Theoretical and Applied Genetics

, Volume 129, Issue 12, pp 2369–2378 | Cite as

Fine mapping of the stem rust resistance gene SrTA10187

  • Andrew T. Wiersma
  • Linda K. Brown
  • Elizabeth I. Brisco
  • Tiffany L. Liu
  • Kevin L. Childs
  • Jesse A. Poland
  • Sunish K. Sehgal
  • Eric L. Olson
Original Article


Key message

SrTA10187 was fine-mapped to a 1.1 cM interval, candidate genes were identified in the region of interest, and molecular markers were developed for marker-assisted selection and Sr gene pyramiding.


Stem rust (Puccinia graminis f. sp. tritici, Pgt) races belonging to the Ug99 (TTKSK) race group pose a serious threat to global wheat (Triticum aestivum L.) production. To improve Pgt host resistance, the Ug99-effective resistance gene SrTA10187 previously identified in Aegilops tauschii Coss. was introgressed into wheat, and mapped to the short arm of wheat chromosome 6D. In this study, high-resolution mapping of SrTA10187 was done using a population of 1,060 plants. Pgt resistance was screened using race QFCSC. PCR-based SNP and STS markers were developed from genotyping-by-sequencing tags and SNP sequences available in online databases. SrTA10187 segregated as expected in a 3:1 ratio of resistant to susceptible individuals in three out of six BC3F2 families, and was fine-mapped to a 1.1 cM region on wheat chromosome 6DS. Marker context sequence was aligned to the reference Ae. tauschii genome to identify the physical region encompassing SrTA10187. Due to the size of the corresponding region, candidate disease resistance genes could not be identified with confidence. Comparisons with the Ae. tauschii genetic map developed by Luo et al. (PNAS 110(19):7940–7945, 2013) enabled identification of a discrete genetic locus and a BAC minimum tiling path of the region spanning SrTA10187. Annotation of pooled BAC library sequences led to the identification of candidate genes in the region of interest—including a single NB-ARC-LRR gene. The shorter genetic interval and flanking KASP™ and STS markers developed in this study will facilitate marker-assisted selection, gene pyramiding, and positional cloning of SrTA10187.


Stem Rust Single Nucleotide Polymorphism Marker Stem Rust Resistance Stem Rust Resistance Gene Defense Response Gene 
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.



Aegilops tauschii sequence used to develop five KASP™ markers and identify candidate genes were obtained from the “Sequencing the Aegilops tauschii Genome” project website at This work was supported in part by the National Science Foundation (Grant no. IOS–1126998 to KLC). We thank Dr. Bob Bowden for critical review of this manuscript.

Compliance with ethical standards

This research complies with the current laws of the United States of America.

Conflict of interest

The authors of this study declare that there is no conflict of interest for this study.


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2 CrossRefPubMedGoogle Scholar
  2. Apweiler R, Bateman A, Martin MJ, O’Donovan C, Magrane M, Alam-Faruque Y et al (2014) Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res 42:D191–D198. doi: 10.1093/nar/gkt1140 CrossRefGoogle Scholar
  3. Campbell MS, Law MY, Holt C, Stein JC, Moghe GD, Hufnagel DE et al (2014) MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. Plant Physiol 164:513–524. doi: 10.1104/pp.113.230144 CrossRefPubMedGoogle Scholar
  4. Cox TS (1997) Deepening the wheat gene pool. J Crop Prod 1(1):1–25CrossRefGoogle Scholar
  5. Cox TS, Harrell LG, Chen P, Gill BS (1991) Reproductive behavior of hexaploid/diploid wheat hybrids. Plant Breed 107:105–118CrossRefGoogle Scholar
  6. Eddy SR (2011) Accelerated profile HMM searches. PLoS Comput Biol 7:16. doi: 10.1371/journal.pcbi.1002195 CrossRefGoogle Scholar
  7. Fetch T, Zegeye T, Park RF, Hodson D, Wanyera R (2016) Detection of wheat stem rust races TTHSK and PTKTK in the Ug99 race group in Kenya in 2014. Plant Dis 100(7):1495. doi: 10.1094/PDIS-11-15-1356-PDN CrossRefGoogle Scholar
  8. Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR et al (2014) Pfam: the protein families database. Nucleic Acids Res 42:D222–D230. doi: 10.1093/nar/gkt1223 CrossRefPubMedGoogle Scholar
  9. Gao L, Kielsmeier-Cook J, Bajgain P, Zhang X, Chao S, Rouse MN, Anderson JA (2015) Development of genotyping by sequencing (GBS)- and array-derived SNP markers for stem rust resistance gene Sr42. Mol Breeding 35:207. doi: 10.1007/s11032-015-0404-4 CrossRefGoogle Scholar
  10. Ghazvini H, Hiebert CW, Zegeye T, Liu S, Dilawari M, Tsilo T, Anderson JA, Rouse MN, Jin Y, Fetch T (2012) Inheritance of resistance to Ug99 stem rust in wheat cultivar Norin 40 and genetic mapping of Sr42. Theor Appl Genet 125:817–824. doi: 10.1007/s00122-012-1874-y CrossRefPubMedGoogle Scholar
  11. Gill BS, Raupp WJ (1987) Direct genetic transfers from Aegilops squarrosa L. to hexaploid wheat. Crop Sci 27:445–450CrossRefGoogle Scholar
  12. Hiebert CW, Fetch TG, Zegeye T, Thomas JB, Somers DJ, Humphreys DG, McCallum BD, Cloutier S, Singh D, Knott DR (2011) Genetics and mapping of seedling resistance to Ug99 stem rust in Canadian wheat cultivars ‘Peace’ and ‘AC Cadillac’. Theor Appl Genet 122:143–149. doi: 10.1007/s00122-010-1430-6 CrossRefPubMedGoogle Scholar
  13. Hiebert CW, McCartney C, Kassa M, You F, Pozniak C, Fobert P, Fetch T (2015) Genetic mapping of resistance to Puccinia graminis race TTKSK in Triumph 64. Borlaug Global Rust Initiative. Accessed 25 July 2016
  14. Jia J et al (2013) Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91–95. doi: 10.1038/nature12028 CrossRefPubMedGoogle Scholar
  15. Jin Y, Singh RP, Ward RW, Wanyera R, Kinyua M, Njau P, Fetch T, Pretorius ZA, Yahyaoui A (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(9):1096–1099. doi: 10.1094/PDIS-91-9-1096
  16. Jin Y, Szabo LJ, Pretorius ZA, Singh RP, Ward R, Fetch T (2008) Detection of virulence to resistance Gene Sr24 within race TTKS of Puccinia graminis f. sp. tritici. Plant Dis 92(6):923–926. doi: 10.1094/PDIS-92-6-0923
  17. Jin Y, Szabo LJ, Rouse MN, Fetch T, Pretorius ZA, Wanyera R, Njau P (2009) Detection of Virulence to Resistance Gene Sr36 Within the TTKS Lineage of Puccinia graminis f. sp. tritici. Plant Dis 93(4):367–370. doi: 10.1094/PDIS-93-4-0367 CrossRefGoogle Scholar
  18. Kassa MT, You FM, Fetch TG, Fobert P, Sharpe A, Pozniak CJ, Menzies JG, Jordan MC, Humphreys G, Zhu T, Luo M, McCartney CA, Hiebert CW (2016) Genetic mapping of SrCad and SNP marker development for marker-assisted selection of Ug99 stem rust resistance in wheat. Theor Appl Genet. doi: 10.1007/s00122-016-2709-z Google Scholar
  19. Kersey PJ, Lawson D, Birney E, Derwent PS, Haimel M, Herrero J, Keenan S, Kerhornou A, Koscielny G, Kahari A, Kinsella RJ, Kulesha E, Maheswari U, Megy K, Nuhn M, Proctor G, Staines D, Valentin F, Vilella AJ, Yates A (2009) Ensembl Geomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res 38(Database):D563–D569Google Scholar
  20. Korf I (2004) Gene finding in novel genomes. BMC Bioinform. doi: 10.1186/1471-2105-5-59 Google Scholar
  21. Liu W, Rouse M, Friebe B, Jin Y, Gill B, Pumphrey MO (2011) Discovery and molecular mapping of a new gene conferring resistance to stem rust, Sr53, derived from Aegilops geniculate and characterization of spontaneous translocation stocks with reduced alien chromatin. Chromosom Res 19:669–682. doi: 10.1007/s10577-011-9226-3 CrossRefGoogle Scholar
  22. Lopez-Vera EE, Nelson S, Singh RP, Basnet BR, Haley SD, Bhavani S, Huerta-Espino J, Xoconostle-Cazares BG, Ruiz-Medrano R, Rouse MN, Singh S (2014) Resistance to stem rust Ug99 in six bread wheat cultivars maps to chromosome 6DS. Theor Appl Genet 127:231–239. doi: 10.1007/s00122-013-2212-8 CrossRefPubMedGoogle Scholar
  23. 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 One 9(1):e1003215Google Scholar
  24. Luo M et al (2013) A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor. PNAS 110(19):7940–7945. doi: 10.1073/pnas.1219082110 CrossRefPubMedPubMedCentralGoogle Scholar
  25. Mago R, Zhang P, Bariana HS, Verlin DC, Bansal UK, Ellis JG, Dundas IS (2009) Development of wheat lines carrying stem rust resistance gene Sr39 with reduced Aegilops speltoides chromatin and simple PCR markers for marker-assisted selection. Theor Appl Genet 119:1441–1450. doi: 10.1007/s00122-009-1146-7 CrossRefPubMedGoogle Scholar
  26. McFadden ES, Sears ER (1944) The artificial synthesis of Triticum spelta. Rec Soc Genet Am 13:26–27Google Scholar
  27. McIntosh RA, Wellings CR, Park RF (1995) Wheat rusts: an atlas of resistance genes. CSIRO Publications, East Melbourne, pp 85–141CrossRefGoogle Scholar
  28. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K (2009) TriFLDB: a database of clustered full-length coding sequences from Triticeae with application to comparative grass genomics. Plant Physiol 150:1135–1146. doi: 10.1104/pp.109.138214 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Olson EL, Rouse MN, Pumphrey MO, Bowden RL, Gill BS, Poland JA (2013a) Simultaneous transfer, introgression, and genomic localization of genes for resistance to stem rust race TTKSK (Ug99) from Aegilops tauschii to wheat. Theor Appl Genet 126:1179–1188. doi: 10.1007/s00122-013-2045-5 CrossRefPubMedGoogle Scholar
  30. Olson EL, Rouse MN, Pumphrey MO, Bowden RL, Gill BS, Poland JA (2013b) Introgression of stem rust resistance genes SrTA10187 and SrTA10171 from Aegilops tauschii to wheat. Theor Appl Genet 126:2477–2484. doi: 10.1007/s00122-013-2148-z CrossRefPubMedGoogle Scholar
  31. Patpour M, Hovmoller MS, Justesen AF, Newcomb M, Olivera P, Jin Y, Szabo LJ, Hodson D, Shahin AA, Wanyera R, Habarurema I, Wobibi S (2016) Emergence of virulence to SrTmp in the Ug99 race group of wheat stem rust, Puccinia graminis f. sp. tritici, in Africa. Plant Dis 100(2):522. doi: 10.1094/PDIS-06-15-0668-PDN CrossRefGoogle Scholar
  32. Periyannan S, Moore J, Ayliffe M, Bansal U, Wang X, Huang L, Deal K, Luo M, Kong X, Bariana H, Mago R, McIntosh R, Dodds P, Dvorak J, Lagudah E (2013) The gene Sr33, an ortholog of barley Mla genes, encodes resistance to wheat stem rust race Ug99. Science 341:786–788. doi: 10.1126/science.1239028 CrossRefPubMedGoogle Scholar
  33. Periyannan S, Bansal U, Bariana H, Deal K, Luo M, Dvorak J, Lagudah E (2014) Identification of a robust molecular marker for the detection of the stem rust resistance gene Sr45 in common wheat. Theor Appl Genet 127:947–955. doi: 10.1007/s00122-014-2270-6 CrossRefPubMedGoogle Scholar
  34. Poland JA, Brown PJ, Sorrells ME, Jannink J (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7(2):e32253CrossRefPubMedPubMedCentralGoogle Scholar
  35. Pretorius Z, Singh R, Wagoire W, Payne T (2000) Detection of virulence to wheat stem rust resistance gene Sr31 in Puccinia graminis f. sp. tritici in Uganda. Plant Dis 84:203CrossRefGoogle Scholar
  36. Pujol V, Forrest KL, Zhang P, Rouse MN, Hayden MJ, Huang L, Tabe L, Lagudah E (2015) Identification of a stem rust resistance locus effective against Ug99 on wheat chromosome 7AL using a RAD-Seq approach. Theor Appl Genet 128:1397–1405. doi: 10.1007/s00122-015-2514-0 CrossRefPubMedGoogle Scholar
  37. Qi LL, Pumphrey MO, Friebe B, Zhang P, Qian C, Bowden RL, Rouse MN, Jin Y, Gill BS (2011) A novel Robertsonian translocation event leads to transfer of a stem rust resistance gene (Sr52) effective against race Ug99 from Dasypyrum villosum into bread wheat. Theor Appl Genet 123:159–167. doi: 10.1007/s00122-011-1574-z CrossRefPubMedGoogle Scholar
  38. Rouse MN, Olson EL, Gill BS, Pumphrey MO, Jin Y (2011) Stem rust resistance in Aegilops tauschii germplasm. Crop Sci 51:2074–2078CrossRefGoogle Scholar
  39. Sears ER, Loegering WQ, Rodenhiser HA (1957) Identification of chromosomes carrying genes for stem rust resistance in four varieties of wheat. Agron J 49:208–212CrossRefGoogle Scholar
  40. Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14. doi: 10.1007/s11032-013-9917-x CrossRefGoogle Scholar
  41. Singh RP, Hodson DP, Huerta-Espino Jin Y, Bhavani S, Njau P, Herrera-Foessel S, Singh PK, Singh S, Govindan V (2011) The emergence of Ug99 races of the stem rust fungus is a threat to world wheat production. Annu Rev Phytopathol 49:465–481. doi: 10.1146/annurev-phyto-072910-095423 CrossRefPubMedGoogle Scholar
  42. Singh RP, Hodson DP, Jin Y, Lagudah ES, Ayliffe MA, Bhavani S, Rouse MN, Pretorius ZA, Szabo LJ, Huerta-Espino J, Basnet BR, Lan C, Hovmoller MS (2015) Emergence and spread of new races of wheat stem rust fungus: continued threat to food security and prospects of genetic control. Phytopathology 105(7):872–884CrossRefPubMedGoogle Scholar
  43. Slater GSC, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinform 6:31. doi: 10.1186/1471-2105-6-31 CrossRefGoogle Scholar
  44. Smit A, Hubley R, Green P (2013) RepeatMasker Open-4.0Google Scholar
  45. Stakman EC, Stewart DM, Loegering WQ (1962) Identification of physiologic races of Puccinia graminis var. tritici. USDA-ARS Sci J Ser 4691:1–53Google Scholar
  46. Stanke M, Waack S (2003) Gene prediction with a hidden Markov model and a new intron submodel. Bioinformatics 19:II215–II225. doi:  10.1093/bioinformatics/btg1080
  47. Trick M, Adamski NM, Mugford SG, Jiang C, Febrer M, Uauy C (2012) Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol 12:14. doi: 10.1186/1471-2229-12-14 CrossRefPubMedPubMedCentralGoogle Scholar
  48. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78CrossRefPubMedGoogle Scholar
  49. Wicker T, Matthews DE, Keller B (2002) TREP: a database for Triticeae repetitive elements. Trends Plant Sci 7:561–562. doi: 10.1016/S1360-1385(02)02372-5 CrossRefGoogle Scholar
  50. Wilkinson PA, Winfield MO, Barker GL, Allen AM, Burridge A, Coghill JA, Edwards KJ (2012) CerealsDB 2.0: an integrated resource for plant breeders and scientists. BMC Bioinform 13:219. doi: 10.1186/1471-2105-13-219 CrossRefGoogle Scholar
  51. Yu L, Barbier H, Rouse MN, Singh S, Singh RP, Bhavani S, Huerta-Espino J, Sorrells ME (2014) A consensus map for Ug99 stem rust resistance loci in wheat. Theor Appl Genet 127:1561–1581. doi: 10.1007/s00122-014-2326-7 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Yu G, Klindworth DL, Friesen TL, Faris JD, Zhong S, Rasmussen JB, Xu SS (2015a) Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat. Theor Appl Genet 128:2367–2374. doi: 10.1007/s00122-015-2590-1 CrossRefPubMedGoogle Scholar
  53. Yu G, Zhang Q, Friesen TL, Rouse MN, Jin Y, Zhong S, Rasmussen JB, Lagudah ES, Xu SS (2015b) Identification and mapping of Sr46 from Aegilops tauschii accession CIae 25 conferring resistance to race TTKSK (Ug99) of wheat stem rust pathogen. Theor Appl Genet 128:431–443. doi: 10.1007/s00122-014-2442-4 CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department of Plant, Soil and Microbial SciencesMichigan State UniversityEast LansingUSA
  2. 2.Department of Plant BiologyMichigan State UniversityEast LansingUSA
  3. 3.Department of Plant Biology and Center for Genomics-Enabled Plant ScienceMichigan State UniversityEast LansingUSA
  4. 4.Department of Plant Pathology, Wheat Genetics Resource CenterKansas State UniversityManhattanUSA
  5. 5.Department of Plant ScienceSouth Dakota State UniversityBrookingsUSA

Personalised recommendations