DNA fingerprint of strawberry varieties developed at Colegio de Postgraduados, Mexico

Martín Aguilar Tlatelpa, Guillermo Calderón Zavala, María Alejandra Gutiérrez Espinosa, Ricardo Lobato Ortiz, Leobigildo Córdoba Téllez, Victor Volke Haller, Marja Liza Fajardo Franco, Amalio Santacruz Varela


In a breeding program for strawberry (Fragaria × ananassa) it is important to have a methodology to evaluate the genetic integrity of the plant in all the stages of increase, from different criteria, such as morphological, physiological and molecular; for this purpose one of the most appropriate tools are the Simple Sequence Repeats (SSR`s) molecular markers, since they allow, for example, identifying populations with a reduced genetic diversity, revealing genealogies, knowing the degree of relatedness between individuals, providing solid elements in the defense of intellectual property, evaluation of the purity of the plant material, identification of somaclonal variation and to avoid the mixture of plant material in germplasm banks. In this sense the objective of this study was to obtain the genetic fingerprint of strawberry varieties CP0201, CP0204, CP0615, CPLE7 developed at Colegio de Postgraduados and variety Festival developed at Florida, US, with the use of nine microsatellite (SSR`s) loci. The process included the DNA extraction from strawberry leaf tissue, as well as the amplification by means of PCR of the SSR`s loci grouped in multiplex reactions. The PCR products were separated by capillary electrophoresis and their size in base pairs was determined with the GeneMapper® v. 4 software. From the allele frequencies distance matrices were calculated the Jaccard and Dice coefficients. 63 different alleles were found, each pair of primers amplified between 3 and 12 alleles. The markers that presented the highest number of alleles were EMFn181 (11 alleles) and EMFv104 (12 alleles). The genetic fingerprint of each variety was generated. Differences between the CP0615, CPLE7 and Festival were found based on their allelic profiles; CP0204 and CP0201 had a similar genetic fingerprint, since they are related through their female parent; the allelic diversity index within the populations ranged from 3.96 to 5.93. The varieties had a low uniformity index due to the high level of polymorphism of the markers used.


Fragaria × ananassa; allelic profile; SSR, molecular markers; genetic diversity


Amom, T., & Nongdam, P. (2017). The Use of Molecular Marker Methods in Plants : A Review. International Journal of Current Research and Review. 9(17):1-7. DOI: 10.7324/IJCRR.2017.9171

Arnau, G., Lallemand J. and Bourgoin M. (2001). Are AFLP markers the best alternative for cultivar identification. Acta Horticulturae 546:301-306. DOI: 10.17660/ActaHortic.2001.546.37

Arnau, G., Lallemand J. and Bourgoin M. (2002). Fast and reliable strawberry cultivar identification using inter simple sequence repeat (ISSR) amplification. Euphytica 129(1):69-79. doi: 10.1023/A:1021509206584.

Ather-uz-Zaman., Al-Khayri J. M., Islam R. (2018). Genetic Improvement of Strawberry (Fragaria ×ananassa Duchesne). In: Al-Khayri J., Jain S., Johnson D. (eds) Advances in Plant Breeding Strategies: Fruits. Springer, Cham. https://doi.org/10.1007/978-3-319-91944-7_6

Beovides, Y., Fregene M, Alves A, Gutiérrez J. P, Buitrago C, Marin A. J, Milián M. D, Rodríguez S, Cruz J. A, Ruiz E, Guerra D, Toledo H, Roca O, Albert J, García J, y Oliva M. (2006). Análisis de diversidad genética mediante microsatélites (SSR) en cultivares del germoplasma cubano de yuca. Biotecnología Vegetal 6(1):9-14.

Brunings, A. M., Moyer C, Peres N, and Folta K. M.(2010). Implementation of simple sequence repeat markers to genotype Florida strawberry varieties. Euphytica 173(1):63-75. doi: 10.1007/s10681-009-0112-4.

Carbone, F., Mourgues F, Biasioli F, Gasperi F, Märk T. D, Rosati C, and Perrotta G. (2006). Development of molecular and biochemical tools to investigate fruit quality traits in strawberry elite genotypes. Molecular Breeding 18(2):127-142. doi: 10.1007/s11032-006-9017-2.

Carrasco, B., Garcés M, Rojas P, Saud G, Herrera R, Retamales J. B, and Caligari P. D. S. (2007). The Chilean strawberry [Fragaria chiloensis (L.) Duch.]: genetic diversity and structure. Journal of the American Society for Horticultural Science 132(4):501-506. DOI: 10.21273/JASHS.132.4.501

Carrasco, B., Retamales J. B, Quiroz K, Garriga M, Caligari P. D. S, García-Gonzales R. (2013). Inter Simple Sequence Repeat Markers Associated with Flowering Time Duration in the Chilean Strawberry (Fragaria chiloensis). Journal of Agricultural Sciences and Tecnology 15(6): 1195-1207. http://jast-old.modares.ac.ir/article_5032.html

Clark, L.V., and Jasieniuk M. (2011). POLYSAT: an R package for polyploid microsatellite analysis. Molecular Ecology Resources 11(3):562-566. doi: 10.1111/j.1755-0998.2011.02985.x.

Congiu, L., Chicca M, Cella R, Rossi R, and Bernacchia G. (2000). The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. Molecular Ecology 9(2):229-232. https://doi.org/10.1046/j.1365-294x.2000.00811.x

Dangl, G. S., Lee E. W, Sim S. T, and Golino D. A. (2007). A new system for strawberry cultivar identification developed at Foundation Plant Services (FPS), University of California, Davis, using simple sequence repeat (SSR) primers. NASS/NASGA Proceedings, p. 118-121. http://fpms.ucdavis.edu/WebSitePDFs/Articles/Straw%20DNA%20ID118-121.pdf

Debnath, S. C., Khanizadeh S, Jamieson A. R, and Kempler C. (2008). Inter simple sequence repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes. Canadian Journal of Plant Science 88(2):313-322. doi: 10.4141/CJPS07088.

Debnath, S. C. and Ricard E. (2009). ISSR, anthocyanin content and antioxidant activity analyses to characterize strawberry genotypes. Journal of Applied Horticulture 11(2):83-89. http://horticultureresearch.net/journal_pdf/200983-89.pdf

Debnath, S. C. (2014). Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars. Biochemical Systematics and Ecology. 54(1):337-347. https://doi.org/10.1016/j.bse.2014.03.018.

Degani, C., Rowland L. J, Saunders J. A, Hokanson S. C, Ogden E. L, Golan-Goldhirsh A, and Galletta G. J. (2001). A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data. Euphytica 117(1):1-12. doi: 10.1023/A:1004008408435.

Degani, C., Rowland L. J, Levi A, Hortynski J. A, and Galleta G. J. (1998). DNA fingerprinting of strawberry (Fragaria × ananassa) cultivars using randomly amplified polymorphic DNA (RAPD) markers. Euphytica 102(2):247-253. DOI: 10.1023/A:1018385715007

Dice, L.R. (1945). Measures of the amount of ecologic association between species. Ecology 26(3): 297-302. https://doi.org/10.2307/1932409

Firas, R. S., y Abdulkareem A. 2015. Molecular markers: An introduction and applications. Eur. J. Mol. Biotechnol. 9(3):118–130. DOI: 10.13187/ejmb.2015.9.118

Folta, K. M., Clancy M. A, Chamala S, Brunings A. M, Dhingra A, Gomide L, Kulathinal R. J, Peres N, Davis K. M, Barbazuk W. B. (2010). A transcript accounting from diverse tissues of a cultivated strawberry. The Plant Genome 3(2):90-105. doi: 10.3835/plantgenome2010.02.0003.

Garcia, M. G., Ontivero M, Diaz Rici J.C, Castagnaro A. (2002). Morphological traits and high resolution RAPD markers for the identification of the main strawberry varieties cultivated in Argentina. Plant Breeding 121(1):76-80. https://doi.org/10.1046/j.1439-0523.2002.00671.x

Gil-Ariza, D. J., Amaya I, López-Aranda J.M, Sánchez-Sevilla J. F, Botella M.Á, Valpuesta V. (2009). Impact of plant breeding on the genetic diversity of cultivated strawberry as revealed by expressed sequence tag-derived simple sequence repeat markers. Journal of the American Society for Horticultural Science 134(3): 337-347. DOI: 10.21273/JASHS.134.3.337

González, A. y Aguirre X. (2007). Inter simple sequence repeats (ISSRs). En Ecología Molecular. Compilado por Luis Eguiarte, Valeria Souza y Xitlali Aguirre, 567-571. Secretaría de Medio Ambiente y Recursos Naturales, Comisión Nacional para el Conocimiento y Uso de la Biodiversidad. México,D.F. https://www.researchgate.net/file.PostFileLoader.html?id=552c1fb0d3df3ee7548b458a&assetKey=AS%3A273756348452864%401442280007420

Govan, C. L., Simpson D. W, Johnson A.W, Tobutt K. R, Sargent D. J. (2008). A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars. Molecular Breeding 22(4):649-661. doi: 10.1007/s11032-008-9206-2.

Graham, J., McNicol R. J, and McNicol J. W. (1996). A comparison of methods for the estimation of genetic diversity in strawberry cultivars. Theoretical and Applied Genetics 93(3):402-406. doi: 10.1007/BF00223182.

Hadonou, A. M., Sargent D. J, Wilson F, James C. M, Simpson D. W. (2004). Development of microsatellite markers in Fragaria, their use in genetic diversity analysis, and their potential for genetic linkage mapping. Genome 47(3):429-438. DOI: 10.1139/g03-142

Han, Z., Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T. (2006). Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theoretical and Applied Genetics 112 (3):430-439. doi: 10.1007/s00122-005-0142-9.

Hancock, James. (2008). Temperate fruit crop breeding: Germplasm to genomics. Springer. http://link.springer.com/chapter/10.1007/978-1-4020-6907-9_13

Hilmarsson, H. S., Hytönen, T, Isobe, S, Göransson, M, Toivainen, T, Hallsson, J. H. (2017). Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers. PloS one, 12(8):1-17. doi:10.1371/journal.pone.0183384

Holleley, C. E., and Geerts P. G. (2009) Multiplex Manager 1.0: a cross-platform computer program that plans and optimizes multiplex PCR. BioTechniques 46(7):511-517. doi: 10.2144/000113156.

Holton, T. A., Christopher J. T, McClure L, Harker N, Henry R. J. (2002). Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Molecular Breeding 9(2):63-71. doi: 10.1023/A:1026785207878.

Hummer, K. (2007). Global conservation strategy for Fragaria(strawberry). Scientia Horticulturae 6. International Society for Horticultural Science, Leuven, Belgium. https://www.ishs.org/scripta-horticulturae/global-conservation-strategy-fragaria-strawberry

Hussein, T. S., Tawfik A. A, and Khalifa M. A. (2008). Molecular identification and genetic relationships of six strawberry varieties using ISSR markers. International Journal of Agriculture and Biology 10(6):677-680. http://www.fspublishers.org/published_papers/77379_.pdf

Hwang, J., Kang J, Son B, Kim K, and Park Y. (2011). Genetic diversity in watermelon cultivars and related species based on AFLPs and EST-SSRs. Notulae Botanicae Horti Agrobotanici Cluj-Napoca 39(2):285-292. http://dx.doi.org/10.15835/nbha3926382

Invitrogene. 2006. ChargeSwitch® gDNA Plant Kit for Purification of Genomic DNA (gDNA) from Plant Samples. p. 24. Version C. User Manual. Carlsbad, CA, USA. https://assets.thermofisher.com/TFS-Assets/LSG/manuals/chargeswitch_plant_man.pdf

Kim, J., Lee, S.Y., Kim, D. Eun-Su L, Hye-Eun L, Koen H, Byoung-Cheorl K. (2019). Genotyping of octoploid strawberry inbred lines by SNP discovery using genotyping-by-sequencing. Horticulture, Environment, and Biotechnology. 60(1): 69-80. https://doi.org/10.1007/s13580-018-0100-5

Kim, H.J., Lee J.N, Soo Cho K.S, Sik Won H, Taek Suh J. (2019). Genetic Diversity and Population Structure Analysis of Ever-Bearing and June-Bearing Strawberry Cultivars Using SSR Markers. Horticultural Science and Technology. 37(1): 108-118. https://doi.org/10.12972/kjhst.20190010

Lim, S., Jeongyeo L, Hyun Joo L, Kun-Hyang P, Dae-Soo K, Sung Ran M, Won Seok J, Tae II K, HyeRan K. (2017). The genetic diversity among strawberry breeding resources based on SSRs. Scientia Agricola, 74(3): 226-234. https://dx.doi.org/10.1590/1678-992x-2016-0046

Melese L. (2018). Marker Assisted Selection in Comparison to Conventional Plant Breeding: Review Article. Agri Res & Tech: Open Access J. 14(2): 1- 10. DOI: 10.19080/ARTOAJ.2018.14.555914

Muhammad, A. N., Muhammad A. N, Muhammad Q. S, Yıldız D, Gonul C, Mehtap Y, Rüştü H, Fiaz A, Ahmad A, Nitin L, Hakan Ö, Gyuhwa C, Faheem S. B. (2018). DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing, Biotechnology & Biotechnological Equipment, 32:2, 261-285, DOI: 10.1080/13102818.2017.1400401

Nantoumé, A. D., Andersen S. B, Jensen B. D. (2013). Genetic differentiation of watermelon landrace types in Mali revealed by microsatellite (SSR) markers. Genetic Resources and Crop Evolution 60(7):2129-2141. doi: 10.1007/s10722-013-9980-5.

Novo, M., Romo S, Rey M, Prado M. J, González M. V. (2010). Identification and sequence characterisation of molecular markers polymorphic between male kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev.) accessions exhibiting different flowering time. Euphytica 175(1):109-121. doi: 10.1007/s10681-010-0192-1.

Nunes, C. F., Ferreira J. L, Fernandes M. C. N, Breves S. S, Leal G. A, Soares B. D. F, Dias M. S. C, Pasqual M, Borem A, Cançado G. M. A. (2011). An improved method for genomic DNA extraction from strawberry leaves. Ciência Rural 41(8):1383-1389. http://dx.doi.org/10.1590/S0103-84782011000800014

Nunes, C. Ferreira., Ferreira J. L, Generoso A. L, Dias M. S, Carvalho P. M, Cançado G. M. de A. (2013). The genetic diversity of strawberry (Fragaria ananassa Duch.) hybrids based on ISSR markers. Acta Scientiarum. Agronomy, 35(4), 443-452. https://dx.doi.org/10.4025/actasciagron.v35i4.16737

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(3):225-238. doi: 10.1007/BF00564200.

Rodríguez-Bautista, G., Calderón-Zavala G. Jaen-Contreras David, Curiel-Rodríguez A. (2012). Capacidad de propagación y calidad de planta de variedades mexicanas y extranjeras de fresa. Revista Chapingo Serie Horticultura, 18(1): 113-123. https://www.redalyc.org/articulo.oa?id=60923315008

Rousseau-Gueutin, M., Lerceteau-Köhler E, Barrot L, Sargent D. J, Monfort A, Simpson D, Arús P, Guérin G, Denoyes-Rothan B. (2008). Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179(4):2045-2060. doi: 10.1534/genetics.107.083840.

Sánchez-Sevilla, J.F, Horvath A, Botella M.A, Gaston A, Folta K, Kilian A, Denoyes B, Amaya I. (2015) Diversity Arrays Technology (DArT) Marker Platforms for Diversity Analysis and Linkage Mapping in a Complex Crop, the Octoploid Cultivated Strawberry (Fragaria × ananassa). Plos One 10(12):1-22. https://doi.org/10.1371/journal.pone.0144960

Sargent, D. J., Hadonou A. M, Simpson D. W. (2003). Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Molecular Ecology Notes 3(4):550-552. doi: 10.1046/j.1471-8286.2003.00507.x.

Sargent, D. J., Clarke J, Simpson D. W, Tobutt K. R, Arús P, Monfort A, Vilanova S, Denoyes-Rothan B, Rousseau M, Folta K. M, Bassil N. V, Battey N. H. (2006). An enhanced microsatellite map of diploid Fragaria. Theoretical and Applied Genetics 112(7):1349-1359. doi: 10.1007/s00122-006-0237-y.

Sargent, D.J., Passey T, Šurbanovski N, Lopez E.G, Kuchta P, Davik J, Harrison R, PasseyA,. Whitehouse A. B, Simpson. (2012). A microsatellite linkage map for the cultivated strawberry (Fragaria × ananassa) suggests extensive regions of homozygosity in the genome that may have resulted from breeding and selection. Theoretical and Applied Genetics. 124(7): 1229-1240. https://doi.org/10.1007/s00122-011-1782-6

Shimomura, K. and Hirashima K. (2006). Development and characterization of simple sequence repeats (SSR) as markers to identify strawberry cultivars (Fragaria × ananassa Duch.) Journal of the Japanese Society for Horticultural Science 75(5):399-402. DOI: 10.2503/jjshs.75.399

Sneath, P.H.A. and Sokal R.R. (1973). Numerical taxonomy. The principles and practice of numerical classification. 573 p. W.H. Freeman and Company. San Francisco, CA, USA. https://www.jstor.org/stable/2412767

SNICS. (2008a). Guia tecnica para la descripcción varietal No. 0976, CP-02-04. Servicio Nacional de Inspeción y Veridicación de Semillas, SAGARPA. México.

SNICS. (2008b). Guia tecnica para la descripcción varietal No. 0975, CP-02-01. Servicio Nacional de Inspeción y Veridicación de Semillas,, SAGARPA. México.

SNICS. (2018). Catalogo nacional de variedades vegetales, 3er trimestre. Servicio Nacional de Inspeción y Veridicación de Semillas, SAGARPA, México. https://www.gob.mx/cms/uploads/attachment/file/401833/CNVV3erTrim18_web_.pdf

Tyrka, M., Dziadczyk P, Hortyński J. A. (2002). Simplified AFLP procedure as a tool for identification of strawberry cultivars and advanced breeding lines. Euphytica 125(2):273-280. doi: 10.1023/A:1015892313900.

Whitaker, V. M. (2011). Applications of molecular markers in strawberry. Journal of Berry Research 1(3):115-127. doi: 10.3233/BR-2011-013.

Whitaker, V.M., Hashing T, Chandler C.K, Ploto A, Baldwin E. (2011). Historical trends in strawberry fruit quality revealed by a trial of University of Florida cultivars and advanced selections. HortScience 46(4): 553-57. https://gcrec.ifas.ufl.edu/static/docs/pdf/Historical_Retrospective.pdf

Yoon, M. Y., Moe K. T, Kim D.Y, Rho I. R, Kim S, Kim K. T, Won M K, Chung J W, Park Y. J. (2012). Genetic diversity and population structure analysis of strawberry (Fragaria × ananassa Duch.) using SSR markers. Electronic Journal of Biotechnology 15(2):1-16. doi: 10.2225/vol15-issue2-fulltext-5.

Zhang, L., Li Z, Wang Y, Jiang Z, Wang S, Huang H. (2010). Vitamin C, flower color and ploidy variation of hybrids from a ploidy-unbalanced Actinidia interspecific cross and SSR characterization. Euphytica 175(1):133-143. doi: 10.1007/s10681-010-0194-z.

DOI: https://doi.org/10.21640/ns.v11i22.1794


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