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Genomeless Genomics in Crop Improvement

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Genomics-Assisted Crop Improvement

Abstract

The DNA sequencing of the entire nuclear genomes from Arabidopsis, rice and poplar has facilitated the broad-adoption of contemporary research techniques that extend far beyond the study of individual genes. New post-genomic technologies such as microarray based genome-scale gene expression profiling and proteome analysis are absolutely dependent on deep sequence coverage of the gene-space, but have an immense potential to drive the research community in exciting new directions. Facets of many crop genomes currently preclude them from complete sequencing, but the broadest adoption of post-genomic technologies is essential to make in-roads in plant biotechnology and crop improvement. A variety of technologies are available that can be used to establish a genomics foothold in even the most recalcitrant of crop plant species. In this review we address the fundamental technologies that are being widely adopted within the crop-plant research community to gain such a foothold. By considering primarily the expressed sequence tag resources, we have explored how even moderately simple genomic resources may be exploited in molecular marker development, candidate gene selection and microarray-based gene expression profiling.

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References

  • Adams KL, Wendel JF (2005) Polyploidy and genome evolution in plants. Curr Opin Plant Biol 8:135–141

    PubMed  CAS  Google Scholar 

  • Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, George RA, Lewis SE, Richards S, Ashburner M, Henderson SN, Sutton GG, Wortman JR, Yandell MD, Zhang Q, Chen LX, Brandon RC, Rogers YH, Blazej RG, Champe M, Pfeiffer BD, Wan KH, Doyle C, Baxter EG, Helt G, Nelson CR, Gabor GL, Abril JF, Agbayani A, An HJ, Andrews-Pfannkoch C, Baldwin D, Ballew RM, Basu A, Baxendale J, Bayraktaroglu L, Beasley EM, Beeson KY, Benos PV, Berman BP, Bhandari D, Bolshakov S, Borkova D, Botchan MR, Bouck J, Brokstein P, Brottier P, Burtis KC, Busam DA, Butler H, Cadieu E, Center A, Chandra I, Cherry JM, Cawley S, Dahlke C, Davenport LB, Davies P, de Pablos B, Delcher A, Deng Z, Mays AD, Dew I, Dietz SM, Dodson K, Doup LE, Downes M, Dugan-Rocha S, Dunkov BC, Dunn P, Durbin KJ, Evangelista CC, Ferraz C, Ferriera S, Fleischmann W, Fosler C, Gabrielian AE, Garg NS, Gelbart WM, Glasser K, Glodek A, Gong F, Gorrell JH, Gu Z, Guan P, Harris M, Harris NL, Harvey D, Heiman TJ, Hernandez JR, Houck J, Hostin D, Houston KA, Howland TJ, Wei MH, Ibegwam C, Jalali M, Kalush F, Karpen GH, Ke Z, Kennison JA, Ketchum KA, Kimmel BE, Kodira CD, Kraft C, Kravitz S, Kulp D, Lai Z, Lasko P, Lei Y, Levitsky AA, Li J, Li Z, Liang Y, Lin X, Liu X, Mattei B, McIntosh TC, McLeod MP, McPherson D, Merkulov G, Milshina NV, Mobarry C, Morris J, Moshrefi A, Mount SM, Moy M, Murphy B, Murphy L, Muzny DM, Nelson DL, Nelson DR, Nelson KA, Nixon K, Nusskern DR, Pacleb JM, Palazzolo M, Pittman GS, Pan S, Pollard J, Puri V, Reese MG, Reinert K, Remington K, Saunders RD, Scheeler F, Shen H, Shue BC, Siden-Kiamos I, Simpson M, Skupski MP, Smith T, Spier E, Spradling AC, Stapleton M, Strong R, Sun E, Svirskas R, Tector C, Turner R, Venter E, Wang AH, Wang X, Wang ZY, Wassarman DA, Weinstock GM, Weissenbach J, Williams SM, Woodage T, Worley KC, Wu D, Yang S, Yao QA, Ye J, Yeh RF, Zaveri JS, Zhan M, Zhang G, Zhao Q, Zheng L, Zheng XH, Zhong FN, Zhong W, Zhou X, Zhu S, Zhu X, Smith HO, Gibbs RA, Myers EW, Rubin GM, Venter JC (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195

    PubMed  Google Scholar 

  • Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF et al (1991) Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252:1651–1656

    PubMed  CAS  Google Scholar 

  • AGI T (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Google Scholar 

  • Aharoni A, Giri AP, Verstappen FW, Bertea CM, Sevenier R, Sun Z, Jongsma MA, Schwab W, Bouwmeester HJ (2004) Gain and loss of fruit flavor compounds produced by wild and cultivated strawberry species. Plant Cell 16:3110–3131

    PubMed  CAS  Google Scholar 

  • Albert VA, Soltis DE, Carlson JE, Farmerie WG, Wall PK, Ilut DC, Solow TM, Mueller LA, Landherr LL, Hu Y, Buzgo M, Kim S, Yoo MJ, Frohlich MW, Perl-Treves R, Schlarbaum SE, Bliss BJ, Zhang X, Tanksley SD, Oppenheimer DG, Soltis PS, Ma H, DePamphilis CW, Leebens-Mack JH (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol 5:5

    PubMed  Google Scholar 

  • Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7:55–65

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Alwine JC, Kemp DJ, Stark GR (1977) Method for detection of specific RNAs in agarose gels by transfer to diazobenzyloxymethyl-paper and hybridization with DNA probes. Proc Natl Acad Sci USA 74:5350–5354

    PubMed  CAS  Google Scholar 

  • Antonius K, Ahokas H (1996) Flow cytometric determination of polyploidy level in spontaneous clones of strawberries. Hereditas 124:285

    Google Scholar 

  • Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 15:487–495

    PubMed  Google Scholar 

  • Barkley NA, Newman ML, Wang ML, Hotchkiss MW, Pederson GA (2005) Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers. Genome 48:731–737

    PubMed  CAS  Google Scholar 

  • Bedell JA, Budiman MA, Nunberg A, Citek RW, Robbins D, Jones J, Flick E, Rholfing T, Fries J, Bradford K, McMenamy J, Smith M, Holeman H, Roe BA, Wiley G, Korf IF, Rabinowicz PD, Lakey N, McCombie WR, Jeddeloh JA, Martienssen RA (2005) Sorghum genome sequencing by methylation filtration. PLoS Biol 3:e13

    PubMed  Google Scholar 

  • Beldade P, Rudd S, Gruber JD, Long AD (2006) A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model. BMC Genomics 7:130

    PubMed  Google Scholar 

  • Bennett M, Leitch I (2003) Plant DNA C-values database. release 2.0, January 2003 edn

    Google Scholar 

  • Blanc G, Wolfe KH (2004a) Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution. Plant Cell 16:1679–1691

    CAS  Google Scholar 

  • Blanc G, Wolfe KH (2004b) Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16:1667–1678

    CAS  Google Scholar 

  • Boguski MS, Lowe TM, Tolstoshev CM (1993) dbEST – database for “expressed sequence tags”. Nat Genet 4:332–333

    PubMed  CAS  Google Scholar 

  • Borevitz J (2006) Genotyping and mapping with high-density oligonucleotide arrays. Methods Mol Biol 323:137–145

    PubMed  CAS  Google Scholar 

  • Buchanan CD, Lim S, Salzman RA, Kagiampakis I, Morishige DT, Weers BD, Klein RR, Pratt LH, Cordonnier-Pratt MM, Klein PE, Mullet JE (2005) Sorghum bicolor’s transcriptome response to dehydration, high salinity and ABA. Plant Mol Biol 58:699–720

    PubMed  CAS  Google Scholar 

  • C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018

    Google Scholar 

  • Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WE, Wetter T, Suhai S (2004) Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Res 14:1147–1159

    PubMed  CAS  Google Scholar 

  • Cochrane G, Aldebert P, Althorpe N, Andersson M, Baker W, Baldwin A, Bates K, Bhattacharyya S, Browne P, van den Broek A, Castro M, Duggan K, Eberhardt R, Faruque N, Gamble J, Kanz C, Kulikova T, Lee C, Leinonen R, Lin Q, Lombard V, Lopez R, McHale M, McWilliam H, Mukherjee G, Nardone F, Pastor MP, Sobhany S, Stoehr P, Tzouvara K, Vaughan R, Wu D, Zhu W, Apweiler R (2006) EMBL nucleotide sequence database: developments in 2005. Nucleic Acids Res 34:D10–15

    PubMed  CAS  Google Scholar 

  • Delseny M, Cooke R, Raynal M, Grellet F (1997) The Arabidopsis thaliana cDNA sequencing projects. FEBS Lett 403:221–224

    PubMed  CAS  Google Scholar 

  • Derory J, Leger P, Garcia V, Schaeffer J, Hauser MT, Salin F, Luschnig C, Plomion C, Glossl J, Kremer A (2006) Transcriptome analysis of bud burst in sessile oak (Quercus petraea). New Phytol 170:723–738

    PubMed  CAS  Google Scholar 

  • Dong Q, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32:D354–359

    PubMed  CAS  Google Scholar 

  • Duplessis S, Courty PE, Tagu D, Martin F (2005) Transcript patterns associated with ectomycorrhiza development in Eucalyptus globulus and Pisolithus microcarpus. New Phytol 165:599–611

    PubMed  CAS  Google Scholar 

  • Egertsdotter U, van Zyl LM, MacKay J, Peter G, Kirst M, Clark C, Whetten R, Sederoff R (2004) Gene expression during formation of earlywood and latewood in loblolly pine: expression profiles of 350 genes. Plant Biol (Stuttg) 6:654–663

    CAS  Google Scholar 

  • Forment J, Gadea J, Huerta L, Abizanda L, Agusti J, Alamar S, Alos E, Andres F, Arribas R, Beltran JP, Berbel A, Blazquez MA, Brumos J, Canas LA, Cercos M, Colmenero-Flores JM, Conesa A, Estables B, Gandia M, Garcia-Martinez JL, Gimeno J, Gisbert A, Gomez G, Gonzalez-Candelas L, Granell A, Guerri J, Lafuente MT, Madueno F, Marcos JF, Marques MC, Martinez F, Martinez-Godoy MA, Miralles S, Moreno P, Navarro L, Pallas V, Perez-Amador MA, Perez-Valle J, Pons C, Rodrigo I, Rodriguez PL, Royo C, Serrano R, Soler G, Tadeo F, Talon M, Terol J, Trenor M, Vaello L, Vicente O, Vidal C, Zacarias L, Conejero V (2005) Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Mol Biol 57:375–391

    PubMed  CAS  Google Scholar 

  • Friedman WE, Cook ME (2000) The origin and early evolution of tracheids in vascular plants: integration of palaeobotanical and neobotanical data. Philos Trans R Soc Lond B Biol Sci 355:857–868

    PubMed  CAS  Google Scholar 

  • Gaafar RM, Hohmann U, Jung C (2005) Bacterial artificial chromosome-derived molecular markers for early bolting in sugar beet. Theor Appl Genet 110:1027–1037

    PubMed  CAS  Google Scholar 

  • Garcia-Hernandez M, Berardini TZ, Chen G, Crist D, Doyle A, Huala E, Knee E, Lambrecht M, Miller N, Mueller LA, Mundodi S, Reiser L, Rhee SY, Scholl R, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P (2002) TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics 2:239–253

    PubMed  CAS  Google Scholar 

  • Gardiner J, Schroeder S, Polacco ML, Sanchez-Villeda H, Fang Z, Morgante M, Landewe T, Fengler K, Useche F, Hanafey M, Tingey S, Chou H, Wing R, Soderlund C, Coe Jr. EH (2004) Anchoring 9,371 maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiol 134:1317–1326

    PubMed  Google Scholar 

  • Graham J, Smith K, MacKenzie K, Jorgenson L, Hackett C, Powell W (2004) The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theor Appl Genet 109:740–749

    PubMed  CAS  Google Scholar 

  • Grapes L, Rudd S, Fernando RL, Megy K, Rocha D, Rothschild MF (2006) Prospecting for pig single nucleotide polymorphisms in the human genome: have we struck gold? J Anim Breed Genet 123:145–151

    PubMed  CAS  Google Scholar 

  • Grif VG, Valovich EM, Levbedeva NV (1980) Parameters of the mitotic cycle in two species of Trillium L. Tsitologiya 22:1331–1338

    CAS  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    PubMed  CAS  Google Scholar 

  • Haberer G, Young S, Bharti AK, Gundlach H, Raymond C, Fuks G, Butler E, Wing RA, Rounsley S, Birren B, Nusbaum C, Mayer KF, Messing J (2005) Structure and architecture of the maize genome. Plant Physiol 139:1612–1624

    PubMed  CAS  Google Scholar 

  • Hegarty MJ, Jones JM, Wilson ID, Barker GL, Coghill JA, Sanchez-Baracaldo P, Liu G, Buggs RJ, Abbott RJ, Edwards KJ, Hiscock SJ (2005) Development of anonymous cDNA microarrays to study changes to the Senecio floral transcriptome during hybrid speciation. Mol Ecol 14:2493–2510

    PubMed  CAS  Google Scholar 

  • Hong CP, Lee SJ, Park JY, Plaha P, Park YS, Lee YK, Choi JE, Kim KY, Lee JH, Lee J, Jin H, Choi SR, Lim YP (2004) Construction of a BAC library of Korean ginseng and initial analysis of BAC-end sequences. Mol Genet Genomics 271:709–716

    PubMed  CAS  Google Scholar 

  • Hubbard T, Andrews D, Caccamo M, Cameron G, Chen Y, Clamp M, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Gilbert J, Hammond M, Herrero J, Hotz H, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Keenan S, Kokocinsci F, London D, Longden I, McVicker G, Melsopp C, Meidl P, Potter S, Proctor G, Rae M, Rios D, Schuster M, Searle S, Severin J, Slater G, Smedley D, Smith J, Spooner W, Stabenau A, Stalker J, Storey R, Trevanion S, Ureta–Vidal A, Vogel J, White S, Woodwark C, Birney E (2005) Ensembl 2005. Nucleic Acids Res 33:D447–453

    PubMed  CAS  Google Scholar 

  • Huntley D, Baldo A, Johri S, Sergot M (2006) SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics 22:495–496

    PubMed  CAS  Google Scholar 

  • Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES (2003) Whole-genome sequence assembly for mammalian genomes: arachne 2. Genome Res 13:91–96

    PubMed  CAS  Google Scholar 

  • Jia Y, Anderson JV, Horvath DP, Gu YQ, Lym RG, Chao WS (2006) Subtractive cDNA libraries identify differentially expressed genes in dormant and growing buds of leafy spurge (Euphorbia esula). Plant Mol Biol 61:329–344

    PubMed  CAS  Google Scholar 

  • Karlowski WM, Schoof H, Janakiraman V, Stuempflen V, Mayer KF (2003) MOsDB: an integrated information resource for rice genomics. Nucleic Acids Res 31:190–192

    PubMed  CAS  Google Scholar 

  • Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR (2005) Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 15:496–504

    PubMed  CAS  Google Scholar 

  • Kim BH, von Arnim AG (2006) The early dark-response in Arabidopsis thaliana revealed by cDNA microarray analysis. Plant Mol Biol 60:321–342

    PubMed  CAS  Google Scholar 

  • Kim KM, Cho SK, Shin SH, Kim GT, Lee JH, Oh BJ, Kang KH, Hong JC, Choi JY, Shin JS, Chung YS (2005) Analysis of differentially expressed transcripts of fungal elicitor- and wound-treated wild rice (Oryza grandiglumis). J Plant Res 118:347–354

    PubMed  CAS  Google Scholar 

  • Kota R, Rudd S, Facius A, Kolesov G, Thiel T, Zhang H, Stein N, Mayer K, Graner A (2003) Snipping polymorphisms from large EST collections in barley (Hordeum vulgare L.). Mol Genet Genomics 270:24–33

    PubMed  CAS  Google Scholar 

  • Kumar A, Bennetzen JL (2000) Retrotransposons: central players in the structure, evolution and function of plant genomes. Trends Plant Sci 5:509–510

    PubMed  CAS  Google Scholar 

  • Lagudah ES, Moullet O, Appels R (1997) Map-based cloning of a gene sequence encoding a nucleotide-binding domain and a leucine-rich region at the Cre3 nematode resistance locus of wheat. Genome 40:659–665

    PubMed  CAS  Google Scholar 

  • Laitinen RA, Immanen J, Auvinen P, Rudd S, Alatalo E, Paulin L, Ainasoja M, Kotilainen M, Koskela S, Teeri TH, Elomaa P (2005) Analysis of the floral transcriptome uncovers new regulators of organ determination and gene families related to flower organ differentiation in Gerbera hybrida (Asteraceae). Genome Res 15:475–486

    PubMed  Google Scholar 

  • Lamoureux D, Peterson DG, Li W, Fellers JP, Gill BS (2005) The efficacy of Cot-based gene enrichment in wheat (Triticum aestivum L.). Genome 48:1120–1126

    PubMed  CAS  Google Scholar 

  • Lawrence CJ, Seigfried TE, Brendel V (2005) The maize genetics and genomics database. The community resource for access to diverse maize data. Plant Physiol 138:55–58

    CAS  Google Scholar 

  • Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C (2005) ESTree db: a tool for peach functional genomics. BMC Bioinform 6:S16

    Google Scholar 

  • Lee Y, Tsai J, Sunkara S, Karamycheva S, Pertea G, Sultana R, Antonescu V, Chan A, Cheung F, Quackenbush J (2005) The TIGR gene indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Res 33:D71–74

    PubMed  CAS  Google Scholar 

  • Lim KJ (2005) Utilization of microarray technology for identification of disease response genes in banana (Musa spp.). Universiti Putra Malaysia

    Google Scholar 

  • Ling P, Chen XM (2005) Construction of a hexaploid wheat (Triticum aestivum L.) bacterial artificial chromosome library for cloning genes for stripe rust resistance. Genome 48:1028–1036

    PubMed  CAS  Google Scholar 

  • Lopez C, Soto M, Restrepo S, Piegu B, Cooke R, Delseny M, Tohme J, Verdier V (2005) Gene expression profile in response to Xanthomonas axonopodis pv. manihotis infection in cassava using a cDNA microarray. Plant Mol Biol 57:393–410

    PubMed  CAS  Google Scholar 

  • Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Huihuang Y, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC (2001) Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44:572–581

    PubMed  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, vSimons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  • Marth GT (2003) Computational SNP discovery in DNA sequence data. Methods Mol Biol 212:85–110

    PubMed  CAS  Google Scholar 

  • Matsuoka K, Demura T, Galis I, Horiguchi T, Sasaki M, Tashiro G, Fukuda H (2004) A comprehensive gene expression analysis toward the understanding of growth and differentiation of tobacco BY-2 cells. Plant Cell Physiol 45:1280–1289

    PubMed  Google Scholar 

  • Matukumalli LK, Grefenstette JJ, Hyten DL, Choi IY, Cregan PB, Van Tassell CP (2006) Application of machine learning in SNP discovery. BMC Bioinform 7:4

    Google Scholar 

  • May RM (1990) How many species? Phil Trans Roy Soc B330:292–304

    Google Scholar 

  • Mayer K, Mewes HW (2002) How can we deliver the large plant genomes? Strategies and perspectives. Curr Opin Plant Biol 5:173–177

    PubMed  CAS  Google Scholar 

  • Meyers BC, Tingey SV, Morgante M (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res 11:1660–1676

    PubMed  CAS  Google Scholar 

  • Mian MA, Saha MC, Hopkins AA, Wang ZY (2005) Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses. Genome 48:637–647

    PubMed  CAS  Google Scholar 

  • Ming R, Liu SC, Moore PH, Irvine JE, Paterson AH (2001) QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane. Genome Res 11:2075–2084

    PubMed  CAS  Google Scholar 

  • Morgante M (2006) Plant genome organisation and diversity: the year of the junk! Curr Opin Biotechnol 17:168–173

    PubMed  CAS  Google Scholar 

  • Moyle RL, Crowe ML, Ripi-Koia J, Fairbairn DJ, Botella JR (2005) PineappleDB: an online pineapple bioinformatics resource. BMC Plant Biol 5:21

    PubMed  Google Scholar 

  • Myers EW (2005) The fragment assembly string graph. Bioinformatics 21:ii79–ii85

    PubMed  CAS  Google Scholar 

  • Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kavitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC (2000) A whole-genome assembly of Drosophila. Science 287:2196–2204

    PubMed  CAS  Google Scholar 

  • Myers EW, Sutton GG, Smith HO, Adams MD, Venter JC (2002) On the sequencing and assembly of the human genome. Proc Natl Acad Sci USA 99:4145–4146

    PubMed  CAS  Google Scholar 

  • Nakano T, Suzuki K, Ohtsuki N, Tsujimoto Y, Fujimura T, Shinshi H (2006) Identification of genes of the plant-specific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana. J Plant Res 119:407–413

    PubMed  CAS  Google Scholar 

  • Nekrutenko A, Baker RJ (2003) Subgenome-specific markers in allopolyploid cotton Gossypium hirsutum: implications for evolutionary analysis of polyploids. Gene 306:99–103

    PubMed  CAS  Google Scholar 

  • Oono Y, Seki M, Satou M, Iida K, Akiyama K, Sakurai T, Fujita M, Yamaguchi-Shinozaki K, Shinozaki K (2006) Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays. Funct Integr Genomics:1–23

    Google Scholar 

  • Palmer LE, Rabinowicz PD, O’Shaughnessy AL, Balija VS, Nascimento LU, Dike S, de la Bastide M, Martienssen RA, McCombie WR (2003) Maize genome sequencing by methylation filtration. Science 302:2115–2117

    PubMed  Google Scholar 

  • Paterson AH (2006) Leafing through the genomes of our major crop plants: strategies for capturing unique information. Nat Rev Genet 7:174–184

    PubMed  CAS  Google Scholar 

  • Peterson DG, Schulze SR, Sciara EB, Lee SA, Bowers JE, Nagel A, Jiang N, Tibbitts DC, Wessler SR, Paterson AH (2002a) Integration of Cot analysis, DNA cloning, and high-throughput sequencing facilitates genome characterization and gene discovery. Genome Res 12:795–807

    CAS  Google Scholar 

  • Peterson DG, Wessler SR, Paterson AH (2002b) Efficient capture of unique sequences from eukaryotic genomes. Trends Genet 18:547–550

    CAS  Google Scholar 

  • Pryer KM, Schneider H, Zimmer EA, Banks JA (2002) Deciding among green plants for whole genome studies. Trends Plant Sci 7:550–554

    PubMed  CAS  Google Scholar 

  • Puthoff DP, Smigocki AC (2007) Insect feeding-induced differential expression of Beta vulgaris root genes and their regulation by defense-associated signals. Plant Cell Rep 26:71–84

    PubMed  CAS  Google Scholar 

  • Rabinowicz PD, McCombie WR, Martienssen RA (2003) Gene enrichment in plant genomic shotgun libraries. Curr Opin Plant Biol 6:150–156

    PubMed  CAS  Google Scholar 

  • Rabinowicz PD, Schutz K, Dedhia N, Yordan C, Parnell LD, Stein L, McCombie WR, Martienssen RA (1999) Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome. Nat Genet 23:305–308

    PubMed  CAS  Google Scholar 

  • Reed JL, Famili I, Thiele I, Palsson BO (2006) Towards multidimensional genome annotation. Nat Rev Genet 7:130–141

    PubMed  CAS  Google Scholar 

  • Rensink WA, Iobst S, Hart A, Stegalkina S, Liu J, Buell CR (2005) Gene expression profiling of potato responses to cold, heat, and salt stress. Funct Integr Genomics 5:201–207

    PubMed  CAS  Google Scholar 

  • Richmond T, Somerville S (2000) Chasing the dream: plant EST microarrays. Curr Opin Plant Biol 3:108–116

    PubMed  CAS  Google Scholar 

  • Rickert AM, Ballvora A, Matzner U, Klemm M, Gebhardt C (2005) Quantitative genotyping of single-nucleotide polymorphisms by allele-specific oligonucleotide hybridization on DNA microarrays. Biotechnol Appl Biochem 42:93–96

    PubMed  CAS  Google Scholar 

  • Rudd S (2003) Expressed sequence tags: alternative or complement to whole genome sequences? Trends Plant Sci 8:321–329

    PubMed  CAS  Google Scholar 

  • Rudd S (2005) openSputnik – a database to ESTablish comparative plant genomics using unsaturated sequence collections. Nucleic Acids Res 33 Database Issue:D622–627

    Google Scholar 

  • Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791

    PubMed  Google Scholar 

  • SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20:43–45

    PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    PubMed  CAS  Google Scholar 

  • Schmidt DD, Voelckel C, Hartl M, Schmidt S, Baldwin IT (2005) Specificity in ecological interactions: attack from the same lepidopteran herbivore results in species-specific transcriptional responses in two solanaceous host plants. Plant Physiol 138:1763–1773

    PubMed  CAS  Google Scholar 

  • Schoof H, Ernst R, Nazarov V, Pfeifer L, Mewes HW, Mayer KF (2004) MIPS Arabidopsis thaliana Database (MAtDB): an integrated biological knowledge resource for plant genomics. Nucleic Acids Res 32:D373–376

    PubMed  CAS  Google Scholar 

  • Schoof H, Spannagl M, Yang L, Ernst R, Gundlach H, Haase D, Haberer G, Mayer KF (2005) Munich information center for protein sequences plant genome resources: a framework for integrative and comparative analyses 1(W). Plant Physiol 138:1301–1309

    PubMed  CAS  Google Scholar 

  • Shi YH, Zhu SW, Mao XZ, Feng JX, Qin YM, Zhang L, Cheng J, Wei LP, Wang ZY, Zhu YX (2006) Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation. Plant Cell 18:651–664

    PubMed  CAS  Google Scholar 

  • Shirasawa K, Shiokai S, Yamaguchi M, Kishitani S, Nishio T (2006) Dot-blot-SNP analysis for practical plant breeding and cultivar identification in rice. Theor Appl Genet 113:147–155

    PubMed  CAS  Google Scholar 

  • Soeda Y, Konings MC, Vorst O, van Houwelingen AM, Stoopen GM, Maliepaard CA, Kodde J, Bino RJ, Groot SP, van der Geest AH (2005) Gene expression programs during Brassica oleracea seed maturation, osmopriming, and germination are indicators of progression of the germination process and the stress tolerance level. Plant Physiol 137:354–368

    PubMed  CAS  Google Scholar 

  • Taylor G, Street NR, Tricker PJ, Sjodin A, Graham L, Skogstrom O, Calfapietra C, Scarascia-Mugnozza G, Jansson S (2005) The transcriptome of populus in elevated CO2. New Phytol 167:143–154

    PubMed  CAS  Google Scholar 

  • Tesfaye M, Samac DA, Vance CP (2006) Insights into symbiotic nitrogen fixation in Medicago truncatula. Mol Plant Microbe Interact 19:330–341

    PubMed  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Torres MJ, Tomilov AA, Tomilova N, Reagan RL, Yoder JI (2005) Pscroph, a parasitic plant EST database enriched for parasite associated transcripts. BMC Plant Biol 5:24

    PubMed  Google Scholar 

  • Vendrely R, Vendrely C (1948) La teneur du noyau cellulaire en acide dèsoxyribonuclèique à travers les organes, les individus et les espéces animales: techniques et premiers rèsultats. Experientia 4:434–436

    CAS  Google Scholar 

  • Weil MM, Pershad R, Wang R, Zhao S (2004) Use of BAC end sequences for SNP discovery. Methods Mol Biol 256:1–6

    PubMed  CAS  Google Scholar 

  • Wellman CH, Gray J (2000) The microfossil record of early land plants. Philos Trans R Soc Lond B Biol Sci 355:717–731; discussion 731–712

    PubMed  CAS  Google Scholar 

  • Wellman CH, Osterloff PL, Mohiuddin U (2003) Fragments of the earliest land plants. Nature 425:282–285

    PubMed  CAS  Google Scholar 

  • Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 34:D173–180

    PubMed  CAS  Google Scholar 

  • Yuan Q, Ouyang S, Liu J, Suh B, Cheung F, Sultana R, Lee D, Quackenbush J, Buell CR (2003a) The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. Nucleic Acids Res 31:229–233

    CAS  Google Scholar 

  • Yuan Y, SanMiguel PJ, Bennetzen JL (2003b) High-Cot sequence analysis of the maize genome. Plant J 34:249–255

    Google Scholar 

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Authors and Affiliations

  1. Centre for Biotechnology, Tykistökatu 6, FIN-20521 Turku, Finland

    Kean Jin Lim, Sini Junttila, Vidal Fey & Stephen Rudd

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  1. Kean Jin Lim
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  2. Sini Junttila
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  3. Vidal Fey
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  4. Stephen Rudd
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Editors and Affiliations

  1. ICRISAT, Patancheru, India

    Rajeev K. Varshney

  2. University of Bologna, Italy

    Roberto Tuberosa

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Lim, K.J., Junttila, S., Fey, V., Rudd, S. (2007). Genomeless Genomics in Crop Improvement. In: Varshney, R.K., Tuberosa, R. (eds) Genomics-Assisted Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-6295-7_7

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