Fine mapping of the wheat powdery mildew resistance gene Pm52 using comparative genomics analysis and the Chinese Spring reference genomic sequence

  • Peipei Wu
  • Jinghuang Hu
  • Jingwei Zou
  • Dan Qiu
  • Yunfeng Qu
  • Yahui Li
  • Teng Li
  • Hongjun Zhang
  • Li Yang
  • Hongwei Liu
  • Yang Zhou
  • Zhongjun Zhang
  • Jingting LiEmail author
  • Zhiyong LiuEmail author
  • Hongjie LiEmail author
Original Article


Key message

A high-resolution genetic linkage map was constructed using the comparative genomics analysis approach and the wheat reference genome, which placed wheat powdery mildew resistance gene Pm52 in a 0.21-cM genetic interval on chromosome arm 2BL.


The gene Pm52 confers resistance to powdery mildew and has been previously mapped on chromosome arm 2BL in winter wheat cultivar Liangxing 99. Because of its effectiveness against the disease, this study was initiated to finely map Pm52 using the comparative genomics analysis approach and the wheat reference genomic sequence. Based on the EST sequences that were located in the chromosome region flanking Pm52, four EST-SSR markers were developed, and another nine SSR markers were developed using the comparative genomics technology. These thirteen markers were integrated into a genetic linkage map using an F2:3 subpopulation of the Liangxing 99 × Zhongzuo 9504 cross. Pm52 was mapped within a 3.2-cM genetic interval in the subpopulation that corresponded to a ~40-Mb genomic interval on chromosome arm 2BL of the Chinese Spring reference genome. The Pm52-flanking markers Xicsl163 and Xicsl62 identified 344 recombinant individuals from 8820 F2 plants. Nine SSR markers generated from the Chinese Spring genomic interval were incorporated into a high-resolution genetic linkage map, which placed Pm52 in a 0.21-cM genetic interval corresponding to 5.6-Mb genomic region. The constructed high-resolution genetic linkage map will facilitate the map-based cloning of Pm52 and its marker-assisted selection.



The authors thank Dr. Robert L. Conner, Morden Research and Developmental Center, Agriculture and Agri-Food Canada, for his critical review of the manuscript. The financial support provided by the National Natural Science Foundation of China (31471491, 31871621, and 31501310), the National Key Research and Development Program of China (2017YFD0101000), the Scientific and Technological Research Project of Henan Province of China (172102110110), and the CAAS Innovation Team is gratefully appreciated.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2019_3291_MOESM1_ESM.pdf (660 kb)
Supplementary material 1 (PDF 661 kb)


  1. Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357:93–97Google Scholar
  2. Brenchley R, Spannagl M, Pfeifer M, Barker GLA, D’Amore R, Allen AM, McKenzie N, Kramer M, Kerhornou A, Bolser D, Kay S, Waite D, Trick M, Bancroft I, Gu Y, Huo NX, Luo M-C, Sehgal S, Gill B, Kianian S, Anderson O, Kersey P, Dvorak J, McCombie WR, Hall A, Mayer KFX, Edwards KJ, Bevan MW, Hall N (2012) Analysis of the bread wheat genome using whole-genome shotgun sequencing. Nature 491:705–710Google Scholar
  3. Chapman JA, Mascher M, Buluç A, Barry K, Georganas E, Session A, Strnadova V, Jenkins J, Sehgal S, Oliker L, Schmutz J, Yelick KA, Scholz U, Waugh R, Poland JA, Muehlbauer GJ, Stein N, Rokhsar DS (2015) A whole-genome shotgun approach for assembling and anchoring the hexaploid bread wheat genome. Genome Biol 16:26Google Scholar
  4. He HG, Zhu SY, Zhao RH, Jiang ZN, Ji YY, Ji J, Qiu D, Li HJ, Bie TD (2018) Pm21, encoding a typical CC-NBS-LRR protein, confers broad-spectrum resistance to wheat powdery mildew disease. Mol Plant 11:879–882Google Scholar
  5. Hu TZ, Li HJ, Liu ZJ, Xie CJ, Zhou YL, Duan XY, Jia X, You MS, Yang ZM, Sun QX, Liu ZY (2008) Identification and molecular mapping of the powdery mildew resistance gene in wheat cultivar Yumai 66. Acta Agron Sin 34:545–550Google Scholar
  6. Hurni S, Brunner S, Buchmann G, Herren G, Jordan T, Krukowski P, Wicker T, Yahiaoui N, Mago R, Keller B (2013) Rye Pm8 and wheat Pm3 are orthologous genes and show evolutionary conservation of resistance function against powdery mildew. Plant J 76:957–969Google Scholar
  7. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800Google Scholar
  8. International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788Google Scholar
  9. Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen SS, Feng LH, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 9:3735Google Scholar
  10. Kourelis J, van der Hoom RAL (2018) Defended to the nines: 25 years of resistance gene cloning identifies nine mechanisms for R protein function. Plant Cell 30:285–299Google Scholar
  11. Lazo GR, Chao S, Hummel DD, Edwards H, Crossman CC, Lui N, Matthews DE, Carollo VL, Hane DL, You FM, Butler GE, Miller RE, Close TJ, Peng JH, Lapitan NLV, Gustafson JP, Qi LL, Echalier B, Gill BS, Dilbirligi M, Randhawa HS, Gill KS, Greene RA, Sorrells ME, Akhunov ED, Dvořák J, Linkiewicz AM, Dubcovsky J, Hossain KG, Kalavacharla V, Kianian SF, Mahmoud AA, Miftahudin Ma X-F, Conley EJ, Anderson JA, Pathan MS, Nguyen HT, McGuire PE, Qualset CO, Anderson OD (2004) Development of an expressed sequence tag (EST) resource for wheat (Triticum aestivum L.). Genetics 168:585–593Google Scholar
  12. Lee H, Cha J, Choi C, Choi N, Ji HS, Park SR, Lee S, Hwang DJ (2018) Rice WRKY11 plays a role in pathogen defense and drought tolerance. Rice 11:5–16Google Scholar
  13. Li HJ, Wang XM, Song FJ, Wu CP, Wu XF, Zhang N, Zhou Y, Zhang XY (2011) Response to powdery mildew and detection of resistance genes in wheat cultivars from China. Acta Agron Sin 37:943–954Google Scholar
  14. Li DL, Qiu ZW, Shao YJ, Chen YT, Guan YT, Liu MZ, Li YM, Gao N, Wang LR, Lu XL, Zhao YX, Liu MY (2013) Heritable gene targeting in the mouse and rat using a CRISPR-Cas system. Nat Biol 31:681–683Google Scholar
  15. Lincoln SE, Daly MJ, Lander ES (1993) Constructing linkage maps with MAPMAKER/Exp version 3.0: a tutorial reference manual, 3rd edn. Whitehead Institute for Medical Research, CambridgeGoogle Scholar
  16. Ling HQ, Ma B, Shi XL, Liu H, Dong LL, Sun H, Cao YH, Gao Q, Zheng SS, Li Y, Yu Y, Du HL, Qi M, Li Y, Lu HW, Yu H, Cui Y, Wang N, Chen CL, Wu HL, Zhao Y, Zhang JC, Li YW, Zhou WJ, Zhang BR, Hu WJ, van Eijk MJT, Tang JF, Witsenboer HMA, Zhao SC, Li ZS, Zhang AM, Wang DW, Liang CZ (2018) Genome sequence of the progenitor of wheat A subgenome Triticum urartu. Nature 557:424–447Google Scholar
  17. Liu Z, Sun Q, Ni Z, Yang T (1999) Development of SCAR markers linked to the Pm21 gene conferring resistance to powdery mildew in common wheat. Plant Breed 118:215–219Google Scholar
  18. Liu WC, Liu ZD, Huang C, Lu MH, Liu J, Yang QP (2016) Statistics and analysis of crop yield losses caused by main disease and insect pests in recent 10 years. Plant Protect 42:1–9Google Scholar
  19. Luo PG, Luo HY, Chang ZJ, Zhang HY, Zhang M, Ren ZL (2009) Characterization and chromosomal location of Pm40 in common wheat: a new gene for resistance to powdery mildew derived from Elytrigia intermedium. Theor Appl Genet 118:1059–1064Google Scholar
  20. Luo M-C, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo NX, Zhu TT, Wang L, Wang Y, McGuire PE, Liu SY, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan LX, Wang ZZ, Xia ZQ, Xiao LC, Anderson OD, Ouyang SH, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai XT, Dawson MW, Müller HG, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu FH, Bevan MW, Leroy P, Li PC, You FM, Sun QX, Liu ZY, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551:498–502Google Scholar
  21. Ma PT, Xu HX, Xu YF, Song LP, Liang SS, Sheng Y, Han GH, Zhang XT, An DG (2018) Characterization of a powdery mildew resistance gene in wheat breeding line 10V-2 and its application in marker-assisted selection. Plant Dis 102:925–931Google Scholar
  22. McIntosh RA, Dubcovsky J, Rogers WJ, Morris C, Appels R, Xia XC (2014) Catalogue of gene symbols for wheat: 2013–2014 supplement. Accessed 10 Apr 2018
  23. Morgounov A, Tufan HA, Sharma R, Akin B, Bagci A, Braun H-J, Kaya Y, Keser M, Payne TS, Sonder K, McIntosh R (2012) Global incidence of wheat rusts and powdery mildew during 1969–2010 and durability of resistance of winter wheat variety Bezostaya 1. Eur J Plant Pathol 132:323–340Google Scholar
  24. Ouyang SH, Zhang D, Han J, Zhao X, Cui Y, Song W, Huo NX, Liang Y, Xie JZ, Wang ZZ, Wu QH, Chen YX, Lu P, Zhang DY, Wang LL, Sun H, Yang T, Keeble-Gagnere G, Appels R, Doležel J, Ling HQ, Luo MC, Gu YQ, Sun QX, Liu ZY (2014) Fine physical and genetic mapping of powdery mildew resistance gene MlIW172 originating from wild emmer (Triticum dicoccoides). PLoS ONE 9:e100160Google Scholar
  25. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang HB, Wang XY, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, WangY Zhang LF, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboob-ur-Rahman Ware D, Westhoff P, Mayer KFX, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556Google Scholar
  26. Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018Google Scholar
  27. Sánchez-Martín J, Steuernagel B, Ghosh S, Herren G, Hurni S, Adamski N, Vrána J, Kubaláková M, Krattinger SG, Wicker T, Doležel J, Keller B, Wulff BBH (2016) Rapid gene isolation in barley and wheat by mutant chromosome sequencing. Genome Biol 17:221–227Google Scholar
  28. Summers RW, Brown JKM (2013) Constraints on breeding for disease resistance in commercially competitive wheat cultivars. Plant Pathol 62:115–121Google Scholar
  29. Tagliaro F, Manetto G, Crivellent F, Smith FP (1998) A brief introduction to capillary electrophoresis. Forensic Sci Int 92:75–88Google Scholar
  30. Tang XL, Cao XR, Luo Y, Ma ZH, Xu XM, Jiang YY, Fan JR, Zhou YL (2017) Effects of climate change on epidemics of powdery mildew in winter wheat in China. Plant Dis 101:1753–1760Google Scholar
  31. The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–717Google Scholar
  32. The International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768Google Scholar
  33. The International Wheat Genome Sequencing Consortium (IWGSC) (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361:eaar7191Google Scholar
  34. Wang ZZ, Li HW, Zhang DY, Guo L, Chen JJ, Chen YX, Wu QH, Xie JZ, Zhang Y, Sun QX, Dvorak J, Luo MC, Liu ZY (2015) Genetic and physical mapping of powdery mildew resistance gene MlHLT in Chinese wheat landrace Hulutou. Theor Appl Genet 128:365–373Google Scholar
  35. Wu PP, Xie JZ, Hu JH, Qiu D, Liu ZY, Li JT, Li MM, Zhang HJ, Yang L, Liu HW, Zhou Y, Zhang ZJ, Li HJ (2018a) Development of molecular markers linked to powdery mildew resistance gene Pm4b by combining SNP discovery from transcriptome sequencing data with bulked segregant analysis (BSR-seq) in wheat. Front Plant Sci 9:95Google Scholar
  36. Wu JH, Zeng QD, Wang QL, Liu SJ, Yu SZ, Mu JM, Huang S, Sela H, Distelfeld A, Huang LL, Han DJ, Kang ZS (2018b) SNP-based pool genotyping and haplotype analysis accelerate fine-mapping of the wheat genomic region containing stripe rust resistance gene Yr26. Theor Appl Genet 131:1481–1496Google Scholar
  37. Xie JZ, Wang LL, Wang Y, Zhang HZ, Zhou SH, Wu QH, Chen YX, Wang ZZ, Wang GX, Zhang DY, Zhang Y, Hu TZ, Liu ZY (2017) Fine mapping of powdery mildew resistance gene PmTm4 in wheat using comparative genomics. J Integr Agric 16:540–550Google Scholar
  38. Xing LP, Hu P, Liu JQ, Witek K, Zhou S, Xu JF, Zhou WH, Gao L, Huang ZP, Zhang RQ, Wang XE, Chen PD, Wang HY, Jones JDG, Karafiátová M, Vrána J, Bartoš J, Doležel J, Tian YC, Wu YF, Cao AZ (2018) Pm21 from Haynaldia villosa encodes a CC-NBS-LRR protein conferring powdery mildew resistance in wheat. Mol Plant 11:874–878Google Scholar
  39. Xu WG, Li CX, Hu L, Zhang L, Zhang JZ, Dong HB, Wang GS (2010) Molecular mapping of powdery mildew resistance gene PmHNK in winter wheat (Triticum aestivum L.) cultivar Zhoumai 22. Mol Breed 26:31–38Google Scholar
  40. Xu WG, Li CX, Hu L, Wang HW, Dong HB, Zhang JZ, Zan XC (2011) Identification and molecular mapping PmHNK54: a novel powdery mildew resistance gene in common wheat. Plant Breed 130:603–607Google Scholar
  41. Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528–538Google Scholar
  42. Yeh YH, Chang YH, Huang PY, Huang JB, Zimmerli L (2015) Enhanced Arabidopsis pattern-triggered immunity by overexpression of cysteine-rich receptor-like kinases. Front Plant Sci 6:322–333Google Scholar
  43. You FM, Huo NX, Gu YQ, Luo MC, Ma YQ, Hane D, Lazo GR, Dvorak J, Anderson OD (2008) BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253–265Google Scholar
  44. Zhao ZH, Sun HG, Song W, Lu M, Huang J, Wu LF, Wang XM, Li HJ (2013) Genetic analysis and detection of the gene MlLX99 on chromosome 2BL conferring resistance to powdery mildew in the wheat cultivar Liangxing 99. Theor Appl Genet 126:3081–3089Google Scholar
  45. Zimin AV, Puiu D, Hall R, Kingan S, Clavijo BJ, Salzberg SL (2017) The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum. GigaScience 6:1–7Google Scholar
  46. Zou JW, Qiu D, Sun YL, Zheng CX, Li JT, Wu PP, Wu XF, Wang XM, Zhou Y, Li HJ (2017) Pm52: effectiveness of the gene conferring resistance to powdery mildew in wheat cultivar Liangxing 99. Acta Agron Sin 43:332–342Google Scholar
  47. Zou SH, Wang H, Li YW, Kong ZS, Tang DZ (2018) The NB-LRR gene Pm60 confers powdery mildew resistance in wheat. New Phytol 218:298–309Google Scholar
  48. Zuo WL, Chao Q, Zhang N, Ye JR, Tan GQ, Li BL, Xing YX, Zhang BQ, Liu HJ, Fengler KA, Zhao J, Zhao XR, Chen YS, Lai JS, Yan JB, Xu ML (2014) A maize wall-associated kinase confers quantitative resistance to head smut. Nat Genet 47:151–159Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
  2. 2.College of Chemistry and Environment EngineeringPingdingshan UniversityPingdingshanChina
  3. 3.Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
  4. 4.Department of Plant PathologyChina Agricultural UniversityBeijingChina
  5. 5.College of Life Science and TechnologyHarbin Normal UniversityHarbinChina

Personalised recommendations