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Journal of Integrative Agriculture  2019, Vol. 18 Issue (11): 2457-2471    DOI: 10.1016/S2095-3119(19)62576-1
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Transcriptome profiling using RNA-seq to provide insights into foxtail millet seedling tolerance to short-term water deficit stress induced by PEG-6000
XU Bing-qin, GAO Xiao-li, GAO Jin-feng, LI Jing, YANG Pu, FENG Bai-li
 
College of Agronomy, Northwest A&F University/State Key Laboratory of Crop Stress Biology for Arid Areas, Ministry of Science and Technology, Yangling 712100, P.R.China
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摘要   

Abstract  
Foxtail millet (Setaria italica L.) with high drought resistance, is grown widely in arid and semi-arid regions of the world, and it is a new model plant for genetic and molecular studies.  To uncover the molecular mechanisms of stress-tolerance in different genotypes of foxtail millet, physiological analyses combined with transcriptional profiling were conducted using a time-course analysis on two foxtail millet genotypes Damaomao (DM) and Hongnian (HN).  The genotype DM performed better than HN under water deficiency, with more moderate relative water content (RWC) and chlorophyll decline.  Further physiological and RNA-seq investigations revealed that the two genotypes possessed high conservatism in some vital biological pathways which respond to drought stress, involving hormone synthesis, proline, and soluble sugar synthesis, and reactive oxygen species (ROS) metabolism.  However, some genes related to these pathways showed different expression profiles.  Likewise, the lower malondialdehyde (MDA) content in HN than DM may be explained by the observation that HN contained more activated genes in the ascorbate-glutathione cycle using KEGG pathway analysis.  Overall, abscisic acid (ABA) response genes, ROS scavengers which were probably involved in signaling responses, a set of enzymes involved in proline and soluble sugar synthesis, channel protein genes, and transcription factors, encompassed the early strategy of foxtail millet response to drought.  These findings provide a comprehensive molecular view of how different foxtail millet genotypes respond to short-term osmotic stress.
Keywords:   transcriptome        foxtail millet       osmotic stress       RNA-seq              gene expression  
Received: 02 July 2018   Accepted:
Fund: 
This work was supported by the earmarked fund for China Agriculture Research System (CARS-06-13.5-A26), the National Natural Science Foundation of China (31371529), and the Minor Grain Crops Research and Development System of Shaanxi Province, China (2014–2017).
Corresponding Authors:  Correspondence FENG Bai-li, Tel: +86-29-87082889, E-mail: fengbaili@nwsuaf.edu.cn    
About author:  XU Bin-qin, Tel: +86-29-87082889, E-mail: xubingqin1224@gmail.com;

Cite this article: 

XU Bing-qin, GAO Xiao-li, GAO Jin-feng, LI Jing, YANG Pu, FENG Bai-li. 2019. Transcriptome profiling using RNA-seq to provide insights into foxtail millet seedling tolerance to short-term water deficit stress induced by PEG-6000. Journal of Integrative Agriculture, 18(11): 2457-2471.

Amedie F A. 2013. Impacts of climate change on plant growth, ecosystem services, biodiversity, and potential adaptation measure. MSc thesis, Department of Biological and Environmental Sciences University of Gothenburg, Sweden.
Anjum F, Yaseen M, Rasool E, Wahid A, Anjum S. 2003. Water stress in barley (Hordeum vulgare L.). II. Effect on chemical composition and chlorophyll contents. Pakistan Journal of Agricultural Sciences, 26, 203–209.
Anjum S A, Xie X Y, Wang L C, Saleem M F, Man C, Lei W. 2011. Morphological, physiological and biochemical responses of plants to drought stress. African Journal of Agricultural Research, 6, 2026–2032.
Bao G, Zhuo C, Qian C, Xiao T, Guo Z, Lu S. 2016. Co-expression of NCED and ALO improves vitamin C level and tolerance to drought and chilling in transgenic tobacco and stylo plants. Plant Biotechnology Journal, 14, 206–214.
Bates L S, Waldren R P, Teare I D. 1973. Rapid determination of free proline for water-stress studies. Plant and Soil, 39, 205–207.
Bennetzen J L, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli A C, Estep M, Feng L, Vaughn J N, Grimwood J. 2012. Reference genome sequence of the model plant Setaria. Nature Biotechnology, 30, 555–561.
Bingham G E. 1974. Rapid Estimates of relative water content. Plant Physiology, 53, 258.
Bray E A. 1987. Plant responses to water deficit. Trends in Plant Science, 2, 48–54.
Chaves M M, Maroco J P, Pereira J S. 2003. Understanding plant responses to drought — from genes to the whole plant. Functional Plant Biology, 30, 239–264.
Dai X D, Qin N, Wang C Y, Yang G H, Yang Y F, Wang Y N, Xu X Z, Li J X. 2017. Response of foxtail millet varieties (lines) with different genotypes to drought stress and drought resistance evaluation. Chinese Agricultural Science Bulletin, 33, 15–19. (in Chinese)
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. 2010. AgriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Research, 38, W64–W70.
Farhad M S, Babak A M, Reza Z M, Hassan R S M, Afshin T. 2011. Response of proline, soluble sugars, photosynthetic pigments and antioxidant enzymes in potato (Solanum tuberosum L.) to different irrigation regimes in greenhouse condition. Australian Journal of Crop Science, 5, 55.
Golldack D, Lüking I, Yang O. 2011. Plant tolerance to drought and salinity: Stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Reports, 30, 1383–1391.
Han J. 1990. The responses of rice (Oryza sativa L.) seedlings to the osmotic stress and relation to the osmotic adjustment. Journal of Agricultural University of Hebei, 1, 17–21. (in Chinese)
Harb A, Krishnan A, Ambavaram M M R, Pereira A. 2010. Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiology, 154, 1254.
Hodges D M, Delong J M, Forney C F, Prange R K. 1999. Improving the thiobarbituric acid-reactive-substances assay for estimating lipid peroxidation in plant tissues containing anthocyanin and other interfering compounds. Planta, 207, 604–611.
Hörtensteiner S, Kräutler B. 2011. Chlorophyll breakdown in higher plants. Biochimica et Biophysica Acta (Bioenergetics), 1807, 977–988.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, R36.
Lafitte R. 2002. Relationship between leaf relative water content during reproductive stage water deficit and grain formation in rice. Field Crops Research, 76, 165–174.
Lata C, Jha S, Dixit V, Sreenivasulu N, Prasad M. 2011. Differential antioxidative responses to dehydration-induced oxidative stress in core set of foxtail millet cultivars [Setaria italica (L.)]. Protoplasma, 248, 817–828.
Lata C, Mishra A K, Muthamilarasan M, Bonthala V S, Khan Y, Prasad M. 2014. Genome-wide investigation and expression profiling of AP2/ERF transcription factor superfamily in foxtail millet (Setaria italica L.). PLoS ONE, 9, e113092.
Lata C, Prasad M. 2013. Setaria genome sequencing: An overview. Journal of Plant Biochemistry & Biotechnology, 22, 257–260.
Lata C, Sahu P P, Prasad M. 2010. Comparative transcriptome analysis of differentially expressed genes in foxtail millet (Setaria italica L.) during dehydration stress. Biochemical and Biophysical Research Communications, 393, 720–727.
McAdam S A M, Brodribb T J. 2016. Linking turgor with ABA biosynthesis: Implications for stomatal responses to vapor pressure deficit across land plants. Plant Physiology, 171, 2008–2016.
Mickelbart M V, Hasegawa P M, Bailey-Serres J. 2015. Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability. Nature Reviews Genetics, 16, 237–251.
Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621–628.
Muthamilarasan M, Khandelwal R, Yadav C B, Bonthala V S, Khan Y, Prasad M. 2014. Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.). PLoS ONE, 9, e109920.
Nations O. 2011. State of the World’s Land and Water Resources for Food and Agriculture. Food and Agriculture Organization of the United Nations and Earthscan. p. 294.
Nayyar H, Walia D P. 2003. Water stress induced proline accumulation in contrasting wheat genotypes as affected by calcium and abscisic acid. Biologia Plantarum, 46, 275–279.
Okcu G. 2005. Effects of salt and drought stresses on germination and seedling growth of pea (Pisum sativum L.). Turkish Journal of Agriculture & Forestry, 29, 237–242.
Puranik S, Jha S, Srivastava P S, Sreenivasulu N, Prasad M. 2011. Comparative transcriptome analysis of contrasting foxtail millet cultivars in response to short-term salinity stress. Journal of Plant Physiology, 168, 280–287.
Puranik S, Sahu P P, Mandal S N, Vs B, Parida S K, Prasad M. 2013. Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.). PLoS ONE, 8, e64594.
Qi X, Xie S J, Liu Y W, Yi F, Yu J J. 2013. Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Molecular Biology, 83, 459–473.
Regan K L, Whan B R, Turner N C. 1993. Evaluation of chemical desiccation as a selection technique for drought resistance in a dryland wheat breeding program. Australian Journal of Agricultural Research, 44, 1683–1691.
Sairam R K, Srivastava G C, Agarwal S, Meena R C. 2005. Differences in antioxidant activity in response to salinity stress in tolerant and susceptible wheat genotypes. Biologia Plantarum, 49, 85–91.
Schefe J H, Lehmann K E, Buschmann I R, Unger T, Funke-Kaiser H. 2006. Quantitative real-time RT-PCR data analysis: Current concepts and the novel ‘gene expression’s CT difference’ formula. Journal of Molecular Medicine, 84, 901–910. 
Stigler S M. 1989. Francis galton’s account of the invention of correlation. Statistical Science, 4, 73–79.
Tang S, Li L, Wang Y, Chen Q, Zhang W, Jia G, Zhi H, Zhao B, Diao X. 2017. Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses). Scientific Reports, 7, 10009.
Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, van Baren M J, Salzberg S L, Wold B J, Pachter L. 2010. Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms. Nature Biotechnology, 28, 511–515.
Vetriventhan M, Upadhyaya H D, Dwivedi S L, Pattanashetti S K, Singh S K. 2016. Finger and foxtail millets. In: Genetic and Genomic Resources for Grain Cereals Improvement. Academic Press, San Diego. pp. 291–319.
Zhang. 2007. Construction and application of EST library from Setaria italica in response to dehydration stress. Genomics, 90, 121–131.
Zhang W Y, Zhi H, Liu B H, LI W, Wang Y F, LI H Q, Jia G Q, Li Y Q, Diao X M. 2011. Relationship between drought tolerance ability and some physiological characteristics of foxtail millet at booting stage. Acta Agriculturae Boreali-Sinica, 26, 128–133.
Zhang Y Y, Zhang B, Ma F F, Ding M J, Hu T G, Li P, Han Y H. 2016. Responses to drought stress and expression analysis of SiZFP252 of seedlings of different foxtail millet varieties. Journal of Shanxi Agricultural University (Natural Science Edition), 36, 614–618. (in Chinese)
Zhu C, Ming C, Xu Z, Li L, Chen X, Ma Y. 2014. Characteristics and expression patterns of the aldehyde dehydrogenase (ALDH) gene superfamily of foxtail millet (Setaria italica L.). PLoS ONE, 9, e101136.
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