Evaluation of genomic prediction methods for fusarium head blight resistance in wheat

Plant Genome

Volumn 5, Issue 2, 2012, Pages 51-61

  Rutkoski, Jessica ^a   Benson, Jared ^b   Jia, Yi ^a   Brown Guedira, Gina ^c   Jannink, Jean Luc ^a   Sorrells, Mark ^a  

^a Department of Obstetrics Gynecology   (United States)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84878558210     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2012.02.0001     Document Type: Article

References (65)

1. Akbari, M., P. Wenzl, V. Caig, J. Carling, L. Xia, S.Y. Yang, G. Uszynski, V. Mohler, A. Lehmensiek, H. Kuchel, M.J. 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. Anderson, J.A., S. Chao, and S. Liu. 2007. Molecular breeding using a major QTL for Fusarium head blight resistance in wheat. Crop Sci. 47(S3):S112-S119. doi:10.2135/cropsci2006.05.0359.
3. Asoro, F.G., M.A. Newell, W.D. Beavis, M.P. Scott, and J.-L. Jannink. 2011. Accuracy and training population design for genomic selection on quantitative traits in elite NorThAmerican oats. Plant Gen. 4:132-144. doi:10.3835/plantgenome2011.02.0007.
4. Bates, D., M. Maechler, and B. Dai. 2009. lme4: Linear mixed-effects models using S4 classes. R package version 0.999375-39. Institute for Statistics and Mathematics, Wien, Austria. http://cran.r-project.org/web/packages/lme4 (accessed 12. May 2010).
5. Benson, J., and G. Brown-Guedira. 2012. Population structure and linkage disequilibrium of winter wheat in regional Fusarium head blight screen nurseries. Plant Genome (in press).
6. Bernardo, A.N., H. Ma, D. Zhang, and G. Bai. 2011. Single nucleotide polymorphism in wheat chromosome region harboring Fhb1 for Fusarium head blight resistance. Mol. Breed. 29:477-488. doi:10.1007/s11032-011-9565-y
7. Breiman, L. 2001. Random Forests. Mach. Learn. 45:5-32. doi:10.1023/A:1010933404324.
8. Buerstmayr, H., T. Ban, and J.A. Anderson. 2009. QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: A review. Plant Breed. 128:1-26. doi:10.1111/j.1439- 0523.2008.01550.x
9. Buerstmayr, H., M. Lemmens, L. Hartl, L. Doldi, B. Steiner, M. Stierschneider, and P. Ruckenbauer. 2002. Molecular mapping of QTLs for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (Type II resistance). Theor. Appl. Genet. 104:84-91. doi:10.1007/s001220200009.
10. Buerstmayr, H., M. Lemmens, M. Schmolke, G. Zimmermann, L. Hartl, F. Mascher, M. Trottet, N.E. Gosman, and P. Nicholson. 2008. Multi-environment evaluation of level and stability of FHB resistance among parental lines and selected offspring derived from several European winter wheat mapping populations. Plant Breed. 127:325-332. doi:10.1111/j.1439-0523.2008.01507.x
11. Carlson, C.S., M.A. Eberle, M.J. Rieder, Q. Yi, L. Kruglyak, and D.A. Nickerson. 2004. Selecting a maximally informative set of singlenucleotide polymorphisms for association analyses using linkage disequilibrium. Am. J. Hum. Genet. 74:106-120. doi:10.1086/381000.
12. Casale, W.L., J.J. Pestka, and L.P. Hart. 1988. Enzyme-linked immunosorbent assay employing monoclonal antibody specific for deoxynivalenol (vomitoxin) and several analogs. J. Agric. Food Chem. 36:663-668. doi:10.1021/jf00081a064.
13. Chen, J., C.A. Griffey, M.A.S. Maroof, E.L. Stromberg, R.M. Biyashev, W. Zhao, M.R. Chappell, T.H. Pridgen, Y. Dong, and Z. Zeng. 2006. Short communication: Validation of two major quantitative trait loci for Fusarium head blight resistance in Chinese wheat line W14. Plant Breed. 101:2003-2005.
14. Crossa, J., G. de los Campos, P. Perez, D. Gianola, J. Burgueno, 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.
15. Cuthbert, P.A., D.J. Somers, and A. Brule-Babel. 2007. Mapping of Fhb2 on chromosome 6BS: A gene controlling Fusarium head blight field resistance in bread wheat (Triticum aestivum L.). Theor. Appl. Genet. 114:429-437. doi:10.1007/s00122-006-0439-3
16. de los Campos, G., D. Gianola, and G.J.M. Rosa. 2009a. Reproducing kernel Hilbert spaces regression: A general framework for genetic evaluation. J. Anim. Sci. 87:1883-1887. doi:10.2527/jas.2008-1259
17. de los Campos, G., H. Naya, D. Gianola, J. Crossa, A. Legarra, E. Manfredi, K. Weigel, and J.M. Cotes. 2009b. Predicting quantitative traits wiThregression models for dense molecular markers and pedigree. Genetics 182:375-385. doi:10.1534/genetics.109.101501
18. de los Campos, G., and P. Perez Rodriguez. 2010. BLR: Bayesian linear regression. R package version 1.2. Institute for Statistics and Mathematics, Wien, Austria. http://cran.r-project.org/web/packages/BLR/index.html (accessed 26. Apr. 2011).
19. Efron, B. 1979. Bootstrap methods: Another look at the jackknife. Ann. Stat. 7:1-26. doi:10.1214/aos/1176344552.
20. Efron, B., and R. Tibshirani. 1986. Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy. Stat. Sci. 1:54-75. doi:10.1214/ss/1177013815.
21. Garrick, D.J., J.F. Taylor, and R.L. Fernando. 2009. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet. Sel. Evol. 41:55. doi:10.1186/1297-9686-41-55.
22. Gianola, D., R.L. Fernando, and A. Stella. 2006. Genomic-assisted prediction of genetic value wiThsemiparametric procedures. Genetics 173:1761-1776. doi:10.1534/genetics.105.049510.
23. Gilbert, J., and S.M. Woods. 2006. Strategies and considerations for multilocation FHB screening nurseries. In: T. Ban, J.M. Lewis, and E.E. Phipps, editors, The Global Fusarium Initiative for International Collaboration: A Strategic Planning Workshop, CIMMYT, El Batan, Mexico. 14-17. Mar. 2006. CIMMYT, El Batan, Mexico. p. 93-102.
24. Gilmour, A.R., B.J. Gogel, B.R. Cullis, and R. Thompson. 2009. ASReml user guide release 3.0. VSN International Ltd, Hemel Hempstead, UK.
25. Gonzalez-Recio, O., and S. Forni. 2011. Genome-wide prediction of discrete traits using Bayesian regressions and machine learning. Genet. Sel. Evol. 43:7. doi:10.1186/1297-9686-43-7.
26. Gosman, N., R. Bayles, P. Jennings, J. Kirby, and P. Nicholson. 2007. Evaluation and characterization of resistance to Fusarium head blight caused by Fusarium culmorum in UK winter wheat cultivars. Plant Pathol. 56:264-276. doi:10.1111/j.1365-3059.2006.01508.x
27. Guo, P.-G., G.-H. Bai, R.-H. Li, G. Shaner, and M. Baum. 2006. Resistance gene analogs associated wiThFusarium head blight resistance in wheat. Euphytica 151:251-261. doi:10.1007/s10681-006-9153-0.
28. Heffner, E.L., J.-L. Jannink, H. Iwata, E. Souza, and M.E. Sorrells. 2011a. Genomic selection accuracy for grain quality traits in biparental wheat populations. Crop Sci. 51:2597-2606. doi:10.2135/ cropsci2011.05.0253.
29. Heffner, E.L., J.-L. Jannink, and M.E. Sorrells. 2011b. Genomic selection accuracy using multifamily prediction models in a wheat breeding program. Plant Gen. 4:65-75. doi:10.3835/plantgenome.2010.12.0029.
30. Heffner, E.L., A.J. Lorenz, J.-L. Jannink, and M.E. Sorrells. 2010. Plant breeding wiThgenomic selection: Gain per unit time and cost. Crop Sci. 50:1681. doi:10.2135/cropsci2009.11.0662.
31. Heslot, N., H.-P. Yang, M.E. Sorrells, and J.-L. Jannink. 2012. Genomic selection in plant breeding: A comparison of models. Crop Sci. 52:146-160.
32. Jiang, G.-L., Y. Dong, J. Shi, and R.W. Ward. 2007a. QTL analysis of resistance to Fusarium head blight in the novel wheat germplasm CJ 9306. II. Resistance to deoxynivalenol accumulation and grain yield loss. Theor. Appl. Genet. 115:1043-1052. doi:10.1007/s00122- 007-0630-1.
33. Jiang, G.-L., J. Shi, and R.W. Ward. 2007b. QTL analysis of resistance to Fusarium head blight in the novel wheat germplasm CJ 9306. I. Resistance to fungal spread. Theor. Appl. Genet. 116:3-13. doi:10.1007/s00122-007-0641-y
34. Kang, H.M., N.A. Zaitlen, C.M. Wade, A. Kirby, D. Heckerman, M.J. Daly, and E. Eskin. 2008. Efficient control of population structure in model organism association mapping. Genetics 178:1709-1723. doi:10.1534/genetics.107.080101.
35. Knapp, S.J., and W.C. Bridges. 1990. Using molecular markers to estimate quantitative trait locus parameters: Power and genetic variances for unreplicated and replicated progeny. Genetics 126:769-777.
36. Kolb, F.L., and L.K. Boze. 2003. An alternative to the FHB index: incidence, severity, kernel rating (ISK) index. In: S.M. Cantry, J. Lewis, and R.W. Ward, editors, Proceedings of the National Fusarium Head Blight Forum, Bloomington, MN. 13-15. Dec. 2003. Michigan State University, East Lansing, MN. p. 259.
37. Liaw, A., and M. Wiener. 2002. Classification and regression by randomForest. R News 2:18-22.
38. Liu, S., M.D. Hall, C.A. Griffey, and A.L. McKendry. 2009. Meta-analysis of QTL associated wiThFusarium head blight resistance in wheat. Crop Sci. 49:1955-1968. doi:10.2135/cropsci2009.03.0115.
39. Lorenz, A.J., S. Chao, F.G. Asoro, E.L. Heffner, T. Hayashi, H. Iwata, K.P. Smith, M.E. Sorrells, and J.-L. Jannink. 2011. Genomic selection in plant breeding: Knowledge and prospects. Adv. Agron. 110:77-123. doi:10.1016/B978-0-12-385531-2.00002-5.
40. 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. (in press).
41. Lorenzana, R.E., and R. Bernardo. 2009. Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor. Appl. Genet. 120:151-161. doi:10.1007/s00122- 009-1166-3.
42. Ma, H.-X., G.-H. Bai, X. Zhang, and W.-Z. Lu. 2006. Main effects, epistasis, and environmental interactions of quantitative trait loci for Fusarium head blight resistance in a recombinant inbred population. Phytopathology 96:534-541. doi:10.1094/PHYTO-96-0534.
43. 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.
44. Miedaner, T., C. Reinbrecht, U. Lauber, M. Schollenberger, and H. Geiger. 2002. Effects of genotype and genotype-environment interaction on deoxynivalenol accumulation and resistance to Fusarium head blight in rye, triticale, and wheat. Plant Breed. 120:97-105. doi:10.1046/j.1439-0523.2001.00580.x
45. Miedaner, T., T. Würschum, H.P. Maurer, V. Korzun, E. Ebmeyer, and J.C. Reif. 2010. Association mapping for Fusarium head blight resistance in European soft winter wheat. Mol. Breed. 28:647-655. doi:10.1007/ s11032-010-9516-z
46. Nganje, W.E., D.A. Bangsund, F.L. Leistritz, W.W. Wilson, and N.M. Tiapo. 2004. Regional economic impacts of Fusarium head blight in wheat and barley. Rev. Agric. Econ. 26:332-347. doi:10.1111/j.1467- 9353.2004.00183.x
47. Pallotta, M.A., P. Warner, R.L. Fox, H. Kuchel, S.J. Jefferies, and P. Langridge. 2003. Marker assisted wheat breeding in the southern region of Australia. In: N.E. Pogna, editor, Proceedings of the 10ThInternational Wheat Genetics Symposium, Paestum, Italy. 1-6. Sept. 2003. Istituto Sperimentale per la Cerealicoltura, Rome, Italy. p. 789-791.
48. Park, T., and G. Casella. 2008. The Bayesian LASSO. J. Am. Stat. Assoc. 103:681-686. doi:10.1198/016214508000000337.
49. Pathre, S.V., and C.J. Mirocha. 1977. Assay methods for trichothecenes and review of their natural occurrence. In: J.V. Rodricks, C.W. Hesseltine, and M.A. Mehlman, editors, Mycotoxins in human and animal health. Pathotox Publishers, Park Forest South, IL. p. 229-253.
50. Paul, P.A., P.E. Lipps, and L.V. Madden. 2005. Relationship between visual estimates of Fusarium head blight intensity and deoxynivalenol accumulation in harvested wheat grain: A meta-analysis. Phytopathology 95:1225-1236. doi:10.1094/PHYTO-95-1225.
51. 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.
52. Pestka, J.J., and A.T. Smolinski. 2005. Deoxynivalenol: Toxicology and potential effects on humans. J. Toxicol. Environ. HealThB 8:39-69. doi:10.1080/10937400590889458.
53. Piepho, H.P. 2009. Ridge regression and extensions for genomewide selection in maize. Crop Sci. 49:1165-1176. doi:10.2135/ cropsci2008.10.0595.
54. Pumphrey, M.O., R. Bernardo, and J.A. Anderson. 2007. Validating the QTL for Fusarium head blight resistance in near-isogenic wheat lines developed from breeding populations. Crop Sci. 47:200-206. doi:10.2135/cropsci2006.03.0206.
55. R Development Core Team. 2010. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.r-project.org (accessed 29. June 2011).
56. SAS Institute. 2010. JMP Genomics user guide. SAS Institute, Cary, NC.
57. Sneller, C., M. Guttieri, P. Paul, J. Costa, and R. Jackwood. 2012. Variation for resistance to kernel infection and toxin accumulation in winter wheat infected wiThFusarium graminearum. Phytopathology 102:306-314. doi:10.1094/PHYTO-05-11-0143.
58. Sneller, C.H., P. Paul, and M. Guttieri. 2010. Characterization of resistance to Fusarium head blight in an eastern U.S. soft red winter wheat population. Crop Sci. 50:123-133. doi:10.2135/ cropsci2008.09.0569.
59. Somers, D.J., G. Fedak, and M. Savard. 2003. Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat. Genome 564:555-564. doi:10.1139/g03-033.
60. Whittaker, J.C., R. Thompson, and M.C. Denham. 2000. Marker-assisted selection using ridge regression. Genet. Res. 75:249-252. doi:10.1017/ S0016672399004462.
61. Windels, C.E. 2000. Economic and social impacts of Fusarium head blight: Changing farms and rural communities in the northern great plains. Phytopathology 90:17-21. doi:10.1094/PHYTO.2000.90.1.17.
62. Yang, Z., J. Gilbert, G. Fedak, and D.J. Somers. 2005. Genetic characterization of QTL associated wiThresistance to Fusarium head blight in a doubled-haploid spring wheat population. Genome 48:187-196. doi:10.1139/g04-104.
63. Yu, J.-B., G.-H. Bai, W.-C. Zhou, Y.-H. Dong, and F.L. Kolb. 2007. Quantitative trait loci for Fusarium head blight resistance in a recombinant inbred population of Wangshuibai/Wheaton. Phytopathology 98:87-94. doi:10.1094/PHYTO-98-1-0087.
64. Yu, J.M., G. Pressoir, W.H. Briggs, I.V. Bi, M. Yamasaki, J.F. Doebley, M.D. McMullen, B.S. Gaut, D.M. Nielsen, J.B. Holland, S. Kresovich, and E.S. Buckler. 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat. Genet. 38:203-208. doi:10.1038/ng1702.
65. Zhou, W., F.L. Kolb, G. Bai, G. Shaner, and L.L. Domier. 2002. Genetic analysis of scab resistance QTL in wheat wiThmicrosatellite and AFLP markers. Genome 727:719-727. doi:10.1139/g02-034