Czech J. Genet. Plant Breed., 2015, 51(2):62-67 | DOI: 10.17221/16/2015-CJGPB

The selection and validation of a marker set for the differentiation of onion cultivars from the Czech RepublicOriginal Paper

Katarína MITROVÁ, Pavel SVOBODA, Jaroslava OVESNÁ
Crop Research Institute, Prague-Ruzyně, Czech Republic

The onion (Allium cepa L.) constitutes an important part of the human diet and is of economic importance on the vegetable market. Methods that allow unambiguous differentiation of cultivars and breeding lines are required for market control and the protection of plant breeders' rights. DNA analyses, such as single sequence repeat polymorphism (SSRs), represent such a tool. Based on the evaluation of polymorphism in 21 SSR loci, we established a panel of 15 easy to score SSR markers that differentiated 16 commercial onion cultivars in the Czech Republic. The polymorphism ranged from 2-3 alleles per locus, indicating a low level of diversity among the cultivars. The panel can also be used to evaluate genetic resources.

Keywords: Allium cepa L.; diversity; genotyping; SSR markers; variety testing

Published: June 30, 2015  Show citation

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MITROVÁ K, SVOBODA P, OVESNÁ J. The selection and validation of a marker set for the differentiation of onion cultivars from the Czech Republic. Czech J. Genet. Plant Breed. 2015;51(2):62-67. doi: 10.17221/16/2015-CJGPB.
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    References

    1. Anandhan S., Mote S.R., Gopal J. (2014): Evaluation of onion varietal identity using SSR markers. Seed Science and Technology, 42: 279-285. Go to original source...
    2. Auger J., Yang W., Arnault I., Pennier F., Potin-Gautier M. (2004): High-performance liquid chromatographic - inductively coupled plasma mass spectrometric evidence for Se-"alliins" in garlic and onion grown in Se-rich soil. Journal of Chromatography, 1032: 103-107. Go to original source... Go to PubMed...
    3. Baldwin S., Pither-Joyce M., Wright K., Chen L., McCallum J. (2012): Development of robust genomic simple sequence repeat markers for estimation of genetic diversity within and among bulb onion (Allium cepa L.) populations. Molecular Breeding, 3: 1401-1411. Go to original source...
    4. Botstein D., White R.L., Skolnick M., Davis R.W. (1980): Construction of a genetic linkage map in man using restriction fragment length polymorphisms. The American Journal of Human Genetics, 32: 314-331.
    5. Buso G.S.C., Paiva M.R., Torres A.C., Resende F.V., Ferreira M.A., Buso J.A., Dusi A.N. (2008): Genetic diversity studies of Brazilian garlic varieties and quality control of garlic-clover production. Genetics and Molecular Research, 7: 534-541. Go to original source... Go to PubMed...
    6. Bustin S.A., Vandesompele J., Pfaffl M.W. (2009): Standardization of qPCR and RT-qPCR. Genetic Engineering & Biotechnology News, 29: 40-43.
    7. Chinnappareddy L.R.D., Khandagale K., Chennareddy A., Ramappa V.G. (2013): Molecular markers in the improvement of Allium crops. Czech Journal of Genetics and Plant Breeding, 49: 131-139. Go to original source...
    8. Cunha C.P., Hoogerheide E.S.S., Zucchi M.I., Monteiro M., Pinheiro J.B. (2012): New microsatellite markers for garlic, Allium sativum (Alliaceae). American Journal of Botany, 99: e17-e19. Go to original source... Go to PubMed...
    9. Favoretto P., Veasey E.A., Tavares De Melo P.C. (2011): Molecular characterization of potato varieties using SSR markers. Horticultura Brasileira, 29: 542-547. Go to original source...
    10. Filjushin M.A., Kholda O.A., Kochieva E.Z., Ryzhova N.N. (2011): AFLP marking of the genotypes of leek (Allium porrum) varieties. Russian Journal of Genetics, 47: 492-496. Go to original source...
    11. Gong L., Deng Z. (2012): Selection and application of SSR markers for variety discrimination, genetic similarity and relation analysis in gerbera (Gerbera hybrida). Scientia Horticulturae, 138: 120-127. Go to original source...
    12. Jakše J., Martin W., Mccallum J., Havey M.J. (2005): Single nucleotide polymorpisms, indels, and simple sequence repeats for onion cultivar identification. Journal of the American Society for Horticultural Science, 130: 912- 917. Go to original source...
    13. Keusgen M., Schulz H., Glodek J., Krest I., Krüger H., Herchert N., Keller J. (2002): Characterization of some Allium hybrids by aroma precursors, aroma profiles, and alliinase activity. Journal of Agricultural and Food Chemistry, 50: 2884-2890. Go to original source... Go to PubMed...
    14. Kim H.H., Cho E.G., Baek H.J., Kim Ch.Y., Chae Y.A. (2003): Genetic distance of Allium section cepa by DNA fingerprint. Korean Journal of Crop Science, 48: 31-37.
    15. Lampasona S.G., Martinez L., Burba J.L. (2003): Genetic diversity among selected Argentinean garlic clones (Allium sativum L.) using AFLP (Amplified Fragment Length Polymorphism). Euphytica, 132: 115-119. Go to original source...
    16. Lanzotti V. (2006): The analysis of onion and garlic. Journal of Chromatography, 1112: 3-22. Go to original source... Go to PubMed...
    17. Lee G.A., Kwon S.J., Park Y.J., Lee M.C., Kim H.H., Lee J.S., Lee S.Y., Gwag J.G., Kim C.K., Ma K.H. (2011): Crossamplification of SSR markers developed from Allium sativum to other Allium species. Scientia Horticulturae, 128: 401-407. Go to original source...
    18. Mallor C., Arnedo-Andrés M.S., Garcés-Claver A. (2014): Assessing the genetic diversity of Spanish Allium cepa landraces for onion breeding using microsatellite markers. Scientia Horticulturae, 170: 24-31. Go to original source...
    19. McCallum J., Thomson S., Pither-Joyce M., Kenel F., Clarke A., Havey M.J. (2008): Genetic diversity analysis and single-nucleotide polymorphism marker development in cultivated bulb onion based on expressed sequence tagsimple sequence repeat markers. Journal of the American Society for Horticultural Science, 133: 810-818. Go to original source...
    20. Mukherjee A., Sikdar B., Ghosh B., Banerjee A., Ghosh E., Bhattacharya M., Roy S.C. (2013): RAPD and ISSR analysis of some economically important species, varieties, and cultivars of the genus Allium (Alliaceae). Turkish Journal of Botany, 37: 605-618. Go to original source...
    21. Nei M. (1973): Analysis of gene diversity in subdivided populations. Proceedings of the National Academy of Sciences of the United States of America, 70: 3321-3323. Go to original source... Go to PubMed...
    22. Ovesná J., Kučera L., Horníčkova J., Svobodová L., Stavělíková H., Velíšek J., Milella L. (2011): Diversity of Salk(en)yl cysteine sulphoxide content within a collection of garlic (Allium sativum L.) and its association with the morphological and genetic background assessed by AFLP. Scientia Horticulturae, 129: 541-547. Go to original source...
    23. Ovesná J., Leišová-Svobodová L., Kučera L. (2014): Microsatellite analysis indicates the specific genetic basis of Czech bolting garlic. Czech Journal of Genetics and Plant Breeding, 50: 226-234. Go to original source...
    24. Paredes M., Becerra V., González M.I. (2008): Low genetic diversity among garlic (Allium sativum L.) accessions detected using random amplified polymorphic DNA (RAPD). Chilean Journal of Agricultural Research, 68: 3-12. Go to original source...
    25. Poczai P., Varga I., Laos M., Cseh A., Bell N., Valkonen J.P.T., Hyvönen J. (2013): Advances in plant gene-targeted and functional markers: a review. Plant Methods, 9: 6. Go to original source... Go to PubMed...
    26. Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S., Rafalski A. (1996): The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Molecular Breeding, 2: 225-238. Go to original source...
    27. R Core Team (2013): A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available at http://www.R-project.org/
    28. Santos C.A.F., Oliveira V.R., Rodrigues M.A., Ribeiro H.L.C., Silva G.O. (2011): Genetic similarity among onion cultivars of different types and origins, based on AFLP markers. Horticultura Brasileira, 29: 32-37. Go to original source...
    29. Simo J., Pascual J., Canizares J., Casanas F. (2014): Spanish onion landraces (Allium cepa L.) as sources of germplasm for breeding calçots: a morphological and molecular survey. Euphytica, 195: 287-300. Go to original source...
    30. Suzuki R., Shimodaira H. (2011): Hierarchical Clustering with P-Values via Multiscale Bootstrap Resampling. R package version 1.2-2. Available at http://CRAN.Rproject.org/package=pvclust
    31. Tedeschi P., Bonetti G., Majetti A., Brandolini V. (2014): Random amplified polymorphic DNA (RAPD) fingerprint and antioxidants profile as markers for Tropea red onion (Allium cepa L.) authenticity. Journal of Food Composition and Analysis, 36: 98-103. Go to original source...
    32. This P., Jung A., Boccacci P., Borrego J., Botta R., Costantini L., Crespan M., Dangl G.S., Eisenheld C., FerreiraMonteiro F., Grando S., Ibanez J., Lacombe T., Laucou V., Magalhaes R., Meredoth C.P., Milani N., Peterlunger E., Regner F., Zulini L., Maul E. (2004): Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theoretical and Applied Genetics, 109: 1448-1458. Go to original source... Go to PubMed...
    33. Wang Y., Wang C., Zhang H., Yue Z., Liu X., Ji W. (2013): Genetic analysis of wheat (Triticum aestivum L.) and related species with SSR markers. Genetic Resources and Crop Evolution, 60: 1105-1117. Go to original source...

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