Genome-wide SNP genotyping to infer the effects on gene functions in tomato

DNA Research

Volumn 20, Issue 3, 2013, Pages 221-233

  Hirakawa, Hideki ^a   Shirasawa, Kenta ^a   Ohyama, Akio ^b   Fukuoka, Hiroyuki ^b   Aoki, Koh ^c   Rothan, Christophe ^d   Sato, Shusei ^a   Isobe, Sachiko ^a   Tabata, Satoshi ^a  

^a KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^b NATIONAL INSTITUTE OF VEGETABLE AND TEA SCIENCE   (Japan)

^c Osaka Prefecture University   (Japan)

^d Univ Bordeaux   (France)

Author keywords

Goldengate assay; Homology modelling; Infinium assay; Single nucleotide polymorphism (SNP); Solanum lycopersicum

Indexed keywords

NUCLEOTIDE;

ALLELE; AMINO ACID SUBSTITUTION; ARTICLE; GENE FUNCTION; GENETIC ASSOCIATION; GENOTYPE; MISSENSE MUTATION; NONHUMAN; PHYLOGENETIC TREE; PROTEIN DATABASE; SINGLE NUCLEOTIDE POLYMORPHISM; TOMATO; WILD TYPE;

GOLDENGATE ASSAY; HOMOLOGY MODELLING; INFINIUM ASSAY; SINGLE NUCLEOTIDE POLYMORPHISM (SNP); SOLANUM LYCOPERSICUM;

BREEDING; CHIMERA; GENES, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; LYCOPERSICON ESCULENTUM; MUTATION, MISSENSE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE HOMOLOGY;

EID: 84876908996     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst005     Document Type: Article

References (31)

1. Varshney, R.K., Nayak, S.N., May, G.D. and Jackson, S.A. 2009, Next-generation sequencing technologies and their implications for crop genetics and breeding, Trends Biotechnol., 27, 522-30.
2. Cao, J., Schneeberger, K., Ossowski, S., et al. 2011, Whole-genome sequencing of multiple Arabidopsis thaliana populations, Nat. Genet., 43, 956-63.
3. Chagné, D., Crowhurst, R.N., Troggio, M., et al. 2012, Genome-wide SNP detection, validation, and development of an 8K SNP array for apple, PLoS One, 7, e31745.
4. Lee, P.H. and Shatkay, H. 2008, F-SNP: computationally predicted functional SNPs for disease association studies, Nucleic Acids Res., 36, D820-4.
5. Yue, P., Melamud, E. and Moult, J. 2006, SNPs3D: candidate gene and SNP selection for association studies, BMC Bioinformatics, 7, 166.
6. Kharabian, A. 2010, An efficient computational method for screening functional SNPs in plants, J. Theor. Biol., 265, 55-62.
7. Tomato Genome Consortium. 2012, The tomato genome sequence provides insights into fleshy fruit evolution, Nature, 485, 635-41.
8. Hamilton, J.P., Sim, S.C., Stoffel, K., et al. 2012, Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis, The Plant Genome, 5, 17-29.
9. Sim, S.C., Van Deynze, A., Stoffel, K., et al. 2012, Highdensity SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding, PLoS One, 7, e45520.
10. Mueller, L.A., Tanksley, S.D., Giovannoni, J.J., et al. 2005, The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL), Comp. Funct. Genomics, 6, 153-8.
11. Yano, K., Watanabe, M., Yamamoto, N., et al. 2006, MiBASE: a database of a miniature tomato cultivar Micro-Tom, Plant Biotechnol. J., 23, 195-8.
12. Shirasawa, K., Isobe, S., Hirakawa, H., et al. 2010, SNP discovery and linkage map construction in cultivated tomato, DNA Res., 17, 381-91.
13. Pilcher, C.D., Wong, J.K. and Pillai, S.K. 2008, Inferring HIV transmission dynamics from phylogenetic sequence relationships, PLoS Med., 5, e69.
14. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol. Biol. Evol., 28, 2731-9.
15. Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. 2007, TASSEL: software for association mapping of complex traits in diverse samples, Bioinformatics, 23, 2633-5.
16. Altschul, S.F., Madden, T.L., Schäffer, A.A., et al. 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389-402.
17. Pearson, W.R. and Lipman, D.J. 1988, Improved tools for biological sequence comparison, Proc. Natl. Acad. Sci. USA, 85, 2444-8.
18. Eswar, N., Webb, B., Marti-Renom, M.A., et al. 2006, Comparative protein structure modeling using Modeller, Curr. Protoc. Bioinformatics. Chapter 2: Unit 2.9.
19. Le Guilloux, V., Schmidtke, P. and Tuffery, P. 2009, Fpocket: an open source platform for ligand pocket detection, BMC Bioinformatics, 10, 168.
20. Garcia-Hernandez, M., Berardini, T.Z., Chen, G., et al. 2002, TAIR: a resource for integrated Arabidopsis data, Funct. Integr. Genomics, 2, 239-53.
21. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., et al. 2003, The COG database: an updated version includes eukaryotes, BMC Bioinformatics, 4, 41-54.
22. Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H. and Kanehisa, M. 1999, KEGG: Kyoto Encyclopedia of Genes and Genomes, Nucleic Acids Res., 27, 29-34.
23. Punta, M., Coggill, P.C., Eberhardt, R.Y., et al. 2012, The Pfam protein families database, Nucleic Acids Res., 40, D290-301.
24. Eddy, S.R. 2011, Accelerated profile HMM searches, PLoS Comput. Biol., 7, e1002195.
25. Saito, A., Matsunaga, H., Yoshida, T., et al. 2007, 'Tomato Chuukanbohon Nou 11', a tomato parental line with a short-internode trait, Bull. Natl. Inst. Veg. Tea Sci., 6, 65-76.
26. Scott, J.W. and Harbaugh, B.K. 1989, Micro-Tom A miniature dwarf tomato, Florida Agr. Expt. Sta. Circ., 370, 1-6.
27. Meissner, R., Chague, V., Zhu, Q., Emmanuel, E., Elkind, Y. and Levy, A.A. 2000, A high throughput system for transposon tagging and promoter trapping in tomato, Plant J., 22, 265-74.
28. Laterrot, H. 1976, Combined use of male sterility and resistance to tobacco mosaic virus in tomato, Ann. Amelio. Plant, 26, 517-21.
29. Fridman, E., Pleban, T. and Zamir, D. 2000, A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene, Proc. Natl. Acad. Sci. USA, 97, 4718-23.
30. Fridman, E., Carrari, F., Liu, Y.S., Fernie, A.R. and Zamir, D. 2004, Zooming in on a quantitative trait for tomato yield using interspecific introgressions, Science, 305, 1786-9.
31. Kumar, R., Kumar, S., Sangwan, S., Yadav, I.S. and Yadav, R. 2011, Protein modeling and active site binding mode interactions of myrosinase-sinigrin in Brassica juncea-an in silico approach, J. Mol. Graph. Model, 29, 740-6.