Molecular characterization of genetic variability and structure of olive (Olea europaea L.) germplasm collection analyzed by agromorphological traits and microsatellite markers

We studied 200 trees belonging to 20 accessions of cultivated olive (O. europaea L.) from 4 regions of origin, evaluated by means of agromorphological traits and simple sequence repeat (SSR) markers. The agromorphological traits showed high variation between genotypes and significant correlation coefficients were obtained among the values recorded in two consecutive years, 2013 and 2014. The maximum coefficient of variation for the quantitative agronomic traits was observed in fruit weight wet (13.45%), while the lowest was found in stone width (3.18%). Fruit shape index, leaf length, leaf width, and lenticel size also showed variability. With both DNA-based and agromorphological descriptors, higher levels of variability were found. Genetic variation observed among the olive germplasm at the DNA level was higher than that of the agromorphological traits, indicating the efficiency of SSR markers for detecting genetic diversity among olive genotypes and their relationships. The lack of consistency between the relationship studies performed with molecular and morphological markers could indicate that each marker system measures different aspects of olive genetic variability. Molecular data obtained by SSR markers together with morphological and agronomical characterization of olive trees confirmed the high diversity and their potential use for olive breeding.

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Abdessemed S, Muzzalupo L, Benbouz H (2015). Assessment of genetic diversity among Algerian olive (Olea europaea L.) cultivars using SSR marker. Sci Hortic 192: 10-20.
Albertini E, Torricelli R, Bitocchi E, Raggi L, Marconi G, Pollastri L, Di Minco G, Battistini A, Papa R, Veronesi F (2011). Structure of genetic diversity in Olea europaea L. cultivars from central Italy. Mol Breed 27: 533-547.
Baldoni L, Belaj A (2009). Olive. In: Vollmann J, Rajcan I, editors. Oil Crops. Berlin, Germany: Springer, pp. 397-421.
Baldoni L, Tosti N, Ricciolini C, Belaj A, Arcioni S, Pannelli G, Germana MA, Mulas M, Porceddu A (2006). Genetic structure of wild and cultivated olives in the Central Mediterranean Basin. Ann Bot 98: 935-942.
Barranco D, Cimato A, Fiorino P, Rallo, L, Touzani A, Castaneda C, Serafíni F, Trujillo I (2000). World Catalogue of Olive Varieties. Madrid, Spain: International Olive Oil Council.
Barranco D, Trujillo I, Rallo L (2005). Elaiografía Hispánica. In: Rallo L, Barranco D, Caballero JM, del Rio C, Martín A, Tous J, Trujillo I, editors. Variedades de olivo en Espana. Junta de Andalucía. Madrid, Spain: MAPA-Ediciones Mundi-Prensa, pp. 48-76 (in Spanish).
Bartolini G, Prevost G, Messeri C, Carignani C (2005). Olive Germplasm: Cultivars and World-wide Collections. Rome, Italy: FAO/Plant Production and Protection.
Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991). Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196: 80-83.
Belaj A, Leon L, Satovic Rosa R (2011). Variability of wild olives (Olea europaea subsp. europaea var. sylvestris) analyzed by agro-morphological traits and SSR markers. Sci Hortic 129: 561-569.
Belaj A, Munoz-Diez C, Baldoni L, Porceddu A, Barranco D, Satovic Z (2007). Genetic diversity and population structure of wild olives from North-Western Mediterranean assessed by SSR markers. Ann Bot 100: 449-458.
Belaj A, Munoz-Diez C, Baldoni L, Satovic Z, Barranco D (2010). Genetic diversity and relationships of wild and cultivated olives at regional level in Spain. Sci Hortic 124: 323-330.
Belaj A, Satovic Z, Rallo L, Trujillo I (2002). Genetic diversity and relationships in olive (Olea europaea L.) germplasm collections as determined by randomly amplified polymorphic DNA. Theor Appl Genet 105: 638-644.
Besnard G, Baradat P, Bervillé A (2001). Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars. Theor Appl Genet 102: 251-258.
Botstein D, White RL, Sholnick M, David RW (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32: 314-331.
Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994). High resolution human evolutionary trees with polymorphic microsatellites. Nature 368: 455-457.
Bracci T, Busconi M, Fogher C, Sebastiani L (2011). Molecular studies in olive (Olea europaea L.): overview on DNA markers applications and recent advances in genome analysis. Plant Cell Rep 30:449-462.
Breton C, Tersac M, Bervillé A (2006). Genetic diversity and gene flow between the wild olive (oleaster Olea europaea L.) and the olive: several Plio-Pleistocene refuge zones in the Mediterranean basin suggested by simple sequence repeats analysis. J Biogeogr 33: 1916-1928.
Cantini C, Cimato A, Sani G (1999). Morphological evaluation of olive germplasm present in Tuscany region. Euphytica 109: 173-181.
Carriero F, Fontanazza G, Cellini F, Giorio G (2002) Identification of simple sequence repeats (SSRs) in olive (Olea europaea L.). Theor Appl Genet 104: 301-307.
Caruso T, Marra FP, Costa F, Campisi G, Macaluso L, Marchese A (2014). Genetic diversity and clonal variation within the main Sicilian olive cultivars based on morphological traits and microsatellite markers. Sci Hortic 180: 130-138.
Cipriani G, Marrazzo MT, Marconi R, Cimato A, Testolin R (2002). Microsatellite markers isolated in olive are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars (Olea europaea L.). Theor Appl Genet 104: 223-228.
Corrado G, La Mura M, Ambrosino O, Pugliano G, Varricchio P, Rao R (2009). Relationships of Campanian olive cultivars: comparative analysis of molecular and phenotypic data. Genome 52: 692-700.
De la Rosa R, James C, Tobutt KR (2002). Isolation and characterization of polymorphic microsatellite in olive (Olea europaea L.) and their transferability to other genera in the Oleacea. Primer note. Mol Ecol Notes 2: 265-267.
Del Río C, Caballero JM, García-Fernández MD, Tous J, Romero A (2005). Rendimiento graso de la aceituna. In: Rallo L, Barranco D, Caballero JM, del Rio C, Martín A, Tous J, Trujillo I, editors. Variedades de olivo en Espana. Junta de Andalucía. Madrid, Spain: MAPA-Ediciones Mundi-Prensa, pp. 347-356 (in Spanish).
Erre P, Chessa I, Munoz-Diez C, Belaj A, Rallo L, Trujillo I (2010). Genetic diversity and relationships between wild and cultivated olives in Sardinia as assessed by SSR markers. Genet Res Crop Evol 57: 41-54.
Evanno G, Regnaut S, Goudet J (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial restriction sites. Genetics 131: 479-491.
Falush D, Stephens M, Pritchard JK (2007). Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7: 574-578.
Felsenstein J (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
García-Donas Díaz M (2001). Caracterización morfológica, agronómica y elaiotécnica de los acebuches de la provincia de Cádiz. Trabajo profesional de fin de carrera. Cordoba, Spain: University of Cordoba (in Spanish).
García-Verdugo C, Forrest AD, Balaguer L, Fay MC, Vargas P (2010). Parallel evolution of insular Olea europaea subspecies based on geographical structuring of plastid DNA variation and phenotypic similarity in leaf traits. Bot J Linn Soc 162: 54-63.
Gemas VJV, Almadanim MC, Tenreiro R, Martins A, Fevereiro P (2004). Genetic diversity in the olive tree (Olea europaea L. subsp. europaea) cultivated in Portugal revealed by RAPD and ISSR markers. Genet Res Evol 51: 501-511.
Gomes S, Martins-Lopes P, Lima-Brito J, Meirinhos J, Lopes J, Martins A, Guedes-Pinto H (2008). Evidence of clonal variation in olive Verdeal-Transmontana cultivar using RAPD, ISSR and SSR markers. J Hortic Sci Biotechnol 83: 395-400.
Guerin J, Mekuria G, Burr M, Collins G, Sedgley M (2003). Selection of olive cultivars. Acta Hortic 622: 231-234.
Hagidimitirou M, Katsiotis A, Menexes G, Pontikis C, Loukas M (2005). Genetic diversity of major Greek olive cultivars using molecular (AFLPs and RAPDs) markers and morphological traits. J Am Soc Hortic Sci 130: 211-217.
Hannachi H, Breton C, Msallem M, Ben El Hadj S, El Gazzah M, Bervillé A (2008). Differences between native and introduced cultivars as revealed by morphology of drupes, oil composition and SSR polymorphism; a case study in Tunisia. Sci Hortic 116: 280-290.
Hannachi H, Sommerlatte H, Breton C, Msallem M, El Gazzah M, Ben El Hadj S, Bervillé A (2009). Oleaster (var. sylvestris) and subsp. cuspidata are suitable genetic resources for improvement of the olive (Olea europaea subsp. europaea var. europaea). Genet Res Crop Evol 56: 393-403.
Ipek A, Barut E, Gulen H, Ipek M (2012). Assessment of inter- and intra-cultivar variations in olive using SSR markers. Sci Agric 69: 327-335.
Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T (1997). Molecular Tools in Plant Genetic Resources Conservation: A Guide to the Technologies. IPGRI Technical Bulletin No. 2. Rome, Italy: International Plant Genetic Resources Institute.
Koehmstedt AM, Aradhya MK, Soleri D, Smith JL, Polito VS (2011). Molecular characterization of genetic diversity, structure, and differentiation in the olive (Olea europaea L.) germplasm collection of the United States Department of Agriculture. Genet Resour Crop Evol 58: 519-531.
León L, Martín LM, Rallo L (2004a). Phenotypic correlations among agronomic traits in olive progenies. J Am Soc Hortic Sci 129: 271-276.
León L, Rallo L, Del Rio C, Martín LM (2004b). Variability and early selection on the seedling stage for agronomic traits in progenies from olive crosses. Plant Breed 123: 73-78.
Lewontin RC (1972). The apportionment of human diversity. Evol Biol 6: 381-398.
Liu J (2002). POWERMARKER. A Powerful Software for Marker Data Analysis. Raleigh, NC, USA: North Carolina State University Bioinformatics Research Center.
Lopes MS, Mendonc AD, Sefc MK, Gil FS, Da Camara Machado A (2004). Genetic evidence of intra-cultivar variability within Iberian olive cultivars. Hort Sci 39: 1562-1565.
Lumaret R, Ouazzani N, Michaud H, Vivier G, Deguilloux MF, Di Giusto F (2004). Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean basin. Heredity 92: 343-351.
Mantel N (1967). The detection of disease clustering and a generalized regression approach. Cancer Res 27: 209-220.
Marra FP, Caruso T, Costa F, Di Vaio C, Mafrica R, Marchese A (2013). Genetic relationships, structure and parentage simulation among the olive tree (Olea europaea L. subsp. europaea) cultivated in Southern Italy revealed by SSR markers. Tree Genet Genomes 9: 961-973.
Martins-Lopes P, Gomes S, Lima-Brito J, Lopes J, Guedes-Pinto H (2009). Assessment of clonal genetic variability in Olea europaea L. Cobrançosa by molecular markers. Sci Hortic 123: 82-89.
Minch E, Ruiz-Linares A, Goldstein D, Feldman M, Cavalli-Sforza LL (1997). MICROSAT. A Computer Program for Calculating Various Statistics on Microsatellite Allele Data. Ver. 1.5d. Stanford, CA, USA: Stanford University.
Mulas M (1999). Characterization of olive wild ecotypes. Acta Hortic 474: 121-124.
Mulas M, Fadda A, Cauli E (2004). Prime osservazioni su cloni di oleastro (Olea europaea var. sylvestris Hoff E Link) selezionati per lutilizzo forestale. Italus Hortus 11: 214-217 (in Italian).
Muzzalupo I, Chiappetta A, Benincasa C, Perri E (2010). Intracultivar variability of three major olive cultivars grown in different areas of central-southern Italy and studied using microsatellite markers. Sci Hortic 126: 324-329.
Noormohammadi Z, Trujillo I, Belaj A, Ataei A, Hosseini-Mazinan M (2014). Genetic structure of Iranian olive cultivars and their relationship with Mediterraneans cultivars revealed by SSR markers. Sci Horti 178: 175-183.
Omrani-Sabbaghi A, Shahriari M, Falahati-Anbaran M, Mohammadi SA, Nankali A, Mardi M, Ghareyazie B (2007). Microsatellite markers based assessment of genetic diversity in Iranian olive (Olea europaea L.) collections. Sci Hortic 112: 439-447.
Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945- 959.
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: 261-266.
Raymond M, Rousset F (1995). GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
Rohlf FJ (2005). NTSYS-PC. Numerical Taxonomy and Multivariate Analysis System, Version 2.10s. Setauket, NY, USA: Department of Ecology and Evolution, State University of New York.
SAS Institute (2004) SAS/STAT® 9.1 Users Guide. Cary, NC, USA: SAS Institute Inc.
Schneider S, Roessli D, Excoffier L (2000) ARLEQUIN. A Software for Population Genetic Data Analysis. Version 2000. Geneva, Switzerland: Genetics and Biometry Laboratory, University of Geneva.
Sedgley M (2000). Wild Olive Selection for Quality Oil Production, Vol. 116. Barton, Australia: Rural Industries Research and Development Corporation.
Sedgley M, Wirthensohn M (2000). The Australian olive improvement program. Olivae 83: 27-30.
Sorkheh K, Shiran B, Gradziel TM, Epperson BK, Martinez-Gomez P, Asadi E (2007). Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond, and its relationships with agronomic traits. Euphytica 156: 237-344.
Strikic F, Mavsar DB, Perica S, Cmelik Z (2010). Genetic variation within the olive (Olea europaea L.) cultivar Oblica detected using amplified fragment length polymorphism (AFLP) markers. Afr J Biot 9: 2880-2883.
Sutherland EK, Hale BJ, Hix DM (2000). Defining species guilds in the Central Hardwood Forest, USA. Plant Ecol 147: 1-19.
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.
Trujillo I, Ojeda MA, Urdiroz NM, Potter D, Barranco D, Rallo L, Diez CM (2014). Identification of the Worldwide Olive Germplasm Bank of Córdoba (Spain) using SSR and morphological markers. Tree Genet Genomes 10: 141-155.
Zaher H, Boulouha B, Baaziz M, Sikaoui L, Gaboun F, Sripada M (2011). Morpho-logical and genetic diversity in olive (Olea europaea subsp. europaea L.) clones and varieties. Plant Omics Journal 4: 370-376.