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

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.

Short-term transcriptomic analysis at organ scale reveals candidate genes involved in low N responses in NUE-contrasting tomato genotypes

“…Transcription factors (TFs), which usually represent around 6% of coding sequences within a plant genome, are important regulators of plant signal transduction pathways under plant nutritional stress (Canales et al, 2014;Hoang et al, 2017). Among them, many TF families such as MYB, bHLH, bZIP, DOF, ERF, FAR1, GLK, NF-YA, NF-YB, and LOB were reported to be involved in plant N deficiency responses (Hao et al, 2011;Goel et al, 2018;Subudhi et al, 2020) and in coordination of nitrogen metabolism enzymes regulation (Zhang J. et al 2020;Zhang X. et al 2021). In our analysis, TFs belonging to the basic helix-loop-helix (bHLH) and Golden2-like (GLK) families were upregulated in RO shoots in early response to LN resupply (Figure 3C).…”

Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency

“…The current knowledge of plant response to low N conditions at the expression level have been mostly obtained in the model plant Arabidopsis thaliana (Krapp et al 2011, Balazadeh et al 2014, Luo et al 2020) or row crops such as durum wheat (Curci et al 2017), wheat (Zhang et al 2021), rapeseed (Ahmad et al 2022), or rice (Shin et al 2018). However, limited information is available on vegetables such as tomato.…”

An Integrated Analysis of Metabolome, Transcriptome, and Physiology Revealed the Molecular and Physiological Response of Citrus sinensis Roots to Prolonged Nitrogen Deficiency

“…Since the adaptive response of plants to N deprivation can be reflected by N starvation-responsive genes and metabolites, it is meaningful to conduct a comprehensive analysis of transcriptome and metabolome to clarify the metabolic and molecular mechanisms of plant adaptions to N starvation. Some researchers investigated N starvation-responsive genes in potato [ 15 ], wheat [ 16 ], Panicum miliaceum [ 17 ], rice [ 18 ], maize [ 19 ], and rapeseed [ 20 ]; and N starvation-responsive metabolites in Isatis indigotica [ 21 ], soybean [ 22 ], tea [ 9 ], and rapeseed [ 23 ]. Few researchers used a comprehensive analysis of transcriptome and metabolome to examine N starvation-responsive genes and metabolites in rice [ 24 ], soybean [ 25 ], poplar [ 26 ], barely [ 27 ], maize [ 14 ], apple [ 28 ], and Arabidopsis thaliana [ 29 ].…”