Skip to main content

From Markers to Cloned Genes: Map-Based Cloning

  • Chapter

Part of the book series: Biotechnology in Agriculture and Forestry ((AGRICULTURE,volume 55))

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Alonso-Blanco C, Koornneef M (2000) Naturally occurring variation in Arabidopsis: an under-exploited resource for plant genetics. Trends Plant Sci 5:22–29

    Article  PubMed  Google Scholar 

  • Alonso-Blanco C, El-Assal SE-D, Coupland G, Koornneef M (1998) Analysis of natural allelic variation at flowering time loci in the Landsberg erecta and Cape Verde Islands ecotypes of Arabidopsis thaliana. Genetics 149:749–764

    PubMed  Google Scholar 

  • Alpert KB, Grandillo S, Tanksley SD (1995) FW-2.2 — a major QTL controlling fruit weight is common to both red-fruited and green-fruited tomato species. Theor Appl Genet 91:994–1000

    Article  Google Scholar 

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

    Google Scholar 

  • Asins MJ (2002) Present and future of quantitative trait locus analysis in plant breeding. Plant Breed 121:281–291

    Article  Google Scholar 

  • Ballvora A, Ercolano MR, Weiß J, Meksem K, Bormann CA, Oberhagemann P, Salamini F, Gebhardt C (2002) The R1 gene for potato resistance to late blight (Phytophthora infestans) belongs to the leucine zipper/NBS/LRR class of resistance genes. Plant J 30:361–371

    Article  PubMed  Google Scholar 

  • Bancroft I (2000) Physical mapping: YACs, BACs, cosmids, and nucleotide sequences. In: Wilson ZA (ed) Practical approach series. Arabidopsis 223:199–224

    Google Scholar 

  • Baumbusch LO, Sundal IK, Hughes DW, Galau GA, Jakobsen KS (2001) Efficient protocols for CAPS-based mapping in Arabidopsis. Plant Mol Biol Rep 19:137–149

    Google Scholar 

  • Berger D, Altmann T (2000) A subtilisin-like serine protease involved in the regulation of stomatal density and distribution in Arabidopsis thaliana. Genes Dev 14:1119–1131

    PubMed  Google Scholar 

  • Breen G, Harold D, Ralston S, Shaw D, St Clair D (2000) Determining SNP allele frequencies in DNA pools. Biotechniques 28:464–470

    Google Scholar 

  • Brueggeman R, Rostoks N, Kudrna D, Kilian A, Han F, Chen J, Druka A, Steffenson B, Kleinhofs A (2002) The barley stem rust-resistance gene Rpg1 is a novel disease-resistance gene with homology to receptor kinases. Proc Natl Acad Sci USA 99:9328–9333

    Article  PubMed  Google Scholar 

  • Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) Single nucleotide polymorphisms (SNPs) as markers in phylogeography. Trends Ecol Evol 18:249–256

    Google Scholar 

  • Buckler ES, Thornsberry JM (2002) Plant molecular diversity and application to genomics. Curr Opin Plant Biol 5:107–111

    Article  PubMed  Google Scholar 

  • Büschges R, Hollricher K, Panstruga R, Simons G, Wolter M, Frijters A, van Daelen R, van der Lee T, Diergaarde P, Groenendijk J, Topsch S, Vos P, Salamini F, Schulze-Lefert P (1997) The barley Mlo gene: a novel control element of plant pathogen resistance. Cell 88:695–705

    Google Scholar 

  • Buetow KH, Edmonson M, MacDonald R, Clifford R, Yip P, Kelley J, Little DP, Strausberg R, Koester H, Cantor CR, Braun A (2001) High-throughput development and characterization of a genome-wide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc Natl Acad Sci USA 98:581–584

    PubMed  Google Scholar 

  • Cai D, Kleine M, Kifle S, Harloff HJ, Sandal NN, Marcker KA, Klein-Lankhorst RM, Salentijn EM, Lange W, Stiekema WJ, Wyss U, Grundler FM, Jung C (1997) Positional cloning of a gene for nematode resistance in sugar beet. Science 275:832–834

    PubMed  Google Scholar 

  • Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S, Higingbottom S, Phimphilai J, Phimphilai D, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Budiman MA, Tomkins JP, Luo M, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA, Wing RA (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545

    Article  PubMed  Google Scholar 

  • Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang W-H, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203–207

    Google Scholar 

  • Civardi L, Xia Y, Edwards KJ, Schnable PS, Nikolau BJ (1994) The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc Natl Acad Sci USA 1994:8268–8272

    Google Scholar 

  • Cong B, Liu J, Tanksley SD (2002) Natural alleles at a tomato fruit size quantitative trait locus differ by heterochronic regulatory mutations. Proc Natl Acad Sci USA 99: 13606–13611

    Article  PubMed  Google Scholar 

  • Copenhaver GP, Browne WE, Preuss D (1998) Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc Natl Acad Sci USA 95:247–252

    PubMed  Google Scholar 

  • Cotton RGH, Edkins E, Forrest S (1998) Mutation detection. IRL Press at Oxford University Press, Oxford

    Google Scholar 

  • Dangl JL, Jones JDG (2001) Plant pathogens and integrated defence responses to infection. Nature 411:826–833

    PubMed  Google Scholar 

  • Dixon MS, Jones DA, Keddie JS, Thomas CM, Hanson K, Jones JDG (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine rich repeats. Cell 84:451–459

    Article  PubMed  Google Scholar 

  • Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM (2000) A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis. Plant Physiol 124:1483–1492

    Article  PubMed  Google Scholar 

  • Durrett RT, Chen KY, Tanksley SD (2002) A simple formula useful for positional cloning. Genetics 160:353–355

    PubMed  Google Scholar 

  • Endre G, Kereszt A, Kevei Z, Mihacea S, Kalo P, Kiss GB (2002) A receptor kinase gene regulating symbiotic nodule development. Nature 417:962–966

    PubMed  Google Scholar 

  • Ernst K, Kumar A, Kriseleit D, Kloos DU, Phillips MS, Ganal MW (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31:127–136

    Article  PubMed  Google Scholar 

  • Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162

    PubMed  Google Scholar 

  • Eshed Y, Zamir D (1996) Less-than-additive epistatic interactions of quantitative trait loci in tomato. Genetics 143:1807–1817

    PubMed  Google Scholar 

  • Fairweather N (1997) Construction and use of cosmid contigs. In: Boultwood J (ed) Gene isolation and mapping protocols. Methods Mol Biol 68:137–148

    Google Scholar 

  • Faris JD, Haen KM, Gill BS (2000) Saturation mapping of a gene-rich recombination hot spot region in wheat. Genetics 154:823–835

    PubMed  Google Scholar 

  • Flor HH (1971) Current status of the gene-for-gene concept. Annu Rev Phytopathol 9:275–296

    Article  Google Scholar 

  • Frary A, Nesbitt TC, Grandillo S, Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB, Tanksley SD (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science 289:85–88

    Article  PubMed  Google Scholar 

  • Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723

    PubMed  Google Scholar 

  • Germer S, Holland MJ, Higuchi R (2000) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res 10:258–266

    Article  PubMed  Google Scholar 

  • Gill KS, Gill BS, Endo TR, Boyko EV (1996) Identification and high-density mapping of generich regions in chromosome group 5 of wheat. Genetics 143:1001–1012

    PubMed  Google Scholar 

  • Gupta PK, Roy JK, Prasad M (2001) Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Curr Sci 80:524–535

    Google Scholar 

  • Gut IG (2001) Automation in genotyping of single nucleotide polymorphisms. Hum Mutat 17:475–492

    Article  PubMed  Google Scholar 

  • Hauser M-T, Adhami F, Dorner M, Fuchs E, Glössl J (1998) Generation of co-dominant PCR-based markers by duplex analysis on high-resolution gels. Plant J 16:117–125

    Article  PubMed  Google Scholar 

  • Hayashi T, Ukai Y (1999) Method of QTL mapping in an F2 population using phenotypic means of F3 lines (article). Breed Sci 49(2):105–114

    Google Scholar 

  • Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere ML, Spurlock G, Austin J, Stephens MK, Buckland PR, Owen MJ, O'Donovan MC (2000) Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Hum Genet 107:488–493

    PubMed  Google Scholar 

  • Horrigan S, Westbrook C (1997) Construction and use of YAC contigs in disease regions. In: Boultwood J (ed) Gene isolation and mapping protocols. Methods Mol Biol 68:123–136

    Google Scholar 

  • Isaacson T, Ronen G, Zamir D, Hirschberg J (2002) Cloning of tangerine from tomato reveals a carotenoid isomerase essential for the production of β-carotene and xanthophylls in plants. Plant Cell 14:333–342

    PubMed  Google Scholar 

  • Jander G, Norris SR, Rounsley SD, Bush DF, Levin IM, Last RL (2002) Arabidopsis map-based cloning in the post-genome era. Plant Physiol 129:440–450

    Article  PubMed  Google Scholar 

  • Jenkins S, Gibson S (2002) High-throughput SNP genotyping. Comp Funct Genom 3:57–66

    Article  Google Scholar 

  • Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246–251

    PubMed  Google Scholar 

  • Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions. Plant Cell Physiol 43:1096–1105

    Article  PubMed  Google Scholar 

  • Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using codominant ecotype-specific PCR-based markers. Plant J 4:403–410

    Article  PubMed  Google Scholar 

  • Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412

    PubMed  Google Scholar 

  • Kwok P (2001) Methods for genotyping single nucleotide polymorphisms. Annu Rev Genom Hum Genet 2:235–258

    Article  Google Scholar 

  • Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CAM, Muir WJ, Blackwood DHR, Porteous DJ, Evans KL (2002) SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi-automated method for data storage and analysis. Nucleic Acids Res 30:74–84

    Article  Google Scholar 

  • Lee I, Michaels SD, Masshardt AS, Amasino RM (1994) The late-flowering phenotype of FRIGIDA and mutations in LUMINIDEPENDENS is suppressed in the Landsberg erecta strain of Arabidopsis. Plant J 6:903–909

    Article  Google Scholar 

  • Lin X, Kaul S, Rounsley S, Shea TP, Benito M-I, Town CD, Fujii CY, Mason T, Bowman CL, Barnstead M, Feldblyum TV, Buell CR, Ketchum KA, Lee J, Ronning CM, Koo HL, Moffat KS, Cronin LA, Shen M, Pai G, Van Aken S, Umayam L, Tallon LJ, Gill JE, Venter JC (1999) Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402:761–768

    Article  PubMed  Google Scholar 

  • Ling H-Q, Koch G, Bäumlein H, Ganal MW (1999) Map-based cloning of chloronerva, a gene involved in iron uptake of higher plants encoding nicotianamine synthase. Proc Natl Acad Sci USA 96:7098–7103

    Article  PubMed  Google Scholar 

  • Ling H-Q, Bauer P, Bereczky Z, Keller B, Ganal M (2002). The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc Natl Acad Sci USA 99:13938–13943

    Article  PubMed  Google Scholar 

  • Liu J, van Eck J, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306

    Article  PubMed  Google Scholar 

  • Lukowitz W, Gillmor CS, Scheible W-R (2000) Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol 123:795–805

    Article  PubMed  Google Scholar 

  • Lukowitz W, Nickle TC, Meinke DW, Last RL, Conklin PL, Somerville CR (2001) Arabidopsis cyt1 mutants are deficient in a mannose-1-phosphate guanylyltransferase and point to a requirement of N-linked glycosylation for cellulose biosynthesis. Proc Natl Acad Sci USA 98:2262–2267

    PubMed  Google Scholar 

  • Mao L, Begum D, Chuang H-W, Budiman MA, Szymkowiak EJ, Irish EE, Wing RA (2000) JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development. Nature 406:910–913

    Article  PubMed  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436

    PubMed  Google Scholar 

  • Martin GB, Frary A, Wu T, Brommonschenkel S, Chunwongse J, Earle ED, Tanksley SD (1994) A member of the tomato Pto gene family confers sensitivity to fenthion resulting in rapid cell death. Plant Cell 11:1543–1552

    Article  Google Scholar 

  • Meyer K, Leube MP, Grill E (1994) A protein phosphatase 2c involved in ABA signal transduction in Arabidopsis thaliana. Science 264:1452–1455

    PubMed  Google Scholar 

  • Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832

    PubMed  Google Scholar 

  • Morgante M, Salamini F (2003) From plant genomics to breeding practice. Curr Op Biotechnol 14:214–219

    Article  Google Scholar 

  • Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22:271–275

    Article  PubMed  Google Scholar 

  • Narang RA, Bruene A, Altmann T (2001) Analysis of phosphate acquisition efficiency in different Arabidopsis accessions. Plant Physiol 124:1786–1799

    Article  Google Scholar 

  • Nataraj AJ, Olivos-Glander I, Kusukawa N, Highsmith WE (1999) Single-strand conformation polymorphism and heteroduplex analysis for gel-based mutation detection. Electrophoresis 20:1177–1185

    Article  PubMed  Google Scholar 

  • Neff MM, Turk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615

    Article  PubMed  Google Scholar 

  • Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, Morris DW, Hoogendoorn B, Owen MJ, O'Donovan MC (2002) Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools. Hum Genet 110:471–478

    PubMed  Google Scholar 

  • O'Donovan M, Oefner PJ, Roberts SC, Austin J, Hoogendoorn B, Guy C, Speight G, Upadhyaya M, Sommer SS, McGuffin P (1998) Blind analysis of denaturing high-performance liquid chromatography as a tool for mutation detection. Genomics 52:44–49

    Article  PubMed  Google Scholar 

  • Pedrosa A, Sandal N, Stougaard J, Schweizer D, Bachmair A (2002) Chromosomal map of the model legume Lotus japonicus. Genetics 161:1661–1672

    PubMed  Google Scholar 

  • Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Zamir D, Lifschitz E (1998). The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125:1979–1989

    PubMed  Google Scholar 

  • Ponce MR, Robles P, Micol JL (1999) High-throughput mapping in Arabidopsis thaliana. Mol Gen Genet 261:408–415

    Article  PubMed  Google Scholar 

  • Ramsay M (1994) Yeast artificial chromosome cloning. Mol Biotechnol 1:181–201

    PubMed  Google Scholar 

  • Risch NJ (2000) Searching for genetic determinants in the new millennium. Nature 405:847–856

    Article  PubMed  Google Scholar 

  • Ronaghi M, Karamohamed S, Pettersson B, Uhlen M, Nyren P (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242:84–89

    Article  PubMed  Google Scholar 

  • Ronaghi M, Nygren M, Lundeberg J, Nyren P (1999) Analyses of secondary structures in DNA by pyrosequencing. Anal Biochem 267:65–71

    Article  PubMed  Google Scholar 

  • Ronen G, Carmel-Goren L, Zamir D, Hirschberg J (2000) An alternative pathway to β-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato. Proc Natl Acad Sci USA 97:11102–11107

    Article  PubMed  Google Scholar 

  • Ross P, Hall L, Haff LA (2000) Quantitative approach to single-nucleotide polymorphism analysis using MALDI-TOF mass spectrometry. Biotechniques 29:620–629

    PubMed  Google Scholar 

  • Sadowski J, Gaubier P, Delseny M, Quiros CF (1996) Genetic and physical mapping in Brassica diploid species of a gene cluster defined in Arabidopsis thaliana. Mol Gen Genet 251:298–306

    PubMed  Google Scholar 

  • Sakai H, Medrano LJ, Meyerowitz EM (1995) Role of SUPERMAN in maintaining Arabidopsis floral whorl boundaries. Nature 378:199–203

    Article  PubMed  Google Scholar 

  • Sandhu D, Gill KS (2002) Gene-containing regions of wheat and the other grass genomes. Plant Physiol 128:803–811

    Article  PubMed  Google Scholar 

  • Scheible W-R, Eshed R, Richmond T, Delmer D, Somerville CR (2001) Modifications of cellulose synthase confer resistance to isoxaben and thiazolidinone herbicides in Arabidopsis Ixr1 mutants. Proc Natl Acad Sci USA 98:10079–10084

    Article  PubMed  Google Scholar 

  • Scheible W-R, Fry B, Kochevenko A, Schindelasch D, Zimmerli L, Somerville S, Loria R, Somerville CR (2003). An Arabidopsis mutant resistant to thaxtomin A, a cellulose synthesis inhibitor from Streptomyces spp. Plant Cell 15:1781–1794

    Article  PubMed  Google Scholar 

  • Schmid KJ, Sorensen TR, Stracke R, Törjek O, Altmann T, Mitchell-Olds T, Weisshaar B (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res 13:1250–1257

    Article  PubMed  Google Scholar 

  • Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H, Bouchez D, Dean C (1995) Physical map and organization of Arabidopsis thaliana chromosome 4. Science 270:480–483

    PubMed  Google Scholar 

  • Schmitz G, Tillmann E, Carriero F, Fiore C, Cellini F, Theres K (2002) The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems. Proc Natl Acad Sci USA 99:1064–1069

    Article  PubMed  Google Scholar 

  • Schumacher K, Schmitt T, Rossberg M, Schmitz G, Theres K (1999) The Lateral suppressor (Ls) gene of tomato encodes a new member of the VHIID protein family. Proc Natl Acad Sci USA 96:290–295

    Article  PubMed  Google Scholar 

  • Shirasu K, Lahaye T, Tan MW, Zhou F, Azevedo C, Schulze-Lefert P (1999) A novel class of eukaryotic zinc-binding proteins is required for disease resistance signaling in barley and development in C. elegans. Cell 99:355–366

    Article  PubMed  Google Scholar 

  • Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 89:8794–8797

    PubMed  Google Scholar 

  • Song W-Y, Wang G-L, Chen L-L, Kim H-S, Pi L-Y, Holsten T, Gardner J, Wang B, Zhai W-X, Zhu L-H, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    PubMed  Google Scholar 

  • Spiegelman JI, Mindrinos MN, Oefner PJ (2000) High-accuracy DNA sequence variation screening by DHPLC. Biotechniques 29:1084–1092

    PubMed  Google Scholar 

  • Stracke S, Kistner C, Yoshida S, Mulder L, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J, Szczyglowski K, Parniske M (2002) A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417:959–962

    Article  PubMed  Google Scholar 

  • Swann KA, Curtis DE, McKusick KB, Voinov AV, Mapa FA, Cancilla MR (2002) High-throughput gene mapping in Caenorhabditis elegans. Genome Res 12:1100–1105

    PubMed  Google Scholar 

  • Syvänen AC (1999) From gels to chips: “minisequencing” primer extension for analysis of point mutations and single nucleotide polymorphisms. Hum Mutat 13:1–10

    Article  PubMed  Google Scholar 

  • Takahashi Y, Shomura A, Sasaki T, Yano M (2001) Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922–7927

    Article  PubMed  Google Scholar 

  • Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    Article  PubMed  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, Messeguer R, Miller JC, Miller L, Paterson AH, Pineda O, Röder MS, Wing RA, Wu W, Young ND (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    PubMed  Google Scholar 

  • Tanksley SD, Ganal MW, Martin GB (1995) Chromosome landing: a paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11:63–68

    Article  PubMed  Google Scholar 

  • Taylor GR (1999) Enzymatical and chemical cleaving methods. Electrophoresis 20:1125–1130

    Article  PubMed  Google Scholar 

  • Törjéek O, Berger D, Meyer R, Müssig C, Schmid K, Rosleff-Sörensen T, Weisshaar B, Mitchell-Olds T, Altmann T (2003) Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J 36:122–140

    Article  PubMed  Google Scholar 

  • Turner M, Schuch W (2000) Post-transcriptional gene-silencing and RNA interference: genetic immunity, mechanisms and applications. J Chem Technol Biotechnol 75:869–882

    Article  Google Scholar 

  • Utz HF, Melchinger AE, Schoen CC (2000) Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics 154:1839–1849

    PubMed  Google Scholar 

  • Van Lisjebettens M, Wang X, Cnops G, Boerjan W, Desnos T, Höfte H, van Montagu M (1996) Transgenic Arabidopsis tester lines with dominant marker genes. Mol Gen Genet 251:365–372

    PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    PubMed  Google Scholar 

  • Wang DG, Fan JB, Siao CJ, Berno A, Young P, Sapolsky R, Ghandour G, Perkins N, Winchester E, Spencer J, Kruglyak L, Stein L, Hsie L, Topaloglou T, Hubbell E, Robinson E, Mittmann M, Morris MS, Shen N, Kilburn D, Rioux J, Nusbaum C, Rozen S, Hudson TJ, Lipshutz R, Chee M, Lander ES (1998) Large-scale identification, mapping, and genotyping of single-nucleotide polymorphisms in the human genome. Science 280:1077–1082

    Article  PubMed  Google Scholar 

  • Weng Y, Lazar MD (2002) Comparison of homoeologous group-6 short arm physical maps of wheat and barley reveals a similar distribution of recombinogenic and gene-rich regions. Theor Appl Genet 104:1078–1085

    Article  PubMed  Google Scholar 

  • Yamamoto T, Kuboki Y, Lin SY, Sasaki T, Yano M (1998) Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3, controlling heading date of rice, as single Mendelian factors. Theor Appl Genet 97:37–44

    Article  Google Scholar 

  • Yano M (2001) Genetic and molecular dissection of naturally occurring variation. Curr Opin Plant Biol 4:130–135

    PubMed  Google Scholar 

  • Yano M, Harushima Y, Nagamura Y, Kurata N, Minobe Y, Saski T (1997) Identification of quantitative trait loci controlling heading date of rice using a high-density linkage map. Theor Appl Genet 95:1025–1032

    Article  Google Scholar 

  • Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene CONSTANS. Plant Cell 12:2473–2484

    Article  PubMed  Google Scholar 

  • Yano M, Kojima S, Takahashi Y, Lin H, Sasaki T (2001) Genetic control of flowering time in rice, a short-day plant. Plant Physiol 127:1425–1429

    Article  PubMed  Google Scholar 

  • Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang ZX, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight-resistance gene in rice, is induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663–1668

    Article  PubMed  Google Scholar 

  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:983–989

    Article  PubMed  Google Scholar 

  • Zhou F, Kurth J, Wei F, Elliott C, Vale G, Yahiaoui N, Keller B, Somerville S, Wise R, Schulze-Lefert P (2001) Cell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1-independent signaling pathway. Plant Cell 13:337–350

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2004 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Scheible, WR., Törjek, O., Altmann, T. (2004). From Markers to Cloned Genes: Map-Based Cloning. In: Lörz, H., Wenzel, G. (eds) Molecular Marker Systems in Plant Breeding and Crop Improvement. Biotechnology in Agriculture and Forestry, vol 55. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-26538-4_4

Download citation

Publish with us

Policies and ethics