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An efficient strategy for developing genotype identification markers based on simple sequence repeats in grapevine

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Microsatellites are valuable resources for breeding and genetic studies of crop species. The development of simple sequence repeat (SSR) markers, which are applied across closely related cultivars, has been slow, labor-intensive, and expensive, with a low success rate. In this study, we demonstrate an efficient strategy for developing cross-species, amplifiable polymorphic SSR markers from grapevine (Vitis vinifera) based on sequence comparison and in silico polymerase chain reaction amplification of the genome sequences of grape cultivars. A total of 21 primer sets targeting unique SSR loci were screened from polymorphism and heterozygosity analyses of 13 grape cultivars and four wild species. The number of alleles varied from 3 to 12, with a mean of 7.52 alleles per locus. The lowest and highest observed heterozygosity values were 0.24 and 0.82, respectively, with an average of 0.54. Polymorphic information content values for the primer sets ranged from 0.32 to 0.86, with an average of 0.70. We successfully identified genetic relationships among 17 grape genotypes using the unweighted pair group method with arithmetic average and principal coordinates analysis of the SSR markers. The results suggest that the strategy developed in this study is applicable to high-throughput cross-amplifiable SSR marker development for the identification of genotype, genetic study, and examination of genetic diversity in grapevines.

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  • Alleweldt G, Dettweiler E (1994) The genetic resources of Vitis: world list of grapevine collections, 2nd edn. Geilweilerhof, Siebeldingen

    Google Scholar 

  • Argade N, Tamhankar S, Karibasappa G, Patil S, Rao V (2009) DNA profiling and assessment of genetic relationships among important seedless grape (Vitis vinifera) varieties in India using ISSR markers. J Plant Biochem Biotechnol 18:45–51

    Article  CAS  Google Scholar 

  • Bowers J, Meredith C (1996) Genetic similarities among wine grape cultivars revealed by restriction fragment-length polymorphism (RFLP) analysis. J Am Soc Hortic Sci 121:620–624

    Article  Google Scholar 

  • D’Onofrio C, De Lorenzis G, Giordani T, Natali L, Cavallini A, Scalabrelli G (2010) Retrotransposon-based molecular markers for grapevine species and cultivars identification. Tree Genet Genomes 6:451–466

    Article  Google Scholar 

  • Dong Q, Cao X, Yang G, Yu H, Nicholas K, Wang C, Fang J (2010) Discovery and characterization of SNPs in Vitis vinifera and genetic assessment of some grapevine cultivars. Sci Hortic 125:233–238

    Article  CAS  Google Scholar 

  • Doyle J (1991) DNA protocols for plants-CTAB total DNA isolation. In: Hewitt GM, Johnston A (eds) Molecular techniques in taxonomy. Springer, Berlin, pp 283–293

    Chapter  Google Scholar 

  • Ergül A, Tuerkoglu M, Soeylemezoglu G (2004) Genetic identification of Amasya (Vitis vinifera L. Cvs.) genotypes based on AFLP markers. Biotechnol Biotechnol Equip 18:39–43

    Article  Google Scholar 

  • FAOSTAT (2016) Food and agricultural commodities production.

  • Guo D, Zhang J, Liu C, Zhang G, Li M, Zhang Q (2012) Genetic variability and relationships between and within grape cultivated varieties and wild species based on SRAP markers. Tree Genet Genomes 8:789–800

    Article  Google Scholar 

  • Hur YY, Choi YJ, Kim EJ, Yoon MS, Park YS, Jung SM, Noh JH, Park SJ, Ma KH et al (2012) Analysis of genetic relationship of grape rootstock cultivars and wild Vitis species using RAPD and SSR markers. Korean J Breed Sci 44:19–28

    Google Scholar 

  • Karata H, Ağaoğlu Y (2008) Genetic diversity among Turkish local grape accessions (Vitis vinifera L.) using RAPD markers. Hereditas 145:58–63

    Article  Google Scholar 

  • Kindiger B (2006) Cross-species amplification of Lolium microsatellites in Poa ssp. Grassl Sci 52:105–115

    Article  CAS  Google Scholar 

  • Liu LY, Li H (2013) Review: research progress in amur grape, Vitis amurensis Rupr. Can J Plant Sci 93:565–575

    Article  Google Scholar 

  • Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129

    Article  CAS  Google Scholar 

  • Liu C, Fan X, Jiang J, Guo D, Sun H, Ying Z, Feng J (2012) Genetic diversity of Chinese wild grape species by SSR and SRAP markers. Biotechnol Biotechnol Equip 26:2899–2903

    Article  Google Scholar 

  • Pelsy F, Hocquigny S, Moncada X, Barbeau G, Forget D, Hinrichsen P, Merdinoglu D (2010) An extensive study of the genetic diversity within seven French wine grape variety collections. Theor Appl Genet 120:1219–1231

    Article  Google Scholar 

  • Pemberton JM, Slate J, Bancroft DR, Barrett JA (1995) Nonamplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252

    Article  CAS  Google Scholar 

  • Porebski S, Baily LG, Baum BR (1997) Modification of a CTAB extraction protocol for plant containing polysaccharide and polyphenol components. Plant Mol Biol Rep 15:8–15

    Article  CAS  Google Scholar 

  • Riahi L, Zoghlami N, El-Heit K, Laucou V, Le Cunff L, Boursiquot J, Lacombe T, Mliki A, Ghorbel A et al (2010) Genetic structure and differentiation among grapevines (Vitis vinifera) accessions from Maghreb region. Genet Resour Crop Evol 57:255–272

    Article  CAS  Google Scholar 

  • Riaz S, Tenscher AC, Smith BP, Ng DA, Walker MA (2008) Use of SSR markers to assess identity, pedigree, and diversity of cultivated Muscadine grapes. J Am Soc Hortic Sci 133:559–568

    Article  Google Scholar 

  • Roa AC, Chavarriaga-Aguirre P, Duque MC, Maya MM, Bonierbale MW, Iglesias C, Tohme J (2000) Cross species amplification of cassava (Manihot esculenta) (Euphorbiaceae) microsatellites: allelic polymorphism and degree of relationship. Am J Bot 87:1647–1655

    Article  CAS  Google Scholar 

  • Rotmistrovsky K, Jang W, Schuler G (2004) A web server for performing electronic PCR. Nucleic Acids Res 32:W108–W112

    Article  CAS  Google Scholar 

  • Sabir A, Tangolar S, Buyukalaca S, Kafkas S (2009) Ampelographic and molecular diversity among grapevine (Vitis spp.) cultivars. Czech J Genet Plant Breed 45:160–168

    Article  CAS  Google Scholar 

  • Sefc KM, Pejic I, Maletic E, Thomas MR, Lefort F (2009) Microsatellite markers for grapevine: tools for cultivar identification and pedigree reconstruction (Chapter 21). In: Roubelakis-Angelakis KA (ed) Grapevine molecular physiology and biotechnology. Kluwer Publishers, Amsterdam, pp 565–596

    Chapter  Google Scholar 

  • Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348

    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

    Article  CAS  Google Scholar 

  • This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L, Crespan M, Dangl GS, Eisenheld C et al (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458

    Article  CAS  Google Scholar 

  • Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primers were designed using Primer3 program. Nucleic Acids Res 40:e115

    Article  CAS  Google Scholar 

  • Vidal J, Coarer M, Defontaine A (1999) Genetic relationships among grapevine varieties grown in different French and Spanish regions based on RAPD markers. Euphytica 109:161–172

    Article  CAS  Google Scholar 

  • Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16

    Article  CAS  Google Scholar 

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This work was supported by grants from the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01242102), by the Rural Development Administration, and by the National Research Foundation of Korea (Grant No. 2016R1A2B4011866).

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Correspondence to Hee-Ju Yu.

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Kim, HJ., Park, S.H., Kim, JH. et al. An efficient strategy for developing genotype identification markers based on simple sequence repeats in grapevine. Hortic. Environ. Biotechnol. 60, 363–372 (2019).

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