Genetic Markers Analyses and Bioinformatic Approaches to Distinguish Between Olive Tree (Olea europaea L.) Cultivars

Interdisciplinary Sciences – Computational Life Sciences

Volumn 8, Issue 4, 2016, Pages 366-373

  Ben Ayed, Rayda ^a   Ben Hassen, Hanen ^b   Ennouri, Karim ^a   Rebai, Ahmed ^a  

^a CENTRE DE BIOTECHNOLOGIE DE SFAX   (Tunisia)

^b University of Sfax   (Tunisia)

Author keywords

Bioinformatic approaches; Classification; Cultivars; Markers; Olea europaea L; Olive oil; PCoA; UPGMA

Indexed keywords

GENETIC MARKER;

BIOLOGY; CLASSIFICATION; GENETIC MARKER; GENETICS; GENOTYPE; OLIVE TREE; PHYLOGENY; PROCEDURES;

COMPUTATIONAL BIOLOGY; GENETIC MARKERS; GENOTYPE; OLEA; PHYLOGENY;

EID: 84995592231     PISSN: 19132751     EISSN: 18671462     Source Type: Journal    
DOI: 10.1007/s12539-016-0155-x     Document Type: Article

References (31)

1. Elloumi J, Ben Ayed R, Aifa S (2012) An overview of olive oil biomolecules. Curr Biotechnol 1(2):115–124. doi:10.2174/2211550111201020115
2. Barranco D, Rallo L (2000) Olive cultivars in Spain. HortTechnology 10(1):107–110
3. Ben Ayed R, Grati-Kamoun N, Moreau F, Rebaï A (2009) Comparative study of microsatellite profiles of DNA from oil and leaves of two Tunisian olive cultivars. Eur Food Res Technol 229(5):757–762. doi:10.1007/s00217-009-1111-3
4. Busconi M, Foroni C, Corradi M, Bongiorni C, Cattapan F, Fogher C (2003) DNA extraction from olive oil and its use in the identification of the production cultivar. Food Chem 83(1):127–134. doi:10.1016/S0308-8146(03)00218-8
5. Grati-Kamoun N, Lamy Mahmoud F, Rebai A, Gargouri A, Panaud O, Saar A (2006) Genetic diversity of Tunisian olive tree (Olea europaea L.) cultivars assessed by AFLP markers. Genet Resour Crop Evol 53:265–275. doi:10.1007/s10722-004-6130-0
6. Pafundo S, Agrimonti C, Marmiroli N (2005) Traceability of plant contribution in olive oil by amplified fragment length polymorphisms. J Agric Food Chem 53(18):6995–7002. doi:10.1021/jf050775x
7. Ben Ayed R, Grati-kamoun N, Sans-grout C, Moreau F, Rebai A (2012) Characterization and authenticity of virgin olive oil (Olea europaea L.) cultivars by microsatellite markers. Eur Food Res Technol 234(2):263–271. doi:10.1007/s00217-011-1631-5
8. Rekik I, Salimonti A, Grati-Kamoun N, Muzzalupo I, Lepais O, Gerber S, Perri E, Rebai A (2008) Characterization and identification of Tunisian olive tree varieties by microsatellite markers. HortScience 43(5):1371–1376
9. Consolandi C, Palmieri L, Doveri S, Maestri E, Marmiroli N, Reale S, Lee D, Baldoni L, Tosti N, Severgnini M, De Bellis G, Castiglioni B (2007) Olive variety identification by ligation detection in a universal array format. J Biotechnol 129(3):565–574. doi:10.1016/j.jbiotec.2007.01.025
10. Consolandi C, Palmieri L, Severgnini M, Maestri E, Marmiroli N, Agrimonti C, Baldoni L, Donini P, De Bellis G, Castiglioni B (2008) A procedure for olive oil traceability and authenticity: DNA extraction, multiplex PCR and LDR-universal array analysis. Eur Food Res Technol 227(5):1429–1438. doi:10.1007/s00217-008-0863-5
11. Rekik-Hakim I, Grati-Kammoun N, Makhloufi E, Rebaï A (2010) Discovery and potential of SNP markers in characterization of Tunisian olive germplasm. Diversity 2:17–27
12. Ben Ayed R, Grati-kamoun N, Rebai A (2013) An overview of the authentication of olive tree and oil. Compr Rev Food Sci Food Saf 12(2):218–227. doi:10.1111/1541-4337.12003
13. Ben Ayed R, Kallel I, Ben Hassen H, Rebai A (2014) SNP marker analysis for validating the authenticity of Tunisian olive oil. J Genet 93(3):148–154. doi:10.1007/s12041-014-0461-1
14. Ben Ayed R, Sans-grout C, Moreau F, Grati-kamoun N, Rebai A (2014) Genetic similarity among tunisian olive cultivars and two unknown feral olive trees estimated through SSR markers. Biochem Genet 52(5–6):258–268. doi:10.1007/s10528-014-9645-x
15. Trigui A, Msallem M (2002) Oliviers de Tunisie: catalogue des variétés autochtones et types locaux. Volume I (Identification variétale and caractérisation morpho-pomologique des ressources génétiques oléicoles de Tunisie). IRESA press, Tunis, p 159
16. Weir BS (1996) Genetic data analysis II: methods for discrete population genetic data. Sinauer Associates, Sunderland, p 376
17. Brenner C, Morris JW (1990) Paternity index calculations in single locus hypervariable DNA probes: validation and other studies. In: Madison WI (ed) International symposium on human identification. Promega Corporation, Madison, pp 21–53
18. Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270
19. Rohlf FJ (1999) NTSYS-pc. Numerical taxonomy and multivariate analysis system. Version 2.1. Exeter Software, Setauket
20. Reale S, Doveri S, Díaz A, Angiolillo A, Lucentini L, Pilla F, Martin A, Donini P, Lee D (2006) SNP-based markers for discriminating olive (Olea europaea L.) cultivars. Genome 49(9):1193–1205
21. Cipriani G, Marrazzo MT, Marconi R, Cimato A, Testolin R (2002) Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars. Theor Appl Genet 104(2–3):223–228
22. Muzzalupo I, Stefanizzi F, Perri E (2009) Evaluation of olives cultivated in southern Italy by simple sequence repeat markers. HortScience 44(3):582–588
23. Besnard G, Breton C, Baradat P, Khadari B, Bervillé A (2001) Cultivar identification in olive (Olea europaea L.) based on RAPD markers. J Am Soc Hortic Sci 126(6):668–675
24. Rao R, La Mura M, Corrado G, Ambrosino O, Foroni I, Perri E, Pugliano G (2009) Molecular diversity and genetic relationships of southern Italian olive cultivars as depicted by AFLP and morphological traits. J Hortic Sci Biotechnol 84(3):261–266
25. Farris JS (1969) On the cophenetic correlation coefficient. Syst Zool 18(3):279–285
26. Saraçli S, Doğan N, Doğan I (2013) Comparison of hierarchical cluster analysis methods by cophenetic correlation. J Inequal Appl 2013:203. doi:10.1186/1029-242X-2013-203
27. Shiria MR, Choukanb R, Aliyevc RT (2014) Study of genetic diversity among maize hybrids using SSR markers and morphological traits under two different irrigation conditions. Crop Breed J 4(1):65–72
28. Belaj A, Trujillo I, de la Rosa R, Rallo L (2001) Polymorphism and discrimination capacity of randomly amplified polymorphic markers in an olive germplasm bank. J Am Soc Hortic Sci 126(1):64–71
29. Taamalli W, Geuna F, Banfi R, Bassi D, Daoud D, Zarrouk M (2007) Using microsatellite markers to characterize the main Tunisian olive cultivars ‘Chemlali’ and ‘Chetoui’. J Hortric Sci Biotechnol 82(1):25–28
30. Ben Ayed R, Ennouri K, Ben Hassen H, Triki MA, Rebai A (2015) Comparaison between DNA-based, pomological and chemical markers accomplished by bioinformatic tools to distinguish within Tunisian olive cultivars. J Fundam Appl Sci 7(3): 408–421
31. Ben Ayed R, Ben Hassen H, Ennouri K, Ben Marzoug K, Rebai A (2015) OGDD (Olive Genetic Diversity Database): a microsatellite markers’ genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability. Database: J Biol Databases Curation 2015:1–9. doi:10.1093/database/bav090