Molecular Breeding

, Volume 27, Issue 4, pp 439–454 | Cite as

Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm

  • J. Massman
  • B. Cooper
  • R. Horsley
  • S. Neate
  • R. Dill-Macky
  • S. Chao
  • Y. Dong
  • P. Schwarz
  • G. J. Muehlbauer
  • K. P. Smith
Article

Abstract

Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for improving complex quantitative traits with low to moderate heritability. Association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To test this approach, we conducted association mapping of two complex traits with moderate heritability; Fusarium head blight (FHB) severity and the grain concentration of mycotoxin associated with disease, deoxynivalenol (DON). To map FHB resistance in barley, 768 breeding lines were evaluated in 2006 and 2007 in four locations. All lines were genotyped with 1,536 SNP markers and QTL were mapped using a mixed model that accounts for relatedness among lines. Average linkage disequilibrium within the breeding germplasm extended beyond 4 cM. Four QTL were identified for FHB severity and eight QTL were identified for the DON concentration in two independent sets of breeding lines. The QTL effects were small, explaining 1–3% of the phenotypic variation, as might be expected for complex polygenic traits. We show that using breeding germplasm to map QTL can complement bi-parental mapping studies by providing independent validation, mapping QTL with more precision, resolving questions of linkage and pleiotropy, and identifying genetic markers that can be applied immediately in crop improvement.

Keywords

Disease resistance Fusarium head blight Deoxynivalenol Quantitative trait loci Association mapping Linkage disequilibrium Barley 

Notes

Acknowledgments

This research was supported by The U.S. Wheat and Barley Scab Initiative Grant No. 59-0790-4-120, the Minnesota Agricultural Experiment Station, and USDA-CSREES-NRI Grant No. 2006-55606-16722 “Barley Coordinated Agricultural Project: Leveraging Genomics, Genetics, and Breeding for Gene Discovery and Barley Improvement.”.

Supplementary material

11032_2010_9442_MOESM1_ESM.doc (1.2 mb)
Supplementary material 1 (DOC 1239 kb)

References

  1. Arbelbide M, Yu J, Bernardo R (2006) Power of mixed-model QTL mapping from phenotypic, pedigree and marker data in self-pollinated crops. Theor Appl Genet 112:876–884PubMedCrossRefGoogle Scholar
  2. Bai G, Shaner G (2004) Management and resistance in wheat and barley to Fusarium head blight. Annu Rev Phytopathol 42:135–161PubMedCrossRefGoogle Scholar
  3. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21:263–265PubMedCrossRefGoogle Scholar
  4. Beavis WD (1998) QTL analyses: power, precision and accuracy. In: Paterson AH (ed) Molecular analysis of complex traits. CRC, Boca Raton, pp 145–161Google Scholar
  5. Belo A, Zheng P, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A (2008) Whole genome scan detects an allelic variant of fad2 associated with increases oleic acid levels in maize. Mol Genet Genomics 279:1–10PubMedCrossRefGoogle Scholar
  6. Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48:1649–1664CrossRefGoogle Scholar
  7. Bilgic H, Steffenson BJ, Hayes PM (2005) Comprehensive genetic analyses reveal differential expression of spot blotch resistance in four populations of barley. Theor Appl Genet 111:1238–1250PubMedCrossRefGoogle Scholar
  8. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635PubMedCrossRefGoogle Scholar
  9. Breseghello F, Sorrells ME (2006) Association mapping of kernel size and milling quality in wheat (Triticium aestivum) cultivars. Genetics 172:1165–1177PubMedCrossRefGoogle Scholar
  10. Buntjer JB, Sorensen AP, Peleman JD (2005) Haplotype diversity: the link between statistical and biological association. Trends Plant Sci 10:1360–1385CrossRefGoogle Scholar
  11. Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567PubMedCrossRefGoogle Scholar
  12. Camus-Kulandaivelu L, Veyrieras JB, Gouesnard B, Charcosset A, Manicacci D (2007) Evaluating the reliability of Structure outputs in case of relatedness between individuals. Crop Sci 47:887–892CrossRefGoogle Scholar
  13. Canci PC, Nduulu LM, Muehlbauer GJ, Dill-Macky R, Rasmusson DC, Smith KP (2004) Validation of quantitative trait loci for Fusarium head blight and kernel discoloration in barley. Mol Breed 14:91–104CrossRefGoogle Scholar
  14. Capettini F, Rasmusson DC, Dill-Macky R, Schiefelbein E, Elakkad A (2003) Inheritance of resistance to Fusarium head blight in four populations of barley. Crop Sci 43:1960–1966CrossRefGoogle Scholar
  15. Close TJ, Bhat PR, Lonardi S, Wu Y, Rostoks N, Ramsay L, Druka A, Stein N, Svensson JT, Wanamaker S, Bozdag S, Roose ML, Moscou MJ, Chao S, Varshney RK, Szűcs P, Sato K, Hayes PM, Matthews DE, Kleinhofs A, Muehlbauer GJ, DeYoung J, Marshall DF, Madishetty K, Fenton RD, Condamine P, Graner A, Waugh R (2009) Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582PubMedCrossRefGoogle Scholar
  16. Dahleen LS, Agrama HA, Horsley RD, Steffenson BJ, Schwarz PB, Mesfin A, Franckowiak JD (2003) Identification of QTLs associated with Fusarium head blight resistance in Zhedar 2 barley. Theor Appl Genet 108:95–104PubMedCrossRefGoogle Scholar
  17. de la Peña RC, Smith KP, Capettini F, Muehlbauer GJ, Gallo-Meagher M, Dill-Macky R, Somers DA, Rasmusson DC (1999) Quantitative trait loci associated with resistance to Fusarium head blight and kernel discoloration in barley. Theor Appl Genet 99:561–569CrossRefGoogle Scholar
  18. Fan JB, Chee MS, Gunderson KL (2006) Highly parallel genomic assays. Nat Rev Genet 7:632–644PubMedCrossRefGoogle Scholar
  19. Fuentes RG, Michelson HR, Busch RH, Dill-Macky R, Evans CK, Thompson WG, Wiersma JV, Xie W, Dong Y, Anderson JA (2005) Resource allocation and cultivar stability in breeding for Fusarium head blight resistance in spring wheat. Crop Sci 45:1965–1972CrossRefGoogle Scholar
  20. Heffner EL, Sorrells ME, Jannink J (2009) Genomic selection for crop improvement. Crop Sci 49:1–12CrossRefGoogle Scholar
  21. Hori K, Kobayashi T, Sato K, Takeda KE (2005) QTL analysis of Fusarium head blight resistance using a high-density linkage map in barley. Theor Appl Genet 111:1661–1672PubMedCrossRefGoogle Scholar
  22. Hori K, Sato K, Kobayashi T, Takeda K (2006) QTL analysis of Fusarium head blight severity in recombinant inbred population derived from a cross between two-rowed barley varieties. Breed Sci 56:25–30CrossRefGoogle Scholar
  23. Horsley RD, Schmierer D, Maier D, Kudrna D, Urrea CA, Steffenson BJ, Schwarz PB, Franckowiak JD, Green MJ, Zhang B, Kleinhofs A (2006) Identification of QTLs associated with Fusarium head blight resistance in barley accession CIho 4196. Crop Sci 46:145–156CrossRefGoogle Scholar
  24. Jannink JL, Bink MCAM, Jansen RC (2001) Using complex plant pedigrees to map valuable genes. Trends Plant Sci 6:337–342PubMedCrossRefGoogle Scholar
  25. Kraakman ATW, Niks RE, Van den Berg PMMM, Stam P, van Eeuwijk FA (2004) Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168:435–446PubMedCrossRefGoogle Scholar
  26. Kraakman ATW, Martínez F, Mussiraliev B, van Eeuwijk FA, Niks RE (2006) Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Mol Breed 17:41–58CrossRefGoogle Scholar
  27. Lynch M, Ritland K (1999) Estimation of relatedness with molecular markers. Genetics 152:1753–1766PubMedGoogle Scholar
  28. Ma Z, Steffenson BJ, Prom LK, Lapitan NLV (2000) Mapping of quantitative trait loci for fusarium head blight resistance in barley. Phytopathology 90:1079–1088PubMedCrossRefGoogle Scholar
  29. Malysheva-Otto LV, Ganal MW, Roder MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genet 7:6PubMedCrossRefGoogle Scholar
  30. McMullen M, Jones R, Gallenberg D (1997) Scab of wheat and barley: a re-emerging disease of devastating impact. Plant Dis 81:1340–1348CrossRefGoogle Scholar
  31. Melchinger AE, Utz HF, Schon CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149:383–403PubMedGoogle Scholar
  32. Mesfin A, Smith KP, Dill-Macky R, Evans CK, Waugh R, Gustus CD, Muehlbauer GJ (2003) Quantitative trait loci for Fusarium head blight resistance in barley detected in a two-rowed by six-rowed population. Crop Sci 43:307–318CrossRefGoogle Scholar
  33. Mirocha CJ, Kolaczkowski E, Xie W, Yu H, Jelen H (1998) Analysis of deoxynivalenol and its derivatives (batch and single kernel) using gas chromatography/mass spectrometry. J Agric Food Chem 46:1414–1418CrossRefGoogle Scholar
  34. Nduulu LM, Mesfin A, Muehlbauer GJ, Smith KP (2007) Analysis of the chromosome 2(2H) region of barley associated with the correlated traits Fusarium head blight resistance and heading date. Theor Appl Genet 115:561–570PubMedCrossRefGoogle Scholar
  35. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  36. R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna. ISBN 3-900051-07-0, http://www.R-project.org
  37. Robertson A (1967) The nature of quantitative genetic variation. In: Brink A (ed) Heritage from Mendel. University of Wisconsin, Madison, pp 265–280Google Scholar
  38. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat P, Roose M, Svensson J, Stein N, Varshney R, Marshall D, Graner A, Close T, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103:18656–18661PubMedCrossRefGoogle Scholar
  39. Rudd JC, Horsley RD, McKendry AL, Elias EM (2001) Host plant resistance genes for Fusarium head blight: sources, mechanisms, and utility in conventional breeding systems. Crop Sci 41:620–627CrossRefGoogle Scholar
  40. SAS Institute (2002) SAS—statistical analysis software for windows, 9.1. SAS Institute, CaryGoogle Scholar
  41. Sato K, Hori K, Takeda K (2008) Detection of Fusarium head blight resistance QTLs using five populations of top-cross progeny derived from two-row × two-row crosses in barley. Mol Breed 22:517–526CrossRefGoogle Scholar
  42. Slotta TAB, Brady L, Chao S (2008) High throughput tissue preparation for large scale genotyping experiments. Mol Ecol Res 8:83–87CrossRefGoogle Scholar
  43. Steffenson BJ (2003) Fusarium head blight of barley: impact, epidemics, management, and strategies for identifying and utilizing genetic resistance. In: Leonard KL, Bushnell WR (eds) Fusarium head blight of wheat and barley. The American Phytopathological Society, St. Paul, pp 241–295Google Scholar
  44. Thornsberry JM, Goodman M, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  45. Van Sanford D, Anderson J, Campbell K, Costa J, Cregan P, Griffey C, Hayes P, Ward R (2001) Discovery and deployment of molecular markers linked to Fusarium head blight resistance: an integrated system for wheat and barley. Crop Sci 41:638–644CrossRefGoogle Scholar
  46. Wang JU, McClean PE, Lee R, Goos RJ, Helms T (2008) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116:777–787PubMedCrossRefGoogle Scholar
  47. Wu Y, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet 4:1–11CrossRefGoogle Scholar
  48. Xu Y, Crouch J (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar
  49. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208PubMedCrossRefGoogle Scholar
  50. Zhao K, Aranzana MJ, Kim S, Clare L, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:71–82CrossRefGoogle Scholar
  51. Zhu H, Gilchrist L, Hayes P, Kleinhofs A, Kudrna D, Liu Z, Prom L, Steffenson BJ, Toojinda T, Vivar HE (1999) Does function follow form? Principal QTLs for Fusarium head blight (FHB) resistance are coincident with QTLs for inflorescence traits and plant height in a doubled-haploid population of barley. Theor Appl Genet 99:1221–1232CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  • J. Massman
    • 1
  • B. Cooper
    • 5
  • R. Horsley
    • 3
  • S. Neate
    • 4
  • R. Dill-Macky
    • 2
  • S. Chao
    • 6
  • Y. Dong
    • 2
  • P. Schwarz
    • 3
  • G. J. Muehlbauer
    • 1
  • K. P. Smith
    • 1
  1. 1.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulUSA
  2. 2.Department of Plant PathologyUniversity of MinnesotaSaint PaulUSA
  3. 3.Department of Plant SciencesNorth Dakota State UniversityFargoUSA
  4. 4.Department of Plant PathologyNorth Dakota State UniversityFargoUSA
  5. 5.Busch Agricultural Resources LLCFt. CollinsUSA
  6. 6.USDA-ARSFargoUSA

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