Analyse of iPBS lenght polymorphism in selected group of Vitis vinifera, L varieties

Authors

  • Jana Žiarovská SPU v Nitre
  • Adam Kováčik
  • Silvia Farkasová
  • Martina Fikselová
  • Jozef Sabo
  • Miroslava Kačániová

Keywords:

Vitis vinifera L, iPBS, DNA markers, polymorphism, genetic distance

Abstract

Here, the specific natural variability of iPBS (Inter Primer Binding Sites Polymorphism) fingerprints in thirteen varieties of Vitis vinifera, L. was performed. All of the analysed biological material was collected in the vineyard of Sabo vinery for describing of the existing genetic polymorphism. Young leaves from a total of thirteen grapevine varieties were obtained in the in the Small Carpathians wine region of Slovakia, Vrbové. Genetic length polymorphism was studied by iPBS markers. A dendrogram of genetic similarity of generated fingerprints was constucted by UPGMA (Unweighted Pair Group Method with Arithmetic mean) and the Jaccard coefficient of genetic similarity was used for the analyse of 13 Vitis vinifera, L varieties. The generated dendrogram is separated into three major clusters at the genetic dissimilarity of 0.58. Cluster 1 is composed of two red varieties – Alibernet and  Cabernet Sauvignon. Cluster 2 was further subdivided into two sub-clusters, where the larger one include all white varieties - Pinot Blanc, Müller-Thurgau, Welschriesling, Irsai Oliver, Grüner Veltliner, Pálava, Weisser Riesling, Sauvignon Blanc and Feteasca Regala. The second subcluster is comprised from two red varieties – Blaufränkisch and Dornfelder.  The analysis prooved the the iPBS technique is an effective retrotransposon based markers to evaluate the variability of  the genome in the germplasm of Vitis vinifera L. cultivated varieties.

References

Aydın, F. et al. (2020). The utility of iPBS retrotransposons markers to analyze genetic variation in yeast. International Journal of Food Microbiology,16, 325,108647.

Baránek, M. et al. (2012). Utility of retrotransposon-derived marker systems for differentiation of presumed clones of the apricot cultivar Velkopavlovická. Scientia Horticulturae, 143, 1–6.

Balážová, Ž. et al. (2014). Genetic diversity of triticale cultivars based on microsatellite and retrotransposon-based markers. Journal of Microbiology, Biotechnology and Food Sciences, 3, 58–60.

Belgorudova, I. et al. (2012). Usability of retrotransposone-based molecular marker system to assess genetic diversity of Liparis loeselii. Acta Biologica Universitatis Daugavpiliensis, 12, 40–43.

Blondon, A.F.A. & Zapater, J.M.M. & Kole, C. (2011). Genetics, genomics and breeding of grapes. Science publishers. ISBN 978-1-57808-717-4

Boronnikova, S.V. & Kalendar, R.N. (2010). Using IRAP markers for analysis of genetic variability in populations of resource and rare species of plants. Russian Journal of Genetics, 46(1), 36–42. https://doi.org/10.1134/S1022795410010060

Bourquin, J.C. et al. (1992). Identification of sixteen grapevine rootstocks by RFLP and RFLP analysis of nuclear DNA extracted from the wood. Journal of Grapevine Research, 31(3), https://doi.org/10.5073/vitis.1992.31.157-162

Buti, M. et al. (2009). HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.). Genome, 52, 904–911.

Castro, I. et al. (2012). Effectiveness of AFLPs and retrotransposon-based markers for the identification of Portuguese grapevine cultivars and clones. Molecular Biotechnology, 52, 26–39.

Collins, G.G. &,Symons, R.H. (1993). Polymorphisms in grapevine DNA detected by the RAPD-PCR technique. Plant Molecular Biology Reporter, 11, 105–111.

Coutinho, J.P. et al. (2018). Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers. Molecular Biology Reporter, 45, 133–142.

De Oliveira, G.L. et al. (2020) Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs. PLoS ONE, 15(10), e0240665. https://doi.org/10.1371/journal.pone.0240665

De Riek, J. et al. (2001). AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theoretical and Applied Genetics, 103, 1254–1265.

Emanuelli, F. et al. (2014). Development of user-friendly functional molecular markers for VvDXS gene conferring muscat flavor in grapevine. Molecular breeding: new strategies in plant improvement, 33, 235–241. https://doi.org/10.1007/s11032-013-9929-6

Gailite, A. & Rungis, D. (2012). An initial investigation of the taxonomic status of Saussurea esthonica Baer ex Rupr. utilising DNA markers and sequencing. Plant Systematics and Evolution, 298, 913–919.

Giannuzzi, G. et al. (2011). Analysis of high-identity segmental duplications in the grapevine genome. BMC Genomics, 12, 436. https://doi.org/10.1186/1471-2164-12-436

Gilbert, J. et al. (1999). Developing an appropriate strategy to assess genetic variability in plant germplasm collections. Theoretical and Applied Genetics, 98, 1125–1131.

Grimplet, J. et al. (2014). The grapevine gene nomenclature system. BMC Genomics, 15(1077), 1–14. https://doi.org/10.1186/1471-2164-15-1077

Guo, D.L. et al. (2014). Molecular diversity analysis of grape varieties based on iPBS markers. Biochemical Systematics and Ecology, 52, 27–32. https://doi.org/10.1016/j.bse.2013.10.008

Ilnitskaya, E., Makarkina, m., Tokmakov, S., Kotlyar. 2020. DNA-marker identification of Rpv3 and Rpv12 resistance loci in genotypes of table and seedless grape varieties, BIO Web Conf., 25, 03004 DOI: https://doi.org/10.1051/bioconf/20202503004

Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Société vaudoise des sciences naturelles, 44(163), 223–270.

Kalendar, R. et al. (2010). iPBS: a universal method for DNA fingerprinting and retrotransposon isolation. Theoretical and Applied Genetics, 121, 1419–1430. https://doi.org/10.1007/s00122-010-1398-2

Kalendar, R. & Amenov, A. & Daniyarov, A. (2019). Use of retrotransposon-derived genetic markers to analyse genomic variability in plants. Functional Plant Biology, 46(1), 15–29. https://doi.org/10.1071/FP18098

Lessig, V.P. (1972). Comparing cluster analyses with cophenetic correlation. Journal of Marketing Research, 9(1), 82–84.

Mangini, G. et al. 2010. Identification of durum wheat cultivars by a minimum number of microsatellite markers. Cereal Research Communication, 38, 155–162.

Milovanov, A. et al. (2019). Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers. Genetica, 147, 91–101.

Monden, Y. J. & Yamaguchi, K. & Tahara, M. (2014ň. Application of iPBS in high-throughput sequencing for the development of retrotransposon-based molecular markers. Current Plant Biology, 1, 40–44. https://doi.org/10.1016/j.cpb.2014.09.001

Rohlf, F. (2005). NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.2. Exeter Software, Setauket, New York.

Saiki, R. et al. (1985). Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 230(4732), 1350–1354. https://doi.org/10.1126/science.2999980

Salunkhe, A. et al. (2013). Molecular genetic diversity analysis in emmer wheat (Triticum dicoccon Schrank.) from India. Genetic Resources and Crop Evolution, 60, 165–174.

Sharma, K. S. & Rao, S.R. & Shamurailatpam, A. (2010). DNA based molecular markers: concept, techniques and comparison. Advances in Applied Biotechnology, 1–22.

Smýkal, P. et al. 2011. Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers. Theoretical and Applied Genetics, 122(7), 1385–1397. https://doi.org/10.1007/s00122-011-1539-2

Terral, J.F. et al. (2009). Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars. Annals of Botany, 105(3), 443–455. https://doi.org/PMC2826248

Tessier, C. et al. (1999). Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theoretical and Applied Genetics, 98, 171–177.

Velasco, R. et al. (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS. ONE, 2, e1326.

Zhou, Y. et al. (2017). Evolutionary genomics of grape (Vitis vinifera ssp. vinifera) domestication. Proceeding of the National Academy of Sciences of the United States of America, 114(44), 11715–11720.

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Published

2022-07-11 — Updated on 2022-10-13

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Plant Science