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Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs

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Abstract

Buffalograss [Buchloe dactyloides (Nutt.) Englem.] is the only native grass that is being used extensively as a turfgrass in the Great Plains region. Its low-growth habit, drought resistance, and low-maintenance requirement make it attractive as a turfgrass species. Our objective was to obtain an overview on the genetic relatedness among and within seeded and vegetative biotype buffalograsses using inter-simple sequence repeats (ISSRs), random amplified polymorphic DNA (RAPDs), sequence-related amplified polymorphisms (SRAPs), and simple sequence repeats (SSRs) markers that were derived from related species (maize, pearl millet, sorghum, and sugarcane). Twenty individuals per cultivar were genotyped using 30 markers from each marker system. All buffalograss cultivars were uniquely fingerprinted by all four marker systems. Mean genetic similarities were estimated at 0.52, 0.51, 0.62, and 0.57 using SSRs, ISSRs, SRAPs, and RAPDs, respectively. Two main clusters separating the seeded-biotype from the vegetative-biotype cultivars were produced using UPGMA analysis. Further subgroupings were unequivocal. The Mantel test resulted in a very good fit (SRAP=0.92, ISSR=0.90) to good fit (RAPD=0.86, SSR=0.88) of cophenetic values. Comparing the four marker systems to each other, RAPD and SRAP similarity indices were highly correlated (r=0.73), while Spearman’s rank correlation coefficient between RAPDs and SSRs was r=0.24 and between ISSRs and SSRs was r=0.66. A genotype-assignment analytical approach might be useful for cultivar identification and property rights protection. Polymorphic SRAPs were abundant and demonstrated genetic diversity among closely related cultivars.

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References

  • Ajmone-Marsan P, Castiglino P, Fusari F, Kuipper M, Motto M (1998) Genetic diversity and its relationship to hybrid performance in maize as revealed by RFLP and AFLP markers. Theor Appl Genet 96:219–227

    Article  Google Scholar 

  • Allouis S, Qi X, Lindup S, Gale MD, Devos K M (2001) Construction of BAC library of pearl millet, Pennisetum glaucum. Theor Appl Genet 102:1200–1205

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Blair MW, Panaud O, McCouch SR (1999) Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet 98:780–792

    Article  CAS  Google Scholar 

  • Budak H, Pedraza F, Baenziger PS, Cregan PB, Dweikat I (2003) Development and utilization of SSR to estimate genetic diversity in a collection of pearl millet germplasm. Crop Sci 43:2284–2290

    CAS  Google Scholar 

  • Budak H, Shearman RC, Parmaksiz I, Gaussoin RE, Riordan TP, Dweikat I (2004) Molecular characterization of buffalograss germplasm using sequence related amplified polymorphism markers. Theor Appl Genet 108:328–334

    Article  CAS  PubMed  Google Scholar 

  • Corderio GM, Taylor GO, Henry RJ (2000) Characterization of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploidy species. Plant Sci 155:161–168

    CAS  PubMed  Google Scholar 

  • Degani C, Rowland LJ, Saunders JA, Hokanson SC, Ogden E, Golan-Goldrish A, Galetta GL (2001) A comparison of genetic relationship measures in strawberry (Frageria ananassa Duch.) based on AFLPs, RAPDs and pedigree data. Euphytica 117:1–12

    Article  CAS  Google Scholar 

  • Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26:297–302

    Google Scholar 

  • Excoffier L, Smouse P, Qattro J (1992) Analysis of molecular variance inferred for metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479–491

    CAS  PubMed  Google Scholar 

  • Eguirta LE, Perez-Naser N, Pinero D (1993) Genetic structure, outcrossing rate and heterosis in Astrocaryum mexicanum (tropical palm): implications for evolution and conservation. Heredity 47:75–87

    Google Scholar 

  • Franco J, Crossa J, Villasenor J, Taba S, Eberhart SA (1997) Classifying Mexican maize accessions using hierarchical and density search methods. Crop Sci 37:972–980

    Google Scholar 

  • Gale MD, Devos KM (1998). Plant comparative genetics after 10 years. Science 282:656–659

    Article  CAS  PubMed  Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Huff DR, Peakall R, Smouse PE (1993) RAPD variation within and among natural populations of outcrossing buffalograss [Buchloe dactyloides (Nutt.) Engelm.]. Theor Appl Genet 86:927–934

    CAS  Google Scholar 

  • Johnson PG, Kenworthy KE, Auld DL, Riordan TP (2001) Distribution of buffalograss polyploid variation in the southern Great Plains. Crop Sci 41:909–913

    Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP) a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461

    Article  CAS  Google Scholar 

  • Mantel M (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Mohammadi SA, Prasanna BM (2003) Analysis of genetic diversity in crop plants-salient stataistical tools and considerations. Crop Sci 43:1235–1248

    Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    CAS  PubMed  Google Scholar 

  • Peakall R, Smouse PE, Huff DR (1995) Evolutionary implications of allozyme and RAPD variation in diploid populations of dioecious buffalograss Buchloe dactyloides. Mol Ecol 4:135–147

    CAS  Google Scholar 

  • Qi X, Lindup S, Pittaway TS, Allouis S, Gale MD, Devos KM (2001) Development of simple sequence repeat markers from bacterial artificial chromosomes without subcloning. BioTechniques 31:355–362

    CAS  PubMed  Google Scholar 

  • Riordan TP, de Shazer SA, Johnson-Cicalese JM, Shearman RC (1993) An overview of breeding and development of buffalograss. Int Turfgrass Soc Res J 7:816–822

    Google Scholar 

  • Rohlf JF (2000) NTSYSpc: numerical taxonomy and multivariate analysis system. Exeter Software, Setauket, New York, USA

  • Rossetto M (2001) Sourcing of SSR markers from related plant species. In: Henry R (ed) Plant genotyping the DNA fingerprinting of plants. CAB International, Wallingford, UK, pp 211–224

  • Russell JR, Fuller JD, Macaulay M, Hatz BG, Jahoor A, Powell W, Waugh R (1997) Direct comparison levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722

    Article  CAS  Google Scholar 

  • Senior ML, Heun M (1993) Mapping maize microsatellites and polymerase chain reaction confirmation of the targeted repeats using CT primer. Genome 36:884–889

    CAS  PubMed  Google Scholar 

  • Taliaferro CM, Springer TL, Ahring RM (1994) Registration of bison buffalograss. Crop Sci 34:304

    Google Scholar 

  • Tessier C, David J, This P, Boursiquot JM, Charrier A (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet 98:171–177

    CAS  Google Scholar 

  • Tivang JG, Nienhuis J, Smith OS (1994) Estimation of sampling variance of molecular marker data using the bootstrap procedure. Theor Appl Genet 89:259–264

    Google Scholar 

  • Van Deynze AE, Sorrels ME, Park WD, Ayres NM, Fu H, Cartinhour SW, Paul E, McCouch SR (1998) Anchor probes for comparative mapping of grass genera. Theor Appl Genet 97:356–369

    Article  Google Scholar 

  • Wagner DB, Furnier MA, Saghai-Maroof SA, Williams SM, Dancik BP, Allard RW (1987) Chloroplast DNA polymorphisms in lodgepole and jack pines and their hybrids. Proc Natl Acad Sci USA 84:2097–2100

    CAS  PubMed  Google Scholar 

  • Weir BS (1990) Genetic data analysis. Sinauer, Sunderland, Mass.

  • Wu L, Lin H (1994) Identifying buffalograss [Buchloe dactyloides (Nutt.) Engelm.] cultivar breeding lines using random amplified polymorphic DNA (RAPD) markers. J Am Soc Hortic Sci 119:126–130

    CAS  Google Scholar 

  • Zietkievicz E, Rafalski A, Labuda D (1994) Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genome 20:176–183

    Article  Google Scholar 

Download references

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Authors and Affiliations

  1. Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA

    H. Budak, R. C. Shearman, I. Parmaksiz & I. Dweikat

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  1. H. Budak
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  2. R. C. Shearman
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  3. I. Parmaksiz
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  4. I. Dweikat
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Correspondence to H. Budak.

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Communicated by B. Friebe

A contribution of the University of Nebraska Agricultural Research Division, Lincoln, Nebraska 68583. Journal Series No. 14398.

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Budak, H., Shearman, R.C., Parmaksiz, I. et al. Comparative analysis of seeded and vegetative biotype buffalograsses based on phylogenetic relationship using ISSRs, SSRs, RAPDs, and SRAPs. Theor Appl Genet 109, 280–288 (2004). https://doi.org/10.1007/s00122-004-1630-z

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  • DOI: https://doi.org/10.1007/s00122-004-1630-z

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