the wild potato S. commersonii, confirming that the identified Dof genes can be grouped in four classes (A, B, C, D), as reported for cultivated potato. A special focus was dedicated to Cycling Dof Factors (CDFs), which play a crucial role in plant responses to abiotic stresses. Analysis of available RNA-seq data confirmed CDF genes as regulated by stresses and often in a tissue specific manner. To ascertain their involvement in the stress response, S. tuberosum and S. commersonii plantlets growing in vitro were subjected to salt stress (80mM NaCl) for short (2 days) and prolonged (7 days) times. Analysis of phenotypic traits and qRT-PCR expression profiles of target CDF genes in aerial and root tissues showed differences between the two species. In addition, after saline treatment, changes in total phenols, proline, and malondialdehyde suggested a diverse perception of saline stress in S. commersonii vs. S. tuberosum. Overall, this study provided useful clues to the involvement of CDF genes in salt response and promoted the identification of potential candidate genes for further functional studies.

Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming

Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3- increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.

Optimized nitrogen application ameliorates the photosynthetic performance and yield potential in peanuts as revealed by OJIP chlorophyll fluorescence kinetics

BACKGROUND

Nitrogen (N) is a crucial element for increasing photosynthesis and crop yields. The study aims to evaluate the photosynthetic regulation and yield formation mechanisms of different nodulating peanut varieties with N fertilizer application.

METHOD

The present work explored the effect of N fertilizer application rates (N0, N45, N105, and N165) on the photosynthetic characteristics, chlorophyll fluorescence characteristics, dry matter, N accumulation, and yield of four peanut varieties.

RESULTS

The results showed that N application increased the photosynthetic capacity, dry matter, N accumulation, and yield of peanuts. The measurement of chlorophyll a fluorescence revealed that the K-phase, J-phase, and I-phase from the OJIP curve decreased under N105 treatment compared with N0, and WOI, ET0/CSM, RE0/CSM, ET0/RC, RE0/RC, φPo, φEo, φRo, and Ψ0 increased, whereas VJ, VI, WK, ABS/RC, TR0/RC, DI0/RC, and φDo decreased. Meanwhile, the photosystem activity and electron transfer efficiency of nodulating peanut varieties decreased with an increase in N (N165). However, the photosynthetic capacity and yield of the non-nodulating peanut variety, which highly depended on N fertilizer, increased with an increase in N.

CONCLUSION

Optimized N application (N105) increased the activity of the photosystem II (PSII) reaction center, improved the electron and energy transfer performance in the photosynthetic electron transport chain, and reduced the energy dissipation of leaves in nodulating peanut varieties, which is conducive to improving the yield. Nevertheless, high N (N165) had a positive effect on the photosystem and yield of non-nodulating peanut. The results provide highly valuable guidance for optimizing peanut N management and cultivation measures.

Identification of a Comprehensive Gene Co-Expression Network Associated with Autotetraploid Potato (Solanum tuberosum L.) Development Using WGCNA Analysis

The formation and development of potato tissues and organs is a complex process regulated by a variety of genes and environmental factors. The regulatory mechanisms underlying the growth and development are still unclear. In this work, we aimed to explore the changes in gene expression patterns and genetic characteristics of potato tissues throughout different developmental stages. To achieve this, we used autotetraploid potato JC14 as an experimental subject to analyze the transcriptome of the root, stem, and leaf at the seedling, tuber formation, and tuber expansion stages. The results revealed thousands of differentially expressed genes, predominantly involved in defense response and carbohydrate metabolism according to KEGG pathway enrichment analysis. Weighted gene co-expression network analysis (WGCNA) revealed a total of 12 co-expressed gene modules, with 4 modules showing the highest correlation with potato stem development. By calculating the connectivity of genes within the module, hub genes were identified, and functional annotations were subsequently performed. A total of 40 hub genes from the four modules were identified, and their functions were found to be related to carbohydrate metabolism, defense response, and transcription factors. These findings provide important insights for further understanding of the molecular regulation and genetic mechanisms involved in potato tissue development.

Transcriptome and Metabolome Reveal the Molecular Mechanism of Barley Genotypes Underlying the Response to Low Nitrogen and Resupply

Nitrogen is one of the most important mineral elements for plant growth and development. Excessive nitrogen application not only pollutes the environment, but also reduces the quality of crops. However, are few studies on the mechanism of barley tolerance to low nitrogen at both the transcriptome and metabolomics levels. In this study, the nitrogen-efficient genotype (W26) and the nitrogen-sensitive genotype (W20) of barley were treated with low nitrogen (LN) for 3 days and 18 days, then treated with resupplied nitrogen (RN) from 18 to 21 days. Later, the biomass and the nitrogen content were measured, and RNA-seq and metabolites were analyzed. The nitrogen use efficiency (NUE) of W26 and W20 treated with LN for 21 days was estimated by nitrogen content and dry weight, and the values were 87.54% and 61.74%, respectively. It turned out to have a significant difference in the two genotypes under the LN condition. According to the transcriptome analysis, 7926 differentially expressed genes (DEGs) and 7537 DEGs were identified in the leaves of W26 and W20, respectively, and 6579 DEGs and 7128 DEGs were found in the roots of W26 and W20, respectively. After analysis of the metabolites, 458 differentially expressed metabolites (DAMs) and 425 DAMs were found in the leaves of W26 and W20, respectively, and 486 DAMs and 368 DAMs were found in the roots of W26 and W20, respectively. According to the KEGG joint analysis of DEGs and DAMs, it was discovered that glutathione (GSH) metabolism was the pathway of significant enrichment in the leaves of both W26 and W20. In this study, the metabolic pathways of nitrogen metabolism and GSH metabolism of barley under nitrogen were constructed based on the related DAMs and DEGs. In leaves, GSH, amino acids, and amides were the main identified DAMs, while in roots, GSH, amino acids, and phenylpropanes were mainly found DAMs. Finally, some nitrogen-efficient candidate genes and metabolites were selected based on the results of this study. The responses of W26 and W20 to low nitrogen stress were significantly different at the transcriptional and metabolic levels. The candidate genes that have been screened will be verified in future. These data not only provide new insights into how barley responds to LN, but also provide new directions for studying the molecular mechanisms of barley under abiotic stress.

Insights on Phytohormonal Crosstalk in Plant Response to Nitrogen Stress: A Focus on Plant Root Growth and Development

Nitrogen (N) is a vital mineral component that can restrict the growth and development of plants if supplied inappropriately. In order to benefit their growth and development, plants have complex physiological and structural responses to changes in their nitrogen supply. As higher plants have multiple organs with varying functions and nutritional requirements, they coordinate their responses at the whole-plant level based on local and long-distance signaling pathways. It has been suggested that phytohormones are signaling substances in such pathways. The nitrogen signaling pathway is closely associated with phytohormones such as auxin (AUX), abscisic acid (ABA), cytokinins (CKs), ethylene (ETH), brassinosteroid (BR), strigolactones (SLs), jasmonic acid (JA), and salicylic acid (SA). Recent research has shed light on how nitrogen and phytohormones interact to modulate physiology and morphology. This review provides a summary of the research on how phytohormone signaling affects root system architecture (RSA) in response to nitrogen availability. Overall, this review contributes to identifying recent developments in the interaction between phytohormones and N, as well as serving as a foundation for further study.