scholarly journals Comparative Transcriptome Analysis Reveals Different Low-Nitrogen-Responsive Genes in Pepper Cultivars

Horticulturae ◽  
2021 ◽  
Vol 7 (5) ◽  
pp. 110
Author(s):  
Chunping Wang ◽  
Yifei Li ◽  
Wenqin Bai ◽  
Xiaomiao Yang ◽  
Hong Wu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Stress Response ◽  
Molecular Mechanisms ◽  
Tricarboxylic Acid Cycle ◽  
Rna Seq ◽  
N Metabolism ◽  
Use Efficiency ◽  
N Starvation ◽  
Low Nitrogen ◽  
N Use

The molecular mechanisms underlying the variation in N-use efficiency (NUE) in pepper (Capsicum annuum L.) genotypes are poorly understood. In this work, two genotypes (750-1, low-N tolerant; ZCFB, low-N sensitive) with contrasting low-N tolerance were selected from 100 pepper cultivars on the basis of their relative leaf areas, shoot dry weights, root dry weights, and plant dry weights at the seedling stage. Subsequently, using RNA-Seq, the transcriptome of these two pepper genotypes under N starvation for 28 days was analyzed. We detected 2621/2470 and 3936/4218 different expressed genes (DEGs) in the leaves/roots of 750-1 and ZCFB, respectively. The changes in the expression of basic N metabolism genes were similar between 750-1 and ZCFB. However, different DEGs not directly involved in N metabolism were identified between the 750-1 and ZCFB cultivars. In 750-1, 110 unique DEGs were detected in the leaves, of which 103 were down-regulated, including genes associated with protein metabolism, photosynthesis, secondary metabolism, cell wall metabolism, stress response, and disease resistance. In ZCFB, 142 unique DEGs were detected in the roots, of which 117 were up-regulated, resulting in enhancement of processes such as protein degradation, secondary metabolites synthesis, lipid metabolism, endocytosis, the tricarboxylic acid cycle (TCA), transcriptional regulation, stress response, and disease resistance. Our results not only facilitate an understanding of the different regulatory process in low-N-tolerant and low-N-sensitive pepper cultivars, but also provide abundant candidate genes for improving the low-N tolerance of pepper cultivars.

scholarly journals The Role of Gibberellins in Regulation of Nitrogen Uptake and Physiological Traits in Maize Responding to Nitrogen Availability

2020 ◽  
Vol 21 (5) ◽  
pp. 1824
Author(s):  
Yubin Wang ◽  
Qingqing Yao ◽  
Yushi Zhang ◽  
Yuexia Zhang ◽  
Jiapeng Xing ◽  
...  
Keyword(s):  
Nitrogen Availability ◽  
Physiological Responses ◽  
N Uptake ◽  
Nitrogen Supply ◽  
Rna Seq ◽  
Uptake Capacity ◽  
Use Efficiency ◽  
Low Nitrogen ◽  
N Use

Modified gibberellin (GA) signaling leads to semi-dwarfism with low nitrogen (N) use efficiency (NUE) in crops. An understanding of GA-mediated N uptake is essential for the development of crops with improved NUE. The function of GA in modulating N uptake capacity and nitrate (NO3−) transporters (NRTs) was analyzed in the GA synthesis-deficient mutant zmga3ox grown under low (LN) and sufficient (SN) N conditions. LN significantly suppressed the production of GA1, GA3, and GA4, and the zmga3ox plants showed more sensitivity in shoots as well as LN stress. Moreover, the higher anthocyanin accumulation and the decrease of chlorophyll content were also recorded. The net NO3− fluxes and 15N content were decreased in zmga3ox plants under both LN and SN conditions. Exogenous GA3 could restore the NO3− uptake in zmga3ox plants, but uniconazole repressed NO3− uptake. Moreover, the transcript levels of ZmNRT2.1/2.2 were downregulated in zmga3ox plants, while the GA3 application enhanced the expression level. Furthermore, the RNA-seq analyses identified several transcription factors that are involved in the GA-mediated transcriptional operation of NRTs related genes. These findings revealed that GAs influenced N uptake involved in the transcriptional regulation of NRTs and physiological responses in maize responding to nitrogen supply.

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

Biology ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1126
Author(s):  
Xinbo Zhang ◽  
Quan Ma ◽  
Fujian Li ◽  
Yonggang Ding ◽  
Yuan Yi ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Nitrogen Use Efficiency ◽  
Molecular Mechanisms ◽  
Nitrogen Deficiency ◽  
Genotypic Difference ◽  
Rna Seq ◽  
Transcriptional Responses ◽  
Nitrogen Use ◽  
Use Efficiency ◽  
Upregulated Genes

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.

scholarly journals Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Qinjun Huang ◽  
Weixi Zhang ◽  
Changjun Ding ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Nitrogen Use Efficiency ◽  
Populus Deltoides ◽  
Hub Genes ◽  
Nitrogen Use ◽  
Group A ◽  
Use Efficiency ◽  
N Starvation ◽  
Low Nitrogen

Abstract Background Nitrogen (N) is one of the main factors limiting the wood yield in poplar cultivation. Understanding the molecular mechanism of N utilization could play a guiding role in improving the nitrogen use efficiency (NUE) of poplar. Results In this study, three N-efficient genotypes (A1-A3) and three N-inefficient genotypes (C1-C3) of Populus deltoides were cultured under low N stress (5 μM NH4NO3) and normal N supply (750 μM NH4NO3). The dry matter mass, leaf morphology, and chlorophyll content of both genotypes decreased under N starvation. The low nitrogen adaptation coefficients of the leaves and stems biomass of group A were significantly higher than those of group C (p < 0.05). Interestingly, N starvation induced fine root growth in group A, but not in group C. Next, a detailed time-course analysis of enzyme activities and gene expression in leaves identified 2062 specifically differentially expressed genes (DEGs) in group A and 1118 in group C. Moreover, the sensitivity to N starvation of group A was weak, and DEGs related to hormone signal transduction and stimulus response played an important role in the low N response this group. Weighted gene co-expression network analysis identified genes related to membranes, catalytic activity, enzymatic activity, and response to stresses that might be critical for poplar’s adaption to N starvation and these genes participated in the negative regulation of various biological processes. Finally, ten influential hub genes and twelve transcription factors were identified in the response to N starvation. Among them, four hub genes were related to programmed cell death and the defense response, and PodelWRKY18, with high connectivity, was involved in plant signal transduction. The expression of hub genes increased gradually with the extension of low N stress time, and the expression changes in group A were more obvious than those in group C. Conclusions Under N starvation, group A showed stronger adaptability and better NUE than group C in terms of morphology and physiology. The discovery of hub genes and transcription factors might provide new information for the analysis of the molecular mechanism of NUE and its improvement in poplar.

scholarly journals Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12492
Author(s):  
Xun Liu ◽  
Xinxia Yang ◽  
Bin Zhang
Keyword(s):  
Salt Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Functional Identification ◽  
Salt Stress Response ◽  
Soybean Seedlings

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

Agronomic performance of maize (Zea mays L.) breeding lines derived from a low nitrogen maize population

2003 ◽  
Vol 141 (2) ◽  
pp. 221-230 ◽  
Author(s):  
A. Y. KAMARA ◽  
J. G. KLING ◽  
A. MENKIR ◽  
O. IBIKUNLE
Keyword(s):  
Zea Mays ◽  
N Uptake ◽  
N Use Efficiency ◽  
Agronomic Performance ◽  
N Accumulation ◽  
Breeding Lines ◽  
Use Efficiency ◽  
Low Nitrogen ◽  
N Use ◽  
Pulling Resistance

Eighteen S1 lines of maize (Zea mays L.) derived from a low nitrogen tolerant pool and two inbred lines were evaluated for agronomic performance under moderate N conditions in the southern Guinea savannah of Nigeria. Generally, the breeding lines differed in yield, growth, vertical root-pulling resistance, N-uptake and N-use efficiency. Breeding lines with high vertical root-pulling resistance took up more N and utilized it more efficiently. They also showed better agronomic performance and recorded higher yields. Principal component and cluster analyses classified the breeding lines into six groups. The results of principal components analyses (PCA) suggest that the most important variables for the classification of the S1 lines were grain yield, plant height, total dry matter during the grain-filling period and at maturity, N-accumulation, N-uptake and N-use efficiency. Other important traits were days to silking, anthesis-silking interval, ears per plant, harvest index and vertical root-pulling resistance. Two groups containing a total of 14 S1 lines that had higher agronomic performance than others are recommended for further evaluation under severe N stress to ascertain their tolerance of low N stress before recombination to form a new population for the next cycle of selection.

Physiological analysis of nitrogen-efficient rice overexpressing alanine aminotransferase under different N regimes

Botany ◽  
2013 ◽  
Vol 91 (12) ◽  
pp. 866-883 ◽  
Author(s):  
Perrin H. Beatty ◽  
Rebecka T. Carroll ◽  
Ashok K. Shrawat ◽  
David Guevara ◽  
Allen G. Good
Keyword(s):  
Transgenic Rice ◽  
Nitrogen Use Efficiency ◽  
Alanine Aminotransferase ◽  
Nitrogen Use ◽  
Physiological Analysis ◽  
Use Efficiency ◽  
Amino Acid Levels ◽  
Transcriptome Response ◽  
Low Nitrogen ◽  
N Use

Cereal crop plants have low nitrogen (N) use efficiency, taking up only 30% to 50% of the applied N fertilizers, with the rest having the potential for loss into the environment as N pollution. One way to address this problem is to improve the nitrogen use efficiency of cereal crops using a transgenic approach. We developed alanine aminotransferase overexpressing rice, and we have previously determined that this modification provided an improved nitrogen-use phenotype to the engineered plants. In this study, the transgenic rice were grown in low, medium, and high nitrogen supply, and morphology, plant N levels, enzymatic activity, metabolite levels, and transcriptome response in the roots and shoots at active and maximum tillering at each N level were measured. The transcriptome response was analysed further using MapMan and PageMan to view multiple comparisons. The transgenic rice plants showed improved nitrogen use efficiency at medium and high N supply, but with few significant changes to the amino acid levels or to the transcriptome. The transgenic plants grown in high N showed up-regulation of transcripts associated with photosynthesis, non-melavonate pathway secondary metabolites, protein degradation, and many unknown function transcripts.

scholarly journals Rapid Generation and Analysis of a Barley Doubled Haploid Line with Higher Nitrogen Use Efficiency Than Parental Lines by F1 Microspore Embryogenesis

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1588
Author(s):  
Hongwei Xu ◽  
Yingbo Li ◽  
Runhong Gao ◽  
Rugen Xu ◽  
Guimei Guo ◽  
...  
Keyword(s):  
Nitrogen Use Efficiency ◽  
Doubled Haploid ◽  
Molecular Mechanisms ◽  
Field Experiments ◽  
Microspore Embryogenesis ◽  
Doubled Haploid Line ◽  
Mapk Signaling ◽  
Nitrogen Use ◽  
Use Efficiency ◽  
Low Nitrogen

Creating varieties with high nitrogen use efficiency (NUE) is crucial for sustainable agriculture development. In this study, a superior barley doubled haploid line (named DH45) with improved NUE was produced via F1 microspore embryogenesis with three rounds of screening in different nitrogen levels by hydroponic and field experiments. The molecular mechanisms responsible for the NUE of DH45 surpassing that of its parents were investigated by RNA-seq analysis. A total of 1027 differentially expressed genes (DEGs) were identified that were up- or down-regulated in DH45 under low nitrogen conditions but showed no significant differences in the parents. GO analysis indicated that genes involved in nitrogen compound metabolic processes were significantly enriched in DH45 compared with the parents. KEGG analysis showed the MAPK signaling pathway plant to be highly enriched in DH45 relative to its parents, as well as genes involved in alanine, aspartate and glutamate metabolism, and arginine biosynthesis. In conclusion, our study revealed the potential to fix trait superiority in a line by combining crossing with F1 microspore culture technologies in future crop breeding and also identified several candidate genes that are expressed in shoots and may enable barley to cope with low-nitrogen stress.

scholarly journals Integrated RNA-seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

2020 ◽  
Vol 21 (13) ◽  
pp. 4615 ◽  
Author(s):  
Weilong Kong ◽  
Chenhao Zhang ◽  
Yalin Qiang ◽  
Hua Zhong ◽  
Gangqing Zhao ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Stress Response ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Growth And Yield ◽  
Rna Seq ◽  
Cold Tolerant ◽  
Stress Related Genes ◽  
Qtls Mapping

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

scholarly journals Cyanobacterial NOS expression improves nitrogen use efficiency, nitrogen-deficiency tolerance and yield in Arabidopsis

2020 ◽  
Author(s):  
Del Castello Fiorella ◽  
Foresi Noelia ◽  
Nejamkin Andrés ◽  
Lindermayr Christian ◽  
Buegger Franz ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Seed Production ◽  
N Uptake ◽  
Nitrogen Deficiency ◽  
N Assimilation ◽  
N Metabolism ◽  
Use Efficiency ◽  
Oxide Synthase ◽  
Positive Effect ◽  
N Use

ABSTRACTDeveloping strategies to improve nitrogen (N) use efficiency (NUE) in plants is a challenge to reduce environmental problems linked to over-fertilization. The nitric oxide synthase (NOS) enzyme from the cyanobacteria Synechococcus PCC 7335 (SyNOS) has been recently identified and characterized. SyNOS catalyzes the conversion of arginine to citrulline and nitric oxide (NO), and then 70% of the produced NO is rapidly oxidized to nitrate by an unusual globin domain in its 5'-terminus. In this study, we assessed whether SyNOS expression in plants affects N metabolism improving NUE and yield. Our results showed that transgenic Arabidopsis plants had higher primary shoot length and shoot branching when grown in N-deficient conditions and higher seed production in N-sufficient and -deficient conditions. Moreover, transgenic plants showed significantly increased NUE in both N conditions. No differences were observed in N uptake for SyNOS lines. However, SyNOS lines presented an increase in N assimilation/remobilization under low N conditions. In addition, SyNOS lines had greater N-deficiency tolerance compared to wt plants. Our results support that SyNOS expression generates a positive effect on N metabolism and seed production in Arabidopsis, and it might be envisaged as a strategy to improve productivity in crops under adverse N environments.

scholarly journals Genome-Wide Investigation of the Role of MicroRNAs in Desiccation Tolerance in the Resurrection Grass Tripogon loliiformis

Plants ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 68 ◽  
Author(s):  
Isaac Njaci ◽  
Brett Williams ◽  
Claudia Castillo-González ◽  
Martin Dickman ◽  
Xiuren Zhang ◽  
...  
Keyword(s):  
Stress Response ◽  
Water Use Efficiency ◽  
Water Use ◽  
Desiccation Tolerance ◽  
Molecular Mechanisms ◽  
Crop Improvement ◽  
Resurrection Plant ◽  
Small Rna Sequencing ◽  
Use Efficiency

Drought causes approximately two-thirds of crop and yield loss worldwide. To sustain future generations, there is a need to develop robust crops with enhanced water use efficiency. Resurrection plants are naturally resilient and tolerate up to 95% water loss with the ability to revive upon watering. Stress is genetically encoded and resilient species may garner tolerance by tightly regulating the expression of stress-related genes. MicroRNAs (miRNAs) post-transcriptionally regulate development and other stress response processes in eukaryotes. However, their role in resurrection plant desiccation tolerance is poorly understood. In this study, small RNA sequencing and miRNA expression profiling was conducted using Tripogon loliiformis plants subjected to extreme water deficit conditions. Differentially expressed miRNA profiles, target mRNAs, and their regulatory processes were elucidated. Gene ontology enrichment analysis revealed that development, stress response, and regulation of programmed cell death biological processes; Oxidoreductase and hydrolyase molecular activities; and SPL, MYB, and WRKY transcription factors were targeted by miRNAs during dehydration stress, indicating the indispensable regulatory role of miRNAs in desiccation tolerance. This study provides insights into the molecular mechanisms of desiccation tolerance in the resurrection plant T. loliiformis. This information will be useful in devising strategies for crop improvement on enhanced drought tolerance and water use efficiency.

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