Gene discovery using mutagen-induced polymorphisms and deep sequencing: Application to plant disease resistance

Genetics

Volumn 192, Issue 1, 2012, Pages 139-146

  Zhu, Ying ^a,b   Mang, Hyung gon ^a,c   Sun, Qi ^a   Qian, Jun ^a   Hipps, Ashley ^a,d   Hua, Jian ^a  

^a Department of Obstetrics Gynecology   (United States)

^b INSTITUTE OF PLANT PROTECTION AND MICROBIOLOGY   (China)

^c Texas State University   (United States)

^d VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL MUTAGEN;

ARTICLE; CONTROLLED STUDY; DISEASE RESISTANCE; DNA MODIFICATION; DNA POLYMORPHISM; DNA SEQUENCE; GENE MAPPING; GENE SEGREGATION; GENETIC ASSOCIATION; MOLECULAR CLONING; MOLECULAR GENETICS; MUTAGEN INDUCED POLYMORPHISM; MUTANT; NEXT GENERATION SEQUENCING; NONHUMAN; PHENOTYPE; PLANT DISEASE; PLANT GROWTH; PRIORITY JOURNAL; WILD TYPE;

ACTIVE TRANSPORT, CELL NUCLEUS; ARABIDOPSIS; CELL NUCLEUS; DISEASE RESISTANCE; GENES, PLANT; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HYBRIDIZATION, GENETIC; MUTAGENESIS; MUTAGENS; PLANT DISEASES; PLANT PROTEINS; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 84866061672     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.141986     Document Type: Article

References (29)

1. Abe, A., S. Kosugi, K. Yoshida, S. Natsume, H. Takagi et al., 2012 Genome sequencing reveals agronomically important loci in rice using MutMap. Nat. Biotechnol. 30: 174-178.
2. Austin, R. S., D. Vidaurre, G. Stamatiou, R. Breit, N. J. Provart et al., 2011 Next-generation mapping of Arabidopsis genes. Plant J. 67: 715-725.
3. Bittner, F., M. Oreb, and R. R. Mendel, 2001 ABA3 is a molybdenum cofactor sulfurase required for activation of aldehyde oxidase and xanthine dehydrogenase in Arabidopsis thaliana. J. Biol. Chem. 276: 40381-40384.
4. Cao, J., K. Schneeberger, S. Ossowski, T. Gunther, S. Bender et al., 2011 Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat. Genet. 43: 956-963.
5. Colbert, T., B. J. Till, R. Tompa, S. Reynolds, M. N. Steine et al., 2001 High-throughput screening for induced point mutations. Plant Physiol. 126: 480-484.
6. Cuperus, J. T., T. A. Montgomery, N. Fahlgren, R. T. Burke, T. Townsend et al., 2010 Identification of MIR390a precursor processing-defective mutants in Arabidopsis by direct genome sequencing. Proc. Natl. Acad. Sci. USA 107: 466-471.
7. Dowell, R. D., O. Ryan, A. Jansen, D. Cheung, S. Agarwala et al., 2010 Genotype to phenotype: a complex problem. Science 328: 469.
8. Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto et al., 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6: e19379.
9. Gan, X., O. Stegle, J. Behr, J. G. Steffen, P. Drewe et al., 2011 Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
10. Gou, M., Z. Shi, Y. Zhu, Z. Bao, G. Wang et al., 2011 The F-box protein CPR1/CPR30 negatively regulates R protein SNC1 accumulation. Plant J. 69: 411-420.
11. Jander, G., S. R. Norris, S. D. Rounsley, D. F. Bush, I. M. Levin et al., 2002 Arabidopsis map-based cloning in the post-genome era. Plant Physiol. 129: 440-450.
12. Li, H., and R. Durbin, 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
13. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., 2009 The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
14. Lister, R., B. D. Gregory, and J. R. Ecker, 2009 Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond. Curr. Opin. Plant Biol. 12: 107-118.
15. Lukowitz, W., C. S. Gillmor, and W. R. Scheible, 2000 Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you. Plant Physiol. 123: 795-805.
16. Mang, H. G., W. Qian, Y. Zhu, J. Qian, H. G. Kang et al., 2012 Abscisic acid deficiency antagonizes high-temperature inhibition of disease resistance through enhancing nuclear accumulation of Resistance proteins SNC1 and RPS4 in Arabidopsis. Plant Cell 24: 1271-1284.
17. Mardis, E. R., 2008 Next-generation DNA sequencing methods. Annu. Rev. Genomics Hum. Genet. 9: 387-402.
18. Pan, X., R. Welti, and X. Wang, 2008 Simultaneous quantification of major phytohormones and related compounds in crude plant extracts by liquid chromatography-electrospray tandem mass spectrometry. Phytochemistry 69: 1773-1781.
19. Peters, J. L., F. Cnudde, and T. Gerats, 2003 Forward genetics and map-based cloning approaches. Trends Plant Sci. 8: 484-491.
20. Schneeberger, K., S. Ossowski, C. Lanz, T. Juul, A. H. Petersen et al., 2009 SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat. Methods 6: 550-551.
21. Shendure, J., and H. Ji, 2008 Next-generation DNA sequencing. Nat. Biotechnol. 26: 1135-1145.
22. Uchida, N., T. Sakamoto, T. Kurata, andM. Tasaka, 2011 Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing. Plant Cell Physiol. 52: 716-722.
23. Wang, K., M. Li, and H. Hakonarson, 2010 ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38: e164.
24. Wang, Y., Z. Bao, Y. Zhu, and J. Hua, 2009 Analysis of temperature modulation of plant defense against biotrophic microbes. Mol. Plant Microbe Interact. 22: 498-506.
25. Xiong, L., M. Ishitani, H. Lee, and J. K. Zhu, 2001 The Arabidopsis LOS5/ABA3 locus encodes a molybdenum cofactor sulfurase and modulates cold stress-and osmotic stress-responsive gene expression. Plant Cell 13: 2063-2083.
26. Yang, S., and J. Hua, 2004 A haplotype-specific Resistance gene regulated by BONZAI1 mediates temperature-dependent growth control in Arabidopsis. Plant Cell 16: 1060-1071.
27. Zhang, Y., S. Goritschnig, X. Dong, and X. Li, 2003 A gain-offunction mutation in a plant disease resistance gene leads to constitutive activation of downstream signal transduction pathways in suppressor of npr1-1, constitutive 1. Plant Cell 15: 2636-2646.
28. Zhu, Y., W. Qian, and J. Hua, 2010 Temperature modulates plant defense responses through NB-LRR proteins. PLoS Pathog. 6: e1000844.
29. Zuryn, S., S. Le Gras, K. Jamet, and S. Jarriault, 2010 A strategy for direct mapping and identification of mutations by wholegenome sequencing. Genetics 186: 427-430.