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EST–SSR markers for asparagus genetic diversity evaluation and cultivar identification

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Abstract

Simple sequence repeat (SSR) markers generated from expressed sequence tag (EST) sequences represent useful tools for genotyping and their development is relatively easy because of the public availability of EST databases. We report design and application of EST–SSRs to assess the level of genetic diversity among thirty-five asparagus cultivars and to fingerprint DePaoli, a new variety released by University of California, Riverside. DNA was isolated from bulks of pooled cladophylls coming from five plants of each variety to reduce the number of DNA extractions and PCR reactions. Allele frequencies were estimated from the intensity of the bands in two bulks and two individual plant samples for each variety. Although asparagus varieties derive from a limited germplasm pool, eight EST–SSR loci differentiated all of the analyzed cultivars. Moreover, UPGMA (unweighted pair group method with arithmetic mean) and neighbor-joining trees, as well as principal components analysis separated the cultivars into clusters corresponding to the geographical areas where they originated.

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Abbreviations

SSR:

Simple sequence repeat

EST:

Expressed sequence tags

UPGMA:

Unweighted pair group method with arithmetic mean

References

  • Aceto S, Sica M, Gamba G, Pontieri S, Farina A, Gaudio L (2003) Isolation and characterization of microsatellite loci from Asparagus acutifolius (Liliaceae). Mol Ecol Notes 3:242–243

    Article  CAS  Google Scholar 

  • Collins HE, Li H, Inda SE, Anderson J, Laiho K, Tuomilehto J, Seldin MF (2000) A simple and accurate method for determination of microsatellite total allele content differences between DNA pools. Hum Genet 106(2):218–226

    Article  PubMed  CAS  Google Scholar 

  • Doré C (1977) In vitro techniques as an efficient tool in asparagus breeding. Acta Hort 78:89–94

    Google Scholar 

  • Ellison JH, Scheer DF, Wagner JJ (1960) Asparagus yield as related to plant vigor, earliness and sex. Proc Am Soc Hortic Sci 75:411–415

    Google Scholar 

  • Flory WS (1932) Genetic, cytological investigations on Asparagus officinalis L. Genetics 17:432–467

    PubMed  CAS  Google Scholar 

  • Geoffriau E, Denoue D, Rameau C (1992) Assessment of genetic variation among asparagus (Asparagus officinalis L.) populations and cultivars: agromorphological and isozymic data. Euphytica 61:169–179

    Article  CAS  Google Scholar 

  • Gonzáles-Castañón ML (1997) Isozyme gene markers in asparagus used to classify fifty asparagus cultivars. Acta Hort 479:77–84

    Google Scholar 

  • Hollingsworth WO, Christie CB, Nichols A, Neilson HF (1998) Detection of variation among and within asparagus hybrids using random amplified DNA (RAPD) markers. New Zeal J Crop Hort 26:1–9

    CAS  Google Scholar 

  • Khandka DK, Nejidat A, Golan-Goldhirsh A (1996) Polymorphism and DNA markers for asparagus cultivars identified by random amplified polymorphic DNA. Euphytica 887:39–44

    Article  Google Scholar 

  • Knaflewski M (1996) Genealogy of asparagus cultivars. Acta Hort 415:87–91

    Google Scholar 

  • Kuhl JC, Havey MJ, Martin WJ, Cheung F, Yuan Q, Landherr L, Hu Y, Leebens-Mack J, Town CD, Sink KC (2005) Comparative genomic analyses in Asparagus. Genome 48:1052–1060

    Article  PubMed  CAS  Google Scholar 

  • Loptien H (1979) Identification of the sex chromosome pair in asparagus (Asparagus officinalis L.). Z Pflanzenzucht 82:162–173

    Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    PubMed  Google Scholar 

  • O’Connell LM, Russell J, Ritland K (2004) Fine-scale estimation of outcrossing in western redcedar with microsatellite assay of bulked DNA. Heredity 93(5):443–449

    Article  PubMed  CAS  Google Scholar 

  • Oetting WS, Lee HK, Flanders DJ, Wiesner GL et al (1995) Linkage analysis with multiplexed short tandem repeat polymorphisms using infrared fluorescence and M13 tailed primers. Genomics 30:450–458

    Article  PubMed  CAS  Google Scholar 

  • Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, NJ, pp 365–386

    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 

  • Yang H-J, Clore WJ (1974) Development of complete plantlets from moderately vigorous shoots of stock plants of asparagus in vitro. HortScience 9:138–140

    Google Scholar 

  • Yang H-J (1977) Tissue culture technique developed for asparagus propagation. HortScience 12(2):140–141

    Google Scholar 

Download references

Acknowledgements

We thank Neil Stone for assistance in collecting the samples, John Ikeda for primer design, Xinrong Ye for the DNA extraction protocol and Lisa Mu for assistance in SSR analysis. Funding was provided by the University of California and the University of Catania.

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Authors and Affiliations

  1. Dipartimento di Ortofloroarboricoltura e Tecnologie Agroalimentari, Sezione Arboricoltura, University of Catania, Catania, 95123, Italy

    Marco Caruso

  2. Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA

    Claire T. Federici & Mikeal L. Roose

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  1. Marco Caruso
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  2. Claire T. Federici
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  3. Mikeal L. Roose
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Correspondence to Mikeal L. Roose.

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Caruso, M., Federici, C.T. & Roose, M.L. EST–SSR markers for asparagus genetic diversity evaluation and cultivar identification. Mol Breeding 21, 195–204 (2008). https://doi.org/10.1007/s11032-007-9120-z

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  • DOI: https://doi.org/10.1007/s11032-007-9120-z

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