Plant Systematics and Evolution

, Volume 302, Issue 9, pp 1301–1309 | Cite as

Phylogenetic relationships of Thinopyrum and Triticum species revealed by SCoT and CDDP markers

  • Jun Guo
  • Xiaocheng Yu
  • Huayan Yin
  • Guojuan Liu
  • Anfei Li
  • Hongwei Wang
  • Lingrang KongEmail author
Original Article


To evaluate the phylogenetic relationships among Thinopyrum species and Triticum species, 7 accessions of Thinopyrum species (2 Th. bessarabicum, 1 Th. elongatum, 2 Th. intermedium and 2. Th. ponticum), 11 accessions of Triticum species (2 Aeglips tauschii, 1 T. monococcum, 1 T. turgidum, 2 T. timopheevii and 5 T. aestivum) together with Hordeum vulgare cv. Golden were analysed using 17 SCoT and 10 CDDP markers. The mean number of observed alleles was 8.5 and 6.6 among the species for SCoT and CDDP markers, respectively. Based on the genetic data produced by the SCoT and CDDP markers, cluster analysis among Thinopyrum species, Triticum species and Hordeum was performed to generate dendrograms. The genetic relationships among Thinopyrum species, Triticum species and H. vulgare revealed by the SCoT markers were in agreement with the results of the CDDP markers. On both dendrograms, these species formed three clusters. The results indicated that Thinopyrum species and Triticum species were the most closely related, whereas H. vulgare was relatively distant from both genera. In addition, seven markers, i.e. SCoT 9, SCoT 31, SCoT 34, WRKY-R1, WRKY-R2, MADS-1 and MADS-4 were developed for monitoring introgression of Thinopyrum chromosomes or chromosome segments into Triticum species.


Marker-assisted introgression Phylogenetic relationships SCoT and CDDP markers Thinopyrum species Triticum species 



We thank Dr. Honggang Wang, Shandong Agricultural University (SDAU), Taian 271018, China, and Dr. Herbert Ohm, Purdue University, West Lafayette, IN 47907-1150, USA for providing seeds of Thinopyrum species. We also thank Dr. Lihui Li, Insititute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China, and Dr. H. Bockelman, NPGS, ARS, USA for providing seeds of Triticum species. We also acknowledge financial supports by the National High-Tech R&D Program of China (2011AA100102 and 2012AA101105), the NSF of China (Grant No. 31171553 and 31471488), Shandong Seed Engineering Project (2015–2019) and the International Collaboration Program (948 Project, 2013-S19).

Compliance with ethical standards

Conflict of interest

The authors declare no conflicts of interest.

Supplementary material

606_2016_1332_MOESM1_ESM.doc (652 kb)
Supplementary material 1 (DOC 652 kb)


  1. Anderson J, Churchill G, Autrique J, Tanksley S, Sorrells M (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186. doi: 10.1139/g93-024 CrossRefPubMedGoogle Scholar
  2. Autrique E, Tanksley SD, Sorrells ME, Singh RP (1995) Molecular markers for four leaf rust resistance genes introgressed into wheat from wild relatives. Genome 38:75–83. doi: 10.1139/g95-009 CrossRefPubMedGoogle Scholar
  3. Cao S, Li Z, Gong C, Xu H, Yang R, Hao S, Wang X, Wang D, Zhang X (2014) Identification and characterization of high-molecular-weight glutenin subunits from Agropyron intermedium. PLoS ONE 9(2):e87477. doi: 10.1371/journal.pone.0087477 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Charpentier X, Polard P, Claverys J-P (2012) Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS? Curr Opin Microbiol 15:570–576. doi: 10.1016/j.mib.2012.08.001 CrossRefPubMedGoogle Scholar
  5. Chen Q, Conner R, Laroche A, Thomas J (1998) Genome analysis of Thinopyrum intermedium and Thinopyrum ponticum using genomic in situ hybridization. Genome 41:580–586. doi: 10.1139/g98-055 CrossRefPubMedGoogle Scholar
  6. Chen Q, Conner R, Laroche A, Ahmad F (2001) Molecular cytogenetic evidence for a high level of chromosome pairing among different genomes in Triticum aestivumThinopyrum intermedium hybrids. Theor Appl Genet 102:847–852. doi: 10.1007/s001220000496 CrossRefGoogle Scholar
  7. Collard BC, Mackill DJ (2009a) Start codon targeted (SCoT) polymorphism: a simple, novel DNA marker technique for generating gene-targeted markers in plants. Pl Molec Biol Rep 27:86–93. doi: 10.1007/s11105-008-0060-5 CrossRefGoogle Scholar
  8. Collard BC, Mackill DJ (2009b) Conserved DNA-derived polymorphism (CDDP): a simple and novel method for generating DNA markers in plants. Pl Molec Biol Rep 27:558–562. doi: 10.1007/s11105-009-0118-z CrossRefGoogle Scholar
  9. Dewey DR (1984) The genomic system of classification as a guide to intergeneric hybridization with the perennial Triticeae. Springer, Berlin, pp 209–279. doi: 10.1007/978-1-4613-2429-4_9 Google Scholar
  10. Dubcovsky J, Dvorak J (2007) Genome plasticity a key factor in the success of polyploid wheat under domestication. Science 316:1862–1866. doi: 10.1126/science.1143986 CrossRefPubMedPubMedCentralGoogle Scholar
  11. Dundas I, Zhang P, Verlin D, Graner A, Shepherd K (2015) Chromosome engineering and physical mapping of the translocation in wheat carrying the rust resistance gene. Crop Sci 55:648–657. doi: 10.2135/cropsci2014.08.0590 CrossRefGoogle Scholar
  12. Feller A, Machemer K, Braun EL, Grotewold E (2011) Evolutionary and comparative analysis of MYB and bHLH plant transcription factors. Pl J 66:94–116. doi: 10.1111/j.1365-313X.2010.04459.x CrossRefGoogle Scholar
  13. Friebe B, Jiang J, Raupp W, McIntosh R, Gill B (1996) Characterization of wheat-alien translocations conferring resistance to diseases and pests: current status. Euphytica 91:59–87. doi: 10.1007/BF00035277 CrossRefGoogle Scholar
  14. Gao YH, Zhu YQ, Tong ZK, Xu ZY, Jiang XF, Huang CH (2014) Analysis of genetic diversity and relationships among genus Lycoris based on start codon targeted (SCoT) marker. Biochem Syst Ecol 57:221–226. doi: 10.1016/j.bse.2014.08.002 CrossRefGoogle Scholar
  15. Guo DL, Zhang JY, Liu CH (2012) Genetic diversity in some grape varieties revealed by SCoT analyses. Molec Biol Rep 39:5307–5313. doi: 10.1007/s11033-011-1329-6 CrossRefGoogle Scholar
  16. Guo J, He F, Cai JJ, Wang HW, Li AF, Wang HG, Kong LR (2015a) Molecular and cytological comparisons of chromosomes 7el1, 7el2, 7Ee, and 7Ei Derived from Thinopyrum. Cytogenet Genome Res 145:68–74. doi: 10.1159/000381838 CrossRefPubMedGoogle Scholar
  17. Guo J, Zhang X, Hou Y, Cai J, Shen X, Zhou T, Xu H, Ohm HW, Wang H, Li A, Han F, Wang H, Kong L (2015b) High-density mapping of the major FHB resistance gene Fhb7 derived from Thinopyrum ponticum and its pyramiding with Fhb1 by marker-assisted selection. Theor Appl Genet 128:2301–2316. doi: 10.1007/s00122-015-2586-x CrossRefPubMedGoogle Scholar
  18. Hamidi H, Talebi R, Keshavarzi F (2014) Comparative efficiency of functional gene-based markers, start codon targeted polymorphism (SCoT) and conserved DNA-derived polymorphism (CDDP) with ISSR markers for diagnostic fingerprinting in wheat (Triticum aestivum L.). Cereal Res Commun 42:558–567. doi: 10.1556/CRC.2014.0010 CrossRefGoogle Scholar
  19. He R, Chang Z, Yang Z, Yuan Z, Zhan H, Zhang X, Liu J (2009) Inheritance and mapping of powdery mildew resistance gene Pm43 introgressed from Thinopyrum intermedium into wheat. Theor Appl Genet 118:1173–1180. doi: 10.1007/s00122-009-0971-z CrossRefPubMedGoogle Scholar
  20. Huang S, Sirikhachornkit A, Su X, Faris J, Gill B, Haselkorn R, Gornicki P (2002) Genes encoding plastid acetyl-CoA carboxylase and 3-phosphoglycerate kinase of the Triticum/Aegilops complex and the evolutionary history of polyploid wheat. Proc Natl Acad Sci USA 99:8133–8138. doi: 10.1073/pnas.072223799 CrossRefPubMedPubMedCentralGoogle Scholar
  21. Ishihama N, Yoshioka H (2012) Post-translational regulation of WRKY transcription factors in plant immunity. Curr Opin Pl Biol 15:431–437. doi: 10.1016/j.pbi.2012.02.003 CrossRefGoogle Scholar
  22. Järve K, Peusha H, Tsymbalova J, Tamm S, Devos K, Enno T (2000) Chromosomal location of a Triticum timopheevii-derived powdery mildew resistance gene transferred to common wheat. Genome 43:377–381. doi: 10.1139/g99-141 CrossRefPubMedGoogle Scholar
  23. Jauhar P (1992) Synthesis and cytological characterization of trigeneric hybrids involving durum wheat, Thinopyrum bassarabicum, and Lophopyrum elongatum. Theor Appl Genet 84:511–519. doi: 10.1007/BF00224146 PubMedGoogle Scholar
  24. Li H, Wang X (2009) Th. ponticum and Th. intermedium: the promising source of resistance to fungal and viral diseases of wheat. J Genet Genomics 36:557–565. doi: 10.1016/S1673-8527(08)60147-2 CrossRefPubMedGoogle Scholar
  25. Liu Z, Li D, Zhang X (2007) Genetic relationships among five basic genomes St, E, A, B and D in Triticeae revealed by genomic southern and in situ hybridization. J Integr Pl Biol 49:1080–1086. doi: 10.1111/j.1672-9072.2007.00462.x CrossRefGoogle Scholar
  26. Lu B, Ellstrand N (2014) World food security and the tribe Triticeae (Poaceae): genetic resources of cultivated, wild, and weedy taxa for crop improvement. J Syst Evol 52:661–666. doi: 10.1111/jse.12131 CrossRefGoogle Scholar
  27. Luo C, He X-H, Chen H, Hu Y, Ou S-J (2012) Genetic relationship and diversity of Mangifera indica L.: revealed through SCoT analysis. Genet Resour Crop Evol 59:1505–1515. doi: 10.1007/s10722-011-9779-1 CrossRefGoogle Scholar
  28. Mason-Gamer RJ, Kellogg EA (1996) Testing for phylogenetic conflict among molecular data sets in the tribe Triticeae (Gramineae). Syst Biol 45:524–545. doi: 10.1093/sysbio/45.4.524 CrossRefGoogle Scholar
  29. Molnár-Láng M, Linc G, Szakács É (2014) Wheat–barley hybridization: the last 40 years. Euphytica 195:315–329. doi: 10.1007/s10681-013-1009-9 CrossRefGoogle Scholar
  30. Monte J, McIntyre C, Gustafson J (1993) Analysis of phylogenetic relationships in the Triticeae tribe using RFLPs. Theor Appl Genet 86:649–655. doi: 10.1007/BF00838722 CrossRefPubMedGoogle Scholar
  31. Oliver R, Xu S, Stack R, Friesen T, Jin Y, Cai X (2006) Molecular cytogenetic characterization of four partial wheat-Th. ponticum amphiploids and their reactions to Fusarium head blight, tan spot, and Stagonospora nodorum blotch. Theor Appl Genet 112:1473–1479. doi: 10.1007/s00122-006-0250-1 CrossRefPubMedGoogle Scholar
  32. Peleg Z, Fahima T, Korol A, Abbo S, Saranga Y (2011) Genetic analysis of wheat domestication and evolution under domestication. J Exp Bot 62:5051–5061. doi: 10.1093/jxb/err206 CrossRefPubMedPubMedCentralGoogle Scholar
  33. Poczai P, Varga I, Bell N, Hyvönen J (2011) Genetic diversity assessment of bittersweet (Solanum dulcamara, Solanaceae) germplasm using conserved DNA-derived polymorphism and intron-targeting markers. Ann Appl Biol 159:141–153. doi: 10.1111/j.1744-7348.2011.00482.x CrossRefGoogle Scholar
  34. Radakovits R, Jinkerson RE, Fuerstenberg SI, Tae H, Settlage RE, Boore JL, Posewitz MC (2012) Draft genome sequence and genetic transformation of the oleaginous alga Nannochloropsis gaditana. Nat Commun 3:686. doi: 10.1038/ncomms1688 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Rohlf J (1997) NTSYS-pc 2.10e: Numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc., SetauketGoogle Scholar
  36. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molec Biol Evol 4:406–425PubMedGoogle Scholar
  37. Smaczniak C, Immink RG, Angenent GC, Kaufmann K (2012) Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 139:3081–3098. doi: 10.1242/dev.074674 CrossRefPubMedGoogle Scholar
  38. Sneath PH, Sokal RR (1973) Numerical taxonomy. The principles and practice of numerical classification, W.H. Freeman and Company, San Francisco, USAGoogle Scholar
  39. Sun GL, Fahima T, Korol AB, Turpeinen T, Grama A, Ronin YI, Nevo E (1997) Identification of molecular markers linked to the Yr15 stripe rust resistance gene of wheat originated in wild emmer wheat, Triticum dicoccoides. Theor Appl Genet 95(4):622–628CrossRefGoogle Scholar
  40. Tripathi P, Rabara RC, Rushton PJ (2014) A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. Planta 239:255–266. doi: 10.1007/s00425-013-1985-y CrossRefPubMedGoogle Scholar
  41. Wang RRC (2011) Agropyron and Psathyrostachys. In: Kole C (ed) Wild crop relatives: genomic and breeding resources, cereals. Springer, Berlin and Heidelberg, pp 77–108CrossRefGoogle Scholar
  42. Wang RRC, Lu B (2014) Biosystematics and evolutionary relationships of perennial Triticeae species revealed by genomic analyses. J Syst Evol 52:697–705. doi: 10.1111/jse.12084 CrossRefGoogle Scholar
  43. Wang RRC, Von Bothmer R, Dvorak J, Fedak G, Linde-Laursen I, Muramatsu M (1994) Genome symbols in the Triticeae (Poaceae). In: Proceedings of the 2nd international Triticeae symposium. Logan, pp 20–24Google Scholar
  44. Wang RRC, Li XM, Hu ZM, Zhang JY, Larson SR, Zhang XY, Grieve CM, Shannon MC (2003) Development of salinity-tolerant wheat recombinant lines from a wheat disomic addition line carrying a Thinopyrum junceum chromosome. Int J Pl Sci 164(1):25–33CrossRefGoogle Scholar
  45. Wang RRC, Larson SR, Jensen KB, Bushman BS, DeHaan LR, Wang SW, Yan XB (2015) Genome evolution in intermediate wheatgrass revealed by newly developed EST-SSR markers of its three progenitor diploid species. Genome 58:63–70CrossRefPubMedGoogle Scholar
  46. Xu S, Niu Z, Klindworth D, Zhang Q, Chao S, Friesen T, Jin Y, Rouse M, Faris J, Cai X (2013) Chromosome engineering for alien gene introgression in wheat: progress and prospective. Meeting Abstract, pp 24–25Google Scholar
  47. Yang Z, Li G, Chang Z, Zhou J, Ren Z (2006) Characterization of a partial amphiploid between Triticum aestivum cv. Chinese Spring and Thinopyrum intermedium ssp. trichophorum. Euphytica 149:11–17. doi: 10.1007/s10681-005-9010-6 CrossRefGoogle Scholar
  48. Yaniv E, Raats D, Ronin Y, Korol AB, Grama A, Bariana H, Dubcovsky J, Schulman AH, Fahima T (2015) Evaluation of marker-assisted selection for the stripe rust resistance gene Yr15, introgressed from wild emmer wheat. Molec Breeding 35:1–12. doi: 10.1007/s11032-015-0238-0 CrossRefGoogle Scholar
  49. Zhang X, Dong Y, Wang RRC (1996) Characterization of genomes and chromosomes in partial amphiploids of the hybrid Triticum aestivum × Th. ponticum by in situ hybridization, isozyme analysis, and RAPD. Genome 39:1062–1071. doi: 10.1139/g96-133 CrossRefPubMedGoogle Scholar
  50. Zhang X, DeHaan LR, Higgins L, Markowski TW, Wyse DL, Anderson JA (2014) New insights into high-molecular-weight glutenin subunits and sub-genomes of the perennial crop Thinopyrum intermedium (Triticeae). J Cereal Sci 59:203–210. doi: 10.1016/j.jcs.2014.01.008 CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2016

Authors and Affiliations

  • Jun Guo
    • 1
    • 2
    • 3
  • Xiaocheng Yu
    • 1
    • 2
  • Huayan Yin
    • 1
    • 2
  • Guojuan Liu
    • 1
    • 2
  • Anfei Li
    • 1
    • 2
  • Hongwei Wang
    • 1
    • 2
  • Lingrang Kong
    • 1
    • 2
    Email author
  1. 1.State Key Laboratory of Crop BiologyShandong Agricultural UniversityTaianChina
  2. 2.Shandong Key Laboratory of Crop Biology, College of AgronomyShandong Agricultural UniversityTaianChina
  3. 3.Crop Research InstituteShandong Academy of Agricultural Sciences (SAAS)JinanChina

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