Abstract
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.
Similar content being viewed by others
References
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
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
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
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
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
Chen Q, Conner R, Laroche A, Ahmad F (2001) Molecular cytogenetic evidence for a high level of chromosome pairing among different genomes in Triticum aestivum–Thinopyrum intermedium hybrids. Theor Appl Genet 102:847–852. doi:10.1007/s001220000496
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Rohlf J (1997) NTSYS-pc 2.10e: Numerical taxonomy and multivariate analysis system. Applied Biostatistics Inc., Setauket
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molec Biol Evol 4:406–425
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
Sneath PH, Sokal RR (1973) Numerical taxonomy. The principles and practice of numerical classification, W.H. Freeman and Company, San Francisco, USA
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):622–628
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
Wang RRC (2011) Agropyron and Psathyrostachys. In: Kole C (ed) Wild crop relatives: genomic and breeding resources, cereals. Springer, Berlin and Heidelberg, pp 77–108
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
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 20–24
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):25–33
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 58:63–70
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 24–25
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
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
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
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
Acknowledgments
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).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare no conflicts of interest.
Additional information
Handling editor: Daniel C. Thomas.
Jun Guo and Xiaocheng Yu have contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Information on Electronic Supplementary Material
Information on Electronic Supplementary Material
Online Resource 1. The genetic relationships among Thinopyrum species, Triticum species and H. vulgare constructed by the unweighted pair-group method with arithmetical averages (a) and by the neighbor jointing method described by Saitou and Nei (1987) (b) based on total markers including 17 SCoT markers and 10 CDDP markers. The scale indicates the coefficient.
Rights and permissions
About this article
Cite this article
Guo, J., Yu, X., Yin, H. et al. Phylogenetic relationships of Thinopyrum and Triticum species revealed by SCoT and CDDP markers. Plant Syst Evol 302, 1301–1309 (2016). https://doi.org/10.1007/s00606-016-1332-4
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00606-016-1332-4