Bioinformatics pp 165-189 | Cite as

Molecular Marker Discovery and Genetic Map Visualisation

  • Chris Duran
  • David Edwards
  • Jacqueline Batley


The bulk of variation at the nucleotide level is often not visible at the phenotypic level. However, this variation can be exploited using molecular genetic marker systems. Molecular genetic markers represent one of the most powerful tools for genome analysis and permit the association of heritable traits with underlying genomic variation. Molecular marker technology has developed rapidly over the last decade, with the development of high-throughput genotyping methods and the availability of large amounts of sequence data for automated marker discovery. Two forms of sequence based marker, Simple Sequence Repeats (SSRs), also known as microsatellites, and Single Nucleotide Polymorphisms (SNPs) are the principal markers currently applied in modern genetic analysis. This are supplemented with anonymous marker systems such as Amplified Fragment Length Polymorphisms (AFLPs; Vos et al. 1995), and Diversity Array Technology (DArT; Jaccoud et al. 2001). The reducing cost of DNA sequencing has led to the availability of large sequence data sets that enable the mining of sequence based markers, such as SSRs and SNPs, which may then be applied to diversity analysis, genetic trait mapping, association studies, and marker assisted selection.


Amplify Fragment Length Polymorphism Heritable Trait Trace File Molecular Genetic Marker Tandem Repeat Finder 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372PubMedCrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P (2005) A haplotype map of the human genome. Nature 437:1299–1320CrossRefGoogle Scholar
  4. Awadalla P, Ritland K (1997) Microsatellite variation and evolution in the Mimulus guttatus species complex with contracting mating systems. Mol Biol Evol 14:1023–1034PubMedGoogle Scholar
  5. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918PubMedCrossRefGoogle Scholar
  6. Barker G, Batley J, O′Sullivan H, Edwards KJ, Edwards D (2003) Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP. Bioinformatics 19:421–422PubMedCrossRefGoogle Scholar
  7. Batley J, Edwards D (2007) SNP applications in plants. In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds) Association Mapping in Plants. Springer, NY, pp 95–102CrossRefGoogle Scholar
  8. Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91PubMedCrossRefGoogle Scholar
  9. Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J et al (2007) Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences. Mol Ecol Notes 7:886–889CrossRefGoogle Scholar
  10. Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580PubMedCrossRefGoogle Scholar
  11. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59PubMedCrossRefGoogle Scholar
  12. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18:249–256CrossRefGoogle Scholar
  13. Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg GC et al (2006) Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Mol Ecol Notes 6:1191–1194CrossRefGoogle Scholar
  14. Burke J, Davison D, Hide W (1999) d2_cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res 9:1135–1142PubMedCrossRefGoogle Scholar
  15. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854PubMedGoogle Scholar
  16. Carollo V, Matthews DE, Lazo GR, Blake TK, Hummel DD, Lui N et al (2005) GrainGenes 2.0. An improved resource for the small-grains community. Plant Physiol 139:643–651PubMedCrossRefGoogle Scholar
  17. Castelo AT, Martins W, Gao GR (2002) TROLL-Tandem Repeat Occurrence Locator. Bioinformatics 18:634–636PubMedCrossRefGoogle Scholar
  18. Cervigni GDL, Paniego N, Diaz M, Selva JP, Zappacosta D, Zanazzi D et al (2008) Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula. Plant Mol Biol 67:1–10PubMedCrossRefGoogle Scholar
  19. Chen CX, Zhou P, Choi YA, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257PubMedCrossRefGoogle Scholar
  20. Chen XF, Laudeman TW, Rushton PJ, Spraggins TA, Timko MP (2007) CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L.) methylation filtered genomic genespace sequences. BMC Bioinformatics 8:129PubMedCrossRefGoogle Scholar
  21. Collins A, Lau W, De la Vega FM (2004) Mapping genes for common diseases: the case for genetic (LD) maps. Hum Hered 58:2–9PubMedCrossRefGoogle Scholar
  22. Corva P, Soria L, Schor A, Villarreal E, Cenci MP, Motter M et al (2007) Association of CAPN1 and CAST gene polymorphisms with meat tenderness in Bos taurus beef cattle from Argentina. Genet Mol Biol 30:1064–1069CrossRefGoogle Scholar
  23. Dierick I, Baets J, Irobi J, Jacobs A, De Vriendt E, Deconinck T et al (2008) Relative contribution of mutations in genes for autosomal dominant distal hereditary motor neuropathies: a genotype–phenotype correlation study. Brain 131:1217–1227PubMedCrossRefGoogle Scholar
  24. Dong QF, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C et al (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol 139:610–618PubMedCrossRefGoogle Scholar
  25. Dong QF, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucleic Acids Res 31:244–247PubMedCrossRefGoogle Scholar
  26. Dong QF, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32:D354–D359PubMedCrossRefGoogle Scholar
  27. Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J et al (2009) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951–3PubMedCrossRefGoogle Scholar
  28. Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ et al (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36:D959–D965PubMedCrossRefGoogle Scholar
  29. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758–760PubMedGoogle Scholar
  30. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred II. Error probabilities. Genome Res 8:186–194PubMedGoogle Scholar
  31. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred I. Accuracy assessment. Genome Res 8:175–185PubMedGoogle Scholar
  32. Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA et al (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861PubMedCrossRefGoogle Scholar
  33. Gai XW, Lal S, Xing LQ, Brendel V, Walbot V (2000) Gene discovery using the maize genome database ZmDB. Nucleic Acids Res 28:94–96PubMedCrossRefGoogle Scholar
  34. Gao H, Kong J (2005) The microsatellites and minisatellites in the genome of Fenneropenaeus chinensis. DNA Seq 16:426–436PubMedGoogle Scholar
  35. Garg K, Green P, Nickerson DA (1999) Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags. Genome Res 9:1087–1092PubMedCrossRefGoogle Scholar
  36. Gibbs RA, Belmont JW, Hardenbol P, Willis TD, Yu FL, Yang HM et al (2003) The international HapMap project. Nature 426:789–796CrossRefGoogle Scholar
  37. Gonzales MD, Archuleta E, Farmer A, Gajendran K, Grant D, Shoemaker R et al (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res 33:D660–D665PubMedCrossRefGoogle Scholar
  38. Gordon D, Abajian C, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8:195–202PubMedGoogle Scholar
  39. Gupta M, Chyi Y-S, Romero-Severson J, Owen JL (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence re-peats. Theor Appl Genet 89:998–1006CrossRefGoogle Scholar
  40. 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 80:524–535Google Scholar
  41. Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP (2004) An interactive bovine in silico SNP database (IBISS). Mamm Genome 15:819–827PubMedCrossRefGoogle Scholar
  42. Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X et al (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. Mol Ecol Notes 7:697–700CrossRefGoogle Scholar
  43. Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F et al (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based in-formation retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29:102–105PubMedCrossRefGoogle Scholar
  44. Huang XQ, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877PubMedCrossRefGoogle Scholar
  45. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25PubMedCrossRefGoogle Scholar
  46. Jaiswal P, Ni JJ, Yap I, Ware D, Spooner W, Youens-Clark K et al (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34:D717–D723PubMedCrossRefGoogle Scholar
  47. Jayashree B, Ferguson M, Ilut D, Doyle J, Crouch JH (2005) Analysis of genomic sequences from peanut (Arachis hypogaea). Electron J Biotechnol 8:3Google Scholar
  48. Jesubatham AM, Burow MD (2006) PeanutMap: an online genome database for comparative molecular maps of peanut. BMC Bioinformatics 7:375PubMedCrossRefGoogle Scholar
  49. Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC et al (2006) SSRPrimer and SSR Taxonomy Tree: Biome SSR discovery. Nucleic Acids Res 34:W656–W659PubMedCrossRefGoogle Scholar
  50. Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A et al (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36:D1034–D1040PubMedCrossRefGoogle Scholar
  51. Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74–78PubMedCrossRefGoogle Scholar
  52. Kasprzyk A, Keefe D, Smedley D, London D, Spooner W, Melsopp C et al (2004) EnsMart: a generic system for fast and flexible access to biological data. Genome Res 14:160–169PubMedCrossRefGoogle Scholar
  53. Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167PubMedGoogle Scholar
  54. Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GC, Edwards D et al (2006) Identification and characterization of simple sequence repeat (SSR) markers from Fragaria × ananassa expressed sequences. Mol Ecol Notes 6:319–322CrossRefGoogle Scholar
  55. Kwok PY, Carlson C, Yager TD, Ankener W, Nickerson DA (1994) Comparative analysis of human DNA variations by fluorescence-based sequencing of PCR products. Genomics 23:138–144PubMedCrossRefGoogle Scholar
  56. Lander E, Abrahamson J, Barlow A, Daly M, Lincoln S, Newburg L et al (1987) Mapmaker: a computer package for constructing genetic-linkage maps. Cytogenet Cell Genet 46:642Google Scholar
  57. Lawrence CJ, Dong OF, Polacco ML, Seigfried TE, Brendel V (2004) MaizeGDB, the community database for maize genetics and genomics. Nucleic Acids Res 32:D393–D397PubMedCrossRefGoogle Scholar
  58. Lazzari B, Caprera A, Vecchietti A, Stella A, Milanesi L, Pozzi C (2005) ESTree db: a tool for peach functional genomics. BMC Bioinformatics 6(Suppl 4):S16PubMedCrossRefGoogle Scholar
  59. Lee SH, Park EW, Cho YM, Lee JW, Kim HY, Lee JH et al (2006) Confirming single nucleotide polymorphisms from expressed sequence tag datasets derived from three cattle cDNA libraries. J Biochem Mol Biol 39:183–188PubMedGoogle Scholar
  60. Li Y-C, Korol AB, Fahima T, Beiles A, Nevo E (2002) Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol Ecol 11:2453–2465PubMedCrossRefGoogle Scholar
  61. Liao W, Collins A, Hobbs M, Khatkar MS, Luo JH, Nicholas FW (2007) A comparative location database (CompLDB): map integration within and between species. Mamm Genome 18:287–299PubMedCrossRefGoogle Scholar
  62. Lim GAC, Jewell EG, Xi L, Erwin TA, Love C, Batley J et al (2007) A comparative map viewer integrating genetic maps for Brassica and Arabidopsis. BMC Plant Biol 7:40PubMedCrossRefGoogle Scholar
  63. Lindqvist C, Scheen AC, Yoo MJ, Grey P, Oppenheimer DG, Leebens-Mack JH et al (2006) An expressed sequence tag (EST) library from developing fruits of an Hawaiian endemic mint (Stenogyne rugosa, Lamiaceae): characterization and microsatellite markers. BMC Plant Biol 6:16PubMedCrossRefGoogle Scholar
  64. Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X et al (2007) Characterization of simple sequence repeat markers derived in silico from Brassica rapa bacterial artificial chromosome sequences and their application in Brassica napus. Mol Ecol Notes 7:273–277CrossRefGoogle Scholar
  65. Mallon AM, Strivens M (1998) DNA sequence analysis and comparative sequencing. Methods 14:160–178PubMedCrossRefGoogle Scholar
  66. Manly KF, Cudmore RH, Meer JM (2001) Map manager QTX, cross-platform software for genetic mapping, Mamm. Genome 12:930–932Google Scholar
  67. Marth GT, Korf I, Yandell MD, Yeh RT, Gu ZJ, Zakeri H et al (1999) A general approach to single-nucleotide polymorphism discovery. Nat Genet 23:452–456PubMedCrossRefGoogle Scholar
  68. Martin ER, Lai EH, Gilbert JR, Rogala AR, Afshari AJ, Riley J et al (2000) SNPing away at complex diseases: analysis of single-nucleotide polymorphisms around APOE in Alzheimer disease. Am J Hum Genet 67:383–394PubMedCrossRefGoogle Scholar
  69. Matthews DE, Carollo VL, Lazo GR, Anderson OD (2003) GrainGenes, the genome database for small-grain crops. Nucleic Acids Res 31:183–186PubMedCrossRefGoogle Scholar
  70. Matukumalli LK, Grefenstette JJ, Hyten DL, Choi I-Y, Cregan PB, Van Tassell CP (2006) SNP–PHAGE – High throughput SNP discovery pipeline. BMC Bioinformatics 7:468PubMedCrossRefGoogle Scholar
  71. Mortimer J, Batley J, Love C, Logan E, Edwards D (2005) Simple Sequence Repeat (SSR) and GC distribution in the Arabidopsis thaliana genome. J Plant Biotechnol 7:17–25Google Scholar
  72. Moxon ER, Wills C (1999) DNA microsatellites: agents of evolution. Sci Am 280:94–99PubMedCrossRefGoogle Scholar
  73. Nickerson DA, Tobe VO, Taylor SL (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res 25:2745–2751PubMedCrossRefGoogle Scholar
  74. Pavy N, Parsons LS, Paule C, MacKay J, Bousquet J (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics 7:174PubMedCrossRefGoogle Scholar
  75. Perez F, Ortiz J, Zhinaula M, Gonzabay C, Calderon J, Volckaert F (2005) Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy. Mar Biotechnol 7:554–569PubMedCrossRefGoogle Scholar
  76. Pertea G, Huang XQ, Liang F, Antonescu V, Sultana R, Karamycheva S et al (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652PubMedCrossRefGoogle Scholar
  77. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
  78. Pumpernik D, Oblak B, Borstnik B (2008) Replication slippage versus point mutation rates in short tandem repeats of the human genome. Mol Gen Genomics 279:53–61CrossRefGoogle Scholar
  79. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  80. Rhee SY, Beavis W, Berardini TZ, Chen GH, Dixon D, Doyle A et al (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31:224–228PubMedCrossRefGoogle Scholar
  81. Robinson AJ, Love CG, Batley J, Barker G, Edwards D (2004) Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20:1475–1476PubMedCrossRefGoogle Scholar
  82. Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC et al (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 33:W493–W495PubMedCrossRefGoogle Scholar
  83. Schlötterer C (2000) Evolutionary dynamics of microsatellite DNA. Nucleic Acids Res 20:211–215CrossRefGoogle Scholar
  84. Sherry ST, Ward MH, Sirotkin K (1999) dbSNP – database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res 9:677–679PubMedGoogle Scholar
  85. Sironi L, Lazzari B, Ramelli P, Gorni C, Mariani P (2006) Single nucleotide polymorphism discovery in the avian Tapasin gene. Poult Sci 85:606–612PubMedGoogle Scholar
  86. Smigielski EM, Sirotkin K, Ward M, Sherry ST (2000) dbSNP: a database of single nucleotide polymorphisms. Nucleic Acids Res 28:352–355PubMedCrossRefGoogle Scholar
  87. Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114PubMedCrossRefGoogle Scholar
  88. Stein LD, Mungall C, Shu SQ, Caudy M, Mangone M, Day A et al (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12:1599–1610PubMedCrossRefGoogle Scholar
  89. Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Biol 4:R13PubMedCrossRefGoogle Scholar
  90. Sullivan JC, Reitzel AM, Finnerty JR (2008) Upgrades to StellaBase facilitate medical and genetic studies on the starlet sea anemone, Nematostella vectensis. Nucleic Acids Res 36:D607–D611PubMedCrossRefGoogle Scholar
  91. Syvanen AC (2001) Genotyping single nucleotide polymorphisms. Nat Rev Genet 2:930–942PubMedCrossRefGoogle Scholar
  92. Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471PubMedCrossRefGoogle Scholar
  93. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  94. 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 106:411–422PubMedGoogle Scholar
  95. Tóth G, Gáspári Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981PubMedCrossRefGoogle Scholar
  96. Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, software for calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  97. Volfovsky N, Haas BJ, Salzberg SL (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol 2(8):RESEARCH0027PubMedCrossRefGoogle Scholar
  98. von Stackelberg M, Rensing SA, Reski R (2006) Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biol 6:9CrossRefGoogle Scholar
  99. Vos P, Hogers R, Bleeker M, Reijans M, Vandelee T, Hornes M et al (1995) AFLP – a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414PubMedCrossRefGoogle Scholar
  100. Wang WL, Zhang GL, Wu LH, Yao MY, Jin J, Jia CK et al (2007) Efficacy of hepatitis B immunoglobulin in relation to the gene polymorphisms of human leukocyte Fc gamma receptor III (CD16) in Chinese liver trans-plant patients. Chin Med J 120:1606–1610PubMedGoogle Scholar
  101. Ware D, Jaiswal P, Ni JJ, Pan XK, Chang K, Clark K et al (2002a) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30:103–105PubMedCrossRefGoogle Scholar
  102. Ware DH, Jaiswal PJ, Ni JJ, Yap I, Pan XK, Clark KY et al (2002b) Gramene, a tool for grass genomics. Plant Physiol 130:1606–1613PubMedCrossRefGoogle Scholar
  103. Weber JL (1990) Informativeness of human (dC–dA)n. (dG–dT) n polymorphisms. Genomics 7:524–530PubMedCrossRefGoogle Scholar
  104. Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts M, De Jonghe P et al (2005) novoSNP, a novel computational tool for sequence variation discovery. Genome Res 15:436–442PubMedCrossRefGoogle Scholar
  105. Weems D, Miller N, Garcia-Hernandez M, Huala E, Rhee SY (2004) Design, implementation and maintenance of a model organism database for Arabidopsis thaliana. Comp Funct Genomics 5:362–369PubMedCrossRefGoogle Scholar
  106. Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, McGuire A et al (2008a) The complete genome of an individual by massively parallel DNA sequencing. Nature 452(7189):872–876PubMedCrossRefGoogle Scholar
  107. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V et al (2008b) Database resources of the national center for biotechnology information. Nucleic Acids Res 36:D13–D21PubMedCrossRefGoogle Scholar
  108. Winton LM, Krohn AL, Leiner RH (2007) Microsatellite markers for Sclerotinia subarctica nom. prov., a new vegetable pathogen of the High North. Mol Ecol Notes 7:1077–1079CrossRefGoogle Scholar
  109. Zhang JH, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W et al (2005) SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol 1:395–404Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  1. 1.Australian Centre for Plant Functional Genomics, ARC Centre of Excellence for Integrative Legume Research, School of Land, Crop and Food SciencesUniversity of QueenslandBrisbaneAustralia

Personalised recommendations