Early molecular events associated with nitrogen deficiency in rice seedling roots

Hsieh, Ping-Han; Kan, Chia-Cheng; Wu, Hsin-Yu; Yang, Hsiu-Chun; Hsieh, Ming‐Hsiun

doi:10.1038/s41598-018-30632-1

Cited by 89 publications

(67 citation statements)

References 88 publications

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“…However, when KNO 3 or NH 4 Cl was resupplied, it was gradually decreased to basal level within 24 hours while KCl control treatment did not alter OsNLP1 transcript level (Fig. 1I and J), consistent with the previous report that OsNLP1 was induced by N starvation in rice roots (Hsieh et al, 2018). All these data imply that OsNLP1 is N responsive and may play some roles in N utilization or signaling…”

Section: Resultssupporting

confidence: 91%

RiceNIN-LIKE PROTEIN 1Rapidly Responds to Nitrogen Deficiency and Improves Yield and Nitrogen Use Efficiency

Alfatih

Zhang

et al. 2020

Preprint

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Nitrogen (N) is indispensable for crop growth and yield, but excessive agricultural application of nitrogenous fertilizers has generated severe environmental problems. A desirable and economical solution to cope with these issues is to improve crop nitrogen use efficiency (NUE). Plant NUE has been a focal point of intensive research worldwide, yet much more has to be learned about its genetic determinants and regulation. Here, we show that rice NIN-LIKE PROTEIN 1 (OsNLP1) plays a fundamental role in N utilization. OsNLP1 protein localizes in nucleus and its transcript level is rapidly induced by N starvation. Overexpression of OsNLP1 improves plant growth, grain yield and NUE under different N conditions while knockout of OsNLP1 impairs grain yield and NUE under N limiting conditions. OsNLP1 regulates nitrate and ammonium utilization by cooperatively orchestrating multiple N uptake and assimilation genes. Chromatin immunoprecipitation and yeast-one-hybrid assays show that OsNLP1 can directly bind to the promoter of these genes to activate their expression. Therefore, our results demonstrate that OsNLP1 is a key regulator of N utilization and represents a potential target for improving NUE and yield in rice.One-sentence summaryOsNLP1 rapidly responds to N availability, enhances N uptake and assimilation, and holds great potential in promoting high yield in rice.

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Section: Resultssupporting

confidence: 91%

RiceNIN-LIKE PROTEIN 1Rapidly Responds to Nitrogen Deficiency and Improves Yield and Nitrogen Use Efficiency

Alfatih

Zhang

et al. 2020

Preprint

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show abstract

“…Nitrogen fertilizer is critical for grain yield and seed quality in many crops, such as wheat, rice, and maize [ 19 , 24 , 25 ]. Moreover, a previous study reported changes of metabolism pathways in rice seedling roots in response to nitrogen deficiency [ 26 ]. However, effects of nitrogen level during seed production on seed vigor are largely unknown in wheat.…”

Section: Discussionmentioning

confidence: 99%

Effects of Nitrogen Level during Seed Production on Wheat Seed Vigor and Seedling Establishment at the Transcriptome Level

Wen

Xie

et al. 2018

IJMS

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Nitrogen fertilizer is a critical determinant of grain yield and seed quality in wheat. However, the mechanism of nitrogen level during seed production affecting wheat seed vigor and seedling establishment at the transcriptome level remains unknown. Here, we report that wheat seeds produced under different nitrogen levels (N0, N168, N240, and N300) showed significant differences in seed vigor and seedling establishment. In grain yield and seed vigor, N0 and N240 treatments showed the minimum and maximum, respectively. Subsequently, we used RNA-seq to analyze the transcriptomes of seeds and seedlings under N0 and N240 at the early stage of seedling establishment. Gene Ontology (GO) term enrichment analysis revealed that dioxygenase-activity-related genes were dramatically upregulated in faster growing seedlings. Among these genes, the top three involved linoleate 9S-lipoxygenase (Traes_2DL_D4BCDAA76, Traes_2DL_CE85DC5C0, and Traes_2DL_B5B62EE11). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that pathways involved in nutrient mobilization and the antioxidant system showed enhanced expression under N240. Moreover, seeds with faster growing seedlings had a higher gene expression level of α-amylase, which was consistent with α-amylase activity. Taken together, we propose a model for seedling establishment and seed vigor in response to nitrogen level during seed production.

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“…Recently, researchers have found that multiple protein genes are related to nitrogen use efficiency in rice.OsCPK12 participates in the response signal pathway of low nitrogen stress, and overexpression of OsCPK12 enhances rice growth under low nitrogen conditions [59] . Hsieh et al [60] found that the N-regulated genes, Os02g0120100, Os02g0807000 and Os06g0692600 etc., which encode transcription factors, protein kinases and protein phosphatases and may be involved in the regulation of early −N responses in rice roots. The serine/threonine/tyrosine (STY) protein kinase, ACTPK1, enhances ammonium uptake and use, and promotes growth of rice seedlings under sufficient ammonium [61] .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

Xiao-ling

Xia

Zeng

et al. 2020

Preprint

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Background: Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family are involved in nitrate uptake and transport. Here, we identied PTR gene family in rice and analyzed their expression level in near-isogenic lines. Results: We identified 96, 85 and 78 PTR genes in Nipponbare, R498and Oryza glaberrima , and the phylogenetic were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanuts (125) and soybeans (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons , and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-Seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-Seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice nitrogen uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. Conclusions: In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in riceNUE, and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.

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Early molecular events associated with nitrogen deficiency in rice seedling roots

Cited by 89 publications

References 88 publications

RiceNIN-LIKE PROTEIN 1Rapidly Responds to Nitrogen Deficiency and Improves Yield and Nitrogen Use Efficiency

RiceNIN-LIKE PROTEIN 1Rapidly Responds to Nitrogen Deficiency and Improves Yield and Nitrogen Use Efficiency

Effects of Nitrogen Level during Seed Production on Wheat Seed Vigor and Seedling Establishment at the Transcriptome Level

Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

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