Genetic variability of commercially important apple varieties (Malus x domestica Borkh.) assessed by CDDP markers

Abstract

Received: 2020-10-13 Accepted: 2021-02-08 Available online: 2021-02-28
https://doi.org/10.15414/afz.2021.24.mi-apa.21-26

Apple stand on the top of the most desirable and most produced fruit species in the world. Despite enormously wide genetic
diversity among existing apple varieties, the current market is mostly oriented on several cultivars of commercially attractive
traits. For the preservation of genetic resources and for breeding programmes, the evaluation of genetic diversity is fundamental.
Number of marker systems have been developed and adopted in the assessment apple germplasm. In the present study, CDDP
marker technique was used to analyse polymorphism within the genomes of fifteen apple varieties which are of large commercial
use. Five primer combinations were used in the PCR amplification: WRKY-F1/WRKY-R1, WRKY-F1/WRKY-R2, WRKY-F1/WRKY-R2B,
WRKY-F1/WRKY-R3 and WRKY-F1/WRKY-R3B. All primer combinations produced polymorphic amplification patterns. In some
primer combinations, identical amplification profiles were observed in few varieties, but amplification patterns of all combinations
merged were specific for each apple variety. Identical profiles were only seen in Red Delicious and Granny Smith in F1/R1 primer
combination, May Gold and Paula Red, and Selena and Melodie in F1/R2 primer combination and May Gold and Paula Red when
F1/R3B primers were used. Based on the CDDP markers, UPGMA algorithm assessed cultivars Paula Red and May Gold as the
most similar (with similarity value of 0.909), whereas Gloster and Ambrosia showed to be the least similar within the analyzed set
(similarity value of 0.200). The study proved CDDP markers to be suitable tool to produce polymorphic amplification patterns in
apple genotypes.

Keywords: conserved DNA-derived polymorphism, genetic variability, WRKY, DNA markers

References
Aouadi , M. et al. (2019). Conserved DNA-derived polymorphism, new markers for genetic diversity analysis of Tunisian Pistacia
vera L. Physiology and Molecular Biology of Plants, 25(5), 1211–1223. https://doi.org/10.1007/s12298-019-00690-4
Atia, M. A. M. (2017). Assessing date palm genetic diversity using different molecular markers. Methods Mol Biol, 1638, 125–142.
https://doi.org/10.1007/978-1-4939-7159-6_12
Collard, B. C. and Mackill, D. J. (2009). Conserved DNA-derived polymorphism (CDDP): a simple and novel method for
generating DNA markers in plants. Plant Molecular Biology Reporter, 27(4), 558–562. https://doi.org/10.1007/s11105-009-0118-z
Cornille, A. et al. (2014). The domestication and evolutionary ecology of apples. Trends in Genetics, 30(2), 57–65. https://doi.
org/10.1016/j.tig.2013.10.002
Davila , J. A. et al. (1998). The use of random amplified microsatellite polymorphic DNA and coefficients of parentage to
determine genetic relationships in barley. Genome, 41, 477–486. https://doi.org/10.1139/g98-044
Dar , J. A. et al. (2020). Assessment of Apple (Malus × domestica Bark.) Germplasm of Kashmir Using RAPD Markers. International
Journal of Fruit Science, 20(3), 635–645. https://doi.org/10.1080/15538362.2019.1639583
Gardiner, S. E. et al. (1996). Isozyme, randomly amplified polymorphic DNA (RAPD), and restriction fragment-length
polymorphism (RFLP) markers used to deduce a putative parent for the ‘Braeburn’ apple. Journal of the American Society
for Horticultural Science, 121(6), 996–1001. https://doi.org/10.21273/JASHS.121.6.99Goulao , L. et al. (2001). Comparing RAPD and AFLPTM analysis in discrimination and estimation of genetic similarities among
apple (Malus domestica Borkh.) cultivars. Euphytica, 119(3), 259–270. https://doi.org/10.1023/A:1017519920447
Goulao , L. and Oliveira , C.M. (2001). Molecular characterisation of cultivars of apple (Malus × domestica Borkh.) using
microsatellite (SSR and ISSR) markers. Euphytica, 122, 81–89. https://doi.org/10.1023/A:1012691814643
Gross , B. L. (2014). Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication. American
Journal of Botany, 101(10), 1770–1779. https://doi.org/10.3732/ajb.1400297
Hajibarat , Z. et al. (2015). Characterization of genetic diversity in chickpea using SSR markers, start codon targeted
polymorphism (SCoT) and conserved DNA-derived polymorphism (CDDP). Physiol Mol Biol Plants, 21(3), 365–373. https://doi.
org/10.1007/s12298-015-0306-2
Jiang, L. and Zang, D. (2018). Analysis of genetic relationships in Rosa rugosa using conserved DNA-derived polymorphism
markers. Biotechnol Biotechnol Equip, 32(1), 88–94. https://doi.org/10. 1080/13102818.2017.1407255
Kafkas , S. et al. (2008). Molecular characterization of mulberry accessions in Turkey by AFLP markers. J Am Soc Hort Sci, 4,
593–597. https://doi.org/10.21273/JASHS.133.4.593
Kyse ľ, M. et al. (2019). Marker profiling of wheat with different drought tolerance by CDDP. Journal of Microbiology, Biotechnology
and Food Sciences, 9(4), 1220–1222. https://doi.org/10.15414/jmbfs.2019.8.5.1220-1222
Li, T. et al. (2013). Genetic diversity assessment of chrysanthemum germplasm using conserved DNA-derived polymorphism
markers. Sci Hortic, 162, 271–277. https://doi.org/10.1016/j.scienta.2013.08.027
Li, Y. Y. and Zheng, C. S. (2013). Genetic diversity of Tree Peony cultivar resources in Heze Revealed by CDDP Marker. Scientia
Agric Sin, 46(13), 2739–2750.
Li, T. et al. (2014). Genetic diversity and construction of fingerprinting of chrysanthemum cultivars by CDDP markers. J Beijing
For Univ, 36(4), 95–101. https://doi.org/10.13332/j.cnki.jbfu.2014.04.018
Myles , S. et al. (2011). Genetic structure and domestication history of the grape. Proceedings of the National Academy of
Sciences, 108(9), 3530–3535. https://doi.org/10.1073/pnas.1009363108
Myles , S. (2013). Improving fruit and wine: what does genomics have to offer? Trends in Genetics, 29(4), 190–196. https://doi.
org/10.1016/j.tig.2013.01.006
Nei, M. (1973). Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci., (70), 3321–3323. doi: 10.1073/
pnas.70.12.3321
Oraguzie , N. C. et al. (2001). Genetic diversity and relationships in Malus sp. germplasm collections as determined by randomly
amplified polymorphic DNA. Journal of the American Society for Horticultural Science, 126(3), 318–328. https://doi.org/10.21273/
JASHS.126.3.318
Oraguzie , N.C. et al. (2005). DNA fingerprinting of apple (Malus spp.) rootstocks using Simple Sequence Repeats. Plant
Breeding, 124, 197–202. https://doi.org/10.1111/j.1439-0523.2004.01064.x
Pavlovic , N. et al. (2012). Characterization of onion genotypes by use of RAPD markers. Genetika, 2, 269–278. https://doi.
org/10.2298/GENSR1202269P
Pereira -Lorenzo , S. et al. (2007). Evaluation of genetic identity and variation of local apple cultivars (Malus × domestica) from
Spain using microsatellite markers. Genetic Resources and Crop Evolution, 54(2), 405–420. https://doi.org/10.1007/s10722-006-0003-7
Royo , J. B. and Itoiz , R. (2004). Evaluation of the discriminance capacity of RAPD, isoenzymes and morphologic markers in
apple (Malus × domestica Borkh.) and the congruence among classifications. Genetic Resources and Crop Evolution. 51(2), 153–160.
https://doi.org/10.1023/B:GRES.0000020857.29125.2b
Sansavini , S. et al. (2004). Advances in apple breeding for enhanced fruit quality and resistance to biotic stresses: new varieties
for the European market. J Fruit Orn Plant Res, 12, 13–51.
Tignon, M. et al. (2001). Distinction between closely related apple cultivars of the belle-fleur family using RFLP and AFLP
markers. Acta Horticulturae, 546, 509–513. https://doi.org/10.17660/ActaHortic.2001.546.70
Velasco , R. et al. (2010). The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet., 42(10), 833–839.
https://doi.org/10.1038/ng.654
Wang, X. et al. (2014). Analysis of genetic relationships in tree peony of different colors using conserved DNA-derived
polymorphism markers. Sci Hortic, 175, 68–73. https://doi.org/10.1016/j.scienta.2014.05.026
Way, R. (1990). Apples. In Moore, J. and Ballington, J. (eds.): Genetic resources of temperate fruit and nut crops. International society
for horticultural science, Wageningen, Netherlands, pp. 1–62.
WAPA (2019). European apple forecast. Available at: http://www.wapa-association.org/docs/2019/European_summary_
reduced.pdf
Yeh, F.C., Yang, R.C. and Boyle , T. (1999). Popgene Software Package Version 1.31 for Population Genetic Analysis. University
of Alberta; Edmonton, AB, Canada.
Žiarovská, J. et al. (2019). Restriction polymorphism of Mal d 1 allergen promotor in apple varieties. Journal of Microbiology,
Biotechnology and Food Sciences, 8(5), 1217–1219. https://doi.org/10.15414/jmbfs.2019.8.5.1217-1219