Theoretical and Applied Genetics

, Volume 119, Issue 4, pp 663–673 | Cite as

Development and functional assessment of EST-derived 2RL-specific markers for 2BS.2RL translocations

  • Tong Geon Lee
  • Min Jeong Hong
  • Jerry W. Johnson
  • Daniel E. Bland
  • Dae Yeon Kim
  • Yong Weon SeoEmail author
Original Paper


ESTs-derived markers are useful for comparative genomic analysis and can also serve as phenotype-linked functional markers. Here, we report the development of EST-derived 2RL-specific markers and the evaluation of the possibility of functional assessment of markers tagging 2RL, which carries Hessian fly resistance genes (loci). To identify transcripts specific to 2RL, unigene sequences in combination with wheat progenitor genomes were used. Total 275 contigs mapped to the long arms of homoeologous group 2 chromosomes were downloaded. To obtain a cluster corresponding to each of the wheat 275 contigs, unigene sequences of wheat, rice, barley, and rye were pooled for cross-species clusters. Out of 275 clusters examined, it was possible to design 112 cross-species primer pairs for genome-specific amplifications. Out of 112 cross-species primer pairs, 45 primer pairs (40%) produced amplicons from at least one species (three wheat progenitors or rye). Among the 45 contigs, 73% were associated with one of known functions and 82% of the contigs associated with known functions were also associated with one of the GO categories. On the basis of the oligonucleotide sequence alignment of each of 45 genome-specific amplifications, 21 amplifications (47%) were suitable for designing RR genome-specific primers, which are specific to translocated rye chromatin 2RL. Six primer pairs (13%) successfully produced amplicons in the 2BS.2RL translocation lines and not in the non-2RLs. Functional assessment of one of the 2RL-specific markers, NSFT03P2_Contig4445, was performed on Hessian fly infested NILs. Under Hessian fly infestation, significantly high expression of a gene tagged by a 2RL-specific marker (NSFT03P2_Contig4445) was observed 1 day after infestation. EST-derived 2RL-specific marker development from this study provides a basis for the development of ESTs-derived markers for detecting wheat–rye translocations. In addition, these markers could be employed in elucidating functional analysis of genes on 2RL.


Translocation Line Homoeologous Group Unigene Sequence Triticeae Tribe Wheat Progenitor 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



The study was supported by a grant (No. 20070301-034-016-009-01-00) from BioGreen 21 Program, Rural Development Administration, Republic of Korea.


  1. Anderson JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560CrossRefGoogle Scholar
  2. Brunell MS, Lukaszewski AJ, Whitkus R (1999) Development of arm specific RAPD markers for rye chromosome 2R in wheat. Crop Sci 39:1702–1706Google Scholar
  3. Chantret N, Salse J, Sabot F, Rahman S, Bellec A, Laubin B, Dubois I, Dossat C, Sourdille P, Joudrier P, Gautier M-F, Cattolico L, Beckert M, Aubourg S, Weissenbach J, Caboche M, Bernard M, Leroy P, Chalhoub B (2005) Molecular basis of evolutionary events that shaped the Hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell 17:1033–1045PubMedCrossRefGoogle Scholar
  4. Choi HW, Kim YJ, Lee SC, Hong JK, Hwang BK (2007) Hydrogen peroxide generation by the pepper extracellular peroxidase CaPO2 activates local and systemic cell death and defense response to bacterial pathogens. Plant Physiol 145:890–904PubMedCrossRefGoogle Scholar
  5. Conley EJ, Conley EJ, Nduati V, Gonzalez-Hernandez JL, Mesfin A, Trudeau-Spanjers M, Chao S, Lazo GR, Hummel DD, Anderson OD, Qi LL, Gill BS, Echalier B, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvořák J, Peng JH, Lapitan NLV, Pathan MS, Nguyen HT, Ma X-F, Miftahudin, Gustafson JP, Greene RA, Sorrells ME, Hossain KG, Kalavacharla V, Kianian SF, Sidhu D, Dilbirligi M, Gill KS, Choi DW, Fenton RD, Close TJ, McGuire PE, Qualset CO, Anderson JA (2004) A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics 168:625–637PubMedCrossRefGoogle Scholar
  6. Devos KM, Moore G, Gale MD (1995) Conservation of marker synteny during evolution. Euphytica 85:367–372CrossRefGoogle Scholar
  7. Dundas IS, Frappell DE, Crack DM, Fisher JM (2001) Deletion mapping of a nematode resistance gene on rye chromosome 6R in wheat. Crop Sci 41:1771–1778Google Scholar
  8. Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH (2006) A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops. Plant Physiol 140:1183–1191PubMedCrossRefGoogle Scholar
  9. Friebe B, Hatchett JH, Sears RG, Gill BS (1990) Transfer of Hessian fly resistance from ‘Chaupon’ rye to hexaploid wheat via a 2BS/2RL wheat–rye chromosome translocation. Theor Appl Genet 79:385–389CrossRefGoogle Scholar
  10. Friebe B, Jiang J, Raupp WJ, McIntosh RA, Gill BS (1996) Characterization of wheat–alien translocations conferring resistance to diseases and pets: current status. Euphytica 91:59–87CrossRefGoogle Scholar
  11. Gupta PK, Rustgi S (2004) Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct Integr Genomics 4:139–162PubMedCrossRefGoogle Scholar
  12. Hackauf B, Wehling P (2005) Approaching the self-incompatibility locus Z in rye (Secale cereale L.) via comparative genetics. Theor Appl Genet 110:832–845PubMedCrossRefGoogle Scholar
  13. Hackauf B, Rudd S, van der Voort JR, Miedaner T, Wehling P (2009) Comparative mapping of DNA sequences in rye (Secale cereale L.) in relation to the rice genome. Theor Appl Genet 118:371–384PubMedCrossRefGoogle Scholar
  14. Hatchett JH, Sears RG, Cox TS (1993) Inheritance of resistance to Hessian fly in rye and in wheat–rye translocation lines. Crop Sci 33:730–734CrossRefGoogle Scholar
  15. Heun M, Friebe B (1990) Introgression of powdery mildew resistance from rye into wheat. Phytopathology 80:242–245CrossRefGoogle Scholar
  16. Hysing SC, Hsam SLK, Singh RP, Huerta-Espino J, Boyd LA, Koebner RMD, Cambron S, Johnson JW, Bland DE, Liljeroth E, Merker A (2007) Agronomic performance and multiple disease resistance in T2BS.2RL wheat–rye translocation lines. Crop Sci 47:254–260CrossRefGoogle Scholar
  17. Ishikawa G, Yonemaru J, Saito M, Nakamura T (2007) PCR-based landmark unique gene (PLUG) markers effectively assign homoeologous wheat genes to A, B and D genomes. BMC Genomics 8:135PubMedCrossRefGoogle Scholar
  18. Jang CS, Kim JY, Haam JW, Lee MS, Kim DS, Li YW, Seo YW (2003) Expressed sequence tags from a wheat–rye translocation line (2BS/2RL) infested by larvae of Hessian fly [Mayetiola destructor (Say)]. Plant Cell Rep 22:150–158PubMedCrossRefGoogle Scholar
  19. Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci 95:2005–2010PubMedCrossRefGoogle Scholar
  20. La Rota M, Sorrells ME (2004) Comparative DNA sequence analysis of mapped wheat ESTs reveals the complexity of genome relationships between rice and wheat. Funct Integr Genomics 4:34–46PubMedCrossRefGoogle Scholar
  21. Lee JH, Graybosch RA, Lee DJ (1994) Detection of rye chromosome 2R-using the polymerase chain reaction and sequence-specific DNA primers. Genome 37:19–22PubMedCrossRefGoogle Scholar
  22. Lee JH, Graybosch RA, Kaeppler SM, Sears RG (1996) A PCR assay for detection of 2RL.2BS wheat–rye chromosome translocation. Genome 39:605–608PubMedCrossRefGoogle Scholar
  23. Liu XM, Gill BS, Chen M-S (2005) Hessian fly resistance gene H13 is mapped to a distal cluster of resistance genes in chromosome 6DS of wheat. Theor Appl Genet 111:243–249PubMedCrossRefGoogle Scholar
  24. Mago R, Miah H, Lawrence GJ, Wellings CR, Spielmeyer W, Bariana HS, McIntosh RA, Pryor AJ, Ellis JG (2005) High-resolution mapping and mutation analysis separate the rust resistance genes Sr31, Lr26 and Yr9 on the short arm of rye chromosome 1. Theor Appl Genet 112:41–50PubMedCrossRefGoogle Scholar
  25. Monte JV, McIntyre CL, Gustafson JP (1993) Analysis of phylogenetic relationships in the Triticeae tribe using RFLPs. Theor Appl Genet 86:649–655CrossRefGoogle Scholar
  26. Naranjo T, Fernández-Rueda P (1991) Homoeology of rye chromosome arms to wheat. Theor Appl Genet 82:577–586CrossRefGoogle Scholar
  27. Nomura T, Ishihara A, Yanagita RC, Endo TR, Iwamura H (2005) Three genomes differentially contribute to the biosynthesis of benzoxazinones in hexaploid wheat. PNAS 102:16490–16495PubMedCrossRefGoogle Scholar
  28. Paterson AH, Bowers JE, Peterson DG, Estill JC, Chapman BA (2003) Structure and evolution of cereal genomes. Curr Opin Genet Dev 13:644–650PubMedCrossRefGoogle Scholar
  29. Saal B, Wricke G (1999) Development of simple sequence repeat markers in rye (Secale cereal L.). Genome 42:964–972PubMedCrossRefGoogle Scholar
  30. Sardesai N, Nemacheck JA, Subramanyam S, Williams CE (2005) Identification and mapping of H32, a new wheat gene conferring resistance to Hessian fly. Theor Appl Genet 111:1167–1173PubMedCrossRefGoogle Scholar
  31. Seo YW, Johnson JW, Jarret RL (1997) A molecular marker associated with the H21 Hessian fly resistance gene in wheat. Mol Breed 3:177–181CrossRefGoogle Scholar
  32. Seo YW, Jang CS, Johnson JW (2001) Development of AFLP and STS markers for identifying wheat–rye translocations possessing 2RL. Euphytica 121:279–287CrossRefGoogle Scholar
  33. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA, Kantety R, Munkvold JD, Miftahudin Mahmoud A, Ma X, Gustafson PJ, Qi LL, Echalier B, Gill BS, Matthews DE, Lazo GR, Chao S, Anderson OD, Edwards H, Linkiewicz AM, Dubcovsky J, Akhunov ED, Dvorak J, Zhang D, Nguyen HT, Peng J, Lapitan NL, Gonzalez-Hernandez JL, Anderson JA, Hossain K, Kalavacharla V, Kianian SF, Choi DW, Close TJ, Dilbirligi M, Gill KS, Steber C, Walker-Simmons MK, McGuire PE, Qualset CO (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818–1827PubMedGoogle Scholar
  34. Tsuchida M, Fukushima T, Nasuda S, Masoudi-Nejad A, Ishikawa G, Nakamura T, Endo TR (2008) Dissection of rye chromosome 1R in common wheat. Genes Genet Syst 83:43–53PubMedCrossRefGoogle Scholar
  35. Zhao HX, Liu XM, Chen M-S (2006) H22, a major resistance gene to the Hessian fly (Mayetiola destructor), is mapped to the distal region of wheat chromosome 1DS. Theor Appl Genet 113:1491–1496PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Tong Geon Lee
    • 1
  • Min Jeong Hong
    • 1
  • Jerry W. Johnson
    • 2
  • Daniel E. Bland
    • 2
  • Dae Yeon Kim
    • 1
  • Yong Weon Seo
    • 1
  1. 1.College of Life Sciences and BiotechnologyKorea UniversitySeoulRepublic of Korea
  2. 2.Department of Crop and Soil SciencesUniversity of GeorgiaGriffinUSA

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