Transcriptomic basis for drought-resistance in Brassica napus L.

Based on transcriptomic data from four experimental settings with drought-resistant and drought-sensitive cultivars under drought and well-watered conditions, statistical analysis revealed three categories encompassing 169 highly differentially expressed genes (DEGs) in response to drought in Brassica napus L., including 37 drought-resistant cultivar-related genes, 35 drought-sensitive cultivar-related genes and 97 cultivar non-specific ones. We provide evidence that the identified DEGs were fairly uniformly distributed on different chromosomes and their expression patterns are variety specific. Except commonly enriched in response to various stimuli or stresses, different categories of DEGs show specific enrichment in certain biological processes or pathways, which indicated the possibility of functional differences among the three categories. Network analysis revealed relationships among the 169 DEGs, annotated biological processes and pathways. The 169 DEGs can be classified into different functional categories via preferred pathways or biological processes. Some pathways might simultaneously involve a large number of shared DEGs, and these pathways are likely to cross-talk and have overlapping biological functions. Several members of the identified DEGs fit to drought stress signal transduction pathway in Arabidopsis thaliana. Finally, quantitative real-time PCR validations confirmed the reproducibility of the RNA-seq data. These investigations are profitable for the improvement of crop varieties through transgenic engineering.

[1]  R. Munns,et al.  Mechanisms of salt tolerance in nonhalophytes. , 1980 .

[2]  Richard A. Johnson,et al.  Applied Multivariate Statistical Analysis , 1983 .

[3]  Ecker.  The ethylene signal transduction pathway in plants , 1995, Science.

[4]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[5]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  Albert,et al.  Emergence of scaling in random networks , 1999, Science.

[7]  Y. Benjamini,et al.  THE CONTROL OF THE FALSE DISCOVERY RATE IN MULTIPLE TESTING UNDER DEPENDENCY , 2001 .

[8]  D. Bartels,et al.  Drought- and desiccation-induced modulation of gene expression in plants. , 2002, Plant, cell & environment.

[9]  Jian-Kang Zhu,et al.  Cell Signaling during Cold, Drought, and Salt Stress Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.000596. , 2002, The Plant Cell Online.

[10]  Jian-Kang Zhu,et al.  Salt and drought stress signal transduction in plants. , 2002, Annual review of plant biology.

[11]  T. Koshiba,et al.  Complex regulation of ABA biosynthesis in plants. , 2002, Trends in plant science.

[12]  S. Mangan,et al.  Structure and function of the feed-forward loop network motif , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  A. Kamei,et al.  Molecular responses to drought, salinity and frost: common and different paths for plant protection. , 2003, Current opinion in biotechnology.

[14]  Plant AP2/ERF transcription factors , 2003 .

[15]  R. Sunkar,et al.  Overexpression of a stress-inducible aldehyde dehydrogenase gene from Arabidopsis thaliana in transgenic plants improves stress tolerance. , 2003, The Plant journal : for cell and molecular biology.

[16]  Viswanathan Chinnusamy,et al.  Molecular genetic perspectives on cross-talk and specificity in abiotic stress signalling in plants. , 2003, Journal of experimental botany.

[17]  D. Hegedus,et al.  Molecular characterization of Brassicanapus NAC domain transcriptional activators induced in response to biotic and abiotic stress , 2003, Plant Molecular Biology.

[18]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[19]  David Botstein,et al.  GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes , 2004, Bioinform..

[20]  Andrea Pitzschke,et al.  Emerging MAP kinase pathways in plant stress signalling. , 2005, Trends in plant science.

[21]  Mayra Rodríguez,et al.  Molecular aspects of abiotic stress in plants , 2005 .

[22]  Yi-feng Chen,et al.  Ethylene signal transduction. , 2005, Annals of botany.

[23]  Weixiong Zhang,et al.  Cis-regulatory element based targeted gene finding: genome-wide identification of abscisic acid- and abiotic stress-responsive genes in Arabidopsis thaliana , 2005, Bioinform..

[24]  Nobuhiro Suzuki,et al.  Enhanced Tolerance to Environmental Stress in Transgenic Plants Expressing the Transcriptional Coactivator Multiprotein Bridging Factor 1c1[w] , 2005, Plant Physiology.

[25]  M. Martínez-Ripoll,et al.  The structure of the Arabidopsis thaliana SOS3: molecular mechanism of sensing calcium for salt stress response. , 2005, Journal of molecular biology.

[26]  L. Sweetlove,et al.  The Mitochondrial Type II Peroxiredoxin F Is Essential for Redox Homeostasis and Root Growth of Arabidopsis thaliana under Stress* , 2005, Journal of Biological Chemistry.

[27]  L. Xiong,et al.  Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance , 2006, Genetics.

[28]  M. Haslbeck,et al.  Identification and Characterization of a Stress-Inducible and a Constitutive Small Heat-Shock Protein Targeted to the Matrix of Plant Peroxisomes1[W] , 2006, Plant Physiology.

[29]  T. Berleth,et al.  Growth and development: Integrating signals and differentiating tissues — the ‘calculus’ of plant development , 2006 .

[30]  H. Nguyen,et al.  Understanding regulatory networks and engineering for enhanced drought tolerance in plants. , 2006, Current opinion in plant biology.

[31]  R. Bruskiewich,et al.  Gene expression microarrays and their application in drought stress research. , 2006 .

[32]  Liisa Holm,et al.  Identifying functional gene sets from hierarchically clustered expression data: map of abiotic stress regulated genes in Arabidopsis thaliana , 2006, Nucleic acids research.

[33]  Yoshihiro Yamanishi,et al.  KEGG for linking genomes to life and the environment , 2007, Nucleic Acids Res..

[34]  D. Repsilber,et al.  Expression profiling of rice cultivars differing in their tolerance to long-term drought stress , 2008, Plant Molecular Biology.

[35]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[36]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[37]  V. Chinnusamy,et al.  Abiotic stress and ABA-inducible Group 4 LEA from Brassica napus plays a key role in salt and drought tolerance. , 2009, Journal of biotechnology.

[38]  Feng Ren,et al.  Identification and expression analysis of genes in response to high-salinity and drought stresses in Brassica napus. , 2010, Acta biochimica et biophysica Sinica.

[39]  K. Shinozaki,et al.  Arabidopsis tiling array analysis to identify the stress-responsive genes. , 2010, Methods in molecular biology.

[40]  M. Farooq,et al.  Plant drought stress: effects, mechanisms and management , 2011, Agronomy for Sustainable Development.

[41]  Yanchun Liang,et al.  Prediction of Drought-Resistant Genes in Arabidopsis thaliana Using SVM-RFE , 2011, PloS one.

[42]  Zhijin Zhang,et al.  The ethylene response factor AtERF98 enhances tolerance to salt through the transcriptional activation of ascorbic acid synthesis in Arabidopsis. , 2012, The Plant journal : for cell and molecular biology.

[43]  K. Mysore,et al.  Glycolate Oxidase Modulates Reactive Oxygen Species–Mediated Signal Transduction during Nonhost Resistance in Nicotiana benthamiana and Arabidopsis[W] , 2012, Plant Cell.

[44]  X. Fang,et al.  Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors , 2013, BMC Genomics.

[45]  Zhu Jiacheng.  Drought Resistance and Identification Method and Evaluation Index in Brassica napus II.Study on Identification Indexes of Drought Resistance at Germination Stage , 2012 .

[46]  Zhu Jiacheng.  Drought Resistance and Identification Method and Evaluation Index in Brassica napus III.Selection of Drought Resistance Identification Index at Seedling Stage , 2012 .

[47]  Arjun Krishnan,et al.  Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq1[W][OA] , 2012, Plant Physiology.

[48]  Y. Rui.  Relationship between the Physiological and Biochemical Substances and the Graft Affinity of Grape Rootstock-scion Combination , 2012 .

[49]  Maciej Ogorzalek,et al.  Global relative parameter sensitivities of the feed-forward loops in genetic networks , 2012, Neurocomputing.

[50]  A. Shanker,et al.  Drought stress responses in crops , 2014, Functional & Integrative Genomics.

[51]  T. Oliver,et al.  Genomic basis for coral resilience to climate change , 2013, Proceedings of the National Academy of Sciences.

[52]  S. Gill,et al.  Drought Stress Responses in Plants, Oxidative Stress, and Antioxidant Defense , 2013 .

[53]  Xinghuo Yu,et al.  Identification and Evolution of Structurally Dominant Nodes in Protein-Protein Interaction Networks , 2014, IEEE Transactions on Biomedical Circuits and Systems.

[54]  T. Nishio,et al.  Comparative Transcriptome Analysis of Leaves and Roots in Response to Sudden Increase in Salinity in Brassica napus by RNA-seq , 2014, BioMed research international.

[55]  Corinne Da Silva,et al.  Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome , 2014, Science.

[56]  L. Xiong,et al.  General mechanisms of drought response and their application in drought resistance improvement in plants , 2014, Cellular and Molecular Life Sciences.

[57]  Lizhong Xiong,et al.  Genetic engineering and breeding of drought-resistant crops. , 2014, Annual review of plant biology.

[58]  Jie Chen,et al.  Transcriptome Profiling and Identification of Transcription Factors in Ramie (Boehmeria nivea L. Gaud) in Response to PEG Treatment, Using Illumina Paired-End Sequencing Technology , 2015, International journal of molecular sciences.

[59]  Cuiling Yang,et al.  Comparative transcriptome analyses of drought-resistant and - susceptible Brassica napus L. and development of EST-SSR markers by RNA-Seq , 2015, Journal of Plant Biology.

[60]  R. Redden,et al.  Identification of Putative Candidate Genes for Water Stress Tolerance in Canola (Brassica napus) , 2015, Front. Plant Sci..

[61]  Qing Liu,et al.  Overexpression of the brassinosteroid biosynthetic gene DWF4 in Brassica napus simultaneously increases seed yield and stress tolerance , 2016, Scientific Reports.

[62]  Maoteng Li,et al.  Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus , 2016, Scientific Reports.

[63]  Han Liu,et al.  Comparative transcriptomic analysis uncovers the complex genetic network for resistance to Sclerotinia sclerotiorum in Brassica napus , 2016, Scientific Reports.

[64]  Guanrong Chen,et al.  Identifying structures of continuously-varying weighted networks , 2016, Scientific Reports.

[65]  H. Shao,et al.  Recent Advances in Utilizing Transcription Factors to Improve Plant Abiotic Stress Tolerance by Transgenic Technology , 2016, Front. Plant Sci..