Whole-Genome Sequencing for Marker Discovery

Molecular Markers in Plants

Volumn , Issue , 2012, Pages 21-34

  Edwards, Mark ^a  

^a SOUTHERN CROSS UNIVERSITY   (Australia)

Author keywords

Comparative with "genome partitioning," or "genomic capture"; Ion Torrent and Pacific Biosciences systems, SMRT technology; MRNA expression, on SGS, biomarker whole genome resequencing; Sequencing plant related "omics," for attaining gains; SGS and large data volume, short sequence reads and low cost; SGS sequencing, short length reads as problems in genome; Targeted, barcode index sequences, to library molecules; Third generation sequencing, or SMS for very long reads; Third generation SMS, epigenetic, GS for GEBVs and low cost; Whole genome sequencing in facilitating marker discovery

Indexed keywords

EID: 84886336692     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118473023.ch2     Document Type: Chapter

References (26)

1. Bentley, D.R. and Smith, A.J. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
2. Birney, E. (2011) Assemblies: the good, the bad, the ugly. Nature Methods, 8, 59-60.
3. Brautigam, A. and Gowik, U. (2010) What can next generation sequencing do for you? Next generation sequencing as a valuable tool in plant research. Plant Biology, 12, 831-841.
4. Clark, T.A., Murray, I.A., Morgan, R.D. et al. (2011) Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing. Nucleic Acids Research, 1-12. doi: 10.1093/nar/gkr1146.
5. Deschamps, S. and Campbell, M.A. (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Molecular Breeding, 25, 553-570.
6. Edwards, M.A. and Henry, R.J. (2011) DNA sequencing methods contributing to new directions in cereal research. Journal of Cereal Science, 54, 395-400.
7. Eid, J., Fehr, A., Turner, S. et al. (2009) Real-time DNA sequencing from single polymerase molecules. Science, 323, 133-138.
8. Glenn, T.C. (2011) Field guide to next-generation DNA sequencers. Molecular Ecology Resources, 11, 759-769.
9. Gupta, P.K., Langridge, P. and Mir, R.R. (2010) Marker-assisted wheat breeding: present status and future possibilities. Molecular Breeding, 26, 145-161.
10. Imelfort, M., Batley, J., Grimmond, S. and Edwards, D. (2009) Genome sequencing approaches and successes, in Methods in Molecular Biology, Plant Genomics, vol. 513 (eds Daryl J. Somers et al.), Humana Press, New York, pp. 345-258
11. Jannink, J.L. (2010) Dynamics of long-term genomic selection. Genetics Selection Evolution, 42, 35. doi: 10.1186/1297-9686-42-35
12. Kircher, M. and Kelso, J. (2010) High-throughput DNA sequencing-concepts and limitations. Bioessays, 32, 524-536.
13. Laird, P.W. (2010). Principles and challenges of genome-wide DNA methylation analysis. Nature Reviews Genetics, 11, 191-203.
14. Langridge, P. and Fleury, D. (2010) Making the most of 'omics' for crop breeding. Trends in Biotechnology, 29, 33-40.
15. Lieberman, K.R., Cherf, G.M., Doody, M.J. et al. (2010) Processive replication of single DNA molecules in a nanopore catalyzed by phi29 DNA polymerase. Journal of the American Chemical Society, 132, 17961-17972.
16. Magi, A., Benelli, M., Gozzini, A. et al. (2010) Bioinformatics for next generation sequencing data. Genes, 1, 294-307.
17. Margulies, M., Egholm, M. and Rothberg, J.M. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376-380.
18. Metzker, M.L. (2010) Sequencing technologies-the next generation. Nature Reviews Genetics, 11, 31-46.
19. Mochida, K. and Shinozaki, K. (2010) Genomics and bioinformatics resources for crop improvement. Plant and Cell Physiology, 51, 497-523.
20. Peterson, T.W., Nam, S.J. and Darby, A. (2010) Next gen sequencing survey, in North America Equity Research, vol. 2010 (ed. T.W. Peterson), JP Morgan Chase & Co., New York.
21. Rival, A., Beule, T., Bertossi, F.A. et al. (2010) Plant epigenetics: From genomes to epigenomes. Notulae Botanicae Horti Agrobotanici Cluj-Napoca, 38, 9-15.
22. Ronaghi, M., Karamohamed, S., Pettersson, B. et al. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Analytical Biochemistry, 242, 84-89.
23. Sanger, F., Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chainterminating inhibitors. Proceedings of the National Academy of Sciences, 74, 5463-5467.
24. Schadt, E.E., Turner, S. and Kasarskis, A. (2010) A window into third-generation sequencing. Human Molecular Genetics, 19, R227-R240.
25. Shendure, J. and Ji, H.L. (2008) Next-generation DNA sequencing. Nature Biotechnology, 26, 1135-1145.
26. Shendure, J., Porreca, G.J., Reppas, N.B. et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728-1732.