Genomic prediction of genetic values for resistance to wheat rusts

Plant Genome

Volumn 5, Issue 3, 2012, Pages 136-148

  Ornella, Leonardo ^a   Sukhwinder Singh, ^b   Perez, Paulino ^c   Burgueño, Juan ^b   Singh, Ravi ^b   Tapia, Elizabeth ^a   Bhavani, Sridhar ^b   Dreisigacker, Susanne ^b   Braun, Hans Joachim ^b   Mathews, Ky ^b   Crossa, Jose ^b  

^a French Argentine International Center for Information and Systems Sciences (CIFASIS)   (Mexico)

^b INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^c Colegio de Postgraduados ^*  (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84878561724     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2012.07.0017     Document Type: Article

References (38)

1. Bhavani, S., R.P. Singh, O. Argillier, J. Huerta-Espino, S. Singh, P. Njau, S. Brun, S. Lacam, and N. Desmouceaux. 2011. Mapping durable adult plant stem rust resistance to the race Ug99 group in six CIMMYT wheats. Borlaug Global Rust Initiative (BGRI) Technical Workshop, St. Paul, MN. 13-16 June 2011. University of Minnesota and USDA Cereal Disease Lab, St. Paul, MN. http://www.globalrust.org/db/attachments/knowledge/122/2/Bhavani-revised .pdf (accessed 6 Jan. 2012).
2. Burgueño, J., G. de los Campos, K. Weigel, and J. Crossa. 2012. Genomic prediction of breeding values when modeling genotype × environment interaction using pedigree and dense molecular markers. Crop Sci. 52:707-719. doi:10.2135/cropsci2011.06.0299
3. Cooper, M., I.H. DeLacy, and K.E. Basford. 1996. Relationships among analytical methods used to analyze genotypic adaptation in multienvironment trials. In: M. Cooper and G.L. Hammer, editors, Plant adaptation and crop improvement. CAB Int., Wallingford, Oxon, UK. p. 193-224.
4. Crossa, J., G. de los Campos, P. Pérez, D. Gianola, J. Burgueño, J.L. Araus, D. Makumbi, R.P. Singh, S. Dreisigacker, J. Yan, V. Arief, M. Banziger, and H.-J. Braun. 2010. Prediction of genetic values of quantitative traits in plant breeding using pedigree and molecular markers. Genetics 186:713-724. doi:10.1534/genetics.110.118521
5. de los Campos, G., D. Gianola, G. Rosa, K. Weigel, and J. Crossa. 2010. Semi-parametric genomic-enabled prediction of genetic values using reproducing kernel Hilbert spaces methods. Genet. Res. 92:295-308. doi:10.1017/S0016672310000285
6. de los Campos, G., H. Naya, D. Gianola, J. Crossa, A. Legarra, E. Manfredi, K. Weigel, and J.M. Cotes. 2009. Predicting quantitative traits with regression models for dense molecular markers and pedigree. Genetics 182:375-385. doi:10.1534/genetics.109.101501
7. Dexter, M. 2007. Eclipse and Java for total beginners companion tutorial document. Eclipse, New York, NY. http://www.eclipsetutorial.sourceforge.net (accessed 6 Apr. 2012).
8. Endelman, J.B. 2011. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Gen. 4:250-255. doi:10.3835/plantgenome2011.08.0024
9. Fox, J. 2005. The R Commander: A basic-statistics graphical user interface to R. J. Stat. Soft ware 14:1-42.
10. Hall, M., E. Frank, G. Holmes, B. Pfahringer, P. Reutemann, and I. Witten. 2009. The WEKA data mining soft ware: An update. SIGKDD Explor. Newsl. 11.
11. Hastie, T., R. Tibshirani, and J. Friedman. 2011. The elements of statistical learning: Data mining, inference, and prediction. Springer, Springer, New York, NY.
12. Heffner, E.L., A.J. Lorenz, J.-L. Jannink, and M.E. Sorrells. 2010. Plant breeding with genomic selection: Gain per unit time and cost. Crop Sci. 50:1681-1690. doi:10.2135/cropsci2009.11.0662
13. Hickey, L.T., P.M. Wilkinson, C.R. Knight, I.D. Godwin, O.Y. Kravchuk, E.A.B. Aitken, U.K. Bansal, H.S. Bariana, I.H. De Lacy, and M.J. Dieters. 2012. Rapid phenotyping for adult-plant resistance to stripe rust in wheat. Plant Breed. 131:54-61. doi:10.1111/j.1439-0523.2011.01925.x
14. Jannink, J.J., A.J. Lorenz, and H. Iwata. 2010. Genomic selection in plant breeding: From theory to practice. Briefings Funct. Genomics 9:166-177. doi:10.1093/bfgp/elq001
15. Long, N., D. Gianola, G. Rosa, and K. Weigel. 2011a. Marker-assisted prediction of non-additive genetic values. Genetica (The Hague) 139:843-854. doi:10.1007/s10709-011-9588-7
16. Long, N., D. Gianola, G.J. Rosa, and K.A. Weigel. 2011b. Application of support vector regression to genome-assisted prediction of quantitative traits. Theor. Appl. Genet. 123:1065-1074. doi:10.1007/s00122-011-1648-y
17. Lorenz, A.J., K.P. Smith, and J.-L. Jannink. 2012. Potential and optimization of genomic selection for Fusarium head blight resistance in six-row barley. Crop Sci. 52:1609-1621. doi:10.2135/cropsci2011.09.0503
18. Mago, R., G. Brown-Guedira, S. Dreisigacker, J. Breen, Y. Jin, R. Singh, R. Appels, E. Lagudah, J. Ellis, and W. Spielmeyer. 2011. An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theor. Appl. Genet 122:735-744. doi:10.1007/s00122-010-1482-7
19. Mann, H. B., and D.R. Whitney. 1947. On a test of whether one of two random variables is stochastically larger than the other. Ann. Math. Stat. 18:50-60. doi:10.1214/aoms/1177730491
20. Meuwissen, T.H.E., B.J. Hayes, and M.E. Goddard. 2001. Prediction of total genetic value using Genome-wide dense marker maps. Genetics 157:1819-1829.
21. Njau, P.N., Y. Jin, J. Huerta-Espino, B. Keller, and R.P. Singh. 2010. Identification and evaluation of sources of resistance to stem rust race Ug99 in wheat. Plant Dis. 94:413-419. doi:10.1094/PDIS-94-4-0413
22. Ober, U., M. Erbe, N. Long, E. Porcu, M. Schlather, and H. Simianer. 2011. Predicting genetic values: A kernel-based best linear unbiased prediction with genomic data. Genetics 188:695-708. doi:10.1534/genetics.111.128694
23. Park, T., and G. Casella. 2008. The Bayesian Lasso. J. Am. Stat. Assoc. 103:681-686. doi:10.1198/016214508000000337
24. Pérez, P., G. de los Campos, J. Crossa, and D. Gianola. 2010. Genomicenabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R. Plant Gen. 3:106-116. doi:10.3835/plantgenome2010.04.0005
25. Peterson, R.F., A.B. Campbell, and A.E. Hannah. 1948. A diagrammatic scale for estimating rust intensity on leaves and stems of cereals. Can. J. Res. 26:496-500. doi:10.1139/cjr48c-033
26. R Development Core Team. 2008. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.R-project.org (accessed 30 June 2012).
27. Rutkoski, J., J. Benson, Y. Jia, G. Brown-Guedira, J.-J. Jannink, and M. Sorrells. 2012. Evaluation of genomic prediction methods for Fusarium head blight resistance in wheat. Plant Gen. 5:51-61. doi:10.3835/plantgenome2012.02.0001
28. Rutkoski, J., E. Heffner, and M. Sorrells. 2011. Genomic selection for durable stem rust resistance in wheat. Euphytica 179:161-173. doi:10.1007/s10681-010-0301-1
29. SAS Institute. 2004. The SAS system for Windows. Release 9.0. SAS Inst., Cary, NC.
30. Shapiro, S.S., and M.B. Wilk. 1965. An analysis of variance test for normality (complete samples). Biometrika 52:591-611.
31. Singh, R.P., D.P. Hodson, J. Huerta-Espino, Y. Jin, S. Bhavani, P. Njau, S. Herrera-Foessel, P.K. Singh, S. Singh, and V. Govindan. 2011. The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu. Rev. Phytopathol. 49:465-481. doi:10.1146/annurev-phyto-072910-095423
32. Singh, R.P., D.P. Hodson, J. Huerta-Espino, Y. Jin, P. Njau, R. Wanyera, S. Herrera-Foessel, and R. Ward. 2008. Will stem rust destroy the world's wheat crop? Adv. Agron. 98:271-309. doi:10.1016/S0065-2113(08)00205-8
33. Singh, R.P., J. Huerta Espino, and H.M. William. 2005. Genetics and breeding for durable resistance to leaf and stripe rusts in wheat. Turk. J. Agric. For. 29:1-7.
34. Singh, S., M.V. Hernandez, J. Crossa, P.K. Singh, N.S. Bains, K. Singh, and I. Sharma. 2012. Multi-trait and multi-environment QTL analyses for resistance to wheat diseases. PLoS ONE 7(6):e38008. doi:10.1371/journal.pone.0038008
35. Smola, A.J., and B. Schölkopf. 2004. A tutorial on support vector regression. Stat. Comput. 14:199-222. doi:10.1023/B:STCO.0000035301.49549.88
36. Van Raden, P.M. 2008. Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414-4423. doi:10.3168/jds.2007-0980
37. Wellings, C. 2011. Global status of stripe rust: A review of historical and current threats. Euphytica 179:129-141. doi:10.1007/s10681-011-0360-y
38. Xu, Y., Y. Lu, C. Xie, S. Gao, J. Wan, and B. Prasanna. 2012. Wholegenome strategies for marker-assisted plant breeding. Mol. Breed. 29:833-854. doi:10.1007/s11032-012-9699-6