Validation of Chromosomal Locations of 90K array single nucleotide polymorphisms in US wheat

Crop Science

Volumn 56, Issue 1, 2016, Pages 364-373

  Liu, Shuyu ^a   Assanga, Silvano Ocheya ^b   Dhakal, Smit ^b   Gu, Xiangkun ^b   Tan, Chor Tee ^a   Yang, Yan ^b   Rudd, Jackie ^a   Hays, Dirk ^b   Ibrahim, Amir ^b   Xue, Qingwu ^a   Chao, Shiaoman ^c   Devkota, Ravindra ^a   Shachter, Cody ^a,d   Huggins, Trevis ^b   Mohammed, Suheb ^b   Fuentealba, Maria Pilar ^a  

^a Texas A and M AgriLife Research   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c U S DEPARTMENT OF AGRICULTURE   (United States)

^d AUSTIN COMMUNITY COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84952791854     PISSN: 0011183X     EISSN: 14350653     Source Type: Journal    
DOI: 10.2135/cropsci2015.03.0194     Document Type: Article

References (28)

1. Akbari, M., P. Wenzl, V. Caig, J. Carling, L. Xia, S. Yang, G. Uszynski, V. Mohler, A. Lehmensiek, H. Kuchel, M. Hayden, N. Howes, P. Sharp, P. Vaughan, B. Rathmell, E. Huttner, and A. Kilian. 2006. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet. 113:1409-1420. doi:10.1007/s00122-006-0365-4
2. 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
3. Allen, A.M., G.L.A. Barker, S.T. Berry, J.A. Coghill, R. Gwilliam, S. Kirby, P. Robinson, R.C. Brenchley, R. D'Amore, N. McKenzie, D. Waite, A. Hall, M. Bevan, N. Hall, and K.J. Edwards. 2011. Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.). Plant Biotechnol. J. 9:1086-1099. doi:10.1111/j.1467-7652.2011.00628.x
4. Cavanagh, C.R., S. Chao, S. Wang, B.E. Huang, S. Stephen, S. Kiani, K. Forrest, C. Saintenac, G.L. Brown-Guedira, A. Akhunova, D. See, G. Bai, M. Pumphrey, L. Tomar, D. Wong, S. Kong, M. Reynolds, M.L. da Silva, H. Bockelman, L. Talbert, J.A. Anderson, S. Dreisigacker, S. Baenziger, A. Carter, V. Korzun, P.L. Morrell, J. Dubcovsky, M.K. Morell, M.E. Sorrells, M.J. Hayden, and E. Akhunov. 2013. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. P. Natl. Acad. Sci. 110:8057-8062. doi:10.1073/pnas.1217133110
5. Dhakal, S. 2014. Resistance sources of hard red winter wheat against wheat curl mite. Ph.D. diss. West Texas A&M Univ., Canyon, TX.
6. Haley, S.D., T.J. Martin, J.S. Quick, D.L. Seifers, J.A. Stromberger, S.R. Clayshulte, B.L. Clifford, F.B. Peairs, J.B. Rudolph, J.J. Johnson, B.S. Gill, and B. Friebe. 2002. Registration of CO960293-2 wheat germplasm resistant to wheat streak mosaic virus and Russian wheat aphid. Crop Sci. 42:1381-1382. doi:10.2135/cropsci2002.1381
7. Kosambi, D.D. 1944. The estimation of map distance from recombination values. Ann. Eugen. 12:172-175. doi:10.1111/j.1469-1809.1943.tb02321.x
8. Lazar, M.D., W.D. Worrall, G.L. Peterson, A.K. Fritz, D. Marshall, L.R. Nelson, and L.W. Rooney. 2004. Registration of 'TAM 111'. Crop Sci. 44:355-356 10.2135/cropsci2004.3550.
9. Liu, S.Y., C. Griffey, M. Hall, A. McKendry, J. Chen, W. Brooks, G. Brown-Guedira, D. Sanford, and D. Schmale. 2013. Molecular characterization of field resistance to Fusarium head blight in two US soft red winter wheat cultivars. Theor. Appl. Genet. 126:2485-2498. doi:10.1007/s00122-013-2149-y
10. Liu, S.Y., J.C. Rudd, G. Bai, S.D. Haley, A.M.H. Ibrahim, Q. Xue, D.B. Hays, R.A. Graybosch, R.N. Devkota, and P. St. Amand. 2014. Molecular markers linked to important genes in hard winter wheat. Crop Sci. 54:1304-1321. doi:10.2135/cropsci2013.08.0564
11. Lu, H., R. Kottke, R. Devkota, P.S. Amand, A. Bernardo, G. Bai, P. Byrne, T.J. Martin, S.D. Haley, and J. Rudd. 2012. Consensus mapping and identification of markers for marker-assisted selection of in wheat. Crop Sci. 52:720-728 10.2135/cropsci2011.07.0363.
12. Lu, H., J. Price, R. Devkota, C. Rush, and J. Rudd. 2011. A dominant gene for resistance to in winter wheat line CO960293-2. Crop Sci. 51:5-12. doi:10.2135/cropsci2010.01.0038
13. Luo, M.C., Y.Q. Gu, F.M. You, K.R. Deal, Y. Ma, Y. Hu, N. Huo, Y. Wang, J. Wang, S. Chen, C.M. Jorgensen, Y. Zhang, P.E. McGuire, S. Pasternak, J.C. Stein, D. Ware, M. Kramer, W.R. McCombie, S.F. Kianian, M.M. Martis, K.F.X. Mayer, S.K. Sehgal, W. Li, B.S. Gill, M.W. Bevan, H. Šimková, J. Doležel, S. Weining, G.R. Lazo, O.D. Anderson, and J. Dvorak. 2013. A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. P. Natl. Acad. Sci. 110:7940-7945. doi:10.1073/pnas.1219082110
14. Paull, J., K. Chalmers, A. Karakousis, J.M. Kretschmer, S. Manning, and P. Langridge. 1998. Genetic diversity in Australian wheat varieties and breeding material based on RFLP data. Theor. Appl. Genet. 96:435-446. doi:10.1007/s001220050760
15. Poland, J.A., M.E. Sorrells, and J.-L. Jannink. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253. doi:10.1371/journal.pone.0032253
16. Reddy, S.K., S. Liu, J.C. Rudd, Q. Xue, P. Payton, S.A. Finlayson, J. Mahan, A. Akhunova, S.V. Holalu, and N. Lu. 2014. Physiology and transcriptomics of water-deficit stress responses in wheat cultivars TAM 111 and TAM 112. J. Plant Physiol. 171:1289-1298. doi:10.1016/j.jplph.2014.05.005
17. Reddy, S.K., Y. Weng, J.C. Rudd, A. Akhunova, and S.Y. Liu. 2013. Transcriptomics of induced defense responses to greenbug aphid feeding in near isogenic wheat lines. Plant Sci. 212:26-36. doi:10.1016/j.plantsci.2013.08.002
18. Röder, M.S., V. Korzun, K. Wendehake, J. Plaschke, M.H. Tixier, P. Leroy, and M.W. Ganal. 1998. A microsatellite map of wheat. Genetics 149:2007-2023.
19. Röder, M.S., J. Plaschke, S.U. König, A. Börner, M.E. Sorrells, S.D. Tanksley, and M.W. Ganal. 1995. Abundance, variability and chromosomal location of microsatellites in wheat. Mol. Gen. Genet. 246:327-333. doi:10.1007/BF00288605
20. Rudd, J.C., R.N. Devkota, J.A. Baker, G.L. Peterson, M.D. Lazar, B. Bean, D. Worrall, T. Baughman, D. Marshall, R. Sutton, L.W. Rooney, R. Nelson, A.K. Fritz, Y. Weng, G.D. Morgan, and B.W. Seabourn. 2014. 'TAM 112' wheat: A greenbug and wheat curl mite resistant cultivar adapted to the dryland production system in the Southern High Plains. J. Plant Reg. 8:291-297. doi:10.3198/jpr2014.03.0016crc
21. Saintenac, C., D. Jiang, S. Wang, and E. Akhunov. 2013. Sequence-Based Mapping of the Polyploid Wheat Genome. G3. Gen. Genom. Genet. 3:1105-1114. doi:10.1534/g3.113.005819
22. Somers, D., P. Isaac, and K. Edwards. 2004. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 109:1105-1114. doi:10.1007/s00122-004-1740-7
23. Song, Q., J. Shi, S. Singh, E. Fickus, J. Costa, J. Lewis, B. Gill, R. Ward, and P. Cregan. 2005. Development and mapping of microsatellite (SSR) markers in wheat. Theor. Appl. Genet. 110:550-560. doi:10.1007/s00122-004-1871-x
24. Sorrells, M.E., J.P. Gustafson, D. Somers, S. Chao, D. Benscher, G. Guedira-Brown, E. Huttner, A. Kilian, P.E. McGuire, K. Ross, J. Tanaka, P. Wenzl, K. Williams, and C.O. Qualset. 2011. Reconstruction of the synthetic W7984 × Opata M85 wheat reference population. Genome 54:875-882. doi:10.1139/g11-054
25. Van Ooijen, J.W. 2006. JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, the Netherlands.
26. 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 a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol. J. 12:787-796. doi:10.1111/pbi.12183
27. Wilkinson, P.A., M.O. Winfield, G.L.A. Barker, A.M. Allen, A. Burridge, J.A. Coghill, A. Burridge, and K.J. Edwards. 2012. CerealsDB 2.0: An integrated resource for plant breeders and scientists. BMC Bioinformatics 13:219. doi:10.1186/1471-2105-13-219
28. Xue, Q., J.C. Rudd, S. Liu, K.E. Jessup, R.N. Devkota, and J.R. Mahan. 2014. Yield determination and water-use efficiency of wheat under water-limited conditions in the U.S. Southern High Plains. Crop Sci. 54:34-47. doi:10.2135/cropsci2013.02.0108