Skip to main content
SpringerLink
Log in

Genomic selection for durable stem rust resistance in wheat

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Inheritance of stem rust (caused by Puccinia graminis f. sp. tritici) resistance in wheat can be either qualitative or quantitative. While quantitative disease resistance is believed to be more durable, it is more difficult to evaluate if it is expressed only in mature plants, i.e. adult plant resistance (APR). Marker-assisted selection (MAS) methods for APR would be useful; however, the multigenic nature of APR impedes the use of MAS efforts that aim to pyramid only a few target genes. A promising alternative is genomic selection (GS), which utilizes genome-wide marker coverage to predict genotypic values for quantitative traits. In turn, GS can reduce the selection cycle length of a breeding program for traits like APR that could take several seasons to generate reliable phenotypes. In this paper, we describe the GS process for use in crop improvement, both specifically for APR and in general. We also propose a GS–based wheat breeding scheme for quantitative resistance to stem rust that, when compared to current breeding schemes, can reduce cycle time by up to twofold and facilitates pyramiding of major genes with APR genes. Thus, GS could be an important tool for achieving the Borlaug Global Rust Initiative’s (BGRI) goal of developing durable stem rust resistance in wheat.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

Abbreviations

AB:

Association breeding

APR:

Adult plant resistance

GasBLUP:

Gene-assisted genomic selection

GEBV:

Genomic estimated breeding value

GS:

Genomic selection

HR:

Hypersensitive response

LD:

Linkage disequilibrium

MABC:

Marker assisted backcrossing

MAS:

Marker assisted selection

MARS:

Marker assisted recurrent selection

RR-BLUP:

Ridge regression best linear unbiased prediction

TP:

Training population

TBV:

True breeding value

SC:

Selection candidate

References

  • Akbari M, Wenzl P, Caig V, Carling J, Xia L, Yang SY, Uszynski G, Mohler V, Lehmensiek A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420

    Article  PubMed  CAS  Google Scholar 

  • Bariana HS, Hayden MJ, Ahmed NU, Bell JA, Sharp PJ, McIntosh RA (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

    Article  CAS  Google Scholar 

  • Beavis WD (1998) QTL Analysis: power, precision and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 145–162

    Google Scholar 

  • Bernardo R (2008) Molecular markers and selection for complex traits in plants: Learning from the last 20 years. Crop Sci 48:1649–1664

    Article  Google Scholar 

  • Bernardo R (2009) Genomewide selection for rapid introgression of exotic germplasm in maize. Crop Sci 49:419–425

    Article  Google Scholar 

  • Bernardo R (2010) Genomewide selection with minimal crossing in self-pollinated crops. Crop Sci 50:624–627

    Article  Google Scholar 

  • Bernardo R, Yu JM (2007) Prospects for genomewide selection for quantitative traits in maize. Crop Sci 47:1082–1090

    Article  Google Scholar 

  • Breseghello F, Sorrells ME (2006) Association mapping of kernal size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177

    Article  PubMed  Google Scholar 

  • Busch RH, Kofoid K (1982) Recurrent selection for kernel weight in spring wheat. Crop Sci 22:568–572

    Article  Google Scholar 

  • Calus MPL (2010) Genomic breeding value prediction: methods and procedures. Animal 4:157–164

    Article  CAS  Google Scholar 

  • Calus MPL, Veerkamp RF (2007) Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. J Anim Breed Genet 124:362–368

    Article  PubMed  CAS  Google Scholar 

  • Concibido VC, Denny RL, Boutin SR, Hautea R, Orf JH, Young ND (1994) DNA marker analysis of loci underlying resistance to soybean cyst-nematode (Heterodera glycines Ichinohe). Crop Sci 34:240–246

    Article  CAS  Google Scholar 

  • de Roos APW, Hayes BJ, Goddard ME (2009) Reliability of genomic predictions across multiple populations. Genetics 183:1545–1553

    Article  PubMed  Google Scholar 

  • Eathington SR, Crosbie TM, Edwards MD, Reiter R, Bull JK (2007) Molecular markers in a commercial breeding program. Crop Sci 47:S154–S163

    Article  Google Scholar 

  • Falconer DS, Mackay TFC (1996) Introduction to quantitative genetics. Longman, New York

  • Fernando RL, Grossman M (1998) Marker assisted selection using best linear unbiased prediction. Genet Sel Evol 21:467–477

    Article  Google Scholar 

  • Flint-Garcia S, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  PubMed  CAS  Google Scholar 

  • Flor HH (1942) Inheritance of pathogenicity in Melampsora lini. Phytopathology 32:653–669

    Google Scholar 

  • Goddard M (2009) Genomic selection: prediction of accuracy and maximisation of long term response. Genetica 136:245–257

    Article  PubMed  Google Scholar 

  • Goddard ME, Hayes BJ (2007) Genomic selection. J Anim Breed Genet 124:323–330

    Article  PubMed  CAS  Google Scholar 

  • Griffiths DJ, Carr AJH (1961) Induced mutation for pathogenicity in Puccinia coronata avenae. Trans Brit Mycol Soc 44:601–607

    Article  Google Scholar 

  • Habier D, Fernando RL, Dekkers JCM (2007) The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389–2397

    PubMed  CAS  Google Scholar 

  • Hallauer AR (1985) Compendium of recurrent selection methods and their application. CRC Crit Rev Plant Sci 3:1–33

    Article  Google Scholar 

  • Hare RA, McIntosh RA (1979) Genetic and cytogenetic studies of durable adult-plant resistances in Hope and related cultivars to wheat rusts. Z Pflanzenzucht 83:350–367

    Google Scholar 

  • Hayes BJ, Bowman PJ, Chamberlain AC, Verbyla K, Goddard ME (2009a) Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genet Sel Evol 41:51

    Article  PubMed  Google Scholar 

  • Hayes BJ, Bowman PJ, Chamberlain AJ, Goddard ME (2009b) Genomic selection in dairy cattle: progress and challenges. J Dairy Sci 92:433–443

    Article  PubMed  CAS  Google Scholar 

  • Heffner EL, Sorrells ME, Jannink JL (2009) Genomic selection for crop improvement. Crop Sci 49:1–12

    Article  CAS  Google Scholar 

  • Heffner EL, Lorenz AJ, Jannink JL, Sorrells ME (2010) Plant breeding with genomic selection: Potential gain per unit time and cost. Crop Sci 50(50):1681–1690

    Article  Google Scholar 

  • Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231

    Article  Google Scholar 

  • Holland JB (2004) Implementation of molecular markers for quantitative traits in breeding programs—challenges and opportunities. In: Fischer T (ed) New directions for a diverse planet: Proc 4th Int Crop Sci Cong, Brisbane, Australia, 26 September–1 October, 2004. http://cropscience.org.au/icsc2004/pdf/203_hollandjb.pdf

  • Ibánẽz-Escriche N (2009) Genomic selection of purebreds for crossbred performance. Genet Sel Evol 41:12

    Article  PubMed  Google Scholar 

  • Jannink J-L, Lorenz AJ, Iwata H (2010) Genomic selection in plant breeding: from theory to practice. Brief Funct Genomics 9:166–177

    PubMed  CAS  Google Scholar 

  • Jin Y, Singh RP, Ward RW, Wanyera R, Kinyua M, Njau P, Pretorius ZA (2007) Characterization of seedling infection types and adult plant infection responses of monogenic Sr gene lines to race TTKS of Puccinia graminis f. sp tritici. Plant Dis 91:1096–1099

    Article  Google Scholar 

  • Jin Y, Szabo LJ, Rouse MN, Fetch T Jr, Pretorius ZA, Wanyera R, Njau P (2009) Detection of virulence to resistance gene Sr36 within the TTKS race lineage of Puccinia graminis f. sp. tritici. Plant Dis 93:367–370

    Article  CAS  Google Scholar 

  • Johnson R (1984) A critical analysis of durable resistance. Annu Rev Phytopathol 22:309–330

    Article  Google Scholar 

  • Johnson R (2004) Marker-assisted selection. Plant Breed Rev 24:293–310

    Google Scholar 

  • Knapp SJ, Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters: Power and genetic variances for unreplicated and replicated progeny. Genetics 126:769–777

    PubMed  CAS  Google Scholar 

  • Knott DR (1982) Multigenic inheritance of stem rust resistance in wheat. Crop Sci 22:393–399

    Article  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743

    PubMed  CAS  Google Scholar 

  • Lee M (1995) DNA markers and plant breeding programs. Adv Agron 55:265–344

    Article  CAS  Google Scholar 

  • Lee SH, van der Werf JHJ, Hayes BJ, Goddard ME, Visscher PM (2008) Predicting unobserved phenotypes for complex traits from whole-genome SNP data. PLoS Genet 4:e1000231

    Article  PubMed  Google Scholar 

  • Lorenzana RE, Bernardo R (2009) Accuracy of genotypic value predictions for marker-based selection in biparental plant populations. Theor Appl Genet 120:151–161

    Article  PubMed  Google Scholar 

  • Mallard S, Gaudet D, Aldeia A, Abelard C, Besnard AL, Sourdille P, Dedryver F (2005) Genetic analysis of durable resistance to yellow rust in bread wheat. Theor Appl Genet 110:1401–1409

    Article  PubMed  CAS  Google Scholar 

  • McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: An atlas of resistance genes. CSIRO Publishing, Melbourne, Australia

    Google Scholar 

  • Messmer MM, Seyfarth R, Keller M, Schachermayr G, Winzeler M, Zanetti S, Feuillet C, Keller B (2000) Genetic analysis of durable leaf rust resistance in winter wheat. Theor Appl Genet 100:419–431

    Article  CAS  Google Scholar 

  • Meuwissen TH (2009) Accuracy of breeding values of ‘unrelated’ individuals predicted by dense SNP genotyping. Genet Sel Evol 41:35

    Article  PubMed  Google Scholar 

  • Meuwissen TH, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    PubMed  CAS  Google Scholar 

  • Muir WM (2007) Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J Anim Breed and Genet 124:342–355

    Article  CAS  Google Scholar 

  • Navabi A, Singh RP, Tewari JP, Briggs KG (2004) Inheritance of high levels of adult-plant resistance to stripe rust in five spring wheat genotypes. Crop Sci 44:1156–1162

    Article  Google Scholar 

  • Navabi A, Tewari JP, Singh RP, McCallum B, Laroche A, Briggs KG (2005) Inheritance and QTL analysis of durable resistance to stripe and leaf rusts in an Australian cultivar, Triticum aestivum ‘Cook’. Genome 48:97–107

    Article  PubMed  CAS  Google Scholar 

  • Nei M, Maruyama T, Chakraborty R (1975) The bottleneck effect and genetic variability in populations. Evolution 29:1–10

    Article  Google Scholar 

  • Odegard J, Sonesson AK, Yazdi MH, Meuwissen TH (2009a) Introgression of a major QTL from an inferior into a superior population using genomic selection. Genet Sel Evol 41:38

    Article  PubMed  Google Scholar 

  • Odegard J, Yazdi MH, Sonesson AK, Meuwissen TH (2009b) Incorporating desirable genetic characteristics from an inferior into a superior population using genomic selection. Genetics 181:737–745

    Article  PubMed  CAS  Google Scholar 

  • Ovenden JR, Peel D, Street R, Courtney AJ, Hoyle SD, Peel SL, Podlich H (2007) The genetic effective and adult census size of an Australian population of tiger prawns (Penaeus esculentus). Mol Ecol 16:127–138

    Article  PubMed  CAS  Google Scholar 

  • Parlevliet JE (2002) Durability of resistance against fungal, bacterial and viral pathogens; present situation. Euphytica 124:147–156

    Article  CAS  Google Scholar 

  • Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210

    Article  PubMed  CAS  Google Scholar 

  • Person C (1959) Gene-for-gene relationships in host: parasite systems. Can J Bot 37:1101–1130

    Article  Google Scholar 

  • Podlich DW, Winkler CR, Cooper M (2004) Mapping as you go: an effective approach for marker-assisted selection of complex traits. Crop Sci 44:1560

    Article  Google Scholar 

  • Rosewarne GM, Singh RP, Huerta-Espino J, Rebetzke GJ (2008) Quantitative trait loci for slow-rusting resistance in wheat to leaf rust and stripe rust identified with multi-environment analysis. Theor Appl Genet 116:1027–1034

    Article  PubMed  CAS  Google Scholar 

  • Schaeffer LR (2006) Strategy for applying genome-wide selection in dairy cattle. J Anim Breed Genet 123:218–223

    Article  PubMed  CAS  Google Scholar 

  • Singh RP, Huerta-Espino J, Rajaram S (2000) Achieving near-immunity to leaf and stripe rusts in wheat by combining slow rusting resistance genes. Acta Phytopathol Entomol Hung 35:133–139

    CAS  Google Scholar 

  • Singh RP, Huerto-Espino J, William HM (2005) Genetics and breeding for durable resistance to leaf and stripe rusts in wheat. Turk J Agr For 29:121–127

    CAS  Google Scholar 

  • Singh RP, Hodson DP, Jin Y, Huerta-Espino J, Kinyua MG, Wanyera R, Njau P, Ward RW (2006) Current status, likely migration and strategies to mitigate the threat to wheat production from race Ug99 (TTKS) of stem rust pathogen. CAB Rev Perspect Agric Vet Sci Nutr Nat Resour 1(054):13

    Google Scholar 

  • Solberg TR, Sonesson AK, Woolliams JA, Meuwissen TH (2008) Genomic selection using different marker types and densities. J Anim Sci 86:2447–2454

    Article  PubMed  CAS  Google Scholar 

  • Stakman EC (1915) Relation between Puccinia graminis and plants highly resistant to its attack. J Agr Res 4:193–299

    Google Scholar 

  • Statler GD (1987) Mutation studies with race 1, Puccinia recondita. Can J Plant Pathol 9:200–204

    Google Scholar 

  • Sunderwirth SD, Roelfs AP (1980) Greenhouse evaluation of the adult-plant resistance of Sr2 to wheat stem rust. Phytopathology 70:634–637

    Article  Google Scholar 

  • ter Braak CJF, Boer MP, Bink M (2005) Extending Xu’s Bayesian model for estimating polygenic effects using markers of the entire genome. Genetics 170:1435–1438

    Article  PubMed  CAS  Google Scholar 

  • Toosi A, Fernando RL, Dekkers JCM (2010) Genomic selection in admixed and crossbred populations. J Anim Sci 88:32–46

    Article  PubMed  CAS  Google Scholar 

  • VanRaden PM, Tassell CP, Wiggans GR, Sonstegard TS, Schanabel RD, Taylor JF, Schenkel FS (2009) Reliability of genomic predictions for North American Holstein bulls. J Dairy Sci 92:16–24

    Article  PubMed  CAS  Google Scholar 

  • Wang GL, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434

    PubMed  CAS  Google Scholar 

  • Wang JK, Chapman SC, Bonnett DG, Rebetzke GJ, Crouch J (2007) Application of population genetic theory and simulation models to efficiently pyramid multiple genes via marker-assisted selection. Crop Sci 47:582–590

    Article  Google Scholar 

  • Wiersma JJ, Busch RH, Fulcher GG, Hareland GA (2001) Recurrent selection for kernel weight in spring wheat. Crop Sci 41:999–1005

    Article  Google Scholar 

  • William HM, Trethowan R, Crosby-Galvan EM (2007) Wheat breeding assisted by markers: CIMMYT’s experience. Euphytica 157:307–319

    Article  Google Scholar 

  • Wong CK, Bernardo R (2008) Genomewide selection in oil palm: increasing selection gain per unit time and cost with small populations. Theor Appl Genet 116:815–824

    Article  PubMed  CAS  Google Scholar 

  • Xu SZ (2003) Estimating polygenic effects using markers of the entire genome. Genetics 163:789–801

    PubMed  CAS  Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391

    Article  Google Scholar 

  • Young ND (1996) QTL mapping and quantitative disease resistance in plants. Annu Rev Phytopathol 34:479–501

    Article  PubMed  CAS  Google Scholar 

  • Zhong S, Dekkers JCM, Fernando RL, Jannink J-L (2009) Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a barley case study. Genetics 182:355–364

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgements

Support for the work of JR was provided by the USDA National Needs Graduate Fellowship Competitive Grant No. 2008-38420-04755 from the National Institute of Food and Agriculture, the Einaudi Center International Research Travel Grant, and the Jeanie Borlaug Women in Triticum Award. Support for the work of EH was provided by USDA National Needs Graduate Fellowship Competitive Grant No. 2005-38420-15785 from the National Institute of Food and Agriculture. Additional funding for this research was provided by USDA—NIFA National Research Initiative CAP grants No. 2005-05130, 2006-55606-16629, and by Hatch 149-402.

Author information

Authors and Affiliations

  1. Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA

    Jessica E. Rutkoski, Elliot L. Heffner & Mark E. Sorrells

Authors
  1. Jessica E. Rutkoski
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elliot L. Heffner
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mark E. Sorrells
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Mark E. Sorrells.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rutkoski, J.E., Heffner, E.L. & Sorrells, M.E. Genomic selection for durable stem rust resistance in wheat. Euphytica 179, 161–173 (2011). https://doi.org/10.1007/s10681-010-0301-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-010-0301-1

Keywords

Search

Navigation