Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.)
详细信息    查看全文
  • 作者:Fantao Zhang ; Xiangdong Luo ; Yi Zhou ; Jiankun Xie
  • 关键词:Dongxiang wild rice ; Drought resistance ; Genetic resource ; High ; throughput sequencing ; microRNA
  • 刊名:Biotechnology Letters
  • 出版年:2016
  • 出版时间:April 2016
  • 年:2016
  • 卷:38
  • 期:4
  • 页码:711-721
  • 全文大小:832 KB
  • 参考文献:Ahmadvand R, Poczai P, Hajianfar R, Kolics B, Gorji AM, Polgár Z, Taller J (2014) Next generation sequencing based development of intron-targeting markers in tetraploid potato and their transferability to other Solanum species. Gene 540:117–121CrossRef PubMed
    Akdogan G, Tufekci ED, Uranbey S, Unver T (2015) miRNA-based drought regulation in wheat. Funct Integr Genomic. doi:10.​1007/​s10142-015-0452-1
    Atwell BJ, Wang H, Scafaro AP (2014) Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? Plant Sci 215–216:48–58CrossRef PubMed
    Barrera-Figueroa BE, Gao L, Diop NN, Wu Z, Ehlers JD, Roberts PA, Close TJ, Zhu JK, Liu R (2011) Identification and comparative analysis of drought-associated microRNAs in two cowpea genotypes. BMC Plant Biol 11:127CrossRef PubMed PubMedCentral
    Bekele WA, Wieckhorst S, Friedt W, Snowdon RJ (2013) High-throughput genomics in sorghum: from whole-genome resequencing to a SNP screening array. Plant Biotechnol J 11:1112–1125CrossRef PubMed
    Bouman BAM, Peng S, Castaòeda AR, Visperas RM (2005) Yield and water use of irrigated tropical aerobic rice systems. Agric Water Manag 74:87–105CrossRef
    Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A (2013) Rfam 11.0: 10 years of RNA families. Nucleic Acids Res 41:D226–D232CrossRef PubMed PubMedCentral
    Chen XR, Yang KS, Fu JR, Zhu CL, Peng XS, He XP, He HH (2008) Identification and genetic analysis of fertility restoration ability in Dongxiang wild rice (Oryza rufipogon). Rice Sci 15:21–28CrossRef
    Chen ZX, Li FL, Yang SN, Dong YB, Yuan QH, Wang F, Li WM, Jiang Y, Jia SR, Pei XW (2013) Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.). PLoS One 8:e82844CrossRef PubMed PubMedCentral
    Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acid Res 39:155–159CrossRef
    Ding YF, Tao YL, Zhu C (2013) Emerging roles of microRNAs in the mediation of drought stress response in plants. J Exp Bot 64:3077–3086CrossRef PubMed
    Dong ZH, Shi L, Wang YW, Chen L, Cai ZM, Wang YN, Jin JB, Li X (2013) Identification and dynamic regulation of microRNAs involved in salt stress responses in functional soybean nodules by high-throughput sequencing. Int J Mol Sci 14:2717–2738CrossRef PubMed PubMedCentral
    Eldem V, Celikkol Akcay U, Ozhuner E, Bakir Y, Uranbey S, Unver T (2012) Genome-wide identification of miRNAs responsive to drought in peach (Prunus persica) by high-throughput deep sequencing. PLoS One 7:e50298CrossRef PubMed PubMedCentral
    Eldem V, Okay S, Unver T (2013) Plant microRNAs: new players in functional genomics. Turk J Agric For 37:1–21
    Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of miRNA genes. PLoS One 2:e219CrossRef PubMed PubMedCentral
    Fang YJ, Xiong LZ (2015) General mechanisms of drought response and their application in drought resistance improvement in plants. Cell Mol Life Sci 72:673–689CrossRef PubMed
    Fujii H, Chiou TJ, Lin SI, Aung K, Zhu JK (2005) A miRNA involved in phosphate-starvation response in Arabidopsis. Curr Biol 15:2038–2043CrossRef PubMed
    Gentile A, Dias LI, Mattos RS, Ferreira TH, Menossi M (2015) microRNAs and drought responses in sugarcane. Front Plant Sci 6:58CrossRef PubMed PubMedCentral
    Grossa BL, Zhao ZJ (2014) Archaeological and genetic insights into the origins of domesticated rice. Proc Natl Acad Sci USA 111:6190–6197CrossRef
    He GM, Luo XJ, Feng T, Li KG, Zhu ZF, Su W, Qian XY, Fu YC, Wang XK, Sun CQ, Yang JS (2006) Haplotype variation in structure and expression of a gene cluster associated with a quantitative trait locus for improved yield in rice. Genome Res 16:618–626CrossRef PubMed PubMedCentral
    Hollister JD (2014) Genomic variation in Arabidopsis: tools and insights from next-generation sequencing. Chromosom Res 22:103–115CrossRef
    Huang XH, Lu TT, Han B (2013) Resequencing rice genomes: an emerging new era of rice genomics. Trend Genet 29:225–232CrossRef
    Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345:646–651CrossRef PubMed
    Jaleel CA, Manivannan P, Wahid A, Farooq M, Somasundaram R, Panneerselvam R (2009) Drought stress in plants: a review on morphological characteristics and pigments composition. Int J Agric Biol 11:100–105
    Kantar M, Unver T, Budak H (2010) Regulation of barley miRNAs upon dehydration stress correlated with target gene expression. Funct Integr Genomic 10:493–507CrossRef
    Kantar M, Lucas SJ, Budak H (2011) miRNA expression patterns of Triticum dicoccoides in response to shock drought stress. Planta 233:471–484CrossRef PubMed
    Koh S, Lee SC, Kim MK, Koh JH, Lee S, An G, Choe S, Kim SR (2007) T-DNA tagged knockout mutation of rice OsGSK1, an orthologue of Arabidopsis BIN2, with enhanced tolerance to various abiotic stresses. Plant Mol Biol 65:453–466CrossRef PubMed
    Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acid Res 42:D68–D73CrossRef PubMed PubMedCentral
    Krannich CT, Maletzki L, Kurowsky C, Horn R (2015) Network candidate genes in breeding for drought tolerant crops. Int J Mol Sci 16:16378–16400CrossRef PubMed PubMedCentral
    Kumar RR, Pathak H, Sharma SK, Kala YK, Nirjal MK, Singh GP, Goswami S, Rai RD (2015) Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.). Funct Integr Genomic 15:323–348CrossRef
    Lacape JM, Claverie M, Vidal RO, Carazzolle MF, Guimarães Pereira GA, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C (2012) Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS One 7:e48855CrossRef PubMed PubMedCentral
    Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854CrossRef PubMed
    Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24:713–714CrossRef PubMed
    Li WB, Wang PP, Li YG, Zhang KX, Ding FQ, Nie TK, Yang X, Lv QX, Zhao L (2015) Identification of microRNAs in response to different day lengths in soybean using high-throughput sequencing and qRT-PCR. PLoS One 10:e0132621CrossRef PubMed PubMedCentral
    Liu X, Zhang H, Zhao Y, Feng Z, Li Q, Yang HQ, Luan S, Li J, He ZH (2013) Auxin controls seed dormancy through stimulation of abscisic acid signaling by inducing ARF-mediated ABI3 activation in Arabidopsis. Proc Natl Acad Sci USA 110:15485–15490CrossRef PubMed PubMedCentral
    Lu TT, Yu SL, Fan DL, Mu J, Shangguan YY, Wang ZX, Minobe Y, Lin ZX, Han B (2008) Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943. DNA Res 15:285–295CrossRef PubMed PubMedCentral
    Luo LJ (2010) Breeding for water-saving and drought-resistance rice (WDR) in China. J Exp Bot 61:3509–3517CrossRef PubMed
    Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM (2015) Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet 11:e1005566CrossRef PubMed PubMedCentral
    Mao DH, Yu L, Chen DZ, Li LY, Zhu YX, Xiao YQ, Zhang DC, Chen CY (2015) Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theor Appl Genet 128:1359–1371CrossRef PubMed
    Pandey R, Joshi G, Bhardwaj AR, Agarwal M, Katiyar-Agarwal S (2014) A comprehensive genome-wide study on tissue-specific and abiotic stress-specific miRNAs in Triticum aestivum. PLoS One 9:e95800CrossRef PubMed PubMedCentral
    Paul S, Datta SK, Datta K (2015) miRNA regulation of nutrient homeostasis in plants. Front Plant Sci 6:232CrossRef PubMed PubMedCentral
    Reuter JA, Spacek DV, Snyder MP (2015) High-throughput sequencing technologies. Mol Cell 58:586–597CrossRef PubMed
    Saha G, Park JI, Jung HJ, Ahmed NU, Kayum MA, Chung MY, Hur Y, Cho YG, Watanabe M, Nou IS (2015) Genome-wide identification and characterization of MADS-box family genes related to organ development and stress resistance in Brassica rapa. BMC Genom 16:178CrossRef
    Saini S, Dongen HK, Enrigh SV (2008) miRBase: tools for microRNA genomics. Nucleic Acid Res 36:D154–D158CrossRef PubMed PubMedCentral
    Sakai H, Itoh T (2010) Massive gene losses in Asian cultivated rice unveiled by comparative genome analysis. BMC Genom 11:121CrossRef
    Swamy BP, Kumar A (2013) Genomics-based precision breeding approaches to improve drought tolerance in rice. Biotechnol Adv 31:1308–1318CrossRef PubMed
    Todaka D, Shinozaki K, Yamaguchi-Shinozaki K (2015) Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants. Front Plant Sci 6:84CrossRef PubMed PubMedCentral
    Unver T, Namuth-Covert DM, Budak H (2009) Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genom 2009:262463
    Vashisht D, Nodine MD (2014) microRNA functions in plant embryos. Biochem Soc Trans 42:352–357CrossRef PubMed
    Wang T, Chen L, Zhao M, Tian Q, Zhang WH (2011) Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing. BMC Genom 12:367CrossRef
    Wei LY, Zhang DF, Xiang F, Zhang ZX (2009) Differentially expressed miRNAs potentially involved in the regulation of defense mechanism to drought stress in maize seedlings. Int J Plant Sci 170:979–989CrossRef
    Wei B, Zhang RZ, Guo JJ, Liu DM, Li AL, Fan RC, Mao L, Zhang XQ (2014) Genome-wide analysis of the MADS-box gene family in Brachypodium distachyon. PLoS One 9:e84781CrossRef PubMed PubMedCentral
    Xie KB, Wu CQ, Xiong LZ (2006) Genomic organization, differential expression, and interaction of SQUAMOSA promoter-binding-like tanscription factors and microRNA156 in rice. Plant Physiol 142:280–293CrossRef PubMed PubMedCentral
    Yoshida S, Cock JH, Parao FT (1972) Physiological aspects of high yield. International Rice Research Institute. Rice Breed pp 455–469
    Zhang XH, Zou Z, Zhang JH, Zhang YY, Han QQ, Hu TX, Xu XG, Liu H, Li HX, Ye ZB (2011) Over-expression of sly-miR156a in tomato results in multiple vegetative and reproductive trait alterations and partial phenocopy of the sft mutant. FEBS Lett 585:435–439CrossRef PubMed
    Zhang FT, Cui FL, Zhang LX, Wen XF, Luo XD, Zhou Y, Li X, Wan Y, Zhang JE, Xie JK (2014) Development and identification of a introgression line with strong drought resistance at seedling stage derived from Oryza sativa L. mating with Oryza rufipogon Griff. Euphytica 200:1–7CrossRef
    Zhang YJ, Wang W, Chen J, Liu JB, Xia MX, Shen FF (2015) Identification of miRNAs and their targets in cotton inoculated with verticillium dahliae by high-throughput sequencing and degradome analysis. Int J Mol Sci 16:14749–14768CrossRef PubMed PubMedCentral
  • 作者单位:Fantao Zhang (1)
    Xiangdong Luo (1)
    Yi Zhou (1)
    Jiankun Xie (1)

    1. College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
  • 刊物类别:Biomedical and Life Sciences
  • 刊物主题:Life Sciences
    Microbiology
    Biotechnology
    Applied Microbiology
    Biochemistry
  • 出版者:Springer Netherlands
  • ISSN:1573-6776
文摘
Objectives To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress.

© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号

地址:北京市海淀区学院路29号 邮编:100083

电话:办公室:(+86 10)66554848;文献借阅、咨询服务、科技查新:66554700