Fine mapping of the stem rust resistance gene SrTA10187
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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.
KeywordsStem Rust Single Nucleotide Polymorphism Marker Stem Rust Resistance Stem Rust Resistance Gene Defense Response Gene
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 http://aegilops.wheat.ucdavis.edu/ATGSP/. 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.
- 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
- 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. http://www.globalrust.org/events/bgri-workshop-abstracts. Accessed 25 July 2016
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- McFadden ES, Sears ER (1944) The artificial synthesis of Triticum spelta. Rec Soc Genet Am 13:26–27Google Scholar
- 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
- 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
- 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
- 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
- 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
- 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
- Smit A, Hubley R, Green P (2013) RepeatMasker Open-4.0Google Scholar
- 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
- 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
- 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
- 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