SNP Discovery by Transcriptome Pyrosequencing
作者： W. Brad Barbazuk , Patrick S. Schnable
DOI: 10.1007/978-1-61779-065-2_15
关键词:
摘要: Single nucleotide polymorphisms (SNPs) are single base differences between haplotypes. SNPs abundant in many species and valuable as markers for genetic map construction, modern molecular breeding programs, quantitative studies. readily mined from genomic DNA or cDNA sequence obtained individuals having two more distinct genotypes. While automated Sanger sequencing has become less expensive over time, it is still costly to acquire deep several "Next-generation" technologies that utilize new chemistries massively parallel approaches have enabled sequences be acquired at extremely high depths of coverage faster cost than traditional sequencing. One such method represented by the Roche/454 Life Sciences GS-FLX Titanium Series, which currently uses pyrosequencing produce up 400-600 million bases sequence/run (>1 reads, ~400 bp/read). This chapter discusses use high-throughput SNP discovery focusing on 454 maize cDNA, development a computational pipeline polymorphism detection, subsequent identification 7,000 putative Mo17 B73 maize. In addition, alternative alignment detection strategies implement Illumina short data processing visualization tools, reduced representation techniques reduce repeat DNA, thus enabling efficient analysis genome sequence, discussed.
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Pablo D. Rabinowicz, Kristin Schutz, Neilay Dedhia, Cristina Yordan, Laurence D. Parnell, Lincoln Stein, W. Richard McCombie, Robert A. Martienssen, Differential methylation of genes and retrotransposons facilitates shotgun sequencing of the maize genome Nature Genetics. ,vol. 23, pp. 305- 308 ,(1999) , 10.1038/15479
Roy J. Britten, Dale E. Graham, Berney R. Neufeld, Analysis of repeating DNA sequences by reassociation Methods in Enzymology. ,vol. 29, pp. 363- 418 ,(1974) , 10.1016/0076-6879(74)29033-5
Gabor T. Marth, Ian Korf, Mark D. Yandell, Raymond T. Yeh, Zhijie Gu, Hamideh Zakeri, Nathan O. Stitziel, LaDeana Hillier, Pui-Yan Kwok, Warren R. Gish, A general approach to single-nucleotide polymorphism discovery Nature Genetics. ,vol. 23, pp. 452- 456 ,(1999) , 10.1038/70570
Nicholas J. Bray, Paul R. Buckland, Michael J. Owen, Michael C. O'Donovan, Cis-acting variation in the expression of a high proportion of genes in human brain. Human Genetics. ,vol. 113, pp. 149- 153 ,(2003) , 10.1007/S00439-003-0956-Y
Jianmin Wang, Xiaoqiu Huang, A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage BMC Bioinformatics. ,vol. 6, pp. 220- 220 ,(2005) , 10.1186/1471-2105-6-220
B Burr, F A Burr, K H Thompson, M C Albertson, C W Stuber, Gene mapping with recombinant inbreds in maize Genetics. ,vol. 118, pp. 519- 526 ,(1988) , 10.1093/GENETICS/118.3.519
Thomas J Albert, Michael N Molla, Donna M Muzny, Lynne Nazareth, David Wheeler, Xingzhi Song, Todd A Richmond, Chris M Middle, Matthew J Rodesch, Charles J Packard, George M Weinstock, Richard A Gibbs, Direct selection of human genomic loci by microarray hybridization. Nature Methods. ,vol. 4, pp. 903- 905 ,(2007) , 10.1038/NMETH1111
Deborah A Nickerson, Vincent O Tobe, Scott L Taylor, PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing Nucleic Acids Research. ,vol. 25, pp. 2745- 2751 ,(1997) , 10.1093/NAR/25.14.2745
Jeffrey L. Bennetzen, Kathrin Schrick, Patricia S. Springer, Willis E. Brown, Phillip SanMiguel, Active maize genes are unmodified and flanked by diverse classes of modified, highly repetitive DNA Genome. ,vol. 37, pp. 565- 576 ,(1994) , 10.1139/G94-081
John P Vogel, David F Garvin, Todd C Mockler, Jeremy Schmutz, Dan Rokhsar, Michael W Bevan, Kerrie Barry, Susan Lucas, Miranda Harmon-Smith, Kathleen Lail, Hope Tice, Jane Grimwood, Neil McKenzie, Naxin Huo, Yong Q Gu, Gerard R Lazo, Olin D Anderson, Frank M You, Ming-Cheng Luo, Jan Dvorak, Jonathan Wright, Melanie Febrer, Dominika Idziak, Robert Hasterok, Erika Lindquist, Mei Wang, Samuel E Fox, Henry D Priest, Sergei A Filichkin, Scott A Givan, Douglas W Bryant, Jeff H Chang, Haiyan Wu, Wei Wu, An-Ping Hsia, Patrick S Schnable, Anantharaman Kalyanaraman, Brad Barbazuk, Todd P Michael, Samuel P Hazen, Jennifer N Bragg, Debbie Laudencia-Chingcuanco, Yiqun Weng, Georg Haberer, Manuel Spannagl, Klaus Mayer, Thomas Rattei, Therese Mitros, Sang-Jik Lee, Jocelyn KC Rose, Lukas A Mueller, Thomas L York, Thomas Wicker, Jan P Buchmann, Jaakko Tanskanen, Alan H Schulman, Heidrun Gundlach, Michael Bevan, Antonio Costa de Oliveira, Luciano da C Maia, William Belknap, Ning Jiang, Jinsheng Lai, Liucun Zhu, Jianxin Ma, Cheng Sun, Ellen Pritham, Jerome Salse, Florent Murat, Michael Abrouk, Remy Bruggmann, Joachim Messing, Noah Fahlgren, Christopher M Sullivan, James C Carrington, Elisabeth J Chapman, Greg D May, Jixian Zhai, Matthias Ganssmann, Sai Guna Ranjan Gurazada, Marcelo German, Blake C Meyers, Pamela J Green, Ludmila Tyler, Jiajie Wu, James Thomson, Shan Chen, Henrik V Scheller, Jesper Harholt, Peter Ulvskov, Jeffrey A Kimbrel, Laura E Bartley, Peijian Cao, Ki-Hong Jung, Manoj K Sharma, Miguel Vega-Sanchez, Pamela Ronald, Christopher D Dardick, Stefanie De Bodt, Wim Verelst, Dirk Inzé, Maren Heese, Arp Schnittger, Xiaohan Yang, Udaya C Kalluri, Gerald A Tuskan, Zhihua Hua, Richard D Vierstra, Yu Cui, Shuhong Ouyang, Qixin Sun, Zhiyong Liu, Alper Yilmaz, Erich Grotewold, Richard Sibout, Kian Hematy, Gregory Mouille, Herman Höfte, Todd Michael, Jérome Pelloux, Devin O’Connor, James Schnable, Scott Rowe, Frank Harmon, Cynthia L Cass, John C Sedbrook, Mary E Byrne, Sean Walsh, Janet Higgins, Pinghua Li, Thomas Brutnell, Turgay Unver, Hikmet Budak, Harry Belcram, Mathieu Charles, Boulos Chalhoub, Ivan Baxter, Genome sequencing and analysis of the model grass Brachypodium distachyon Nature. ,vol. 463, pp. 763- 768 ,(2010) , 10.1038/NATURE08747