A SNP genotyping array for hexaploid oat

Plant Genome

Volumn 7, Issue 3, 2014, Pages

  Tinker, Nicholas A ^a   Chao, Shiaoman ^b   Lazo, Gerard R ^b   Oliver, Rebekah E ^d   Huang, Yung Fen ^a   Poland, Jesse A ^c   Jellen, Eric N ^f   Maughan, Peter J ^f   Kilian, Andrzej ^g   Jackson, Eric W ^e  

^a AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^b AGRICULTURAL RESEARCH SERVICE   (United States)

^c KANSAS STATE UNIVERSITY   (United States)

^d NORTH DAKOTA STATE UNIVERSITY   (United States)

^e General Mills Inc   (United States)

^f BRIGHAM YOUNG UNIVERSITY   (United States)

^g Diversity Arrays Technology Pty Ltd   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84908430289     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2014.03.0010     Document Type: Article

References (15)

1. Akhunov, E., C. Nicolet, and J. Dvorak. 2009. Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina GoldenGate assay. Theor. Appl. Genet. 119:507-517. doi:10.1007/s00122-009-1059-5
2. Ankerst, M., M.M. Breunig, H.-P. Kriegel, and J. Sander. 1999. OPTICS: Ordering points to identify the clustering structure. SIGMOD Rec. 28:49-60. doi:10.1145/304181.304187
3. Ester, M., H.-P. Kriegel, J. Sander, and X. Xu. 1996. A density-based algorithm for discovering clusters in large spatial databases with noise. KDD 96:226-231.
4. Fan, J.-B., A. Oliphan, R. Shen, B.G. Kermani, F. Garcia, K.L. Gunderson, M. Hansen, F. Steemers, L.S. Butler, P. Deloukas, L. Galver, S. Hunt, C. McBride, M. Bibikova, T. Rubano, J. Chen, E. Wickham, D. Doucet, W. Chang, D. Campbell, B. Zhang, S. Kruglyak, D. Bentley, J. Haas, P. Rigault, L. Zhou, J. Stuelpnagel, and M.S. Chee. 2003. Highly parallel SNP genotyping. Cold Spring Harb. Symp. Quant. Biol. 68:69-78. doi:10.1101/sqb.2003.68.69
5. Götz, S., J.M. Garcia-Gomez, J. Terol, T.D. Williams, S.H. Nagaraj, M.J. Nueda, M. Robles, M. Talon, J. Dopazo, and A. Conesa. 2008. Highthroughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36:3420-3435. doi:10.1093/nar/gkn176
6. International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763-768. doi:10.1038/nature08747
7. Kono, T.J., K. Seth, J.A. Poland, and P.L. Morrell. 2014. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Mol. Ecol. Resour. 14:419-425. doi:10.1111/1755-0998.12183
8. Mayer, K.F., R. Waugh, J.W. Brown, A. Schulman, P. Langridge, M. Platzer, G.B. Fincher, G.J. Muehlbauer, K. Sato, T.J. Close, R.P. Wise, and N. Stein. 2012. A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711-716.
9. Oliver, R.E., G.R. Lazo, J.D. Lutz, M.J. Rubenfield, N.A. Tinker, J.M. Anderson, N.H. Wisniewski Morehead, D. Adhikary, E.N. Jellen, P.J. Maughan, G.L. Brown Guedira, S. Chao, A.D. Beattie, M.L. Carson, H.W. Rines, D.E. Obert, J.M. Bonman, and E.W. Jackson. 2011. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 12:77. doi:10.1186/1471-2164-12-77
10. Oliver, R.E., N.A. Tinker, G.R. Lazo, S. Chao, E.N. Jellen, M.L. Carson, H.W. Rines, D.E. Obert, J.D. Lutz, I. Shackelford, A.B. Korol, C.P. Wight, K.M. Gardner, J. Hattori, A.D. Beattie, A. Bjornstad, J.M. Bonman, J.L. Jannink, M.E. Sorrells, G.L. Brown-Guedira, J.W. Mitchell Fetch, S.A. Harrison, C.J. Howarth, A. Ibrahim, F.L. Kolb, M.S. McMullen, J.P. Murphy, H.W. Ohm, B.G. Rossnagel, W. Yan, K.J. Miclaus, J. Hiller, P.J. Maughan, R.R. Redman Hulse, J.M. Anderson, E. Islamovic, and E.W. Jackson. 2013. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS ONE 8:E58068. doi:10.1371/journal.pone.0058068
11. Ouyang, S., W. Zhu, J. Hamilton, H. Lin, M. Campbell, K. Childs, F. Thibaud-Nissen, R.L. Malek, Y. Lee, L. Zheng, J. Orvis, B. Haas, J. Wortman, and C.R. Buell. 2007. The TIGR Rice Genome Annotation Resource: Improvements and new features. Nucleic Acids Res. 35:D883-D887. doi:10.1093/nar/gkl976
12. Perrier, X., and J.P. Jacquemoud-Collet. 2006. DARwin: Dissimilarity analysis and representation for Windows. 5.0.158. http://darwin. cirad.fr/ (verified 2 July 2014).
13. Poland, J., J. Endelman, J. Dawson, J. Rutkoski, S. Wu, Y. Manes, S. Dreisigacker, J. Crossa, H. Sánchez-Villeda, M. Sorrells, and J.L. Jannink. 2012. Genomic selection in wheat breeding using genotyping- by-sequencing. Plant Gen. 5:103-113. doi:10.3835/plantgenome2012.06.0006
14. Tinker, N.A., A. Kilian, C.P. Wight, K. Heller-Uszynska, P. Wenzl, H.W. Rines, A. Bjornstad, C.J. Howarth, J.L. Jannink, J.M. Anderson, B.G. Rossnagel, D.D. Stuthman, M.E. Sorrells, E.W. Jackson, S. Tuvesson, F.L. Kolb, O. Olsson, L.C. Federizzi, M.L. Carson, H.H. Ohm, S.J. Molnar, G.J. Scoles, P.E. Eckstein, J.M. Bonman, A. Ceplitis, and T. Langdon. 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics 10:39. doi:10.1186/1471-2164-10-39
15. Wang, S., D. Wong, K. Forrest, A. Allen, S. Chao, B.E. Huang, M. Maccaferri, S. Salvi, S.G. Milner, L. Cattivelli, A.M. Mastrangelo, A. Whan, S. Stephen, G. Barker, R. Wieseke, J. Plieske, International Wheat Genome Sequencing Consortium, M. Lillemo, D. Mather, R. Appels, R. Dolferus, G. Brown-Guedira, A. Korol, A.R. Akhunova, C. Feuillet, J. Salse, M. Morgante, C. Pozniak, M.-C. Luo, J. Dvorak, M. Morell, J. Dubcovsky, M. Ganal, R. Tuberosa, C. Lawley, I. Mikoulitch, C. Cavanagh, K.J. Edwards, M. Hayden, and E. Akhunov. 2014. Characterization of polyploid wheat genomic diversity using the high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol. J. 10.1111/pbi.12183.