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Abstract

Plant biotechnology depends on robust control of trait gene expression to produce an adequate level of protein or RNA in the appropriate cells at the correct time. Early biotechnology products depended on high protein production in most plant cells, and relied on relatively few well-characterized “promoters.” This demand continues and has expanded into other classes of expression control, such as tissue specificity and environmental responsiveness, as new trait technologies are pursued. Genomic information can be leveraged to meet this demand now and well into the future. A method has been developed of identifying donor genes in genomic data, and simplifying their annotation to facilitate design and development of effective expression cassettes. This approach greatly reduces the effort and expense of producing novel trait gene expression tools. Coupled with chemical DNA synthesis technology, this approach makes it possible to develop reliable expression cassettes from virtually any plant gene.

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References

  • Allen GC, Spiker S, Thompson WF (2000) Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol 43:361–376

    Article  CAS  PubMed  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Alvarez-Buylla ER, Liljegren SJ, Pelaz S, Gold SE, Burgeff C, Ditta GS, Vergara-Silva F, Yanofsky MF (2000) MADS-box gene evolution beyond flowers: expression in pollen, endosperm, guard cells, roots and trichomes. Plant J 24:457–466

    Article  CAS  PubMed  Google Scholar 

  • An G (1986) Development of plant promoter expression vectors and their use for analysis of differential activity of nopaline synthase promoter in transformed tobacco cells. Plant Physiol 81:86–91

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ancillo G, Hoegen E, Kombrink E (2003) The promoter of the potato chitinase C gene directs expression to epidermal cells. Planta 217:566–576

    Article  CAS  PubMed  Google Scholar 

  • Barker T, Campos H, Cooper M, Dolan D, Edmeades G, Habben J, Schussler J, Write D, Zinselmeier C (2005) Improving drought tolerance in maize. Plant Breed Rev 25:173–253

    CAS  Google Scholar 

  • Bartlett JG, Snape JW, Harwood WA (2009) Intron-mediated enhancement as a method for increasing transgene expression levels in barley. Plant Biotechnol J 7:856–866

    Article  CAS  PubMed  Google Scholar 

  • Benfey PN, Chua NH (1990) The cauliflower mosaic virus 35S promoter: combinatorial regulation of transcription in plants. Science 250:959–966

    Article  CAS  PubMed  Google Scholar 

  • Birch RG (1997) PLANT TRANSFORMATION: problems and strategies for practical application. Annu Rev Plant Physiol Plant Mol Biol 48:297–326

    Article  CAS  PubMed  Google Scholar 

  • Brodersen P, Voinnet O (2006) The diversity of RNA silencing pathways in plants. Trends Genet 22:268–280

    Article  CAS  PubMed  Google Scholar 

  • Butaye KM, Goderis IJ, Wouters PF, Pues JM, Delaure SL, Broekaert WF, Depicker A, Cammue BP, De Bolle MF (2004) Stable high-level transgene expression in Arabidopsis thaliana using gene silencing mutants and matrix attachment regions. Plant J 39:440–449

    Article  CAS  PubMed  Google Scholar 

  • Cattivelli L, Rizza F, Badeck F-W, Mazzucotelli E, Mastrangelo AM, Francia E, Mare C, Tondelli A, Stanca AM (2008) Drought tolerance improvement in crop plants: an integrated view from breeding to genomics. Field Crops Res 105:1–14

    Article  Google Scholar 

  • Chang CW, Sun TP (2002) Characterization of cis-regulatory regions responsible for developmental regulation of the gibberellin biosynthetic gene GA1 in Arabidopsis thaliana. Plant Mol Biol 49:579–589

    Article  CAS  PubMed  Google Scholar 

  • Chen QJ, Zhou HM, Chen J, Wang XC (2006) A Gateway-based platform for multigene plant transformation. Plant Mol Biol 62:927–936

    Article  CAS  PubMed  Google Scholar 

  • Chodavarapu RK, Feng S, Bernatavichute YV, Chen PY, Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Kramer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466:388–392.

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Christensen AH, Quail PH (1996) Ubiquitin promoter-based vectors for high-level expression of selectable and/or screenable marker genes in monocotyledonous plants. Transgenic Res 5:213–218

    Article  CAS  PubMed  Google Scholar 

  • Cominelli E, Galbiati M, Vavasseur A, Conti L, Sala T, Vuylsteke M, Leonhardt N, Tonelli C (2005) A guard-cell-specific MYB transcription factor regulates stomatal movements and plant drought tolerance. Current Biol 15:1196–1200

    Article  CAS  Google Scholar 

  • Dalakouras A, Dadami E, Zwiebel M, Krczal G, Wassenegger M (2012) Transgenerational maintenance of transgene body CG but not CHG and CHH methylation. Epigenetics 7:1071–1078

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Das M, Harvey I, Chu LL, Sinha M, Pelletier J (2001) Full-length cDNAs: more than just reaching the ends. Physiol Genomics 6:57–80

    CAS  PubMed  Google Scholar 

  • De Bodt S, Raes J, Van de Peer Y, Theissen G (2003) And then there were many: MADS goes genomic. Trends Plant Sci 8:475–483

    Article  CAS  PubMed  Google Scholar 

  • Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36:D959–965

    Google Scholar 

  • Emami S, Arumainayagam D, Korf I, Rose AB (2013) The effects of a stimulating intron on the expression of heterologous genes in Arabidopsis thaliana. Plant Biotechnol J 11:555–563

    Article  CAS  PubMed  Google Scholar 

  • Flavell RB (1994) Inactivation of gene expression in plants as a consequence of specific sequence duplication. Proc Natl Acad Sci U S A 91:3490–3496

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Fujisawa M, Takita E, Harada H, Sakurai N, Suzuki H, Ohyama K, Shibata D, Misawa N (2009) Pathway engineering of Brassica napus seeds using multiple key enzyme genes involved in ketocarotenoid formation. J Exp Bot 60:1319–1332

    Article  CAS  PubMed  Google Scholar 

  • Gallie DR, Walbot V (1992) Identification of the motifs within the tobacco mosaic virus 5′-leader responsible for enhancing translation. Nucleic Acids Res 20:4631–4638

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gibson DG, Benders GA, Axelrod KC, Zaveri J, Algire MA, Moodie M, Montague MG, Venter JC, Smith HO, Hutchison CA 3rd (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic mycoplasma genitalium genome. Proc Natl Acad Sci U S A 105:20404–20409

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang RY, Algire MA, Benders GA, Montague MG, Ma L, Moodie MM, Merryman C, Vashee S, Krishnakumar R, Assad-Garcia N, Andrews-Pfannkoch C, Denisova EA, Young L, Qi ZQ, Segall-Shapiro TH, Calvey CH, Parmar PP, Hutchison CA, 3rd, Smith HO, Venter JC (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52–56

    Article  CAS  PubMed  Google Scholar 

  • Giuliano G, Pichersky E, Malik VS, Timko MP, Scolnik PA, Cashmore AR (1988) An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene. Proc Natl Acad Sci U S A 85:7089–7093

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Gleave AP (1992) A versatile binary vector system with a T-DNA organisational structure conducive to efficient integration of cloned DNA into the plant genome. Plant Mol Biol 20:1203–1207

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. Japonica). Science 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • Gruissem W (1990) Of fingers, zippers and boxes. Plant Cell 2:827–828

    Article  PubMed Central  Google Scholar 

  • Halpin C (2005) Gene stacking in transgenic plants–the challenge for 21st century plant biotechnology. Plant Biotechnol J 3:141–155

    Article  CAS  PubMed  Google Scholar 

  • Halpin C, Cooke SE, Barakate A, Amrani AE, Ryan MD (1999) Self-processing 2A-polyproteins-a system for co-ordinate expression of multiple proteins in transgenic plants. Plant J 17:453–459

    Article  CAS  PubMed  Google Scholar 

  • Hunt AG (1994) Messenger RNA 3′ end formation in plants. Annu Rev Plant Biol 45:47–60

    Article  CAS  Google Scholar 

  • Hunt AG (2008) Messenger RNA 3′ end formation in plants. Curr Top Microbiol Immunol 326:151–177

    CAS  PubMed  Google Scholar 

  • Ingelbrecht IL, Herman LM, Dekeyser RA, Van Montagu MC, Depicker AG (1989) Different 3′ end regions strongly influence the level of gene expression in plant cells. Plant Cell 1:671–680

    PubMed Central  CAS  PubMed  Google Scholar 

  • Ingham DJ, Beer S, Money S, Hansen G (2001) Quantitative real-time PCR assay for determining copy number in transformed plants. Biotech 31:132–140

    CAS  Google Scholar 

  • Jiang L, Yu X, Qi X, Yu Q, Deng S, Bai B, Li N, Zhang A, Zhu C, Liu B, Pang J (2013) Multigene engineering of starch biosynthesis in maize endosperm increases the total starch content and the proportion of amylose. Transgenic Res 22:1133–1142

    Article  CAS  PubMed  Google Scholar 

  • Jordano J, Almoguera C, Thomas TL (1989) A sunflower helianthinin gene upstream sequence ensemble contains an enhancer and sites of nuclear protein interaction. Plant Cell 1:855–866

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458:362–366

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ (2003) The UCSC Genome Browser Database. Nucleic Acids Res 31:51–54

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Katagiri F, Chua NH (1992) Plant transcription factors: present knowledge and future challenges. Trends Genet 8:22–27

    Article  CAS  PubMed  Google Scholar 

  • Kebeish R, Niessen M, Thiruveedhi K, Bari R, Hirsch HJ, Rosenkranz R, Stabler N, Schonfeld B, Kreuzaler F, Peterhansel C (2007) Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana. Nature Biotechnol 25:593–599

    Article  CAS  Google Scholar 

  • Khurana R, Kapoor S, Tyagi AK (2013) Spatial and temporal activity of upstream regulatory regions of rice anther-specific genes in transgenic rice and Arabidopsis. Transgenic Res 22:31–46

    Article  CAS  PubMed  Google Scholar 

  • Kohli A, Griffiths S, Palacios N, Twyman RM, Vain P, Laurie DA, Christou P (1999) Molecular characterization of transforming plasmid rearrangements in transgenic rice reveals a recombination hotspot in the CaMV 35S promoter and confirms the predominance of microhomology mediated recombination. Plant J 17:591–601

    Article  CAS  PubMed  Google Scholar 

  • Korf IF, Rose AB (2009) Applying word-based algorithms: the IMEter. Methods Mol Biol 553:287–301

    Article  CAS  PubMed  Google Scholar 

  • Koyama T, Ono T, Shimizu M, Jinbo T, Mizuno R, Tomita K, Mitsukawa N, Kawazu T, Kimura T, Ohmiya K, Sakka K (2005) Promoter of Arabidopsis thaliana phosphate transporter gene drives root-specific expression of transgene in rice. J Biosci Bioengineer 99:38–42

    Article  CAS  Google Scholar 

  • Kozak M (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299:1–34

    Article  CAS  PubMed  Google Scholar 

  • Koziel MG, Carozzi NB, Desai N (1996) Optimizing expression of transgenes with an emphasis on post-transcriptional events. Plant Mol Biol 32:393–405

    Article  CAS  PubMed  Google Scholar 

  • Kudla G, Murray AW, Tollervey D, Plotkin JB (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255–258

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Law JA, Jacobsen SE (2009) Dynamic DNA methylation. Science 323:1568–1569

    Article  CAS  PubMed  Google Scholar 

  • Lee M, Nuccio M, Clarke J, Inventors (2013) Plant regulatory Sequences. United States Patent 8,344,209, granted January 1, 2013

    Google Scholar 

  • Lessard PA, Kulaveerasingam, H, York, GM, Strong, A, Sinskey, AJ (2002) Manipulating gene expression for the metabolic engineering of plants. Metabolic Eng 4:67–79

    Article  CAS  Google Scholar 

  • Liang C, Jaiswal P, Hebbard C, Avraham S, Buckler ES, Casstevens T, Hurwitz B, McCouch S, Ni J, Pujar A, Ravenscroft D, Ren L, Spooner W, Tecle I, Thomason J, Tung CW, Wei X, Yap I, Youens-Clark K, Ware D, Stein L (2008) Gramene: a growing plant comparative genomics resource. Nucleic Acids Res 36:D947–953

    Article  Google Scholar 

  • Lidder P, Gutierrez RA, Salome PA, McClung CR, Green PJ (2005) Circadian control of messenger RNA stability. association with a sequence-specific messenger RNA decay pathway. Plant Physiol 138:2374–2385

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Liu ZZ, Wang JL, Huang X, Xu WH, Liu ZM, Fang RX (2003) The promoter of a rice glycine-rich protein gene, Osgrp-2, confers vascular-specific expression in transgenic plants. Planta 216:824–833

    CAS  PubMed  Google Scholar 

  • Lopez I, Anthony RG, Maciver SK, Jiang CJ, Khan S, Weeds AG, Hussey PJ (1996) Pollen specific expression of maize genes encoding actin depolymerizing factor-like proteins. Proc Natl Acad Sci U S A 93:7415–7420

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Luehrsen KR, Walbot V (1991) Intron enhancement of gene expression and the splicing efficiency of introns in maize cells. Mol Gen Genet 225:81–93

    Article  CAS  PubMed  Google Scholar 

  • Maas C, Laufs J, Grant S, Korfhage C, Werr W (1991) The combination of a novel stimulatory element in the first exon of the maize Shrunken-1 gene with the following intron 1 enhances reporter gene expression up to 1000-fold. Plant Mol Biol 16:199–207

    Article  CAS  PubMed  Google Scholar 

  • McElroy D, Zhang W, Cao J, Wu R (1990) Isolation of an efficient actin promoter for use in rice transformation. Plant Cell 2:163–171

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Mehrotra R, Gupta G, Sethi R, Bhalothia P, Kumar N, Mehrotra S (2011) Designer promoter: an artwork of cis engineering. Plant Mol Biol 75:527–536

    Article  CAS  PubMed  Google Scholar 

  • Moore MJ, Proudfoot NJ (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136:688–700

    Article  CAS  PubMed  Google Scholar 

  • Naqvi S, Zhu C, Farre G, Ramessar K, Bassie L, Breitenbach J, Perez Conesa D, Ros G, Sandmann G, Capell T, Christou P (2009) Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways. Proc Natl Acad Sci U S A 106:7762–7767

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Nuccio M, Inventor (2013) Guard cell expression cassettes compositions and methods of use thereof. United States Patent Application No. 61/787,781, filed 15 March 2013

    Google Scholar 

  • Nuccio M, Richmond A, Inventors (2013) Epidermal tissue promoter derived from potato for monocots. United States Patent 8,304,607, granted 6 Nov 2012

    Google Scholar 

  • Nuccio ML (1997) Identification and characterization of ATS1 and ATS3, two novel seed-specific genes in Arabidopsis thaliana. PhD Thesis, Texas A & M University, College Station

    Google Scholar 

  • Nuccio ML, Lagrimini LM, Meghji M, Inventors (2012) Regulatory sequences for expressing gene products in plant reproductive tissue. United States Patent 8,129,588, granted 6 March 2012

    Google Scholar 

  • Nunberg AN, Li Z, Bogue MA, Vivekananda J, Reddy AS, Thomas TL (1994) Developmental and hormonal regulation of sunflower helianthinin genes: proximal promoter sequences confer regionalized seed expression. Plant Cell 6:473–486

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, Childs K, Thibaud-Nissen F, Malek RL, Lee Y, Zheng L, Orvis J, Haas B, Wortman J, Buell CR (2007) The TIGR rice genome annotation resource: improvements and new features. Nucleic Acids Res 35:D883–887

    Article  Google Scholar 

  • Palmer KE, Thomson JA, Rybicki EP (1999) Generation of maize cell lines containing autonomously replicating maize streak virus-based gene vectors. Arch Virol 144:1345–1360

    Article  CAS  PubMed  Google Scholar 

  • Parra G, Bradnam K, Rose AB, Korf I (2011) Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants. Nucleic Acids Res 39:5328–5337

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Peremarti A, Twyman RM, Gomez-Galera S, Naqvi S, Farre G, Sabalza M, Miralpeix B, Dashevskaya S, Yuan D, Ramessar K, Christou P, Zhu C, Bassie L, Capell T (2010) Promoter diversity in multigene transformation. Plant Mol Biol 73:363–378

    Article  CAS  PubMed  Google Scholar 

  • Pimentel DS, Raven PH (2000) Bt corn pollen impacts on nontarget lepidoptera: assessment of effects in nature. Proc Natl Acad Sci U S A 97:8198–8199

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Potenza C, Aleman L, Sengupta-Gopalan C (2004) Targeting Transgene expression in research, agrigultural, and environmental applications: promoters used in plant transformation. In Vitro Cell Dev Biol Plant 40:1–22

    Article  CAS  Google Scholar 

  • Que Q, Chilton MD, de Fontes CM, He C, Nuccio M, Zhu T, Wu Y, Chen JS, Shi L (2010) Trait stacking in transgenic crops: challenges and opportunities. GM Crops 1:220–229

    Article  PubMed  Google Scholar 

  • Raab JR, Kamakaka RT (2010) Insulators and promoters: closer than we think. Nat Rev Genet 11:439–446

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Ritchie SW, Hanway JJ, Benson GO (1992) How a corn plant develops. Special Report No. 48, Iowa State University of Science and Technology, Ames, Iowa: 1–21

    Google Scholar 

  • Rombauts S, Florquin K, Lescot M, Marchal K, Rouze P, van de Peer Y (2003) Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol 132:1162–1176

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rose AB (2004) The effect of intron location on intron-mediated enhancement of gene expression in Arabidopsis. Plant J 40:744–751

    Article  CAS  PubMed  Google Scholar 

  • Rose AB, Elfersi T, Parra G, Korf I (2008) Promoter-proximal introns in Arabidopsis thaliana are enriched in dispersed signals that elevate gene expression. Plant Cell 20:543–551

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Rothnie HM (1996) Plant mRNA 3′-end formation. Plant Mol Biol 32:43–61

    Article  CAS  PubMed  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Press, Cold Spring Harbor, pp 999

    Google Scholar 

  • Sanger M, Daubert S, Goodman RM (1990) Characteristics of a strong promoter from figwort mosaic virus: comparison with the analogous 35S promoter from cauliflower mosaic virus and the regulated mannopine synthase promoter. Plant Mol Biol 14:433–443

    Article  CAS  PubMed  Google Scholar 

  • Schulze-Lefert P, Becker-Andre M, Schulz W, Hahlbrock K, Dangl JL (1989) Functional architecture of the light-responsive chalcone synthase promoter from parsley. Plant Cell 1:707–714

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Schünmann PHD, Surin B, Waterhouse PM (2003) A suite of novel promoters and terminators for plant biotechnology. II. The pPLEX series for use in monocots. Funct Plant Biol 30:453–460

    Article  Google Scholar 

  • Sieburth LE, Meyerowitz EM (1997) Molecular dissection of the AGAMOUS control region shows that cis elements for spatial regulation are located intragenically. Plant Cell 9:355–365

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Skirycz A, Vandenbroucke K, Clauw P, Maleux K, De Meyer B, Dhondt S, Pucci A, Gonzalez N, Hoeberichts F, Tognetti VB, Galbiati M, Tonelli C, Van Breusegem F, Vuylsteke M, Inze D (2011) Survival and growth of Arabidopsis plants given limited water are not equal. Nature Biotechnol 29:212–214

    Article  CAS  Google Scholar 

  • Springer NM (2013) Epigenetics and crop improvement. Trends Genet 29:241–247

    Article  CAS  PubMed  Google Scholar 

  • Vaucheret H (2006) Post-transcriptional small RNA pathways in plants: mechanisms and regulations. Genes Dev 20:759–771

    Article  CAS  PubMed  Google Scholar 

  • Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17:29–35

    Article  CAS  PubMed  Google Scholar 

  • Venter M (2007) Synthetic promoters: genetic control through cis engineering. Trends Plant Sci 12:118–124

    Article  CAS  PubMed  Google Scholar 

  • Voinnet O, Vain P, Angell S, Baulcombe DC (1998) Systemic spread of sequence-specific transgene RNA degradation in plants is initiated by localized introduction of ectopic promoterless DNA. Cell 95:177–187

    Article  CAS  PubMed  Google Scholar 

  • Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR (2007) Riboswitch control of gene expression in plants by splicing and alternative 3′ end processing of mRNAs. Plant Cell 19:3437–3450

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Walschus U, Witt S, Wittmann C (2002) Development of monoclonal antibodies against Cry1Ab protein from Bacillus thuringiensis and their application in an ELISA for detection of transgenic Bt-maize. Food Agric Immunol 14:231–240

    Article  CAS  Google Scholar 

  • Wheelan SJ, Church DM, Ostell JM (2001) Spidey: a tool for mRNA-to-genomic alignments. Genome Res 11:1952–1957

    PubMed Central  CAS  PubMed  Google Scholar 

  • Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS (2001) Assessing gene significance from cDNA microarray expression data via mixed models. J Comput Biol 8:625–637

    Article  CAS  PubMed  Google Scholar 

  • Xing A, Moon BP, Mills KM, Falco SC, Li Z (2010) Revealing frequent alternative polyadenylation and widespread low-level transcription read-through of novel plant transcription terminators. Plant Biotechnol J 8:772–782

    Article  CAS  PubMed  Google Scholar 

  • Yang Y, Costa A, Leonhardt N, Siegel RS, Schroeder JI (2008) Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool. Plant Methods 4:1–15

    Article  Google Scholar 

  • Yu H, Goh CJ (2000) Identification and characterization of three orchid MADS-box genes of the AP1/AGL9 subfamily during floral transition. Plant Physiol 123:1325–1336

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhao H, Zheng J, Li QQ (2011) A novel plant in vitro assay system for pre-mRNA cleavage during 3′-end formation. Plant Physiol 157:1546–1554

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zhu C, Naqvi S, Breitenbach J, Sandmann G, Christou P, Capell T (2008) Combinatorial genetic transformation generates a library of metabolic phenotypes for the carotenoid pathway in maize. Proc Natl Acad Sci U S A 105:18232–18237

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W (2004) GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol 136:2621–2632

    Article  PubMed Central  CAS  PubMed  Google Scholar 

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Nuccio, M., Chen, X., Conville, J., Zhou, A., Liu, X. (2015). Plant Trait Gene Expression Cassette Design. In: Azhakanandam, K., Silverstone, A., Daniell, H., Davey, M. (eds) Recent Advancements in Gene Expression and Enabling Technologies in Crop Plants. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-2202-4_2

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