High throughput RNA sequencing of a hybrid maize and its parents shows different mechanisms responsive to nitrogen limitation

BackgroundDevelopment 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.ResultsA different set of genes were found to be N-responsive in the three genotypes. Many biological processes important for N metabolism such as the cellular nitrogen compound metabolic process and the cellular amino acid metabolic process were enriched in the N-responsive gene list from the hybrid shoots but not from the parental lines’ shoots. Coupled to this, sugar, carbohydrate, monosaccharide, glucose, and sorbitol transport pathways were all up-regulated in the hybrid, but not in the parents under N limitation. Expression patterns also differed between shoots and roots, such as the up-regulation of the cytokinin degradation pathway in the shoots of the hybrid and down-regulation of that pathway in the roots. The change of gene expression under N limitation in the hybrid resembled the parent with the higher NUE trait. The transcript abundances of alleles derived from each parent were estimated using polymorphic sites in mapped reads in the hybrid. While there were allele abundance differences, there was no correlation between these and the expression differences seen between the hybrid and the two parents.ConclusionsGene expression in two parental inbreds and the corresponding hybrid line in response to N limitation was surveyed using the mRNA-Seq technology. The data showed that the three genotypes respond very differently to N-limiting conditions, and the hybrid clearly has a unique expression pattern compared to its parents. Our results expand our current understanding of N responses and will help move us forward towards effective strategies to improve NUE and enhance crop production.

[1]  B. Ney,et al.  The challenge of improving nitrogen use efficiency in crop plants: towards a more central role for genetic variability and quantitative genetics within integrated approaches. , 2007, Journal of experimental botany.

[2]  S. Rothstein,et al.  Understanding plant response to nitrogen limitation for the improvement of crop nitrogen use efficiency. , 2011, Journal of experimental botany.

[3]  Rodrigo A Gutiérrez,et al.  Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1 , 2008, Proceedings of the National Academy of Sciences.

[4]  T. Zhu,et al.  Genome-wide analysis of Arabidopsis responsive transcriptome to nitrogen limitation and its regulation by the ubiquitin ligase gene NLA , 2007, Plant Molecular Biology.

[5]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[6]  William R. Raun,et al.  Improving Nitrogen Use Efficiency for Cereal Production , 1999 .

[7]  Rongchen Wang,et al.  Genomic Analysis of a Nutrient Response in Arabidopsis Reveals Diverse Expression Patterns and Novel Metabolic and Potential Regulatory Genes Induced by Nitrate , 2000, Plant Cell.

[8]  Yong-Mei Bi,et al.  A Developmental Transcriptional Network for Maize Defines Coexpression Modules1[C][W][OA] , 2013, Plant Physiology.

[9]  C. Masclaux-Daubresse,et al.  Exploring nitrogen remobilization for seed filling using natural variation in Arabidopsis thaliana , 2011, Journal of experimental botany.

[10]  Tong Zhu,et al.  Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis , 2007, BMC Genomics.

[11]  Rongchen Wang,et al.  Nitrite Acts as a Transcriptome Signal at Micromolar Concentrations in Arabidopsis Roots1[W][OA] , 2007, Plant Physiology.

[12]  H. Geiger,et al.  Improving Nitrogen‐Use Efficiency in European Maize , 2003 .

[13]  Francesca Chiaromonte,et al.  Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis , 2007, Genome Biology.

[14]  K. Sayre,et al.  Genetic progress in wheat yield and nitrogen use efficiency under four nitrogen rates , 1997 .

[15]  Lior Pachter,et al.  Identification of novel transcripts in annotated genomes using RNA-Seq , 2011, Bioinform..

[16]  Xianghua Li,et al.  Expression Profiles of 10,422 Genes at Early Stage of Low Nitrogen Stress in Rice Assayed using a cDNA Microarray , 2006, Plant Molecular Biology.

[17]  F. Daniel-Vedele,et al.  REVIEW: PART OF A SPECIAL ISSUE ON PLANT NUTRITION Nitrogen uptake, assimilation and remobilization in plants: challenges for sustainable and productive agriculture , 2010 .

[18]  S. Rothstein.  Returning to Our Roots: Making Plant Biology Research Relevant to Future Challenges in Agriculture , 2007, The Plant Cell Online.

[19]  Rafael A. Cañas,et al.  Can genetic variability for nitrogen metabolism in the developing ear of maize be exploited to improve yield? , 2012, The New phytologist.

[20]  Zhou Du,et al.  agriGO: a GO analysis toolkit for the agricultural community , 2010, Nucleic Acids Res..

[21]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[22]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[23]  O. Crasta,et al.  Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis , 2006, Theoretical and Applied Genetics.

[24]  G. Coruzzi,et al.  Nitrogen and carbon nutrient and metabolite signaling in plants. , 2001, Plant physiology.

[25]  Steven J. M. Jones,et al.  FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology , 2008, Bioinform..

[26]  LiHeng,et al.  The Sequence Alignment/Map format and SAMtools , 2009 .

[27]  Ashverya Laxmi,et al.  Global Transcription Profiling Reveals Multiple Sugar Signal Transduction Mechanisms in Arabidopsis , 2004, The Plant Cell Online.

[28]  J. Veyrieras,et al.  Genetic variation for N-remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. 3. QTL detection and coincidences , 2008, Theoretical and Applied Genetics.

[29]  P. Juskiw,et al.  Genetic Variability in Nitrogen Use Efficiency of Spring Barley , 2009 .

[30]  B. Andrieu,et al.  Nitrogen management and senescence in two maize hybrids differing in the persistence of leaf greenness: agronomic, physiological and molecular aspects. , 2005, The New phytologist.

[31]  A. Glass.  Nitrogen Use Efficiency of Crop Plants: Physiological Constraints upon Nitrogen Absorption , 2003 .

[32]  J. Harrow,et al.  Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene , 2013, Genome Biology.

[33]  Cole Trapnell,et al.  Improving RNA-Seq expression estimates by correcting for fragment bias , 2011, Genome Biology.

[34]  G. Weiller,et al.  A gene expression atlas of the model legume Medicago truncatula. , 2008, The Plant journal : for cell and molecular biology.

[35]  Liang Chen,et al.  Studying alternative splicing regulatory networks through partial correlation analysis , 2009, Genome Biology.

[36]  T. Ericsson.  Growth and shoot: root ratio of seedlings in relation to nutrient availability , 2004, Plant and Soil.

[37]  X. Yang,et al.  Gene Expression Biomarkers Provide Sensitive Indicators of in Planta Nitrogen Status in Maize[W][OA] , 2011, Plant Physiology.

[38]  N. Friedman,et al.  Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.

[39]  Y. Fukuta,et al.  Genetic variations in dry matter production and physiological nitrogen use efficiency in rice (Oryza sativa L.) varieties , 2009 .

[40]  S. Rothstein,et al.  Over-expression of STP13, a hexose transporter, improves plant growth and nitrogen use in Arabidopsis thaliana seedlings. , 2009, Plant, cell & environment.

[41]  Mark Stitt,et al.  Genome-Wide Reprogramming of Primary and Secondary Metabolism, Protein Synthesis, Cellular Growth Processes, and the Regulatory Infrastructure of Arabidopsis in Response to Nitrogen1[w] , 2004, Plant Physiology.

[42]  D. Beghin,et al.  Genetic differences for nitrogen uptake and nitrogen utilisation efficiencies in winter wheat. , 2000 .

[43]  G. Coruzzi,et al.  Cell-specific nitrogen responses mediate developmental plasticity , 2008, Proceedings of the National Academy of Sciences.

[44]  Hitoshi Sakakibara,et al.  Interactions between nitrogen and cytokinin in the regulation of metabolism and development. , 2006, Trends in plant science.

[45]  Roger Sylvester-Bradley,et al.  Analysing nitrogen responses of cereals to prioritize routes to the improvement of nitrogen use efficiency. , 2009, Journal of experimental botany.

[46]  Rongchen Wang,et al.  Microarray Analysis of the Nitrate Response in Arabidopsis Roots and Shoots Reveals over 1,000 Rapidly Responding Genes and New Linkages to Glucose, Trehalose-6-Phosphate, Iron, and Sulfate Metabolism1[w] , 2003, Plant Physiology.

[47]  Rafael A. Cañas,et al.  Nitrogen metabolism in the developing ear of maize (Zea mays): analysis of two lines contrasting in their mode of nitrogen management. , 2009, The New phytologist.

[48]  T. Brutnell,et al.  Exploring plant transcriptomes using ultra high-throughput sequencing. , 2010, Briefings in functional genomics.

[49]  Gloria M Coruzzi,et al.  Genome-wide patterns of carbon and nitrogen regulation of gene expression validate the combined carbon and nitrogen (CN)-signaling hypothesis in plants , 2004, Genome Biology.

[50]  Sandrine Dudoit,et al.  Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments , 2010, BMC Bioinformatics.

[51]  F. Wilcoxon.  Individual Comparisons by Ranking Methods , 1945 .

[52]  S. Krawetz,et al.  Identification of artifactual microarray probe signals constantly present in multiple sample types. , 2012, BioTechniques.

[53]  H. Keulen,et al.  Quantifying N response and N use efficiency in rice–wheat (RW) cropping systems under different water management , 2009, The Journal of Agricultural Science.

[54]  C. Masclaux-Daubresse,et al.  Exploring NUE in crops and in Arabidopsis ideotypes to improve yield and seed quality. , 2012, Journal of experimental botany.

[55]  R. C. Muchow.  NITROGEN UTILIZATION EFFICIENCY IN MAIZE AND GRAIN SORGHUM , 1998 .

[56]  S. Rothstein,et al.  Exploring the Molecular and Metabolic Factors Contributing to the Adaptation of Maize Seedlings to Nitrate Limitation , 2011, Front. Plant Sci..

[57]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[58]  H. Geiger,et al.  Improving Nitrogen-Use Efficiency in European Maize : Estimation of Quantitative Genetic Parameters , 2003 .

[59]  A. Good,et al.  Can less yield more? Is reducing nutrient input into the environment compatible with maintaining crop production? , 2004, Trends in plant science.