Abstract
Major advances have been made in the various “omics” fields in recent years, driven by new genomics technology, particularly DNA sequencing and high-throughput genotyping. The ability to interrogate the genome of diverse organisms enables the characterization of allelic variants underlying important agronomic traits. Advances in bioinformatics support the analysis of the genomic data flood, and applied genome informatics has grown rapidly over recent years in parallel with the expansion of genomics. As we face the perfect storm of increasing population and increasing climatic variation, advances in genomics, phenomics and related research, supported by bioinformatics, offer the greatest potential for accelerating food production and sustainability. An increasing number of crop genomes are being sequenced, and large-scale diversity studies, performed at the whole genome level, are being undertaken for the major crops. The analysis of this data is facilitated by customized databases, statistical methods and visualization tools. Through the integration and interrogation of the various “omics” data and the application of these resources for crop improvement, we have the potential to maintain and improve food security during a period of increasing climate variability.
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References
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 114:359–372
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, Totowa, NJ, pp 19–40
Arabidopsis_Genome_Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JSS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Berard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma ZR, Zhang YF, Brown S, Bourge M, Golser W, Song XA, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D’Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C (2011) The genome of Theobroma cacao. Nat Genet 43:101–108
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 99:186–192
Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS (2007) SNP discovery via 454 transcriptome sequencing. Plant J 51:910–918
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 19:421–422
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 95–102
Batley J, Edwards D (2009a) Genome sequence data: management, storage, and visualization. Biotechniques 46:333–336
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, Totowa, NJ, pp 303–322
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 132:84–91
Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Li X, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC, Edwards D (2007a) Identification and characterization of simple sequence repeat markers from Brassica napus expressed sequences. Mol Ecol Notes 7:886–889
Batley J, Jewell E, Edwards D (2007b) Automated discovery of Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) molecular genetic markers. In: Edwards D (ed) Plant bioinformatics. Humana, Totowa, NJ, pp 473–494
Benson G (1999) Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res 27:573–580
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 9:768–775
Berkman PJ, Lai K, Lorenc MT, Edwards D (2012a) Next generation sequencing applications for wheat crop improvement. Am J Bot 99:365–371
Berkman PJ, Skarshewski A, Manoli S, Lorenc MT, Stiller J, Lars, 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 124:423–432
Bertioli DJ, Moretzsohn MC, Madsen LH, Sandal N, Leal-Bertioli SCM, Guimaraes PM, Hougaard BK, Fredslund J, Schauser L, Nielsen AM, Sato S, Tabata S, Cannon SB, Stougaard J (2009) An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 10:45
Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg GC, Edwards D, Batley J (2006) Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Mol Ecol Notes 6:1191–1194
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang XH, Mudge J, Vasdewani J, Scheix T, Spannagl M, Monaghan E, Nicholson C, Humphray SJ, Schoof H, Mayer KFX, Rogers J, Quetier F, Oldroyd GE, Debelle F, Cook DR, Retzel EF, Roe BA, Town CD, Tabata S, Van de Peer Y, Young ND (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Natl Acad Sci USA 103:14959–14964
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 156:847–854
Carollo V, Matthews DE, Lazo GR, Blake TK, Hummel DD, Lui N, Hane DL, Anderson OD (2005) GrainGenes 2.0. An improved resource for the small-grains community. Plant Physiol 139:643–651
Castelo AT, Martins W, Gao GR (2002) TROLL-tandem repeat occurrence locator. Bioinformatics 18:634–636
Cervigni GDL, Paniego N, Diaz M, Selva JP, Zappacosta D, Zanazzi D, Landerreche I, Martelotto L, Felitti S, Pessino S, Spangenberg G, Echenique V (2008) Expressed sequence tag analysis and development of gene associated markers in a near-isogenic plant system of Eragrostis curvula. Plant Mol Biol 67:1–10
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 77–94
Chen CX, Zhou P, Choi YA, Huang S, Gmitter FG (2006) Mining and characterizing microsatellites from citrus ESTs. Theor Appl Genet 112:1248–1257
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
Chia J-M, Song C, Bradbury PJ, Costich D, de Leon N, Doebley J, Elshire RJ, Gaut B, Geller L, Glaubitz JC, Gore M, Guill KE, Holland J, Hufford MB, Lai J, Li M, Liu X, Lu Y, McCombie R, Nelson R, Poland J, Prasanna BM, Pyhajarvi T, Rong T, Sekhon RS, Sun Q, Tenaillon MI, Tian F, Wang J, Xu X, Zhang Z, Kaeppler SM, Ross-Ibarra J, McMullen MD, Buckler ES, Zhang G, Xu Y, Ware D (2012) Maize HapMap2 identifies extant variation from a genome in flux. Nat Genet 44:803–807
Dong QF, Roy L, Freeling M, Walbot V, Brendel V (2003) ZmDB, an integrated database for maize genome research. Nucleic Acids Res 31:244–247
Dong QF, Schlueter SD, Brendel V (2004) PlantGDB, plant genome database and analysis tools. Nucleic Acids Res 32:D354–D359
Dong QF, Lawrence CJ, Schlueter SD, Wilkerson MD, Kurtz S, Lushbough C, Brendel V (2005) Comparative plant genomics resources at PlantGDB. Plant Physiol 139:610–618
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–D953
Duran C, Appleby N, Edwards D, Batley J (2009b) Molecular genetic markers: discovery, applications, data storage and visualisation. Curr Bioinformatics 4:16–27
Duran C, Appleby N, Vardy M, Imelfort M, Edwards D, Batley J (2009c) Single nucleotide polymorphism discovery in barley using autoSNPdb. Plant Biotechnol J 7:326–333
Duran C, Edwards D, Batley J (2009d) Genetic maps and the use of synteny. In: Somers D, Langridge P, Gustafson J (eds) Plant genomics. Humana, Totowa, NJ, pp 41–56
Duran C, Boskovic Z, Imelfort M, Batley J, Hamilton NA, Edwards D (2010a) CMap3D: a 3D visualisation tool for comparative genetic maps. Bioinformatics 26:273–274
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 53:1017–1023
Duran C, Boskovic Z, Batley J, Edwards D (2011) Role of bioinformatics as a tool for vegetable Brassica species. In: Sadowski J, Kole C (eds) Vegetable Brassicas. Science, Enfield, NH, pp 406–418
Duvick J, Fu A, Muppirala U, Sabharwal M, Wilkerson MD, Lawrence CJ, Lushbough C, Brendel V (2008) PlantGDB: a resource for comparative plant genomics. Nucleic Acids Res 36:D959–D965
Edwards D (2007) Bioinformatics and plant genomics for staple crops improvement. In: Kang MS, Priyadarshan PM (eds) Breeding major food staples. Blackwell, Ames, IA, pp 93–106
Edwards D (2011) Wheat bioinformatics. In: Bonjean A, Angus W, Van Ginkel M (eds) The world wheat book. Lavoisier, Paris, pp 851–875
Edwards D, Batley J (2004) Plant bioinformatics: from genome to phenome. Trends Biotechnol 22:232–237
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, Enfield, NH, pp 269–302
Edwards D, Batley J (2010) Plant genome sequencing: applications for crop improvement. Plant Biotechnol J 7:1–8
Edwards D, Wang X (2012) Genome sequencing initiatives. In: Edwards D, Parkin IAP, Batley J, Kole C (eds) Genetics, genomics and breeding of oilseed brassicas. Science, Enfield, NH, pp 152–157
Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758
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 41–52
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 53–76
Edwards D, Hansen D, Stajich J (2009) DNA sequence databases. In: Edwards D, Hanson D, Stajich J (eds) Applied bioinformatics. Humana, Totowa, NJ, pp 1–11
Edwards D, Batley J, Snowdon R (2012a) Accessing complex crop genomes with next-generation sequencing. Theor Appl Genet 126(1):1–11
Edwards D, Wilcox S, Barrero RA, Fleury D, Cavanagh CR, Forrest KL, Hayden MJ, Moolhuijzen P, Keeble-Gagnère G, Bellgard MI, Lorenc MT, Shang CA, Baumann U, Taylor JM, Morell MK, Langridge P, Appels R, Fitzgerald A (2012b) Bread matters: a national initiative to profile the genetic diversity of Australian wheat. Plant Biotechnol J 10(6):703–708
Gai XW, Lal S, Xing LQ, Brendel V, Walbot V (2000) Gene discovery using the maize genome database ZmDB. Nucleic Acids Res 28:94–96
Gao H, Kong J (2005) The microsatellites and minisatellites in the genome of Fenneropenaeus chinensis. DNA Seq 16:426–436
Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100
Gonzales MD, Archuleta E, Farmer A, Gajendran K, Grant D, Shoemaker R, Beavis WD, Waugh ME (2005) The Legume Information System (LIS): an integrated information resource for comparative legume biology. Nucleic Acids Res 33:D660–D665
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
Hayward A, Dalton-Morgan J, Mason A, Zander M, Edwards D, Batley J (2012a) SNP discovery and applications in Brassica napus. J Plant Biotechnol 39(1):49–61
Hayward A, Vighnes HG, Delay G, Samian MR, Manoli SM, Stiller J, McKenzie M, Edwards D, Batley J (2012b) Second generation sequencing for gene discovery in the Brassicaceae. Plant Biotechnol J 10(6):750–759
Hernandez P, Martis M, Dorado G, Pfeifer M, Gálvez S, Schaaf S, Jouve N, Šimková H, Valárik M, Doležel J, Mayer KFX (2012) NGS and syntenic integration of flow-sorted arms of wheat chromosome 4A exposes the chromosome structure and gene content. Plant J 69(3):377–386
Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Lim GAC, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D, Batley J (2007) Sixteen new simple sequence repeat markers from Brassica juncea expressed sequences and their cross-species amplification. Mol Ecol Notes 7:697–700
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang MZ, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29:102–105
Hufford MB, Xu X, van Heerwaarden J, Pyhajarvi T, Chia J-M, Cartwright RA, Elshire RJ, Glaubitz JC, Guill KE, Kaeppler SM, Lai J, Morrell PL, Shannon LM, Song C, Springer NM, Swanson-Wagner RA, Tiffin P, Wang J, Zhang G, Doebley J, McMullen MD, Ware D, Buckler ES, Yang S, Ross-Ibarra J (2012) Comparative population genomics of maize domestication and improvement. Nat Genet 44:808–811
Hyten DL, Song Q, Zhu Y, Choi I-Y, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671
Imelfort M, Edwards D (2009) De novo sequencing of plant genomes using second-generation technologies. Brief Bioinformatics 10:609–618
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, Totowa, NJ, pp 345–358
Imelfort M, Duran C, Batley J, Edwards D (2009b) Discovering genetic polymorphisms in next-generation sequencing data. Plant Biotechnol J 7:312–317
International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768
Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:E25
Jaiswal P, Ni JJ, Yap I, Ware D, Spooner W, Youens-Clark K, Ren LY, Liang CZ, Zhao W, Ratnapu K, Faga B, Canaran P, Fogleman M, Hebbard C, Avraham S, Schmidt S, Casstevens TM, Buckler ES, Stein L, McCouch S (2006) Gramene: a bird’s eye view of cereal genomes. Nucleic Acids Res 34:D717–D723
Jayashree B, Ferguson M, Ilut D, Doyle J, Crouch JH (2005) Analysis of genomic sequences from peanut (Arachis hypogaea). Electron J Biotechnol 8:226–237
Jesubatham AM, Burow MD (2006) PeanutMap: an online genome database for comparative molecular maps of peanut. BMC Bioinformatics 7:375
Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GAC, Li X, Batley J, Spangenberg GC, Edwards D (2006) SSRPrimer and SSR taxonomy tree: biome SSR discovery. Nucleic Acids Res 34:W656–W659
Jiang Q, Yen SH, Stiller J, Edwards D, Scott PT, Gresshoff PM (2012) Diversity analysis of the tree legume Pongamia pinnata using PISSRs (pongamia inter-simple sequence repeats). J Plant Genome Sci 1(3):54–67
Jiao Y, Zhao H, Ren L, Song W, Zeng B, Guo J, Wang B, Liu Z, Chen J, Li W, Zhang M, Xie S, Lai J (2012) Genome-wide genetic changes during modern breeding of maize. Nat Genet 44:812–815
Jung S, Staton M, Lee T, Blenda A, Svancara R, Abbott A, Main D (2008) GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data. Nucleic Acids Res 36:D1034–D1040
Katti MV, Ranjekar PK, Gupta VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol Biol Evol 18:1161–1167
Keniry A, Hopkins CJ, Jewell E, Morrison B, Spangenberg GC, Edwards D, Batley J (2006) Identification and characterization of simple sequence repeat (SSR) markers from Fragaria × ananassa expressed sequences. Mol Ecol Notes 6:319–322
Lai K, Berkman PJ, Lorenc MT, Duran C, Smits L, Manoli S, Stiller J, Edwards D (2012a) WheatGenome.info: an integrated database and portal for wheat genome information. Plant Cell Physiol 53:1–7
Lai K, Duran C, Berkman PJ, Lorenc MT, Stiller J, Manoli S, Hayden M, Forrest KL, Fleury D, Baumann U, Zander M, Mason A, Batley J, Edwards D (2012b) Single nucleotide polymorphism discovery from wheat next generation sequence data. Plant Biotechnol J 10(6):743–749
Lai K, Lorenc MT, Edwards D (2012c) Genomic databases for crop improvement. Agronomy 2:62–73
Lam HM, Xu X, Liu X, Chen WB, Yang GH, Wong FL, Li MW, He WM, Qin N, Wang B, Li J, Jian M, Wang JA, Shao GH, Wang J, Sun SSM, Zhang GY (2010) Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat Genet 42:1053–1059
Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Lawrence CJ (2007) MaizeGDB - the maize genetics and genomics database. In: Edwards D (ed) Methods in molecular biology. Humana, Totowa, NJ, pp 331–345
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–D397
Lee H, Lai K, Lorenc MT, Imelfort M, Duran C, Edwards D (2012) Bioinformatics tools and databases for analysis of next generation sequence data. Brief Funct Genomics 2:12–24
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 18:287–299
Lim GAC, Jewell EG, Xi L, Erwin TA, Love C, Batley J, Spangenberg G, Edwards D (2007) A comparative map viewer integrating genetic maps for Brassica and Arabidopsis. BMC Plant Biol 7:40
Lindqvist C, Scheen AC, Yoo MJ, Grey P, Oppenheimer DG, Leebens-Mack JH, Soltis DE, Soltis PS, Albert VA (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 6:16
Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiewicz M, Spangenberg G, Edwards D, Batley J (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 7:273–277
Lorenc MT, Boskovic Z, Stiller J, Duran C, Edwards D (2012a) Role of bioinformatics as a tool for oilseed Brassica species. In: Edwards D, Parkin IAP, Batley J, Kole C (eds) Genetics, genomics and breeding of oilseed brassicas. Science, Enfield, NH, pp 194–205
Lorenc MT, Hayashi S, Stiller J, Lee H, Manoli S, Ruperao P, Visendi P, Berkman PJ, Lai K, Batley J, Edwards D (2012b) Discovery of single nucleotide polymorphisms in complex genomes using SGSautoSNP. Biology 1:370–382
Manly KF, Cudmore RH, Meer JM (2001) Map manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932
Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, 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, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380
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 6:19
Matthews DE, Carollo VL, Lazo GR, Anderson OD (2003) GrainGenes, the genome database for small-grain crops. Nucleic Acids Res 31:183–186
Ming R, Hou SB, Feng Y, Yu QY, Dionne-Laporte A, Saw JH, Senin P, Wang W, Ly BV, Lewis KLT, Salzberg SL, Feng L, Jones MR, Skelton RL, Murray JE, Chen CX, Qian WB, Shen JG, Du P, Eustice M, Tong E, Tang HB, Lyons E, Paull RE, Michael TP, Wall K, Rice DW, Albert H, Wang ML, Zhu YJ, Schatz M, Nagarajan N, Acob RA, Guan PZ, Blas A, Wai CM, Ackerman CM, Ren Y, Liu C, Wang JM, Wang JP, Na JK, Shakirov EV, Haas B, Thimmapuram J, Nelson D, Wang XY, Bowers JE, Gschwend AR, Delcher AL, Singh R, Suzuki JY, Tripathi S, Neupane K, Wei HR, Irikura B, Paidi M, Jiang N, Zhang WL, Presting G, Windsor A, Navajas-Perez R, Torres MJ, Feltus FA, Porter B, Li YJ, Burroughs AM, Luo MC, Liu L, Christopher DA, Mount SM, Moore PH, Sugimura T, Jiang JM, Schuler MA, Friedman V, Mitchell-Olds T, Shippen DE, dePamphilis CW, Palmer JD, Freeling M, Paterson AH, Gonsalves D, Wang L, Alam M (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–997
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 7:17–25
Mun J-H, Kwon S-J, Seol Y-J, Kim JA, Jin M, Kim JS, Lim M-H, Lee S-I, Hong JK, Park T-H, Lee S-C, Kim B-J, Seo M-S, Baek S, Lee M-J, Shin JY, Hahn J-H, Hwang Y-J, Lim K-B, Park JY, Lee J, Yang T-J, Yu H-J, Choi I-Y, Choi B-S, Choi SR, Ramchiary N, Lim YP, Fraser F, Drou N, Soumpourou E, Trick M, Bancroft I, Sharpe AG, Parkin IAP, Batley J, Edwards D, Park B-S (2010) Sequence and structure of Brassica rapa chromosome A3. Genome Biol 11:R94
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–e371
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 7:554–569
Powell W, Machray GC, Provan J (1996) Polymorphism revealed by simple sequence repeats. Trends Plant Sci 1:215–222
Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100
Raman H, Raman R, Eckermann P, Coombes N, Manoli S, Zou X, Meng J, Prangnell R, Stiller J, Batley J, Luckett D, Wratten N, Dennis E (2012) Physical mapping of flowering time loci in oilseed rape (Brassica napus L.). Theor Appl Genet 126(1):119–132
Rhee SY, Beavis W, Berardini TZ, Chen GH, Dixon D, Doyle A, Garcia-Hernandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu YH, Xu I, Yoo D, Yoon J, Zhang PF (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 31:224–228
Robinson AJ, Love CG, Batley J, Barker G, Edwards D (2004) Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20:1475–1476
Safar J, Bartos J, Janda J, Bellec A, Kubalakova M, Valarik M, Pateyron S, Weiserova J, Tuskova R, Cihalikova J, Vrana J, Simkova H, Faivre-Rampant P, Sourdille P, Caboche M, Bernard M, Dolezel J, Chalhoub B (2004) Dissecting large and complex genomes: flow sorting and BAC cloning of individual chromosomes from bread wheat. Plant J 39:960–968
Sato S, Nakamura Y, Kaneko T, Asamizu E, Kato T, Nakao M, Sasamoto S, Watanabe A, Ono A, Kawashima K, Fujishiro T, Katoh M, Kohara M, Kishida Y, Minami C, Nakayama S, Nakazaki N, Shimizu Y, Shinpo S, Takahashi C, Wada T, Yamada M, Ohmido N, Hayashi M, Fukui K, Baba T, Nakamichi T, Mori H, Tabata S (2008) Genome structure of the legume, Lotus japonicus. DNA Res 15:227–239
Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GAC, Mongin E, Barker G, Spangenberg GC, Edwards D (2005) SNPServer: a real-time SNP discovery tool. Nucleic Acids Res 33:W493–W495
Schlotterer C (2000) Evolutionary dynamics of microsatellite DNA. Chromosoma 109:365–371
Schlueter JA, Scheffler BE, Jackson S, Shoemaker RC (2008) Fractionation of synteny in a genomic region containing tandemly duplicated genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana. J Hered 99:390–395
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X-C, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183
Schnable PS, Ware D, Fulton RS, Stein JC, Wei FS, Pasternak S, Liang CZ, Zhang JW, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du FY, Kim K, Abbott RM, Cotton M, Levy A (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–1115
Shulaev V, Korban SS, Sosinski B, Abbott AG, Aldwinckle HS, Folta KM, Iezzoni A, Main D, Arus P, Dandekar AM, Lewers K, Brown SK, Davis TM, Gardiner SE, Potter D, Veilleux RE (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003
Shulaev V, Sargent DJ, Crowhurst RN, Mockler TC, Folkerts O, Delcher AL, Jaiswal P, Mockaitis K, Liston A, Mane SP, Burns P, Davis TM, Slovin JP, Bassil N, Hellens RP, Evans C, Harkins T, Kodira C, Desany B, Crasta OR, Jensen RV, Allan AC, Michael TP, Setubal JC, Celton JM, Rees DJG, Williams KP, Holt SH, Rojas JJR, Chatterjee M, Liu B, Silva H, Meisel L, Adato A, Filichkin SA, Troggio M, Viola R, Ashman TL, Wang H, Dharmawardhana P, Elser J, Raja R, Priest HD, Bryant DW, Fox SE, Givan SA, Wilhelm LJ, Naithani S, Christoffels A, Salama DY, Carter J, Girona EL, Zdepski A, Wang WQ, Kerstetter RA, Schwab W, Korban SS, Davik J, Monfort A, Denoyes-Rothan B, Arus P, Mittler R, Flinn B, Aharoni A, Bennetzen JL, Salzberg SL, Dickerman AW, Velasco R, Borodovsky M, Veilleux RE, Folta KM (2011) The genome of woodland strawberry (Fragaria vesca). Nat Genet 43:109–151
Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109:1105–1114
Tautz D (1989) Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Res 17:6463–6471
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 11:1441–1452
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641
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
Tollenaere R, Hayward A, Dalton-Morgan J, Campbell E, McLanders J, Lorenc M, Manoli S, Stiller J, Raman R, Raman H, Edwards D, Batley J (2012) Identification and characterisation of candidate Rlm4 blackleg resistance genes in Brassica napus using next generation sequencing. Plant Biotechnol J 10(6):709–715
Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981
Van Ooijen JW, Voorrips RE (2001) JoinMap® version 3.0: software for the calculation of genetic linkage maps. Plant Research International, Wageningen
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagne D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouze P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833
Volfovsky N, Haas BJ, Salzberg SL (2001) A clustering method for repeat analysis in DNA sequences. Genome Biol 2(8):RESEARCH0027
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 6:9
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
Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park B-S, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IAP, Batley J, Kim J-S, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S-J, Choi S-R, Lee T-H, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039
Ware D, Jaiswal P, Ni JJ, Pan XK, Chang K, Clark K, Teytelman L, Schmidt S, Zhao W, Cartinhour S, McCouch S, Stein L (2002a) Gramene: a resource for comparative grass genomics. Nucleic Acids Res 30:103–105
Ware DH, Jaiswal PJ, Ni JJ, Yap I, Pan XK, Clark KY, Teytelman L, Schmidt SC, Zhao W, Chang K, Cartinhour S, Stein LD, McCouch SR (2002b) Gramene, a tool for grass genomics. Plant Physiol 130:1606–1613
Weber JL (1990) Informativeness of human (Dc-Da)N. (Dg-Dt)N polymorphisms. Genomics 7:524–530
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 5:362–369
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Khovayko O, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Ostell J, Pruitt KD, Schuler GD, Shumway M, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Tatusov RL, Tatusova TA, Wagner L, Yaschenko E (2008) Database resources of the national center for biotechnology information. Nucleic Acids Res 36:D13–D21
Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, Barkan A (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy mutator lines of maize. Plant J 63:167–177
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 7:1077–1079
Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DMA, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejia N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, del Rosario Herrera M, Giuliano G, Pietrella M, Perrotta G, Facella P, O’Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa A, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ, Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JME, Nielsen KL, Sonderkaer M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CWB, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert BTL, Goverse A, van Ham RCHJ, Visser RGF, Potato Genome Sequencing Consortium (2011) Genome sequence and analysis of the tuber crop potato. Nature 475:189–194
Yu J, Hu SN, Wang J, Wong GKS, Li SG, Liu B, Deng YJ, Dai L, Zhou Y, Zhang XQ, Cao ML, Liu J, Sun JD, Tang JB, Chen YJ, Huang XB, Lin W, Ye C, Tong W, Cong LJ, Geng JN, Han YJ, Li L, Li W, Hu GQ, Huang XG, Li WJ, Li J, Liu ZW, Li L, Liu JP, Qi QH, Liu JS, Li L, Li T, Wang XG, Lu H, Wu TT, Zhu M, Ni PX, Han H, Dong W, Ren XY, Feng XL, Cui P, Li XR, Wang H, Xu X, Zhai WX, Xu Z, Zhang JS, He SJ, Zhang JG, Xu JC, Zhang KL, Zheng XW, Dong JH, Zeng WY, Tao L, Ye J, Tan J, Ren XD, Chen XW, He J, Liu DF, Tian W, Tian CG, Xia HG, Bao QY, Li G, Gao H, Cao T, Wang J, Zhao WM, Li P, Chen W, Wang XD, Zhang Y, Hu JF, Wang J, Liu S, Yang J, Zhang GY, Xiong YQ, Li ZJ, Mao L, Zhou CS, Zhu Z, Chen RS, Hao BL, Zheng WM, Chen SY, Guo W, Li GJ, Liu SQ, Tao M, Wang J, Zhu LH, Yuan LP, Yang HM (2002) A draft sequence of the rice genome (Oryza sativa L. ssp indica). Science 296:79–92
Zharkikh A, Troggio M, Pruss D, Cestaro A, Eldrdge G, Pindo M, Mitchell JT, Vezzulli S, Bhatnagar S, Fontana P, Viola R, Gutin A, Salamini F, Skolnick M, Velasco R (2008) Sequencing and assembly of highly heterozygous genome of Vitis vinifera L. cv Pinot Noir: problems and solutions. J Biotechnol 136:38–43
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Edwards, D. (2013). Bioinformatics Tools to Assist Breeding for Climate Change. In: Kole, C. (eds) Genomics and Breeding for Climate-Resilient Crops. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37045-8_10
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