Advantages and limitations of multiple-trait genomic prediction for Fusarium head blight severity in hybrid wheat (Triticum aestivum L.)
Predictabilities for wheat hybrids less related to the estimation set were improved by shifting from single- to multiple-trait genomic prediction of Fusarium head blight severity.
Breeding for improved Fusarium head blight resistance (FHBr) of wheat is a very laborious and expensive task. FHBr complexity is mainly due to its highly polygenic nature and because FHB severity (FHBs) is greatly influenced by the environment. Associated traits plant height and heading date may provide additional information related to FHBr, but this is ignored in single-trait genomic prediction (STGP). The aim of our study was to explore the benefits in predictabilities of multiple-trait genomic prediction (MTGP) over STGP of target trait FHBs in a population of 1604 wheat hybrids using information on 17,372 single nucleotide polymorphism markers along with indicator traits plant height and heading date. The additive inheritance of FHBs allowed accurate hybrid performance predictions using information on general combining abilities or average performance of both parents without the need of markers. Information on molecular markers and indicator trait(s) improved FHBs predictabilities for hybrids less related to the estimation set. Indicator traits must be observed on the predicted individuals to benefit from MTGP. Magnitudes of genetic and phenotypic correlations along with improvements in predictabilities made plant height a better indicator trait for FHBs than heading date. Thus, MTGP having only plant height as indicator trait already maximized FHBs predictabilities. Provided a good indicator trait was available, MTGP could reduce the impacts of genotype environment \(\times\) interaction on STGP for hybrids less related to the estimation set.
Best linear unbiased estimation(s)
Best linear unbiased prediction(s)
Fusarium head blight (resistance/severity)
General combining ability
Genome-wide association mapping studies
Quantitative trait loci
Specific combining ability
Single nucleotide polymorphism
This research work was conducted within the scope of the HYWHEAT project funded by BMBF (Grant no. FKZ031–5945D).
Compliance with ethical standards
Conflict of interest
All authors declare that they have no conflict of interest.
All experiments were performed under the current laws of Germany.
- Arruda MP, Lipka AE, Brown PJ, Krill AM, Thurber C, Brown-Guedira G, Dong Y, Foresman BJ, Kolb FL (2016) Comparing genomic selection and marker-assisted selection for Fusarium head blight resistance in wheat (Triticum aestivum L.). Mol Breed 36:84. https://doi.org/10.1007/s11032-016-0508-5 CrossRefGoogle Scholar
- Borlaug NE (1968) Wheat breeding and its impact on world food supply. Australian Academy of Science, Australia, pp 1–36Google Scholar
- Butler DG, Cullis BR, Gilmour AR, Gogel B (2009) ASReml-R reference manual. The State of Queensland, Department of Primary Industries and Fisheries, BrisbaneGoogle Scholar
- Draeger R, Gosman N, Steed A, Chandler E, Srinivasachary MT, Schondelmaier J, Buerstmayr H, Lemmens M, Schmolke M, Mesterházy A, Nicholson P (2007) Identification of QTLs for resistance to Fusarium head blight, DON accumulation and associated traits in the winter wheat variety Arina. Theor Appl Genet 115:617–625CrossRefPubMedGoogle Scholar
- Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics, 4th edn. Ronald Press Company, New YorkGoogle Scholar
- Jiang Y, Zhao Y, Rodemann B, Plieske J, Kollers S, Korzun V, Ebmeyer E, Argillier O, Hinze M, Ling J, Röder MS, Ganal MW, Mette MF, Reif JC (2015b) Potential and limits to unravel the genetic architecture and predict the variation of Fusarium head blight resistance in European winter wheat (Triticum aestivum L.). Heredity 114:318–326CrossRefPubMedGoogle Scholar
- Marchal A, Legarra A, Tisné S, Carasco-Lacombe C, Manez A, Suryana E, Omoré A, Nouy B, Durand-Gasselin T, Sánchez L, Bouvet JM, Cros D (2016) Multivariate genomic model improves analysis of oil palm (Elaeis guineensis Jacq.) progeny tests. Mol Breed 36:2. https://doi.org/10.1007/s11032-015-0423-1 CrossRefGoogle Scholar
- Mirdita V, He S, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y (2015a) Potential and limits of whole genome prediction of resistance to Fusarium head blight and Septoria tritici blotch in a vast Central European elite winter wheat population. Theor Appl Genet 128:2471–2481CrossRefPubMedGoogle Scholar
- Mirdita V, Liu G, Zhao Y, Miedaner T, Longin CFH, Gowda M, Mette MF, Reif JC (2015b) Genetic architecture is more complex for resistance to Septoria tritici blotch than to Fusarium head blight in Central European winter wheat. BMC Genom 16:430. https://doi.org/10.1186/s12864-015-1628-8 CrossRefGoogle Scholar
- Piepho HP, Williams ER, Fleck M (2006) A note on the analysis of designed experiments with complex treatment structure. HortScience 41:446–452Google Scholar
- Pisanello D (2014) EU regulations on chemicals in foods. In: Pisanello D (ed) Chemistry of foods: EU legal and regulatory approaches. SpringerBriefs in Molecular Science, Springer, Cham, pp 15–77Google Scholar
- R Core Team (2016) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org. Accessed 21 June 2016
- Rutkoski J, Poland J, Mondal S, Autrique E, González Pérez L, Crossa J, Reynolds M, Singh R (2016) Canopy temperature and vegetation indices from high-throughput phenotyping improve accuracy of pedigree and genomic selection for grain yield in wheat. G3 6:2799–2808CrossRefPubMedPubMedCentralGoogle Scholar
- Schrag TA, Frisch M, Dhillon BS, Melchinger AE (2009) Marker-based prediction of hybrid performance in maize single-crosses involving doubled haploids. Maydica 54:353–362Google Scholar
- Schulthess AW, Reif JC, Ling J, Plieske J, Kollers S, Ebmeyer E, Korzun V, Argillier O, Stiewe G, Ganal MW, Röder MS, Jiang Y (2017) The roles of pleiotropy and close linkage as revealed by association mapping of yield and correlated traits of wheat (Triticum aestivum L.). J Exp Bot 68:4089–4101CrossRefPubMedGoogle Scholar
- Searle SR (2006) Matrix algebra useful for statistics, 2nd edn. Wiley, New YorkGoogle Scholar
- Wang Y, Mette MF, Miedaner T, Gottwald M, Wilde P, Reif JC, Zhao Y (2014a) The accuracy of prediction of genomic selection in elite hybrid rye populations surpasses the accuracy of marker-assisted selection and is equally augmented by multiple field evaluation locations and test years. BMC Genom 15:556. https://doi.org/10.1186/1471-2164-15-556 CrossRefGoogle Scholar
- Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E, International Wheat Genome Sequencing C (2014b) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotech J 12:787–796CrossRefGoogle Scholar
- Windhausen VS, Atlin GN, Hickey JM, Crossa J, Jannink JL, Sorrels ME, Raman B, Cairns JE, Tarekegne A, Semagn K, Beyene Y, Grudloyma P, Technow F, Riedelsheimer C, Melchinger AE (2012) Effectiveness of genomic prediction of maize hybrid performance in different breeding populations and environments. G3 2:1427–1436CrossRefPubMedPubMedCentralGoogle Scholar
- Würschum T, Langer SM, Longin CFH, Korzun V, Akhunov E, Ebmeyer E, Schachschneider R, Schacht J, Kazman E, Reif JC (2013) Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet 126:1477–1486CrossRefPubMedGoogle Scholar
- Zhao Y, Li Z, Liu G, Jiang Y, Maurer HP, Würschum T, Mock HP, Matros A, Ebmeyer E, Schachschneider R, Kazman E, Schacht J, Gowda M, Longin CFH, Reif JC (2015) Genome-based establishment of a high-yielding heterotic pattern for hybrid wheat breeding. Proc Natl Acad Sci USA 112:15624–15629PubMedPubMedCentralGoogle Scholar