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Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits

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Abstract

Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice’s coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs.

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References

  1. Lodhi MA, Reisch BI (1995) Nuclear DNA content of species, cultivars, and other genera of the Vitaceae. Theor Appl Genet 90:11–16

    CAS  PubMed  Google Scholar 

  2. McGovern PE (2019) Ancient wine: the search for the origins of viniculture. Princeton University Press, Princeton

    Google Scholar 

  3. Amiri M (2006) The status of genetic resources of deciduous, tropical, and subtropical fruit species in Iran. In XXVII International Horticultural Congress-IHC2006: International Symposium on Asian Plants with Unique Horticultural 769, pp 159–167

  4. Doulaty Baneh H, Grassi F, Mohammadi A, Nazemieh A, De Mattia F, Imazio S, Labra M (2007) The use of AFLP and morphological markers to study Iranian grapevine germplasm to avoid genetic erosion. J Hortic Sci Biotechnol 82:745–752

    Google Scholar 

  5. Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E et al (2013) Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 13:39

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet 5:103–107

    CAS  PubMed  Google Scholar 

  7. Flavell AJ, Dunbar E, Anderson R, Pearce SR, Hartley R, Kumar A (1992) Ty1–copia group retrotransposons are ubiquitous and heterogeneous in higher plants. Nucleic Acids Res 20:3639–3644

    CAS  PubMed  PubMed Central  Google Scholar 

  8. Waugh R, McLean K, Flavell A, Pearce S, Kumar A, Thomas B, Powell W (1997) Genetic distribution of Bare–1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP). Mol Gen Genet 253:687–694

    CAS  PubMed  Google Scholar 

  9. Flavell AJ, Knox MR, Pearce SR, Ellis TN (1998) Retrotransposon-based insertion polymorphisms (RBIP) for high throughput marker analysis. Plant J 16:643–650

    CAS  PubMed  Google Scholar 

  10. Kalendar R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711

    CAS  Google Scholar 

  11. Paux E, Roger D, Badaeva E, Gay G, Bernard M, Sourdille P, Feuillet C (2006) Characterizing the composition and evolution of homoeologous genomes in hexaploid wheat through BAC-end sequencing on chromosome 3B. Plant J 48:463–474

    CAS  PubMed  Google Scholar 

  12. Wanjugi H, Coleman-Derr D, Huo N, Kianian SF, Luo M-C, Wu J, Anderson O, Gu YQ (2009) Rapid development of PCR-based genome-specific repetitive DNA junction markers in wheat. Genome 52:576–587

    CAS  PubMed  Google Scholar 

  13. Mandoulakani BA, Piri Y, Darvishzadeh R, Bernoosi I, Jafari M (2012) Retroelement insertional polymorphism and genetic diversity in Medicago sativa populations revealed by IRAP and REMAP markers. Plant Mol Biol Rep 30:286–296

    Google Scholar 

  14. Kalendar R, Schulman AH (2006) IRAP and REMAP for retrotransposon-based genotyping and fingerprinting. Nat Protoc 1:2478

    CAS  PubMed  Google Scholar 

  15. Pereira HS, Barão A, Delgado M, Morais-Cecílio L, Viegas W (2005) Genomic analysis of grapevine retrotransposon 1 (Gret1) in Vitis vinifera. Theor Appl Genet 111:871–878

    CAS  PubMed  Google Scholar 

  16. Fujita K, Shimazaki M, Furiya T, Takayanagi T, Suzuki S (2009) Genetic variation among Koshu (Vitis vinifera L.) accessions generated by retrotransposon insertion into genome. Am J Enol Viticult 60:490–496

    CAS  Google Scholar 

  17. Verries C, Bes C, This P, Tesniere C (2000) Cloning and characterization of Vine-1, a LTR-retrotransposon-like element in Vitis vinifera L., and other Vitis species. Genome 43:366–376

    CAS  PubMed  Google Scholar 

  18. Pelsy F, Merdinoglu D (2002) Complete sequence of Tvv1, a family of Ty1 copia-like retrotransposons of Vitis vinifera L., reconstituted by chromosome walking. Theor Appl Genet 105:614–621

    CAS  PubMed  Google Scholar 

  19. Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463

    CAS  PubMed  Google Scholar 

  20. Velasco R, Zharkikh A, Troggio M, Cartwright DA, Cestaro A, Pruss D, Pindo M, FitzGerald LM, Vezzulli S et al (2007) A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE 2:e1326

    PubMed  PubMed Central  Google Scholar 

  21. Villano C, Carputo D, Frusciante L, Santoro X, Aversano R (2014) Use of SSR and retrotransposon-based markers to interpret the population structure of native grapevines from Southern Italy. Mol Biotechnol 56(11):1011–1020

    CAS  PubMed  Google Scholar 

  22. Castro I, D’Onofrio C, Martı´n JP, Marı´a Ortiz J, De Lorenzis G, Ferreira V, Pinto-Carnide O (2011) Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Mol Biotechnol 52(1):26–39

    Google Scholar 

  23. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  24. 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

    Google Scholar 

  25. Rohlf J, Rohlf F, Rohlf E, Rohlf J (1993) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Software, Setauket, New York, NY, USA

  26. Lanes EC, Viana JM, Paes GP, Paula MF, Maia C, Caixeta ET, Miranda GV (2014) Population structure and genetic diversity of maize inbreds derived from tropical hybrids. Genet Mol Res 13:7365–7376. https://doi.org/10.4238/2014.September.12.2

    Article  CAS  PubMed  Google Scholar 

  27. Lynch M, Milligan BG (1994) Analysis of population genetic structure with RAPD markers. Mol Ecol 3:91–99

    CAS  PubMed  Google Scholar 

  28. Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  29. Perrier X, Jacquemoud-Collet J (2016) DARwin software: dissimilarity analysis and representation for Windows (version 6.0. 010)

  30. Jombart T, Devillard S, Balloux F (2010) Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. BMC Genet 11(1):94

    PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Khadivi-Khub A, Salimpour A, Rasouli M (2014) Analysis of grape germplasm from Iran based on fruit characteristics. Braz J Bot 37(2):105–113

    Google Scholar 

  33. Boz Y, Bakir M, Cerlikkol BP, Kazan K, Yilmaz F, Cakir B, Aslantas S (2011) Genetic characterization of grape (Vitis vinifera L.) germplasm from Southeast Anatolia by SSR markers. Vitis 50:99–106

    Google Scholar 

  34. 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 

  35. Rold´an-Ruiz I, Dendauw J, Van Bockstaele E, Depicker A, De Loose M (2000) AFLP markers reveal high polymorphic rates in ryegrasses (Lolium spp.). Mol Breeding 6:125–134

    Google Scholar 

  36. Fatahi R, Ebadi A, Bassil N, Mehlenbacher S, Zamani Z (2003) Characterization of Iranian grapevine cultivars using microsatellite markers. Vitis 42:185–192

    CAS  Google Scholar 

  37. Crespan M, Milani N (2001) The Muscats: a molecular analysis of synonyms, homonyms and genetic relationships within a large family of grapevine cultivars. Vitis 40:23–30

    CAS  Google Scholar 

  38. Regner F, Stadlbauer A, Eisenheld C, Kaserer H (2000) Genetic relationships among Pinots and related cultivars. Am J Enol Viticult 51:7–14

    CAS  Google Scholar 

  39. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-induced mutations in grape skin color. Science 304:982–982

    PubMed  Google Scholar 

  40. 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

    PubMed  Google Scholar 

  41. Forneck A (2005) Plant breeding: clonality—a concept for stability and variability during vegetative propagation. In: Luttge U et al (eds) Progress in Botany. Springer, New York, pp 164–183

    Google Scholar 

  42. Hocquigny S, Pelsy F, Dumas V, Kindt S, Heloir M, Merdinoglu D (2004) Diversification within grapevine cultivars goes through chimeric states. Genome 47:579–589

    CAS  PubMed  Google Scholar 

  43. Moncada X, Pelsy F, Merdinoglu D, Hinrichsen P (2006) Genetic diversity and geographical dispersal in grapevine clones revealed by microsatellite markers. Genome 49:1459–1472

    CAS  PubMed  Google Scholar 

  44. Wegscheider E, Benjak A, Forneck A (2009) Clonal variation in Pinot noir revealed by S-SAP involving universal retrotransposon-based sequences. Am J Enol Viticult 60:104–109

    CAS  Google Scholar 

  45. Benjak A, Forneck A, Casacuberta JM (2008) Genome-wide analysis of the “cut-and-paste” transposons of grapevine. PLoS ONE 3:3107

    Google Scholar 

  46. Moisy C, Garrison KE, Meredith CP, Pelsy F (2008) Characterization of ten novel Ty1/copia-like retrotransposon families of the grapevine genome. BMC Genom 9:469

    Google Scholar 

  47. Silvestroni O, Di Pietro D, Intrieri C, Vignani R, Filippetti I, Del Casino C, Scali M, Cresti M (1997) Detection of genetic diversity among clones of cv. Fortana (Vitis vinifera L.) by microsatellite DNA polymorphism analysis. Vitis 36:147–150

    Google Scholar 

  48. Frazer KA, Murray SS, Schork NJ, Topol EJ (2009) Human genetic variation and its contribution to complex traits. Nat Rev Genet 10:241–251

    CAS  PubMed  Google Scholar 

  49. Tautz D, Renz M (1984) Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Bennetzen JL (2000) Transposable element contributions to plant gene and genome evolution. Plant Mol Biol 42:251–269

    CAS  PubMed  Google Scholar 

  51. Kidwell MG, Lisch D (1997) Transposable elements as sources of variation in animals and plants. Proc Natl Acad Sci USA 94:7704–7711

    CAS  PubMed  Google Scholar 

  52. Laucou V, Lacombe T, Dechesne F, Siret R, Bruno J-P, Dessup M, Dessup T, Ortigosa P, Parra P et al (2011) High throughput analysis of grape genetic diversity as a tool for germplasm collection management. Theor Appl Genet 122:1233–1245

    CAS  PubMed  Google Scholar 

  53. Robinson J, Harding J, Vouillamoz J (2013) Wine grapes: a complete guide to 1,368 vine varieties, including their origins and flavours. Penguin Books, London

    Google Scholar 

  54. Grassi F, Labra M, Imazio S, Spada A, Sgorbati S, Scienza A, Sala F (2003) Evidence of a secondary grapevine domestication centre detected by SSR analysis. Theor Appl Genet 107:1315–1320

    CAS  PubMed  Google Scholar 

  55. Snoussi H, Slimane MHB, Ruiz-García L, Martínez-Zapater JM, Arroyo-García R (2004) Genetic relationship among cultivated and wild grapevine accessions from Tunisia. Genome 47:1211–1219

    CAS  PubMed  Google Scholar 

  56. Cornille A, Gladieux P, Smulders MJ, Roldan-Ruiz I, Laurens F, Le Cam B, Nersesyan A, Clavel J, Olonova M et al (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet 8:1002703

    Google Scholar 

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Acknowledgements

Authors thank the Support of the University of Zanjan (Iran) in the stay of Mitra Razi at CEBAS-CSIC of Murcia (Spain).

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Authors and Affiliations

  1. Department of Horticulture, University of Zanjan, P.O. Box 45371-38791, Zanjan, Iran

    M. Razi & M. E. Amiri

  2. Institute of Biotechnology, Urmia University, Shahid Beheshti St, Urmia, Iran

    R. Darvishzadeh

  3. Department of Plant Production and Genetics, Urmia University, P.O. Box 165, 11 Kilometer Sero Road, Daneshgah Boulevard, Urmia, Iran

    R. Darvishzadeh & H. Alipour

  4. Horticultural Crops Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, AREEO, Sanandaj, Iran

    H. Doulati Baneh

  5. Plant Breeding Department, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo, Murcia, Spain

    P. Martínez-Gómez

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  1. M. Razi
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Contributions

MR contributed to all the experimental activities, data analysis and results explanations as well as writing the paper. MEA and RD designed and supervised the work. HDB involved in preparing the plant materials. HA contributed to analyze part of the data. PM-G and RD contributed to review and edit of manuscript. All authors contributed to the discussion. The authors accept full responsibility for the context of the manuscript.

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Correspondence to R. Darvishzadeh.

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Razi, M., Amiri, M.E., Darvishzadeh, R. et al. Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits. Mol Biol Rep 47, 7593–7606 (2020). https://doi.org/10.1007/s11033-020-05827-3

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