Transcriptomic Study for Identification of Major Nitrogen Stress Responsive Genes in Australian Bread Wheat Cultivars

Sultana, Nigarin; Islam, Shahidul; Juhász, Angéla; Yang, Rongchang; She, Maoyun; Alhabbar, Zaid; Zhang, Jingjuan; Ma, Wujun

doi:10.3389/fgene.2020.583785

Cited by 39 publications

(46 citation statements)

References 183 publications

(181 reference statements)

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“…Moreover, RNA-seq data also indicated the glutamate synthesis genes, such as GATB, the homologous gene to At1g74260, and GLR3.4 genes were expressed at high levels (Supplementary Table 3), which might enhance the accumulation of glutamate. The top up-regulated genes found in wheat grain at 10 DAP were glutamate dehydrogenase and glutamine synthase (Sultana et al, 2020), which was a tolerance mechanism to low N conditions, in agreement with the results. Interestingly, although amino acid levels in grain decreased, the TGW increased under N-deficiency conditions.…”

Section: Adaptive Mechanism Of Amino Acids and Sugars Metabolism Under N-deficiency Conditionssupporting

confidence: 90%

“…The last two decades have delivered tremendous progress in understanding the yield, quality, genetic regulations of NUE, as well as the morphological, physiological, and biochemical effects of N deficiency. However, these studies mainly focused on roots and leaves in bread wheat seedlings (Wang et al, 2019 ; Xin et al, 2020 ), or only investigated the transcriptome response to N-starvation (Sultana et al, 2020 ) or metabolome response to high-N condition (Zhen et al, 2016 ) of bread wheat in filling grain. Furthermore, the variation in gene expressions and metabolite levels at the medium stage of grain filling changed to the greatest degree and closely influenced the yield and quality of grain (Zhen et al, 2016 ; Henry et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

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

Wang

Tao

et al. 2021

Front. Plant Sci.

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Nitrogen (N) supplementation is essential to the yield and quality of bread wheat (Triticum aestivum L.). The impact of N-deficiency on wheat at the seedling stage has been previously reported, but the impact of distinct N regimes applied at the seedling stage with continuous application on filling and maturing wheat grains is lesser known, despite the filling stage being critical for final grain yield and flour quality. Here, we compared phenotype characteristics such as grain yield, grain protein and sugar quality, plant growth, leaf photosynthesis of wheat under N-deficient and N-sufficient conditions imposed prior to sowing (120 kg/hm2) and in the jointing stage (120 kg/hm2), and then evaluated the effects of this continued stress through RNA-seq and GC-MS metabolomics profiling of grain at the mid-filling stage. The results showed that except for an increase in grain size and weight, and in the content of total sugar, starch, and fiber in bran fraction and white flour, the other metrics were all decreased under N-deficiency conditions. A total of 761 differentially expressed genes (DEGs) and 77 differentially accumulated metabolites (DAMs) were identified. Under N-deficiency, 51 down-regulated DEGs were involved in the process of impeding chlorophyll synthesis, chloroplast development, light harvesting, and electron transfer functions of photosystem, which resulted in the SPAD and Pn value decreased by 32 and 15.2% compared with N-sufficiency, inhibited photosynthesis. Twenty-four DEGs implicated the inhibition of amino acids synthesis and protein transport, in agreement with a 17–42% reduction in ornithine, cysteine, aspartate, and tyrosine from metabolome, and an 18.6% reduction in grain protein content. However, 14 DEGs were implicated in promoting sugar accumulation in the cell wall and another six DEGs also enhanced cell wall synthesis, which significantly increased fiber content in the endosperm and likely contributed to increasing the thousands-grain weight (TGW). Moreover, RNA-seq profiling suggested that wheat grain can improve the capacity of DNA repair, iron uptake, disease and abiotic stress resistance, and oxidative stress scavenging through increasing the content levels of anthocyanin, flavonoid, GABA, galactose, and glucose under N-deficiency condition. This study identified candidate genes and metabolites related to low N adaption and tolerance that may provide new insights into a comprehensive understanding of the genotype-specific differences in performance under N-deficiency conditions.

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Section: Adaptive Mechanism Of Amino Acids and Sugars Metabolism Under N-deficiency Conditionssupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

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

Wang

Tao

et al. 2021

Front. Plant Sci.

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“…In this study we did not nd signi cant differences for Lettuce NRT1.1 gene expression under HN or LN condition con rming the role of NRT1.1 gene in nitrate perception. In contrast to our nding, Sultana et al (2020) found that in wheat the expression of most of the dual a nity nitrate transporters (like NRT1.1) decreased under nitrogen stress and suggested that the reduced expression of NRT1.1 genes may lead to retarded growth, low grain protein content and low grain yield of nitrogen stressed plants. We observed that the expression of many high a nity nitrate transporter NRT2 genes was altered under low nitrogen conditions.…”

Section: Discussioncontrasting

confidence: 99%

Insights into Nitrogen Metabolism in the Wild and Cultivated Lettuce as Revealed by Transcriptome and Weighted Gene Co-Expression Network Analysis.

Kumar

Eriksen

Šimko

et al. 2021

Preprint

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Large amounts of nitrogen fertilizers applied during lettuce production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (Lactuca sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressing genes (DEGs) were identified. Key enriched biological processes included photosynthesis, oxidation-reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor (ERF) family and basic helix-loop-helix (bHLH) family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis (WGCNA) we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II (PSII). Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen.

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“…In particular, the MAPK cascade is an evolutionarily conserved signal transduction module in plants. The MAPK signaling pathway is involved in the wheat plant response to low-N stress (Wen et al, 2015;Sultana et al, 2020; Figure 1). TaMPK14, a MAPK family gene in wheat, is characterized for its role in mediating the N starvation response.…”

Section: Ros Protein Kinases/phosphatases and Nomentioning

confidence: 99%

“…Plant hormones are important components of signal transduction for N stress (Sultana et al, 2020). A large body of studies has demonstrated the existence of interactions between N nutrition and auxin signaling and revealed the roles of auxin polar transport and signal transduction in the regulation of RSA modifications in response to N availability.…”

Section: Auxinmentioning

confidence: 99%

Signaling Responses to N Starvation: Focusing on Wheat and Filling the Putative Gaps With Findings Obtained in Other Plants. A Review

Kong

Zhang

et al. 2021

Front. Plant Sci.

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Wheat is one of the most important food crops worldwide. In recent decades, fertilizers, especially nitrogen (N), have been increasingly utilized to maximize wheat productivity. However, a large proportion of N is not used by plants and is in fact lost into the environment and causes serious environmental pollution. Therefore, achieving a low N optimum via efficient physiological and biochemical processes in wheat grown under low-N conditions is highly important for agricultural sustainability. Although N stress-related N capture in wheat has become a heavily researched subject, how this plant adapts and responds to N starvation has not been fully elucidated. This review summarizes the current knowledge on the signaling mechanisms activated in wheat plants in response to N starvation. Furthermore, we filled the putative gaps on this subject with findings obtained in other plants, primarily rice, maize, and Arabidopsis. Phytohormones have been determined to play essential roles in sensing environmental N starvation and transducing this signal into an adjustment of N transporters and phenotypic adaptation. The critical roles played by protein kinases and critical kinases and phosphatases, such as MAPK and PP2C, as well as the multifaceted functions of transcription factors, such as NF-Y, MYB, DOF, and WRKY, in regulating the expression levels of their target genes (proteins) for low-N tolerance are also discussed. Optimization of root system architecture (RSA) via root branching and thinning, improvement of N acquisition and assimilation, and fine-tuned autophagy are pivotal strategies by which plants respond to N starvation. In light of these findings, we attempted to construct regulatory networks for RSA modification and N uptake, transport, assimilation, and remobilization.

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Transcriptomic Study for Identification of Major Nitrogen Stress Responsive Genes in Australian Bread Wheat Cultivars

Cited by 39 publications

References 183 publications

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

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

Insights into Nitrogen Metabolism in the Wild and Cultivated Lettuce as Revealed by Transcriptome and Weighted Gene Co-Expression Network Analysis.

Signaling Responses to N Starvation: Focusing on Wheat and Filling the Putative Gaps With Findings Obtained in Other Plants. A Review

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