Molecular Breeding

, Volume 29, Issue 2, pp 477–488 | Cite as

Single nucleotide polymorphism in wheat chromosome region harboring Fhb1 for Fusarium head blight resistance

  • Amy N. Bernardo
  • Hongxiang Ma
  • Dadong Zhang
  • Guihua Bai


Fusarium head blight (FHB) is a destructive disease that reduces wheat grain yield and quality. To date, the quantitative trait locus on 3BS (Fhb1) from Sumai 3 has shown the largest effect on FHB resistance. Single nucleotide polymorphism (SNP) is the most common form of genetic variation and is suitable for high-throughput marker-assisted selection (MAS). We analyzed SNPs derived from 23 wheat expressed sequence tags (ESTs) that previously mapped near Fhb1 on chromosome 3BS. Using 71 Ning 7840/Clark BC7F7 recombinant inbred lines and the single-base extension method, we mapped seven SNP markers between Xgwm533 and Xgwm493, flanking markers for Fhb1. Five of the SNPs explained 45–54% of the phenotypic variation for FHB resistance. Haplotype analysis of 63 wheat accessions from eight countries based on SNPs in EST sequences, simple sequence repeats, and sequence tagged sites in the Fhb1 region identified four major groups: (1) US-Clark, (2) Asian, (3) US-Ernie, and (4) Chinese Spring. The Asian group consisted of Chinese and Japanese accessions that carry Fhb1 and could be differentiated from other groups by marker Xsnp3BS-11. All Sumai 3-related accessions formed a subgroup within the Asian group and could be sorted out by Xsnp3BS-8. The SNP markers identified in this study should be useful for MAS of Fhb1 and fine mapping to facilitate cloning of the Fhb1 resistance gene.


Single nucleotide polymorphism Fhb1 Fusarium graminearum Marker-assisted selection Genetic diversity 

Supplementary material

11032_2011_9565_MOESM1_ESM.docx (13 kb)
Supplementary material 1 (DOCX 13 kb)
11032_2011_9565_MOESM2_ESM.docx (21 kb)
Supplementary material 2 (DOCX 22 kb)
11032_2011_9565_MOESM3_ESM.pdf (194 kb)
Supplementary material 3 (PDF 193 kb)


  1. Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploid wheat with the Illumina goldengate assay. Theor Appl Genet 119:507–517PubMedCrossRefGoogle Scholar
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  3. Andersen AL (1948) The development of Gibberella zeae headblight of wheat. Phytopathology 38:595–611Google Scholar
  4. Bai G, Zhou C, Qian C, Ge Y (1989) A study on scab resistance in new wheat cultivars and advanced breeding lines. Jiangsu Agr Sci 7:20–22Google Scholar
  5. Bai G, Kolb F, Shaner G, Domier L (1999) Amplified fragment length polymorphism markers linked to a major quantitative trait locus controlling scab resistance in wheat. Phytopathology 89:343–348PubMedCrossRefGoogle Scholar
  6. Bai G, Shaner G, Ohm H (2000) Inheritance of resistance to Fusarium graminearum in wheat. Theor Appl Genet 100:1–8CrossRefGoogle Scholar
  7. Bai G, Guo P, Kolb FL (2003) Genetic relationships among head blight resistant cultivars of wheat assessed on the basis of molecular markers. Crop Sci 43:498–507CrossRefGoogle Scholar
  8. Beales J, Laurie D, Devos K (2005) Allelic variation at the linked AP1 and PhyC loci in hexaploid wheat is associated but not perfectly correlated with vernalization response. Theor Appl Genet 110:1099–1107PubMedCrossRefGoogle Scholar
  9. Bernardo AN, Bradbury PJ, Ma H, Hu S, Bowden RL, Buckler ES, Bai G (2009) Discovery and mapping of single feature polymorphisms in wheat using Affymetrix arrays. BMC Genomics 10:251PubMedCrossRefGoogle Scholar
  10. Buerstmayr H, Ban T, Anderson JA (2009) QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review. Plant Breeding 128:1–26CrossRefGoogle Scholar
  11. Cuthbert PA, Somers DJ, Thomas J, Cloutier S, Brule-Babel A (2006) Fine mapping Fhb1, a major gene controlling Fusarium head blight resistance in bread wheat (Triticum aestivum L.). Theor Appl Genet 112:1465–1472PubMedCrossRefGoogle Scholar
  12. Desjardins AE, Hohn TM (1997) Mycotoxins in plant pathogenesis. Mol Plant-Microbe Interact 10:147–152CrossRefGoogle Scholar
  13. Garcés-Claver A, Fellman S, Gil-Ortega R, Jahn M, Arnedo-Andrés M (2007) Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theor Appl Genet 115:907–916PubMedCrossRefGoogle Scholar
  14. Grausgruber H, Lemmens M, Bürstmayr H, Ruckenbauer P (2004) Resistance of ‘Chinese Spring’ substitution sines carrying chromosomes from ‘Cheyenne’, ‘Hope’ and ‘Lutescens 62’ wheats to head blight caused by Fusarium culmorum. Hereditas 130:57–63CrossRefGoogle Scholar
  15. Ha B-K, Hussey RS, Boerma HR (2007) Development of SNP assays for marker-assisted selection of two southern root-knot nematode resistance QTL in soybean. Crop Sci 47:S-73–S-82CrossRefGoogle Scholar
  16. Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220PubMedCrossRefGoogle Scholar
  17. Jayatilake DV, Bai GH, Dong YH (2011) A novel quantitative trait locus for Fusarium head blight resistance in chromosome 7A of wheat. Theor Appl Genet 22:1189–1198CrossRefGoogle Scholar
  18. Jin Q, Waters D, Cordeiro GM, Henry RJ, Reinke RF (2003) A single nucleotide polymorphism (SNP) marker linked to the fragrance gene in rice (Oryza sativa L.). Plant Sci 165:359–364CrossRefGoogle Scholar
  19. Kaczorowski KA, Kim K-S, Diers BW, Hudson ME (2008) Microarray-based genetic mapping using soybean near-isogenic lines and generation of SNP markers in the Rag1 aphid-resistance interval. Plant Gen 1:89–98CrossRefGoogle Scholar
  20. Koebner RMD, Summers RW (2003) 21st century wheat breeding: plot selection or plate detection? Trends Biotechnol 21:59–63PubMedCrossRefGoogle Scholar
  21. Konishi S, Izawa T, Lin S, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) A SNP caused loss of seed shattering during rice domestication. Science 312:1392–1396PubMedCrossRefGoogle Scholar
  22. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  23. Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen H (2007) Single feature polymorphism discovery in rice. PLoS One 2:e284PubMedCrossRefGoogle Scholar
  24. Liu S, Abate ZA, Lu H, Musket T, Davis GL, McKendry AL (2007) QTL associated with Fusarium head blight resistance in the soft red winter wheat Ernie. Theor Appl Genet 115:417–427PubMedCrossRefGoogle Scholar
  25. Liu S, Anderson JA (2003) Marker assisted evaluation of Fusarium head blight resistant wheat germplasm. Crop Sci 43:760–766CrossRefGoogle Scholar
  26. Liu S, Pumphrey MO, Gill BS, Trick HN, Zhang JX, Dolezel J, Chalhoub B, Anderson JA (2008) Toward positional cloning of Fhb1, a major QTL for Fusarium head blight resistance in wheat. Cereal Res Commun 36:195–201CrossRefGoogle Scholar
  27. Ma H-X, Bai G-H, Gill BS, Hart LP (2006) Deletion of a chromosome arm altered wheat resistance to Fusarium head blight and deoxynivalenol accumulation in Chinese Spring. Plant Dis 90:1545–1549CrossRefGoogle Scholar
  28. Marshall O (2004) PerlPrimer: cross-platform, graphical primer design for standard, bisulphite and real-time PCR. Bioinformatics 20:2471–2472PubMedCrossRefGoogle Scholar
  29. 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
  30. Mesterhazy A (1977) Reaction of winter wheat varieties to four Fusarium species. Phytopathol Z 90:104–112CrossRefGoogle Scholar
  31. Mochida K, Yamazaki Y, Ogihara Y (2004) Discrimination of homoeologous gene expression in hexaploid wheat by SNP analysis of contigs grouped from a large number of expressed sequence tags. Mol Gen Genomics 270:371–377CrossRefGoogle Scholar
  32. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5:94–100PubMedCrossRefGoogle Scholar
  33. Roby J, Nelson JC (2008) QGene 4.0, an extensible Java QTL-analysis platform. Bioinformatics 24:2788–2789CrossRefGoogle Scholar
  34. Rohlf FJ (1998) NTSYSpc: numerical taxonomy system, ver. 2.02i. Exeter Publishing, Ltd, Setauket, NYGoogle Scholar
  35. Saghai-Maroof M, Soliman K, Jorgensen R, Allard R (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018PubMedCrossRefGoogle Scholar
  36. Sattarzadeh A, Achenbach U, Lübeck J, Strahwald J, Tacke E, Hofferbert H-R, Rothsteyn T, Gebhardt C (2006) Single nucleotide polymorphism (SNP) genotyping as basis for developing a PCR-based marker highly diagnostic for potato varieties with high resistance to Globodera pallida pathotype Pa2/3. Mol Breed 18:301–312CrossRefGoogle Scholar
  37. Schroeder H, Christensen J (1963) Factors affecting resistance of wheat to scab caused by Gibberella zeae. Phytopathology 53:831–838Google Scholar
  38. Schwieger F, Tebbe CC (1998) A new approach to utilize PCR-single-strand-conformation polymorphism for 16S rRNA gene-based microbial community analysis. Appl Environ Microbiol 64:4870–4876PubMedGoogle Scholar
  39. Smith D, Flavell R (1975) Characterization of the wheat genome by renaturation kinetics. Chromosoma 50:223–242CrossRefGoogle Scholar
  40. Sneller CH, Garcia G, Gupta A, Nolan R, Lipps P, Herald L, Johnston A (2004) Genetics of FHB resistance in the soft red winter wheat cultivar “Freedom”. In: Proceedings of the 2nd international symposium on Fusarium head blight. Orlando, FL, p 166Google Scholar
  41. Snijders CHA (1990) Genetic variation for resistance to Fusarium head blight in bread wheat. Euphytica 50:171–179CrossRefGoogle Scholar
  42. Somers D, Kirkpatrick R, Moniwa M, Walsh A (2003) Mining single-nucleotide polymorphisms from hexaploid wheat ESTs. Genome 46:431–437PubMedCrossRefGoogle Scholar
  43. Sun X, Bai G, Carver B (2009) Molecular markers for wheat leaf rust resistance gene Lr41. Mol Breed 23:311–321CrossRefGoogle Scholar
  44. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  45. Waldron BL, Moreno-Sevilla B, Anderson JA, Stack RW, Frohberg RC (1999) RFLP mapping of QTL for Fusarium head blight resistance in wheat. Crop Sci 39:805–811CrossRefGoogle Scholar
  46. Wilcoxson RD, Busch RH, Ozmon EA (1992) Fusarium head blight resistance in spring wheat cultivars. Plant Dis 76:658–661CrossRefGoogle Scholar
  47. Yu GH, Ma HX, Bai GH, Tang KX (2008a) Single-strand conformational polymorphism markers associated with a major QTL for fusarium head blight resistance in wheat. Mol Biol (Mosk) 42:571–580CrossRefGoogle Scholar
  48. Yu JB, Bai GH, Zhou WC, Dong YH, Kolb FL (2008b) Quantitative trait loci for Fusarium head blight resistance in a recombinant inbred population of Wangshuibai/Wheaton. Phytopathology 98:87–94PubMedCrossRefGoogle Scholar
  49. Zhang X, Zhou M, Ren L, Bai G, Ma H, Scholten OE, Guo P, Lu W (2004) Molecular characterization of Fusarium head blight resistance from wheat variety Wangshuibai. Euphytica 139:59–64CrossRefGoogle Scholar
  50. Zhang JX, Jin Y, Rudd JC, Bockelman HE (2008) New Fusarium head blight resistant spring wheat germplasm identified in the USDA national small grains collection. Crop Sci 48:223–235CrossRefGoogle Scholar
  51. Zhou W, Kolb FL, Bai G, Domier LL, Yao JB (2002a) Effect of individual Sumai 3 chromosomes on resistance to scab spread within spikes and deoxynivalenol accumulation within kernels in wheat. Hereditas 137:81–89PubMedCrossRefGoogle Scholar
  52. Zhou W, Kolb FL, Bai G, Shaner Gregory, Domier LL (2002b) Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers. Genome 45:719PubMedCrossRefGoogle Scholar
  53. Zhou W, Kolb FL, Yu J, Bai G, Boze LK, Domier LL (2004) Molecular characterization of Fusarium head blight resistance in Wangshuibai with simple sequence repeat and amplified fragment length polymorphism markers. Genome 47:1137–1143PubMedCrossRefGoogle Scholar
  54. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphisms in soybean. Genetics 163:1123–1134PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. (outside the USA) 2011

Authors and Affiliations

  • Amy N. Bernardo
    • 1
  • Hongxiang Ma
    • 2
    • 3
  • Dadong Zhang
    • 3
  • Guihua Bai
    • 3
    • 4
  1. 1.Department of Plant PathologyKansas State UniversityManhattanUSA
  2. 2.Plant Genetics and BiotechnologyJAASNanjingChina
  3. 3.Department of AgronomyKansas State UniversityManhattanUSA
  4. 4.Hard Winter Wheat Genetics Research UnitUSDA-ARSManhattanUSA

Personalised recommendations