Skip to main content
SpringerLink
Log in

Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers

  • Published:
Molecular Breeding Aims and scope Submit manuscript

Abstract

Bermudagrass (Cynodon spp.) is extensively cultivated for forage and turf in the the southern United States and in parts of Asia, Africa, southern Europe, Australia and South America. However, few simple sequence repeat (SSR) markers are available for bermudagrass genetics research. Accordingly, the objective of this study was to develop SSR markers in bermudagrass by transferring sorghum genomic SSR primers and by exploring bermudagrass expressed sequence tags (ESTs) from the National Center for Biotechnology Information (NCBI) database. The transferability of 354 tested sorghum SSRs was 57% to C. transvaalensis T577 (2n = 2x = 18), 27% to C. dactylon Tifton 10 (2n = 6x = 54) and 22% to Zebra (2n = 4x = 36). Among the transferred SSRs, 65 primer pairs generated reproducible SSR bands across the three genotypes. From 20,237 Cynodon ESTs at NCBI, 303 designed SSR primer pairs amplified target bands in at least one of C. dactylon var. aridus (2n = 2x = 18), C. transvaalensis T577, C. dactylon cv. Tifton 10, and C. dactylon var. dactylon Zebra. Of the effective EST SSRs, 230 primer pairs produced reproducible bands in all four genotypes. The study demonstrated that EST sequences and sorghum SSR primers are useful sources for the development of SSR markers for bermudagrass. The developed SSR markers will make a valuable contribution to the molecular identification of commercial cultivars, construction of genetic maps, and marker-assisted breeding in bermudagrass.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Assefa S, Taliaferro CM, Anderson MP, de los Reyes BG, Edwards RM (1999) Diversity among Cynodon accessions and taxa based on DNA amplification fingerprinting. Genome 42:465–474

    PubMed  CAS  Google Scholar 

  • Beard JB (1973) Turfgrass: science and culture. Prentice-Hall Inc, Englewood Cliffs, pp 9–15 and 658

  • Bethel CM, Sciara EB, Estill JC, Bowers JE, Hanna WW, Paterson AH (2006) A frame linkage map of bermudagrass (Cynodon dactylon × transvaalensis) based on single-dose restriction fragments. Theor Appl Genet 112:727–737

    Article  PubMed  CAS  Google Scholar 

  • Bhattramakki D, Dong J, Chhabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002

    PubMed  CAS  Google Scholar 

  • Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 93:190–198

    Article  CAS  Google Scholar 

  • Burton GW (1947) Breeding bermudagrass for the south-eastern United States. J Am Soc Agron 39:551–569

    Article  Google Scholar 

  • Caetano-Anolles G, Callahan LM, Williams PE, Weaver KR, Gresshoff PM (1995) DNA amplification fingerprinting analysis of bermudagrass: genetic relationships between species and interspecific crosses. Theor Appl Genet 91:228–235

    Article  CAS  Google Scholar 

  • Cai HW, Yuyama N, Tamaki H, Yoshizawa A (2003) Isolation and characterization of simple sequence repeat markers in the hexaploid forage grass timothy (Phleum pratense L.). Theor Appl Genet 107:1337–1349

    Article  PubMed  CAS  Google Scholar 

  • Cordeiro GM, Casu R, McIntyre SL, Manners JM, Henry RJ (2001) Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci 160:1115–1123

    Article  PubMed  CAS  Google Scholar 

  • da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A (2008) SSR locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics 2008:412696

  • Dayanandan S, Bawa KS, Kesseli RV (1997) Conservation of microsatellites among tropical trees (Leguminosae). Am J Bot 84:1658–1663

    Article  PubMed  CAS  Google Scholar 

  • Dean RE, Dahlberg JA, Hopkins MS, Mitchell SE, Kresovich S (1999) Genetic redundancy and diversity among ‘Orange’ accessions in the US National Sorghum Collection as assessed with simple sequence repeat (SSR) markers. Crop Sci 39:1215–1221

    Article  Google Scholar 

  • Hanna WW, Burton GW, Johnson AW (1990) Registration of ‘Tifton 10’ turf bermudagrass. Crop Sci 30:1355–1356

    Article  Google Scholar 

  • Harlan JR, de Wet JMJ, Rawal KM, Felder MR, Richardson WL (1970a) Cytogenetic studies in Cynodon L.C. Rich. (Gramineae). Crop Sci 10:288–291

    Article  Google Scholar 

  • Harlan JR, de Wet JMJ, Huffine WW, Deakin JR (1970b) A guide to the species of Cynodon (Gramineae). OSU Agricultural Experiment Station Bulletin B673

  • Hernandez P, Oorado G, Laurie D, Martin A, Snape J (2001) Microsatellites and RFLP probes from maize are efficient sources of molecular markers for the biomass energy crop Miscanthus. Theor Appl Genet 102:616–622

    Article  CAS  Google Scholar 

  • Johnston RA, Taliaferro CM (1975) Effects of temperature and light intensity on the expression of a variegated leaf pattern in bermudagrass. Crop Sci 15:445–447

    Article  Google Scholar 

  • Kantety RV, Rota ML, Mathews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510

    Article  PubMed  CAS  Google Scholar 

  • Kong L, Dong J, Hart GE (2000) Characteristics, linkage-map positions and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple sequence repeats (SSRs). Theor Appl Genet 101:438–448

    Article  CAS  Google Scholar 

  • Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3:175–182

    Article  PubMed  CAS  Google Scholar 

  • NCBI (2008) http://www.ncbi.nlm.nih.gov/. Accessed 08 Dec 2008

  • 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 H, Wang X, 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, Wang Y, Zhang L, 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 457:551–556

  • Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier M, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  CAS  Google Scholar 

  • Rohlf FJ (2002) NTSYS-pc. Numerical taxonomy and multivariate analysis system, Version 2.10. Exeter Software, New York

    Google Scholar 

  • Roodt R, Spies JJ, Burger TH (2002) Preliminary DNA fingerprinting of the turf grass Cynodon dactylon (Poaceae: Chlorideae). Bothalia 32:117–122

    Google Scholar 

  • Saghai Maroof MA, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proc Natl Acad Sci USA 91:5466–5470

    Article  PubMed  CAS  Google Scholar 

  • Saha MC, Mian MAR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791

    Article  PubMed  Google Scholar 

  • Saha MC, Cooper JD, Mian MAR, Chekhovskiy K, May GD (2006) Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 113:1449–1458

    Article  PubMed  CAS  Google Scholar 

  • Schloss SJ, Mitchell SE, White GM, Kukatla R, Bowers JE, Paterson AH, Kresovich S (2002) Characterization of RFLP probe sequences for genediscovery and SSR development in Sorghum bicolor (L.) Moench. Theor Appl Genet 105:912–920

    Article  PubMed  CAS  Google Scholar 

  • Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Long MJ, Liscum E, Cone K, Davis G, Coe EH (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481

    Article  PubMed  CAS  Google Scholar 

  • Taliaferro CM (2003) Bermudagrass (Cynodon (L.) Rich). In: Casler MD, Duncan RR (eds) Turfgrass biology, genetics and breeding. John Wiley and Sons Inc, New Jersey, pp 235–257

    Google Scholar 

  • Taramino G, Tarchini R, Ferrario S, Lee M, Pe ME (1997) Characterization and mapping of simple sequence repeats (SSRs) in Sorghum bicolor. Theor Appl Genet 95:66–72

    Article  CAS  Google Scholar 

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55

    Article  PubMed  CAS  Google Scholar 

  • Wang Z, Wu YQ, Martin DL, Gao HW, Samuels T, Tan CC (2010) Identification of vegetatively propagated turf bermudagrass cultivars using simple sequence repeat markers. Crop Sci 50:2103–2111

    Article  CAS  Google Scholar 

  • Wu YQ, Huang Y (2006) An SSR genetic map of Sorghum bicolor (L.) Moench and its comparison to a published genetic map. Genome 50:84–89

    Google Scholar 

  • Wu YQ, Taliaferro CM, Bai GH, Martin DL, Anderson JA, Anderson MP, Edwards RM (2007) Genetic analyses of Chinese Cynodon accessions by flow cytometry and AFLP markers. Crop Sci 46:917–926

    Article  Google Scholar 

  • Zhang LH, Ozias-Akins P, Kochert G, Kresovich S, Dean R, Hanna W (1999) Differentiation of bermudagrass (Cynodon spp.) genotypes by AFLP analysis. Theor Appl Genet 98:895–902

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge Mr. Gary Williams and Mrs. Sharon Williams for their help with field work. The work has been supported, in part, by the United States Golf Association and the Hatch Project OKL01361 (YQW).

The experiments comply with the current laws of the United States of America in which they were performed.

Author information

Authors and Affiliations

  1. Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA

    Chengcheng Tan, Yanqi Wu, Charles M. Taliaferro, Michael P. Anderson & Tim Samuels

  2. Department of Natural Resource Ecology and Management, Oklahoma State University, Stillwater, OK, 74078, USA

    Chuck Tauer

Authors
  1. Chengcheng Tan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yanqi Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Charles M. Taliaferro
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Michael P. Anderson
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chuck Tauer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Tim Samuels
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yanqi Wu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 299 kb)

Supplementary material 2 (PDF 1121 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tan, C., Wu, Y., Taliaferro, C.M. et al. Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers. Mol Breeding 29, 23–30 (2012). https://doi.org/10.1007/s11032-010-9521-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-010-9521-2

Keywords

Search

Navigation