Genetic gain from phenotypic and genomic selection for quantitative resistance to stem rust of wheat

Plant Genome

Volumn 8, Issue 2, 2015, Pages

  Rutkoski, J ^a,b   Singh, R P ^b   Huerta Espino, J ^b,c   Bhavani, S ^d   Poland, J ^e   Jannink, J L ^f   Sorrells, M E ^f  

^a Program on Infrastructure Policy   (United States)

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

^c INSTITUTO NACIONAL DE INVESTIGACIONES FORESTALES   (Mexico)

^d WORLD AGROFORESTRY CENTRE ICRAF   (Kenya)

^e KANSAS STATE UNIVERSITY   (United States)

^f Cornell Univ ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PUCCINIA GRAMINIS F. SP. TRITICI; TRITICUM AESTIVUM;

EID: 84937010785     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2014.10.0074     Document Type: Article

References (46)

1. Abedon, B.G., and W.F. Tracy. 1998. Direct and indirect effects of fullsib recurrent selection for resistance to common rust (Puccinia sorghi Schw.) in three sweet corn populations. Crop Sci. 38:56–61. doi:10.2135/cropsci1998.0011183X003800010010x
2. Asoro, F.G., M.A. Newell, W.D. Beavis, M.P. Scott, N.A. Tinker, and J.-L. Jannink. 2013. Genomic, marker-assisted, and pedigree-BLUP selection methods for β-glucan concentration in elite oat. Crop Sci. 53:1894–1906. doi:10.2135/cropsci2012.09.0526
3. Bariana, H.S., M.J. Hayden, N.U. Ahmed, J.A. Bell, P.J. Sharp, and R.A. McIntosh. 2001. Mapping of durable adult plant and seedling resistances to stripe rust and stem rust diseases in wheat. Aust. J. Agric. Res. 52:1247–1255. doi:10.1071/AR01040
4. Bates, D., and M. Maechler. 2010. lme4: Linear mixed-effects models using S4 classes. http://cran.r-project.org/package=lme4 (accessed 1 Feb. 2011).
5. Bhowal, J.G., and M.N. Narkhende. 1981. Genetics of pseudo-black chaff in wheat. Z. Pflanzenzüchtg 86:298–304.
6. Casellas, J., and L. Varona. 2011. Short communication: Effect of mutation age on genomic predictions. J. Dairy Sci. 94:4224–4229. doi:10.3168/jds.2011-4186
7. Ceballos, H., J.A. Deutsch, and H. Gutiérrez. 1991. Recurrent selection for resistance to Exserohilum turcicum in eight subtropical maize populations. Crop Sci. 31:964–971. doi:10.2135/cropsci1991.0011183X00310 0040025x
8. Combs, E., and R. Bernardo. 2013. Genomewide selection to introgress semidwarf maize germplasm into U.S. Corn Belt inbreds. Crop Sci. 53:1427–1436. doi:10.2135/cropsci2012.11.0666
9. Daetwyler, H.D., B. Villanueva, P. Bijma, and J.A. Woolliams. 2007. Inbreeding in genome-wide selection. J. Anim. Breed. Genet. 124:369–376. doi:10.1111/j.1439-0388.2007.00693.x
10. Dekkers, J.C.M. 2007. Prediction of response to marker-assisted and genomic selection using selection index theory. J. Anim. Breed. Genet. 124:331–341. doi:10.1111/j.1439-0388.2007.00701.x
11. de Roos, A.P.W., C. Schrooten, R.F. Veerkamp, and J.A.M. van Arendonk. 2011. Effects of genomic selection on genetic improvement, inbreeding, and merit of young versus proven bulls. J. Dairy Sci. 94:1559–1567. doi:10.3168/jds.2010-3354
12. Díaz-Lago, J.E., D.D. Stuthman, and T.E. Abadie. 2002. Recurrent selection for partial resistance to crown rust in oat. Crop Sci. 42:1475–1482. doi:10.2135/cropsci2002.1475
13. Elshire, R.J., J.C. Glaubitz, Q. Sun, J.A. Poland, K. Kawamoto, E.S. Buckler, and S.E. Mitchell. 2011. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species (L Orban, Ed.). PLoS One 6: E19379.
14. 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
15. Falconer, D.S., and T.F.C. Mackay. 1996. Introduction to quantitative genetics. 4th ed. Longman, New York.
16. Federer, W.T. 2002. Construction and analysis of an augmented lattice square design. Biometrical J. 44:251–257. doi:10.1002/1521-4036(200203)44:2<251::AID-BIMJ251>3.0.CO;2-N
17. Gilmour, A.R., B.R. Cullis, and A.P. Verbyla. 1997. Accounting for natural and extraneous variation in the analysis of field experiments. J. Agric. Biol. Environ. Stat. 2:269–293. doi:10.2307/1400446
18. 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.
19. Grundy, B., B. Villanueva, and J.A. Woolliams. 1998. Dynamic selection procedures for constrained inbreeding and their consequences for pedigree development. Genet. Res. 72:159–168. doi:10.1017/S0016672398003474
20. Hagborg, W.A.F. 1942. Classification revision in Xanthomonas translucens. Can. J. Res. 20c:312–326. doi:10.1139/cjr42c-028
21. Hallauer, A.R., M.J. Carena, and J.B. Miranda Filho. 2010. Quantitative genetics in maize breeding. Iowa State Univ. Press, Ames, IA.
22. Hare, R.A., and R.A. McIntosh. 1979. Genetic and cytogenetic studies of durable adult-plant resistances in Hope and related cultivars to wheat rusts. Plant Pathol. 83:350–367.
23. Hayes, B.J., P.M. Visscher, and M.E. Goddard. 2009. Increased accuracy of selection by using the realized relationship matrix. Genet. Res. 91:47–60. doi:10.1017/S0016672308009981
24. Heffner, E.L., M.E. Sorrells, and J.L.L. Jannink. 2009. Genomic selection for crop improvement. Crop Sci. 49:1–12. doi:10.2135/cropsci2008.08.0512
25. Hill, W.G. 1977. Variation in response to selection. In: E. Pollak, O. Kempthorne, and T.B. Bailey, editors, Proceedings of the International Conference on Quantitative Genetics, Ames, IA. 16–21 Aug. 1976. Iowa State Univ. Press, Ames, IA. p. 343–365.
26. Jannink, J.L. 2010. Dynamics of long-term genomic selection. Genet. Sel. Evol. 42:35. doi:10.1186/1297-9686-42-35
27. Jin, Y., L.J. Szabo, Z.A. Pretorius, R.P. Singh, R. Ward, and T. Fetch. 2008. Detection of virulence to resistance gene Sr24 within race TTKS of Puccinia graminis f. sp tritici. Plant Dis. 92:923–926. doi:10.1094/PDIS-92-6-0923
28. Jin, Y., L.J. Szabo, M.N. Rouse, T. Fetch, Z.A. Pretorius, R. Wanyera, P. Njau, and T. Fetch. 2009. Detection of virulence to resistance gene Sr36 within the TTKS race lineage of Puccinia graminis f. sp. tritici. Plant Dis. 93:367–370. doi:10.1094/PDIS-93-4-0367
29. Kempthorne, O., and R.N. Curnow. 1961. The partial diallel cross. Biometrics 17:229–250. doi:10.2307/2527989
30. Long, J., J.B. Holland, G.P. Munkvold, and J.L. Jannink. 2006. Responses to selection for partial resistance to crown rust in oat. Crop Sci. 46:1260–1265. doi:10.2135/cropsci2005.06-0169
31. Lorenz, A.J., S. Chao, F.G. Asoro, E.L. Heffner, T. Hayashi, H. Iwata, K.P. Smith, M.E. Sorrells, and J. 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
32. Massman, J.M., H.J.G. Jung, and R. Bernardo. 2013. Genomewide selection versus marker-assisted recurrent selection to improve grain yield and stover-quality traits for cellulosic ethanol in maize. Crop Sci. 53:58–66. doi:10.2135/cropsci2012.02.0112
33. Meuwissen, T.H.E. 1997. Maximizing the response of selection with a predefined rate of inbreeding. J. Anim. Sci. 75:934–940.
34. Meuwissen, T.H.E., and J.A. Woolliams. 1994. Maximizing genetic response in breeding schemes of dairy cattle with constraints on variance of response. J. Dairy Sci. 77:1905–1916. doi:10.3168/jds.S0022-0302(94)77133-2
35. Park, R.F. 2007. Stem rust of wheat in Australia. Aust. J. Agric. Res. 58: 558–566.
36. Parlevliet, J.E. 2002. Durability of resistance against fungal, bacterial and viral pathogens; present situation. Euphytica 124:147–156. doi:10.1023/A:1015601731446
37. 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
38. 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
39. R Development Core Team. 2010. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
40. Rutkoski, J.E., J. Poland, J.L. Jannink, and M.E. Sorrells. 2013. Imputation of unordered markers and the impact on genomic selection accuracy. G3 (Bethesda) 3:427–439.
41. Rutkoski, J.E., J.A. Poland, R.P. Singh, J. Huerta-Espino, S. Bhavani, H. Barbier, M.N. Rouse, J.L. Jannink, and M.E. Sorrells. 2014. Genomic selection for quantitative adult plant stem rust resistance in wheat. Plant Gen. 7(3). doi:10.3835/plantgenome2014.02.0006
42. Sargolzaei, M., and H. Iwaisaki. 2005. Comparison of four direct algorithms for computing inbreeding coefficients. Anim. Sci. J. 76:401–406. doi:10.1111/j.1740-0929.2005.00282.x
43. Singh, R.P., D.P. Hodson, J. Huerta-Espino, Y. Jin, P. Njau, R. Wanyera, S.A. Herrera-Foessel, and R.W. Ward. 2008. Will stem rust destroy the world’s wheat crop? Adv. Agron. 98:271–309. doi:10.1016/S0065-2113(08)00205-8
44. Singh, S., R.P. Singh, S. Bhavani, J. Huerta-Espino, and E.E. Lopez-Vera. 2013. QTL mapping of slow-rusting, adult plant resistance to race Ug99 of stem rust fungus in PBW343/Muu RIL population. Theor. Appl. Genet. 126:1367–1375. doi:10.1007/s00122-013-2058-0
45. Vazquez, A.I., D.M. Bates, G.J.M. Rosa, D. Gianola, and K.A. Weigel. 2010. Technical note: An R package for fitting generalized linear mixed models in animal breeding. J. Anim. Sci. 88:497–504. doi:10.2527/jas.2009-1952
46. Yu, L.X., A. Lorenz, J. Rutkoski, R.P. Singh, S. Bhavani, J. Huerta-Espino, and M.E. Sorrells. 2011. Association mapping and gene-gene interaction for stem rust resistance in CIMMYT spring wheat germplasm. Theor. Appl. Genet. 123:1257–1268. doi:10.1007/s00122-011-1664-y