Oryza sativa Indica Group cultivar:Aditya and Vikramarya
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ABSTRACT:
PROVIDER: PRJNA987388 | ENA |
REPOSITORIES: ENA
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Project description:The development of crop genotypes with high nitrogen utilization efficiency (NUE) under low nitrogen (LN) conditions is of great significance for ensuring food security worldwide. However, different crops have different responses to LN stress, and the regulatory mechanisms involved remain unclear. Comparative transcriptomic of wheat genotypes with contrasting NUE is a strategy to reveal the genetic mechanism of wheat in response to LN stress. In this study, we employed RNA-sequencing (RNA-seq) to investigate the difference between the transcriptome profiles of two wheat genotypes differing in NUE under different N treatments. The results indicated that wheat with high and low NUE genotypes exhibited different gene expression patterns under LN conditions. To identify potential key genes, we classify these N-responsive genes into two major categories: pre-expressed genes and stress-expressed genes. In total, the pre-expressed genes identified in the genotypes with high NUE were 2.97 times that of wheat with low NUE. In summary, the identified candidate genes may provide new insights into comprehensive understanding of the genotypic difference and improving NUE in wheat.
2026-08-21 | GSE319103 | GEO
Project description:Nitrogen (N) is an essential macronutrient for agricultural production, and its excessive use causes not only economic but also environmental damage. However, improving nitrogen use efficiency (NUE) remains a complex task for achieving more productive crops under conditions of limited nitrogen availability. To the best of our knowledge, this is the first study aiming to integrate the morphophysiological responses and proteomic profiles of leaves and roots of popcorn (Zea mays everta). For this, two inbred lines contrasting for NUE, i.e., P2 (high NUE) and L80 (low NUE), were cultivated under high (100% of N supply) and low (10% of N supply) nitrogen conditions. Morphological and physiological traiits such as photochemical quenching (qP), non-photochemical quenching (NPQ), quantum yield of photosystem II (ΦPSII), and potential photosynthesis (Apot) were evaluated. P2 showed more pronounced vegetative growth under low N, as well as higher values of qP, NPQ, and ΦPSII. Comparative proteomic analysis of the leaves identified 215 differentially accumulated proteins (DAPs) in P2 and 168 DAPs in L80, while in roots, 127 DAPs were observed in P2 and 172 in L80. In leaves, DAPs involved in the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, DAPs involved in nitrate transport, ammonium assimilation, and amino acid metabolism seem to have contributed to the improved NUE in P2. This study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.
2025-03-11 | PXD048990 | Pride
Project description:Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the nitrogen application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. The use of near-isogenic lines (NILs) in transcriptome analysis can reduce genetic background noise. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling in NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions. The results showed that 7,023 DEGs (4,738 up-regulated and 2,285 down-regulated) were identified in the 1Y vs 1W comparison. The responses of 1Y and 1W to normal nitrogen differed significantly in the transcriptional regulation mechanisms. Several genes belonging to the GS and GOGAT gene families were up-regulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members such as ERF, WRKY, NAC, and MYB were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE
2021-08-31 | GSE179179 | GEO
Project description:Nitrogen availability strongly influences sorghum growth, physiology, and yield, making enhanced nitrogen use efficiency (NUE) critical for agricultural sustainability. To characterize transcriptional responses to nitrate availability in sorghum, we profiled genome-wide gene expression changes under nitrate-sufficient, nitrate-limiting, and nitrate-recovery conditions. This dataset provides temporal resolution of nitrate-responsive regulation in roots and leaves, enabling comparative insights into nitrogen signaling and assimilation.
2025-12-30 | GSE312411 | GEO
Project description:Drought responsive transcriptome profiling in roots of contrasting rice genotypes IR20 and Nootripathu
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Project description:Transcriptome Profiling Reveals Differences in Key Genes between Wheat Genotypes with Contrasting Nitrogen Use Efficiency (NUE) in Response to Nitrogen Deficiency
| PRJNA1422093 | ENA
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).
2014-05-01 | GSE54705 | GEO
Project description:Among the mineral elements necessary for plant growth, nitrogen (N) is the macronutrient required in larger amounts. The optimization of N use efficiency (NUE) in maize could be obtained through both genetic improvement and agronomic practices in order to enhance production and reduce the negative impact of the N fertilizer use on the environment. Physiological characterizations of inbred lines with different NUE are available in maize.
2014-05-19 | GSE49681 | GEO
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). RNAseq deep sequencing
2014-05-01 | E-GEOD-54705 | biostudies-arrayexpress
Project description:Development of crop varieties with high nitrogen use efficiency (NUE) is crucial for minimizing N loss, reducing environmental pollution and decreasing input cost. Maize is one of the most important crops cultivated worldwide and its productivity is closely linked to the amount of fertilizer used. A survey of the transcriptomes of shoot and root tissues of a maize hybrid line and its two parental inbred lines grown under sufficient and limiting N conditions by mRNA-Seq has been conducted to have a better understanding of how different maize genotypes respond to N limitation.
2014-01-09 | E-MTAB-4410 | biostudies-arrayexpress