Sequence Based DNA Markers and Genotyping for Cereal Genomics and Breeding

  • David Edwards
  • Pushpendra K. Gupta


The last three decades has seen the rapid evolution of a variety of DNA-based molecular markers that are powerful tools for genome analysis and marker-trait association (MTA) studies. Recently, high-throughput sequence-based methods have been developed for use in plant breeding. Sequence-based markers include simple sequence repeats (SSRs; also known as microsatellites) and single nucleotide polymorphisms (SNPs), which now dominate applications in modern genetic analysis. Insertion site-based polymorphisms (ISBPs), copy number variations (CNVs) and presence and absence variations (PAVs) constitute another group of markers that are being applied in a variety of plant systems. Markers may be used for a variety of purposes including diversity analysis, linkage-based QTL mapping, LD-based association mapping and marker assisted selection (MAS). Large sequence datasets (including both, genomic sequences and expressed sequences) are available for many cereals, enabling the mining for large numbers of SSRs, SNPs, ISBPs and CNVs/PAVs. Recombination bins are being used as markers for genotyping mapping populations and QTL analysis in crops such as rice, where reference genome sequences are available. In this chapter we describe the discovery and application of molecular markers using automated sequencing platforms including those based on next generation sequencing (NGS).


Genomic Estimate Breeding Value Exome Capture Reduce Representation Library True SNPs Cereal Crop Improvement 
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. Seifollah K, Alina A, Akhunov E (2013) Application of next-generation sequencing technologies for genetic diver-sity analysis in cereals. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, BerlinGoogle Scholar
  2. Alkan C, Coe BP, Eichler EE (2011) Genome structural variation discovery and genotyping. Nat Rev Genet 12:363–376PubMedCrossRefGoogle Scholar
  3. Allen AM, Barker GLA, Berry ST, Coghill JA, Gwilliam R, Kirby S, Robinson P, Brenchley RC, D’Amore R, McKenzie N, Waite D, Hall A, Bevan M, Hall N, Edwards KJ (2011) Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol J 9(9):1086–1099PubMedCrossRefGoogle Scholar
  4. Allentoft ME, Schuster SC, Holdaway RN, Hale ML, McLay E, Oskam C, Gilbert MTP, Spencer P, Willerslev E, Bunce M (2009) Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data. Biotechniques 46:195PubMedCrossRefGoogle Scholar
  5. Altshuler D, Pollara V, Cowles C, Van Etten W, Baldwin J, Linton L, Lander E (2000) An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature 407:513–516PubMedCrossRefGoogle Scholar
  6. Ammiraju JSS, Luo M, Goicoechea JL, Wang W, Kudrna D, Mueller C, Talag J, Kim H, Sisneros NB, Blackmon B, Fang E, Tomkins JB, Brar D, MacKill D, McCouch S, Kurata N, Lambert G, Galbraith DW, Arumuganathan K, Rao K, Walling JG, Gill N, Yu Y, SanMiguel P, Soderlund C, Jackson S, Wing RA (2006) The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza. Genome Res 16:140–147PubMedCrossRefGoogle Scholar
  7. Ammiraju JSS, Song X, Luo M, Sisneros N, Angelova A, Kudrna D, Kim H, Yu Y, Goicoechea JL, Lorieux M, Kurata N, Brar D, Ware D, Jackson S, Wing RA (2010) The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives. Breed Sci 60:536–543CrossRefGoogle Scholar
  8. Appleby N, Edwards D, Batley J (2009) New technologies for ultra-high throughput genotyping in plants. In: Somers D, Langridge P, Gustafson J (eds) Plant genomics. Humana Press, New York, pp 19–40CrossRefGoogle Scholar
  9. Awadalla P, Ritland K (1997) Microsatellite variation and evolution in the Mimulus guttatus species complex with contrasting mating systems. Mol Biol Evol 14:1023–1034PubMedCrossRefGoogle Scholar
  10. Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, Jones JDG, Varshney RK (2012) Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. Am J Bot 99:186–192PubMedCrossRefGoogle Scholar
  11. Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918PubMedCrossRefGoogle Scholar
  12. 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
  13. Batley J, Edwards D (2007) SNP applications in plants. In: Oraguzie N, Rikkerink E, Gardiner S, De Silva H (eds) Association mapping in plants. Springer, New York, pp 95–102CrossRefGoogle Scholar
  14. Batley J, Edwards D (2009a) Genome sequence data: management, storage, and visualization. Biotechniques 46:333–336PubMedCrossRefGoogle Scholar
  15. Batley J, Edwards D (2009b) Mining for single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) molecular genetic markers. In: Posada D (ed) Bioinformatics for DNA sequence analysis. Humana Press, New York, pp 303–322CrossRefGoogle Scholar
  16. Batley J, Barker G, O’Sullivan H, Edwards KJ, Edwards D (2003a) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol 132:84–91PubMedCrossRefGoogle Scholar
  17. Batley J, Mogg R, Edwards D, O’Sullivan H, Edwards KJ (2003b) A high-throughput SNuPE assay for genotyping SNPs in the flanking regions of Zea mays sequence tagged simple sequence repeats. Mol Breeding 11:111–120CrossRefGoogle Scholar
  18. Batley J, Jewell E, Edwards D (2007) Automated discovery of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) molecular genetic markers. In: Edwards D (ed) Plant bioinformatics. Humana Press, New York, pp 473–494CrossRefGoogle Scholar
  19. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C, Ling EYS, Stiller J, Smits L, Imelfort M, Manoli S, McKenzie M, Kubalakova M, Simkova H, Batley J, Fleury D, Dolezel J, Edwards D (2011) Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol J 9:768–775PubMedCrossRefGoogle Scholar
  20. Berkman PJ, Lai K, Lorenc MT, Edwards D (2012a) Next generation sequencing applications for wheat crop improvement. Am J Bot 99:365–371PubMedCrossRefGoogle Scholar
  21. Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Smits L, Lai K, Campbell E, Kubalakova M, Simkova H, Batley J, Dolezel J, Hernandez P, Edwards D (2012b) Sequencing wheat chromosome arm 7BS delimits the 7BS/4AL translocation and reveals homoeologous gene conservation. Theor Appl Genet 124:423–432PubMedCrossRefGoogle Scholar
  22. Brockman W, Alvarez P, Young S, Garber M, Giannoukos G, Lee WL, Russ C, Lander ES, Nusbaum C, Jaffe DB (2008) Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res 18:763–770PubMedCrossRefGoogle Scholar
  23. Chagné D, Batley J, Edwards D, Forster JW (2007) Single nucleotide polymorphism genotyping in plants. In: Oraguzie N, Rikkerink E, Gardiner S, De Silva H (eds) Association mapping in plants. Springer, New York, pp 77–94CrossRefGoogle Scholar
  24. Ching A, Caldwell K, Jung M, Dolan M, Smith O, Tingey S, Morgante M, Rafalski A (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19PubMedCrossRefGoogle Scholar
  25. Close T, Bhat P, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson J, Wanamaker S, Bozdag S, Roose M, Moscou M, Chao S, Varshney R, Szucs P, Sato K, Hayes P, Matthews D, Kleinhofs A, Muehlbauer G, DeYoung J, Marshall D, Madishetty K, Fenton R, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582PubMedCrossRefGoogle Scholar
  26. Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D (2009a) AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res 37:D951–D953PubMedCrossRefGoogle Scholar
  27. Duran C, Appleby N, Edwards D, Batley J (2009b) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinform 4:16–27CrossRefGoogle Scholar
  28. Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J (2009c) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnol J 7:326–333PubMedCrossRefGoogle Scholar
  29. Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA, Edwards D (2010a) CMap3D: a 3D visualisation tool for comparative genetic maps. Bioinformatics 26:273–274PubMedCrossRefGoogle Scholar
  30. Duran C, Eales D, Marshall D, Imelfort M, Stiller J, Berkman PJ, Clark T, McKenzie M, Appleby N, Batley J, Basford K, Edwards D (2010b) Future tools for association mapping in crop plants. Genome 53:1017–1023PubMedCrossRefGoogle Scholar
  31. Edwards D (2007) Bioinformatics and plant genomics for staple crops improvement. In: Kang MS, Priyadarshan PM (eds) Breeding major food staples. Blackwell, Oxford, pp 93–106CrossRefGoogle Scholar
  32. Edwards D (2011) Wheat bioinformatics. In: Bonjean A, Angus W, Van Ginkel M (eds) The world wheat book. Lavoisier, France, pp 851–875Google Scholar
  33. Edwards D, Batley J (2004) Plant bioinformatics: from genome to phenome. Trends Biotechnol 22:232–237PubMedCrossRefGoogle Scholar
  34. Edwards D, Batley J (2008) Bioinformatics: fundamentals and applications in plant genetics, mapping and breeding. In: Kole C, Abbott AG (eds) Principles and practices of plant genomics. Science Publishers Inc., USA, pp 269–302Google Scholar
  35. Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 7:1–8CrossRefGoogle Scholar
  36. Edwards D, Wang X (2012) Genome Sequencing Initiatives. In: Edwards D, Parkin IAP, Batley J (eds) Genetics, genomics and breeding of Oilseed Brassicas. Science Publishers Inc., New Hampshire, pp 152–157Google Scholar
  37. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758PubMedGoogle Scholar
  38. Edwards D, Forster JW, Chagné D, Batley J (2007a) What are SNPs? In: Oraguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds) Association mapping in plants. Springer, New York, pp 41–52CrossRefGoogle Scholar
  39. Edwards D, Forster JW, Cogan NOI, Batley J, Chagné D (2007b) Single nucleotide polymorphism discovery. In: Oraguzie N, Rikkerink E, Gardiner S, De Silva H (eds) Association mapping in plants. Springer, New York, pp 53–76CrossRefGoogle Scholar
  40. Edwards D, Hansen D, Stajich J (2009) DNA sequence databases. In: Edwards D HDaSJ (ed) Bioinformatics: tools and applications. Springer, Berlin, pp 1–11Google Scholar
  41. Edwards D, Batley J, Snowdon R (2012a) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126:1–11PubMedCrossRefGoogle Scholar
  42. Edwards D, Henry RJ, Edwards KJ (2012b) Preface: advances in DNA sequencing accelerating plant biotechnology. Plant Biotechnol J 10:621–622PubMedCrossRefGoogle Scholar
  43. Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Gagnere GK, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A (2012c) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol J 10:703–708PubMedCrossRefGoogle Scholar
  44. Eisenstein M (2012) Oxford nanopore announcement sets sequencing sector abuzz. Nat Biotech 30:295–296CrossRefGoogle Scholar
  45. Emberton J, Ma J, Yuan Y, SanMiguel P, Bennetzen JL (2005) Gene enrichment in maize with hypomethylated partial restriction (HMPR) libraries. Genome Res 15:1441–1446PubMedCrossRefGoogle Scholar
  46. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res 14:1812–1819PubMedCrossRefGoogle Scholar
  47. Fu Y, Springer NM, Gerhardt DJ, Ying K, Yeh C-T, Wu W, Swanson-Wagner R, D’Ascenzo M, Millard T, Freeberg L, Aoyama N, Kitzman J, Burgess D, Richmond T, Albert TJ, Barbazuk WB, Jeddeloh JA, Schnable PS (2010) Repeat subtraction-mediated sequence capture from a complex genome. Plant J 62:898–909PubMedCrossRefGoogle Scholar
  48. Glenn TC (2011) Field guide to next-generation DNA sequencers. Mol Ecol Resour 11:759–769PubMedCrossRefGoogle Scholar
  49. Gore M, Chia J, Elshire R, Sun Q, Ersoz E, Hurwitz B, Peiffer J, McMullen M, Grills G, Ross-Ibarra J (2009) A first-generation haplotype map of maize. Science 326:1115–1117PubMedCrossRefGoogle Scholar
  50. Gupta PK (2008) Single-molecule DNA sequencing technologies for future genomics research. Trends Biotechnol 26:602–611PubMedCrossRefGoogle Scholar
  51. Gupta M, Chyi YS, Romeroseverson J, Owen JL (1994) Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor Appl Genet 89:998–1006Google Scholar
  52. 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
  53. 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 270:315–323PubMedCrossRefGoogle Scholar
  54. Gupta PK, Rustgi S, Mir RR (2013) Array-based high-throughput DNA markers and genotyping platforms for cereal genetics and genomics. In: Gupta PK, Varshney RK (eds) Cereal genomics II. Springer, BerlinGoogle Scholar
  55. Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schon C-C, Taudien S, Scholz U, Stein N, Mayer K, Bauer E (2011) From RNA-seq to large-scale genotyping—genomics resources for rye (Secale cereale L.). BMC Plant Biol 11:131PubMedCrossRefGoogle Scholar
  56. Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076PubMedCrossRefGoogle Scholar
  57. Huang XH, Wei XH, Sang T, Zhao QA, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang A, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian QA, Zhang QF, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42:U961–U976CrossRefGoogle Scholar
  58. Hyten D, Cannon S, Song Q, Weeks N, Fickus E, Shoemaker R, Specht J, Farmer A, May G, Cregan P (2010a) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11:38PubMedCrossRefGoogle Scholar
  59. Hyten D, Song Q, Fickus E, Quigley C, Lim J, Choi I, Hwang E, Pastor-Corrales M, Cregan P (2010b) High-throughput SNP discovery and assay development in common bean. BMC Genomics 11:475PubMedCrossRefGoogle Scholar
  60. Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Briefings Bioinf 10:609–618CrossRefGoogle Scholar
  61. Imelfort M, Batley J, Grimmond S, Edwards D (2009a) Genome sequencing approaches and successes. In: Somers D, Langridge P, Gustafson J (eds) Plant genomics. Humana Press, New York, pp 345–358CrossRefGoogle Scholar
  62. Imelfort M, Duran C, Batley J, Edwards D (2009b) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J 7:312–317PubMedCrossRefGoogle Scholar
  63. Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC, Edwards D (2006) SSR Primer and SSR Taxonomy Tree: biome SSR discovery. Nucleic Acids Res 34:W656–W659PubMedCrossRefGoogle Scholar
  64. Kashi Y, King D, Soller M (1997) Simple sequence repeats as a source of quantitative genetic variation. Trends Genet 13:74–78PubMedCrossRefGoogle Scholar
  65. Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167PubMedCrossRefGoogle Scholar
  66. 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 vulgareL.). Mol Genet Genomics 270:24–33PubMedCrossRefGoogle Scholar
  67. Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6:127–134PubMedCrossRefGoogle Scholar
  68. Lai JS, Li RQ, Xu X, Jin WW, Xu ML, Zhao HN, Xiang ZK, Song WB, Ying K, Zhang M, Jiao YP, Ni PX, Zhang JG, Li D, Guo XS, Ye KX, Jian M, Wang B, Zheng HS, Liang HQ, Zhang XQ, Wang SC, Chen SJ, Li JS, Fu Y, Springer NM, Yang HM, Wang JA, Dai JR, Schnable PS, Wang J (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:U1027–U1158CrossRefGoogle Scholar
  69. Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2012a) an integrated database and portal for wheat genome information. Plant Cell Physiol 53:1–7CrossRefGoogle Scholar
  70. Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden MJ, Forrest KL, Fleury D, Baumann U, Zander M, Mason AS, Batley J, Edwards D (2012b) Single nucleotide polymorphism discovery from wheat next-generation sequence data. Plant Biotechnol J 10:743–749PubMedCrossRefGoogle Scholar
  71. Lai K, Lorenc MT, Edwards D (2012c) Genomic databases for crop improvement. Agronomy 2:62–73CrossRefGoogle Scholar
  72. Landjeva S, Korzun V, Borner A (2007) Molecular markers: actual and potential contributions to wheat genome characterization and breeding. Euphytica 156:271–296CrossRefGoogle Scholar
  73. Lee H, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D (2012) Bioinformatics tools and databases for analysis of next generation sequence data. Briefings Funct Genom 2:12–24CrossRefGoogle Scholar
  74. Liu L, Li Y, Li S, Hu N, He Y, Pong R, Lin D, Lu L, Law M (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012:11Google Scholar
  75. Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J, Edwards D (2012) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1:370–382CrossRefGoogle Scholar
  76. Love CG, Batley J, Edwards D (2003) Applied computational tools for crop genome research. J Plant Biotechnol 5:193–195Google Scholar
  77. Mammadov J, Chen W, Ren R, Pai R, Marchione W, Yalçin F, Witsenboer H, Greene T, Thompson S, Kumpatla S (2010) Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding. Theor Appl Genet 121:577–588PubMedCrossRefGoogle Scholar
  78. Marshall D, Hayward A, Eales D, Imelfort M, Stiller J, Berkman P, Clark T, McKenzie M, Lai K, Duran C, Batley J, Edwards D (2010) Targeted identification of genomic regions using TAGdb. Plant Methods 6:19PubMedCrossRefGoogle Scholar
  79. McCouch SR, Zhao K, Wright M, Tung C-W, Ebana K, Thomson M, Reynolds A, Wang D, DeClerck G, Ali ML, McClung A, Eizenga G, Bustamante C (2010) Development of genome-wide SNP assays for rice. Breed Sci 60:524–535CrossRefGoogle Scholar
  80. McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc National Acad Sci 106(30):12273–12278CrossRefGoogle Scholar
  81. Metzker ML (2010) Applications of next-generation sequencing, Sequencing technologies—the next generation. Nat Rev Genet 11:31–46PubMedCrossRefGoogle Scholar
  82. Miller MR, Dunham JP, Amores A, Cresko WA, Johnson EA (2007) Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers. Genome Res 17:240–248PubMedCrossRefGoogle Scholar
  83. Mogg R, Batley J, Hanley S, Edwards D, O’Sullivan H, Edwards KJ (2002) Characterization of the flanking regions of Zea mays microsatellites reveals a large number of useful sequence polymorphisms. Theor Appl Genet 105:532–543PubMedCrossRefGoogle Scholar
  84. 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
  85. Moxon ER, Wills C (1999) DNA microsatellites: agents of evolution? Sci Am 280:94–99PubMedCrossRefGoogle Scholar
  86. Nie X, Li B, Wang L, Liu P, Biradar SS, Li T, Dolezel J, Edwards D, Luo MC, Weining S (2012) Development of chromosome-arm-specific microsatellite markers in Triticum aestivum (Poaceae) using NGS technology. Am J Bot 99:e369–e371PubMedCrossRefGoogle Scholar
  87. Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant J, Sourdille P, Balfourier F, Le Paslier M, Chauveau A (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210PubMedCrossRefGoogle Scholar
  88. Pennisi E (2012) Search for pore-fection. Science 336:534–537PubMedCrossRefGoogle Scholar
  89. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253PubMedCrossRefGoogle Scholar
  90. Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222Google Scholar
  91. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  92. Ravel C, Martre P, Romeuf I, Dardevet M, El-Malki R, Bordes J, Duchateau N, Brunel D, Balfourier F, Charmet G (2009) Nucleotide polymorphism in the wheat transcriptional activator spa influences its pattern of expression and has pleiotropic effects on grain protein composition, dough viscoelasticity, and grain hardness. Plant Physiol 151:2133–2144PubMedCrossRefGoogle Scholar
  93. 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
  94. Rustgi S, Bandopadhyay R, Balyan HS, Gupta PK (2009) EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure. Czech J Genet Plant Breed 45:106–116Google Scholar
  95. Saintenac C, Jiang D, Akhunov E (2011) Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome. Genome Biol 12:R88PubMedCrossRefGoogle Scholar
  96. Santana QC, Coetzee MPA, Steenkamp ET, Mlonyeni OX, Hammond GNA, Wingfield MJ, Wingfield BD (2009) Microsatellite discovery by deep sequencing of enriched genomic libraries. Biotechniques 46:217–223PubMedCrossRefGoogle Scholar
  97. Schulman AH, Flavell AJ, Ellis THN (2004) The application of LTR retrotransposons as molecular markers in plants. Mob Genet Elem: Protoc Genomic Appl 260:145–173CrossRefGoogle Scholar
  98. Sharma PC, Grover A, Kahl G (2007) Mining microsatellites in eukaryotic genomes. Trends Biotechnol 25:490–498PubMedCrossRefGoogle Scholar
  99. Shen Y-J, Jiang H, Jin J-P, Zhang Z-B, Xi B, He Y–Y, Wang G, Wang C, Qian L, Li X, Yu Q-B, Liu H-J, Chen D-H, Gao J-H, Huang H, Shi T-L, Yang Z-N (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205PubMedCrossRefGoogle Scholar
  100. Shendure J, Ji HL (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145PubMedCrossRefGoogle Scholar
  101. Subramanian S, Mishra RK, Singh L (2003) Genome-wide analysis of microsatellite repeats in humans: their abundance and density in specific genomic regions. Genome Bio 4(2):R13CrossRefGoogle Scholar
  102. Tautz D, Schlotterer C (1994) Concerted evolution, molecular drive and natural-selection—reply. Current Biol 4:1165–1166CrossRefGoogle Scholar
  103. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res 10:967–981PubMedCrossRefGoogle Scholar
  104. Trebbi D, Maccaferri M, de Heer P, Sørensen A, Giuliani S, Salvi S, Sanguineti M, Massi A, van der Vossen E, Tuberosa R (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum). Theor Appl Genet 123:555–569PubMedCrossRefGoogle Scholar
  105. Trick M, Adamski N, Mugford S, Jiang C-C, Febrer M, Uauy C (2012) Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 12:14PubMedCrossRefGoogle Scholar
  106. van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, van Eijk MJT (2007) Complexity reduction of polymorphic sequences (crops™): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2:e1172PubMedCrossRefGoogle Scholar
  107. Varshney RK, Sigmund R, Börner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168:195–202CrossRefGoogle Scholar
  108. Winfield MO, Wilkinson PA, Allen AM, Barker GLA, Coghill JA, Burridge A, Hall A, Brenchley RC, D’Amore R, Hall N, Bevan MW, Richmond T, Gerhardt DJ, Jeddeloh JA, Edwards KJ (2012) Targeted re-sequencing of the allohexaploid wheat exome. Plant Biotechnol J 10:733–742PubMedCrossRefGoogle Scholar
  109. Wing R, Kim H, Foicoechea J, Yu Y, Kudrna D, Zuccolo A, Ammiraju J, Luo M, Nelson W, Ma J (2007) The oryza map alignment project (omap): a new re-source for comparative genome studies within oryza. In: Upadhyaya NM (ed) Rice functional genomics. Springer, New York, pp 395–409CrossRefGoogle Scholar
  110. Xu X, Liu X, Ge S, Jensen JD, Hu F, Li X, Dong Y, Gutenkunst RN, Fang L, Huang L, Li J, He W, Zhang G, Zheng X, Zhang F, Li Y, Yu C, Kristiansen K, Zhang X, Wang J, Wright M, McCouch S, Nielsen R, Wang J, Wang W (2012) Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotech 30:105–111CrossRefGoogle Scholar
  111. Yamamoto T, Nagasaki H, Yonemaru J-i, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11:267PubMedCrossRefGoogle Scholar
  112. You F, Huo N, Deal K, Gu Y, Luo M-C, McGuire P, Dvorak J, Anderson O (2011) Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence. BMC Genomics 12:59PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  1. 1.Australian Centre for Plant Functional Genomics and School of Agriculture and Food SciencesUniversity of QueenslandBrisbaneAustralia
  2. 2.Ch Charan Singh UniversityMeerutIndia

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