Genome-wide identification and comparative analysis of grafting-responsive mRNA in watermelon grafted onto bottle gourd and squash rootstocks by high-throughput sequencing

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• 作者：Na Liu ; Jinghua Yang ; Xinxing Fu ; Li Zhang ; Kai Tang…
• 关键词：Grafting ; Watermelon ; Rootstock ; RNA ; Seq ; Gene regulation
• 刊名：Molecular Genetics and Genomics
• 出版年：2016
• 出版时间：April 2016
• 年：2016
• 卷：291
• 期：2
• 页码：621-633
• 全文大小：2,284 KB
• 参考文献：Aloni B, Cohen R, Karni L, Aktas H, Edelstein M (2010) Hormonal signaling in rootstock-scion interactions. Sci Hortic-Amsterdam 127:119–126CrossRef
  Baiges I, Schaffner AR, Affenzeller MJ, Mas A (2002) Plant aquaporins. Physiol Plantarum 115:175–182CrossRef
  Bressan R, Bohnert H, Zhu JK (2009) Abiotic stress tolerance: from gene discovery in model organisms to crop improvement. Mol Plant 2:1–2CrossRef PubMed PubMedCentral
  Colla G, Rouphael Y, Leonardi C, Bie ZL (2010) Role of grafting in vegetable crops grown under saline conditions. Sci Hortic-Amsterdam 127:147–155CrossRef
  Collins JK, Wu GY, Perkins-Veazie P, Spears K, Claypool PL, Baker RA, Clevidence BA (2007) Watermelon consumption increases plasma arginine concentrations in adults. Nutrition 23:261–266 CrossRef PubMed
  Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676CrossRef PubMed
  Conte SS, Walker EL (2012) Genetic and biochemical approaches for studying the yellow stripe-like transporter family in plants. Curr Top Membr 69:295–322CrossRef PubMed
  Cookson SJ, Ollat N (2013) Grafting with rootstocks induces extensive transcriptional re-programming in the shoot apical meristem of grapevine. BMC Plant Biol 13:147CrossRef PubMed PubMedCentral
  Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR (2010) Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61:651–679CrossRef PubMed
  Davis AR, Perkins-Veazie P, Sakata Y, Lopez-Galarza S, Maroto JV, Lee SG, Huh YC, Sun ZY, Miguel A, King SR, Cohen R, Lee JM (2008) Cucurbit grafting. Crit Rev. Plant Sci 27:50–74CrossRef
  Dugas DV, Bartel B (2004) MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol 7:512–520CrossRef PubMed
  Fujii H, Chinnusamy V, Rodrigues A, Rubio S, Antoni R, Park SY, Cutler SR, Sheen J, Rodriguez PL, Zhu JK (2009) In vitro reconstitution of an abscisic acid signalling pathway. Nature 462:660–664CrossRef PubMed PubMedCentral
  Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q, Chen Z, Mauceli E, Hacohen N, Gnirke A, Rhind N, di Palma F, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRef PubMed PubMedCentral
  Gregory PJ, Atkinson CJ, Bengough AG, Else MA, Fernandez-Fernandez F, Harrison RJ, Schmidt S (2013) Contributions of roots and rootstocks to sustainable, intensified crop production. J Exp Bot 64:1209–1222CrossRef PubMed
  Guo SG, Zhang JG, Sun HH, Salse J, Lucas WJ, Zhang HY, Zheng Y, Mao LY, Ren Y, Wang ZW, Min JM, Guo XS, Murat F, Ham BK, Zhang ZL, Gao S, Huang MY, Xu YM, Zhong SL, Bombarely A, Mueller LA, Zhao H, He HJ, Zhang Y, Zhang ZH, Huang SW, Tan T, Pang EL, Lin K, Hu Q, Kuang HH, Ni PX, Wang B, Liu JA, Kou QH, Hou WJ, Zou XH, Jiang J, Gong GY, Klee K, Schoof H, Huang Y, Hu XS, Dong SS, Liang DQ, Wang J, Wu K, Xia Y, Zhao X, Zheng ZQ, Xing M, Liang XM, Huang BQ, Lv T, Wang JY, Yin Y, Yi HP, Li RQ, Wu MZ, Levi A, Zhang XP, Giovannoni JJ, Wang J, Li YF, Fei ZJ, Xu Y (2013) The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions. Nat Genet 45:51–58CrossRef PubMed
  He JN, Duan Y, Hua DP, Fan GJ, Wang L, Liu Y, Chen ZZ, Han LH, Qu LJ, Gong ZZ (2012) DEXH box RNA helicase-mediated mitochondrial reactive oxygen species production in arabidopsis mediates crosstalk between abscisic acid and auxin signaling. Plant Cell 24:1815–1833CrossRef PubMed PubMedCentral
  Jensen PJ, Rytter J, Detwiler EA, Travis JW, McNellis TW (2003) Rootstock effects on gene expression patterns in apple tree scions. Plant Mol Biol 53:493–511CrossRef PubMed
  Jensen PJ, Halbrendt N, Fazio G, Makalowska I, Altman N, Praul C, Maximova SN, Ngugi HK, Crassweller RM, Travis JW, McNellis TW (2012) Rootstock-regulated gene expression patterns associated with fire blight resistance in apple. BMC Genom 13:9CrossRef
  Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y (2008) KEGG for linking genomes to life and the environment. Nucleic Acids Res 36:D480–D484CrossRef PubMed PubMedCentral
  Karpinski S, Reynolds H, Karpinska B, Wingsle G, Creissen G, Mullineaux P (1999) Systemic signaling and acclimation in response to excess excitation energy in Arabidopsis. Science 284:654–657CrossRef PubMed
  Khraiwesh B, Zhu JK, Zhu JH (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Bba-Gene Regul Mech 1819:137–148
  Kumari A, Kumar J, Kumar A, Chaudhury A, Singh SP (2015) Grafting triggers differential responses between scion and rootstock. PLoS One 10:e0124438CrossRef PubMed PubMedCentral
  Lee JM, Kubota C, Tsao SJ, Bie Z, Echevarria PH, Morra L, Oda M (2010) Current status of vegetable grafting: diffusion, grafting techniques, automation. Sci Hortic-Amsterdam 127:93–105CrossRef
  Lee S, Ryoo N, Jeon JS, Guerinot ML, An G (2012) Activation of rice yellow stripe1-Like 16 (OsYSL16) enhances iron efficiency. Mol Cells 33:117–126CrossRef PubMed PubMedCentral
  Li RQ, Yu C, Li YR, Lam TW, Yiu SM, Kristiansen K, Wang J (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967CrossRef PubMed
  Liu Y, He JN, Chen ZZ, Ren XZ, Hong XH, Gong ZZ (2010) ABA overly-sensitive 5 (ABO5), encoding a pentatricopeptide repeat protein required for cis-splicing of mitochondrial nad2 intron 3, is involved in the abscisic acid response in Arabidopsis. Plant J 63:749–765CrossRef PubMed
  Liu N, Yang JH, Guo SG, Xu Y, Zhang MF (2013) Genome-Wide identification and comparative analysis of conserved and novel micrornas in grafted watermelon by high-throughput sequencing. PLoS ONE 8:e57359CrossRef PubMed PubMedCentral
  Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(T)(−Delta Delta C) method. Methods 25:402–408CrossRef PubMed
  Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38:S31–S36CrossRef PubMed
  Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141CrossRef PubMed
  Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517CrossRef PubMed PubMedCentral
  Mishra AK, Puranik S, Prasad M (2012) Structure and regulatory networks of WD40 protein in plants. J Plant Biochem Biot 21:S32–S39CrossRef
  Miyazono K, Miyakawa T, Sawano Y, Kubota K, Kang HJ, Asano A, Miyauchi Y, Takahashi M, Zhi YH, Fujita Y, Yoshida T, Kodaira KS, Yamaguchi-Shinozaki K, Tanokura M (2009) Structural basis of abscisic acid signalling. Nature 462:609–614CrossRef PubMed
  Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264CrossRef PubMed
  Mortazavi A, Williams BA, Mccue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628CrossRef PubMed
  Nookaew I, Papini M, Pornputtapong N, Scalcinati G, Fagerberg L, Uhlen M, Nielsen J (2012) A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 40:10084–10097CrossRef PubMed PubMedCentral
  Perkins-Veazie P, Collins JK, Davis AR, Roberts W (2006) Carotenoid content of 50 watermelon cultivars. J Agr Food Chem 54:2593–2597CrossRef
  Rouphael Y, Cardarelli M, Colla G, Rea E (2008) Yield, mineral composition, water relations, and water use efficiency of grafted mini-watermelon plants under deficit irrigation. HortScience 43:730–736
  Rouphael Y, Schwarz D, Krumbein A, Colla G (2010) Impact of grafting on product quality of fruit vegetables. Sci Hortic-Amsterdam 127:172–179CrossRef
  Savvas D, Papastavrou D, Ntatsi G, Ropokis A, Olympios C, Hartmann H, Schwarz D (2009) Interactive effects of grafting and manganese supply on growth, yield, and nutrient uptake by tomato. HortScience 44:1978–1982
  Savvas D, Colla G, Rouphael Y, Schwarz D (2010) Amelioration of heavy metal and nutrient stress in fruit vegetables by grafting. Sci Hortic-Amsterdam 127:156–161CrossRef
  Shen Y, Zhang YZ, Chen J, Lin HJ, Zhao MJ, Peng HW, Liu L, Yuan GS, Zhang SZ, Zhang ZM, Pan GT (2013) Genome expression profile analysis reveals important transcripts in maize roots responding to the stress of heavy metal Pb. Physiol Plantarum 147:270–282CrossRef
  Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63CrossRef PubMed PubMedCentral
  Wilhelm BT, Landry JR (2009) RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Methods 48:249–257CrossRef PubMed
  Zahaf O, Blanchet S, de Zelicourt A, Alunni B, Plet J, Laffont C, de Lorenzo L, Imbeaud S, Ichante JL, Diet A, Badri M, Zabalza A, Gonzalez EM, Delacroix H, Gruber V, Frugier F, Crespi M (2012) Comparative transcriptomic analysis of salt adaptation in roots of contrasting medicago truncatula genotypes. Mol Plant 5:1068–1081CrossRef PubMed
  Zhao ZG, Tan LL, Dang CY, Zhang H, Wu QB, An LZ (2012) Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant. Chorispora bungeana. BMC Plant Biol 12:222CrossRef PubMed
  Zheng LQ, Yamaji N, Yokosho K, Ma JF (2012) YSL16 Is a phloem-localized transporter of the copper-nicotianamine complex that is responsible for copper distribution in rice. Plant Cell 24:3767–3782CrossRef PubMed PubMedCentral
  Zhu JK (2002) Salt and drought stress signal transduction in plants. Annu Rev Plant Biol 53:247–273CrossRef PubMed PubMedCentral
  
• 作者单位：Na Liu (1) (2)
  Jinghua Yang (1)
  Xinxing Fu (1)
  Li Zhang (1)
  Kai Tang (3)
  Kateta Malangisha Guy (1)
  Zhongyuan Hu (1)
  Shaogui Guo (4)
  Yong Xu (4)
  Mingfang Zhang (1)
  
  1. Laboratory of Genetic Resources and Functional Improvement for Horticultural Plants, Department of Horticulture, Zhejiang University, Hangzhou, 310058, People’s Republic of China
  2. Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People’s Republic of China
  3. Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
  4. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, People’s Republic of China
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Cell Biology
  Biochemistry
  Microbial Genetics and Genomics
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1617-4623

文摘

Grafting is an important agricultural technique widely used to improve plant growth, yield, and adaptation to either biotic or abiotic stresses. However, the molecular mechanisms underlying grafting-induced physiological processes remain unclear. Watermelon (Citrullus lanatus L.) is an important horticultural crop worldwide. Grafting technique is commonly used in watermelon production for improving its tolerance to stresses, especially to the soil-borne fusarium wilt disease. In the present study, we used high-throughput sequencing to perform a genome-wide transcript analysis of scions from watermelon grafted onto bottle gourd and squash rootstocks. Our transcriptome and digital gene expression (DGE) profiling data provided insights into the molecular aspects of gene regulation in grafted watermelon. Compared with self-grafted watermelon, there were 787 and 3485 genes differentially expressed in watermelon grafted onto bottle gourd and squash rootstocks, respectively. These genes were associated with primary and secondary metabolism, hormone signaling, transcription factors, transporters, and response to stimuli. Grafting led to changes in expression of these genes, suggesting that they may play important roles in mediating the physiological processes of grafted seedlings. The potential roles of the grafting-responsive mRNAs in diverse biological and metabolic processes were discussed. Obviously, the data obtained in this study provide an excellent resource for unraveling the mechanisms of candidate genes function in diverse biological processes and in environmental adaptation in a graft system.