Impacts of Nitrogen Deficiency on Wheat (Triticum aestivum L.) Grain During the Medium Filling Stage: Transcriptomic and Metabolomic Comparisons

Cereals can trap endophytic bacteria with potential beneficial traits when grown ex-situ in harsh soils

Microbial communities associated with plants growing in harsh conditions, including salinity and water deficiency, have developed adaptive features which permit them to grow and survive under extreme environmental conditions. In the present study, an ex-situ plant trapping method has been applied to collect the culturable microbial diversity associated with the soil from harsh and remote areas. Oryza sativa cv. Baldo and Triticum durum Primadur plants were used as recruiters, while the soil surrounding the roots of Oryza glaberrima plants from remote regions of Mali (West Africa) was used as substrate for their growth. The endophytic communities recruited by the two plant species belonged to Proteobacteria and Firmicutes, and the dominant genera were Bacillus, Kosakonia, and Enterobacter. These endophytes were characterized by analyzing some of the most common plant growth promoting traits. Halotolerant, inorganic phosphate-solubilizing and N-fixing strains were found, and some of them simultaneously showing these three traits. We verified that 'Baldo' recruited mostly halotolerant and P-solubilizers endophytes, while the endophytes selected by 'Primadur' were mainly N-fixers. The applied ex-situ plant trapping method allowed to isolate endophytes with potential beneficial traits that could be applied for the improvement of rice and wheat growth under adverse environmental conditions.

Transcriptomic and Metabolomic Analyses Reveal the Importance of Lipid Metabolism and Photosynthesis Regulation in High Salinity Tolerance in Barley (Hordeum vulgare L.) Leaves Derived from Mutagenesis Combined with Microspore Culture

Barley is the most salt-tolerant cereal crop. However, little attention has been paid to the salt-tolerant doubled haploids of barley derived from mutagenesis combined with isolated microspore culture. In the present study, barley doubled haploid (DH) line 20, which was produced by mutagenesis combined with isolated microspore culture, showed stably and heritably better salt tolerance than the wild type H30 in terms of fresh shoot weight, dry shoot weight, K+/Na+ ratio and photosynthetic characteristics. Transcriptome and metabolome analyses were performed to compare the changes in gene expression and metabolites between DH20 and H30. A total of 462 differentially expressed genes (DEGs) and 152 differentially accumulated metabolites (DAMs) were identified in DH20 compared to H30 under salt stress. Among the DAMs, fatty acids were the most accumulated in DH20 under salt stress. The integration of transcriptome and metabolome analyses revealed that nine key biomarkers, including two metabolites and seven genes, could distinguish DH20 and H30 when exposed to high salt. The pathways of linoleic acid metabolism, alpha-linolenic acid metabolism, glycerolipid metabolism, photosynthesis, and alanine, aspartate and glutamate metabolism were significantly enriched in DH20 with DEGs and DAMs in response to salt stress. These results suggest that DH20 may enhance resilience by promoting lipid metabolism, maintaining energy metabolism and decreasing amino acids metabolism. The study provided novel insights for the rapid generation of homozygous mutant plants by mutagenesis combined with microspore culture technology and also identified candidate genes and metabolites that may enable the mutant plants to cope with salt stress.

Integrated transcriptomic and metabolomic analyses reveal key metabolic pathways in response to potassium deficiency in coconut (Cocos nucifera L.) seedlings

Potassium ions (K⁺) are important for plant growth and crop yield. However, the effects of K⁺ deficiency on the biomass of coconut seedlings and the mechanism by which K⁺ deficiency regulates plant growth remain largely unknown. Therefore, in this study, we compared the physiological, transcriptome, and metabolite profiles of coconut seedling leaves under K⁺-deficient and K⁺-sufficient conditions using pot hydroponic experiments, RNA-sequencing, and metabolomics technologies. K⁺ deficiency stress significantly reduced the plant height, biomass, and soil and plant analyzer development value, as well as K content, soluble protein, crude fat, and soluble sugar contents of coconut seedlings. Under K⁺ deficiency, the leaf malondialdehyde content of coconut seedlings were significantly increased, whereas the proline (Pro) content was significantly reduced. Superoxide dismutase, peroxidase, and catalase activities were significantly reduced. The contents of endogenous hormones such as auxin, gibberellin, and zeatin were significantly decreased, whereas abscisic acid content was significantly increased. RNA-sequencing revealed that compared to the control, there were 1003 differentially expressed genes (DEGs) in the leaves of coconut seedlings under K⁺ deficiency. Gene Ontology analysis revealed that these DEGs were mainly related to "integral component of membrane," "plasma membrane," "nucleus", "transcription factor activity," "sequence-specific DNA binding," and "protein kinase activity." Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated that the DEGs were mainly involved in "MAPK signaling pathway-plant," "plant hormone signal transduction," "starch and sucrose metabolism," "plant-pathogen interaction," "ABC transporters," and "glycerophospholipid metabolism." Metabolomic analysis showed that metabolites related to fatty acids, lipidol, amines, organic acids, amino acids, and flavonoids were generally down-regulated in coconut seedlings under K⁺ deficiency, whereas metabolites related to phenolic acids, nucleic acids, sugars, and alkaloids were mostly up-regulated. Therefore, coconut seedlings respond to K⁺ deficiency stress by regulating signal transduction pathways, primary and secondary metabolism, and plant-pathogen interaction. These results confirm the importance of K⁺ for coconut production, and provide a more in-depth understanding of the response of coconut seedlings to K⁺ deficiency and a basis for improving K⁺ utilization efficiency in coconut trees.

Dissection of Crop Metabolome Responses to Nitrogen, Phosphorus, Potassium, and Other Nutrient Deficiencies

Crop growth and yield often face sophisticated environmental stresses, especially the low availability of mineral nutrients in soils, such as deficiencies of nitrogen, phosphorus, potassium, and others. Thus, it is of great importance to understand the mechanisms of crop response to mineral nutrient deficiencies, as a basis to contribute to genetic improvement and breeding of crop varieties with high nutrient efficiency for sustainable agriculture. With the advent of large-scale omics approaches, the metabolome based on mass spectrometry has been employed as a powerful and useful technique to dissect the biochemical, molecular, and genetic bases of metabolisms in many crops. Numerous metabolites have been demonstrated to play essential roles in plant growth and cellular stress response to nutrient limitations. Therefore, the purpose of this review was to summarize the recent advances in the dissection of crop metabolism responses to deficiencies of mineral nutrients, as well as the underlying adaptive mechanisms. This review is intended to provide insights into and perspectives on developing crop varieties with high nutrient efficiency through metabolite-based crop improvement.

Source-Sink Dynamics in Field-Grown Durum Wheat Under Contrasting Nitrogen Supplies: Key Role of Non-Foliar Organs During Grain Filling

The integration of high-throughput phenotyping and metabolic approaches is a suitable strategy to study the genotype-by-environment interaction and identify novel traits for crop improvement from canopy to an organ level. Our aims were to study the phenotypic and metabolic traits that are related to grain yield and quality at canopy and organ levels, with a special focus on source-sink coordination under contrasting N supplies. Four modern durum wheat varieties with contrasting grain yield were grown in field conditions under two N fertilization levels in north-eastern Spain. We evaluated canopy vegetation indices taken throughout the growing season, physiological and metabolic traits in different photosynthetic organs (flag leaf blade, sheath, peduncle, awn, glume, and lemma) at anthesis and mid-grain filling stages, and agronomic and grain quality traits at harvest. Low N supply triggered an imbalance of C and N coordination at the whole plant level, leading to a reduction of grain yield and nutrient composition. The activities of key enzymes in C and N metabolism as well as the levels of photoassimilates showed that each organ plays an important role during grain filling, some with a higher photosynthetic capacity, others for nutrient storage for later stages of grain filling, or N assimilation and recycling. Interestingly, the enzyme activities and sucrose content of the ear organs were positively associated with grain yield and quality, suggesting, together with the regression models using isotope signatures, the potential contribution of these organs during grain filling. This study highlights the use of holistic approaches to the identification of novel targets to improve grain yield and quality in C₃ cereals and the key role of non-foliar organs at late-growth stages.

Transcriptome Analysis Reveals Different Responsive Patterns to Nitrogen Deficiency in Two Wheat Near-Isogenic Lines Contrasting for Nitrogen Use Efficiency

Simple Summary

Nitrogen (N) limitation is the key factor for wheat production worldwide. Therefore, the development of genotypes with improved nitrogen use efficiency (NUE) is a prerequisite for sustainable and productive agriculture. Exploring the molecular mechanisms of low N stress tolerance is significant for breeding wheat cultivars with high NUE. To clarify the underlying molecular mechanisms of enhanced resilience to low N in high-NUE wheat, we performed an RNA sequencing (RNA-seq) analysis. In the current research, two wheat near-isogenic lines (NILs) differing dramatically in NUE were used to measure gene expression differences under different N treatments. There was a dramatic difference between two wheat NILs in response to N deficiency at the transcriptional level, and the classification of identified candidate genes may provide new valuable insights into the resilience mechanism of wheat.

Abstract

The development of crop cultivars with high nitrogen use efficiency (NUE) under low-N fertilizer inputs is imperative for sustainable agriculture. However, there has been little research on the molecular mechanisms underlying enhanced resilience to low N in high-NUE plants. The comparison of the transcriptional responses of genotypes contrasting for NUE will facilitate an understanding of the key molecular mechanism of wheat resilience to low-N stress. In the current study, the RNA sequencing (RNA-seq) technique was employed to investigate the genotypic difference in response to N deficiency between two wheat NILs (1Y, high-NUE, and 1W, low-NUE). In our research, high- and low-NUE wheat NILs showed different patterns of gene expression under N-deficient conditions, and these N-responsive genes were classified into two major classes, including “frontloaded genes” and “relatively upregulated genes”. In total, 103 and 45 genes were identified as frontloaded genes in high-NUE and low-NUE wheat, respectively. In summary, our study might provide potential directions for further understanding the molecular mechanism of high-NUE genotypes adapting to low-N stress.