Molecular Breeding

, 36:51

Genotyping-by-sequencing to remap QTL for type II Fusarium head blight and leaf rust resistance in a wheat–tall wheatgrass introgression recombinant inbred population

  • Xiangye Xiao
  • Herbert W. Ohm
  • Greg J. Hunt
  • Jesse A. Poland
  • Lingrang Kong
  • Jill A. Nemacheck
  • Christie E. Williams
Article

Abstract

Fusarium graminearum Schwabe (Fusarium head blight, FHB) and Puccinia triticina Eriks (leaf rust) are two major fungal pathogens posing a continuous threat to the wheat crop; consequently, identifying resistance genes from various sources is always of importance to wheat breeders. We identified tightly linked single nucleotide polymorphism (SNP) markers for the FHB resistance quantitative trait locus (QTL) Qfhs.pur-7EL and the leaf rust resistance locus Lr19 using genotyping-by-sequencing (GBS) in a wheat–tall wheatgrass introgression-derived recombinant inbred line (RIL) population. One thousand and seven hundred high-confidence SNPs were used to conduct the linkage and QTL analysis. Qfhs.pur-7EL was mapped to a 2.9 cM region containing four markers within a 43.6 cM segment of wheatgrass chromosome 7el2 that was translocated onto wheat chromosome 7DL. Lr19 from 7el1 was mapped to a 1.21 cM region containing two markers in the same area, in repulsion. Five lines were identified with the resistance-associated SNP alleles for Qfhs.pur-7EL and Lr19 in coupling. Two SNP markers in the Qfhs.pur-7EL region were converted into PCR-based KASP markers. Investigation of the genetic characteristics of the parental lines of this RIL population indicated that they are translocation lines in two different wheat cultivar genetic backgrounds instead of 7E–7D substitution lines in Thatcher wheat background, as previously reported in the literature.

Keywords

Fusarium head blight resistance Leaf rust resistance Wheat Tall wheatgrass Substitution lines KASP assay 

Supplementary material

11032_2016_472_MOESM1_ESM.docx (23 kb)
Supplementary material 1 (DOCX 22 kb)
11032_2016_472_MOESM2_ESM.docx (38 kb)
Supplementary material 2 (DOCX 37 kb)
11032_2016_472_MOESM3_ESM.docx (58 kb)
Supplementary material 3 (DOCX 58 kb)
11032_2016_472_MOESM4_ESM.docx (30 kb)
Supplementary material 4 (DOCX 29 kb)

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Anderson JA, Chao S, Liu S (2007) Molecular breeding using a major QTL for Fusarium head blight resistance in wheat. Crop Sci 47:S-112–S-119Google Scholar
  3. Bai G, Shaner G (2004) Management and resistance in wheat and barley to Fusarium head blight. Annu Rev Phytopathol 42:135–161CrossRefPubMedGoogle Scholar
  4. Beavis WD (1998) QTL analyses: power, precision, and accuracy. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 145–162Google Scholar
  5. Beyer M, Aumann J (2008) Effects of Fusarium infection on the amino acid composition of winter wheat grain. Food Chem 111:750–754. doi:10.1016/j.foodchem.2008.04.047 CrossRefGoogle Scholar
  6. Bhardwaj SC, Prashar M, Kumar S, Jain SK, Datta D (2005) Lr19 resistance in wheat becomes susceptible to Puccinia triticina in India. Plant Dis 89:1360. doi:10.1094/PD-89-1360A CrossRefGoogle Scholar
  7. Brachi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232CrossRefPubMedPubMedCentralGoogle 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 23:2633–2635CrossRefPubMedGoogle Scholar
  9. Brinkman M, Frey KJ (1977) Yield-component analysis of oat isolines that produce different grain yields. Crop Sci 17:165–168CrossRefGoogle Scholar
  10. Bushnell W (1984) The cereal rusts: origins, specificity, structure, and physiology, vol 1. Elsevier, USGoogle Scholar
  11. Chen S, Xia G, Quan T, Xiang F, Jin Y, Chen H (2004) Introgression of salt-tolerance from somatic hybrids between common wheat and Thinopyrum ponticum. Plant Sci 167:773–779CrossRefGoogle Scholar
  12. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971PubMedPubMedCentralGoogle Scholar
  13. Cox C, Murray T, Jones S (2002) Perennial wheat germ plasm lines resistant to eyespot, Cephalosporium stripe, and wheat streak mosaic. Plant Dis 86:1043–1048CrossRefGoogle Scholar
  14. Cuthbert PA, Somers DJ, Thomas J, Cloutier S, Brulé-Babel A (2006) Fine mapping Fhb1, a major gene controlling Fusarium head blight resistance in bread wheat (Triticum aestivum L.). Theor Appl Genet 112:1465–1472CrossRefPubMedGoogle Scholar
  15. Dupuis J, Siegmund D (1999) Statistical methods for mapping quantitative trait loci from a dense set of markers. Genetics 151:373–386PubMedPubMedCentralGoogle Scholar
  16. Dvořák J (1975) Meiotic pairing between single chromosomes of diploid Agropyron elongatum and decaploid A. elongatum in Triticum aestivum. Can J Genet Cytol 17:329–336CrossRefGoogle Scholar
  17. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. doi:10.1371/journal.pone.0019379 CrossRefPubMedPubMedCentralGoogle Scholar
  18. FDA (2010) Guidance for industry and FDA: advisory levels for deoxynivalenol (DON) in finished wheat products for human consumption and grains and grain by-products used for animal feed. http://www.fda.gov/downloads/Food/GuidanceRegulation/UCM217558.pdf
  19. Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324CrossRefPubMedGoogle Scholar
  20. Huerta-Espino J, Singh R (1994) First report of virulence to wheat with leaf rust resistance gene Lr19 in Mexico. Plant Dis 78:640CrossRefGoogle Scholar
  21. IWGSC (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. doi:10.1126/science.1251788 Google Scholar
  22. Kim N-S, Armstrong K, Knott D (1993) Molecular detection of Lophopyrum chromatin in wheat-Lophopyrum recombinants and their use in the physical mapping of chromosome 7D. Theor Appl Genet 85:561–567CrossRefPubMedGoogle Scholar
  23. Knott D (1968) Agropyrons as a source of rust resistance in wheat breeding. In: 3rd international wheat genetics symposium, Canberra, Australia, pp 204–212Google Scholar
  24. Knott D (1980) Mutation of a gene for yellow pigment linked to Lr19 in wheat. Can J Genet Cytol 22:651–654CrossRefGoogle Scholar
  25. Knott D, Dvořák J, Nanda J (1977) The transfer to wheat and homoeology of an Agropyron elongatum chromosome carrying resistance to stem rust. Can J Genet Cytol 19:75–79CrossRefGoogle Scholar
  26. Kosambi D (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175CrossRefGoogle Scholar
  27. Kumar LS (1999) DNA markers in plant improvement: an overview. Biotechnol Adv 17:143–182CrossRefPubMedGoogle Scholar
  28. Lind V, Gultyaeva E (2007) Virulence frequences of Puccinia triticina in Germany and the European regions of the Russian Federation. J Phytopathol 155:13–21. doi:10.1111/j.1439-0434.2006.01182.x CrossRefGoogle Scholar
  29. Lu F, Lipka AE, Glaubitz J, Elshire R, Cherney JH, Casler MD, Buckler ES, Costich DE (2013) Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol. PLoS Genet 9:e1003215. doi:10.1371/journal.pgen.1003215 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Marais GF, Marais AS (1990) The assignment of a Thinopyrum distichum (Thunb.) Löve-derived translocation to the long arm of wheat chromosome 7D using endopeptidase polymorphisms. Theor Appl Genet 79:182–186. doi:10.1007/BF00225949 CrossRefPubMedGoogle Scholar
  31. 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
  32. Nganje WE, Bangsund DA, Leistritz FL, Wilson WW, Tiapo NM (2004) Regional economic impacts of Fusarium head blight in wheat and barley. Appl Econ Perspect Pol 26:332–347. doi:10.1111/j.1467-9353.2004.00183.x Google Scholar
  33. Ordonez ME, Kolmer JA (2007) Virulence phenotypes of a worldwide collection of Puccinia triticina from durum wheat. Phytopathology 97:344–351. doi:10.1094/phyto-97-3-0344 CrossRefPubMedGoogle Scholar
  34. Parry DW, Jenkinson P, Mcleod L (1995) Fusarium ear blight (scab) in small-grain cereals—a review. Plant Pathol 44:207–238. doi:10.1111/j.1365-3059.1995.tb02773.x CrossRefGoogle Scholar
  35. Poland JA, Rife TW (2012) Genotyping-by-sequencing for plant breeding and genetics. The Plant Genome 5:92–102CrossRefGoogle Scholar
  36. Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012a) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:e32253. doi:10.1371/journal.pone.0032253 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Poland JA, Endelman J, Dawson J, Rutkoski J, Wu S, Manes Y, Dreisigacker S, Crossa J, Sánchez-Villeda H, Sorrells ME (2012b) Genomic selection in wheat breeding using genotyping-by-sequencing. Plant Genome 5:103–113CrossRefGoogle Scholar
  38. Riley R (1958) Chromosome pairing and haploids in wheat. 10th International Congress of Genetics. Montreal, Canada, pp 234–235Google Scholar
  39. Samborski D (1985) Wheat leaf rust. In: Roelfs AP, Bushnell WR (eds) The cereal rusts, vol 2. Academic Press, Orlando, pp 39–59Google Scholar
  40. Samborski D, Peturson B (1960) Effect of leaf rust on the yield of resistant wheats. Can J Plant Sci 40:620–622CrossRefGoogle Scholar
  41. Schroeder H, Christensen J (1963) Factors affecting resistance of wheat to scab caused by Gibberella zeae. Phytopathology 53:831–838Google Scholar
  42. Sears E, Okamoto M (1958) Intergenomic chromosome relationships in hexaploid wheat. In: 10th international congress of genetics, Montreal, Canada, pp 258–259Google Scholar
  43. Sharma D, Knott D (1966) The transfer of leaf-rust resistance from Agropyron to Triticum by irradiation. Can J Genet Cytol 8:137–143CrossRefGoogle Scholar
  44. Shen X, Ohm H (2007) Molecular mapping of Thinopyrum-derived Fusarium head blight resistance in common wheat. Mol Breed 20:131–140CrossRefGoogle Scholar
  45. Van Ooijen J (2006) JoinMap (R) 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  46. Van Ooijen J (2009) MapQTL (R) 6, Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, WageningenGoogle Scholar
  47. Wang RR-C (2011) Agropyron and Psathyrostachys. In: Kole C (ed) Wild crop relatives: genomic and breeding resources. Springer, Berlin, pp 77–108CrossRefGoogle Scholar
  48. Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around the Tm-2 locus of tomato during backcross breeding. Theor Appl Genet 77:353–359. doi:10.1007/BF00305828 CrossRefPubMedGoogle Scholar
  49. Zhang X, Shen X, Hao Y, Cai J, Ohm HW, Kong L (2011) A genetic map of Lophopyrum ponticum chromosome 7E, harboring resistance genes to Fusarium head blight and leaf rust. Theor Appl Genet 122:263–270CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht (outside the USA) 2016

Authors and Affiliations

  • Xiangye Xiao
    • 1
  • Herbert W. Ohm
    • 1
  • Greg J. Hunt
    • 2
  • Jesse A. Poland
    • 3
  • Lingrang Kong
    • 4
  • Jill A. Nemacheck
    • 5
  • Christie E. Williams
    • 1
    • 5
  1. 1.Department of AgronomyPurdue UniversityWest LafayetteUSA
  2. 2.Department of EntomologyPurdue UniversityWest LafayetteUSA
  3. 3.Department of Plant PathologyKansas State UniversityManhattanUSA
  4. 4.State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianChina
  5. 5.USDA-ARS, Crop Production and Pest Control Research UnitWest LafayetteUSA

Personalised recommendations