A consensus list of microsatellite markers for olive genotyping

Cultivar identification is a primary concern for olive growers, breeders, and scientists. This study was aimed at examining the SSR markers retrieved from the literature and currently used in olive study, in order to select those most effective in characterizing the olive accessions and to make possible the comparison of data obtained by different laboratories. Olive microsatellite profiles were assessed by four independent laboratories, which analyzed 37 pre-selected SSR loci on a set of 21 cultivars. These SSR markers were initially tested for their reproducibility, power of discrimination and number of amplified loci/alleles. Independent segregation was tested for each pair of SSRs in a controlled cross and the allelic error rate was quantified. Some of them were finally selected as the most informative and reliable. Most of the alleles were sequenced and their sizes were determined. Profiles of the reference cultivars and a list of alleles with their sizes obtained by sequencing are reported. Several genetic parameters have been analysed on a larger set of cultivars allowing for a deeper characterization of the selected loci. Results of this study provide a list of recommended markers and protocols for olive genotyping as well as the allelic profile of a set of reference cultivars that would be useful for the establishment of a universal database of olive accessions.

[1]  A. Musacchio,et al.  DNA Sequence Analysis of Microsatellite Markers Enhances Their Efficiency for Germplasm Management in an Italian Olive Collection , 2006 .

[2]  Jack Edmonds,et al.  Maximum matching and a polyhedron with 0,1-vertices , 1965 .

[3]  M. Morgante,et al.  A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping , 2008, BMC Plant Biology.

[4]  F. Cellini,et al.  Identification of simple sequence repeats (SSRs) in olive (Olea europaea L.) , 2002, Theoretical and Applied Genetics.

[5]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[6]  P. Hatzopoulos,et al.  AFLP reveals structural details of genetic diversity within cultivated olive germplasm from the Eastern Mediterranean , 2005, Theoretical and Applied Genetics.

[7]  P. Hatzopoulos,et al.  Genetic diversity among accessions of an ancient olive variety of Cyprus. , 2003, Genome.

[8]  C. Fogher,et al.  Standardization of a set of microsatellite markers for use in cultivar identification studies in olive (Olea europaea L.) , 2008 .

[9]  B. Jayashree,et al.  Laboratory Information Management Software for genotyping workflows: applications in high throughput crop genotyping , 2006, BMC Bioinformatics.

[10]  J. Brookfield.  A simple new method for estimating null allele frequency from heterozygote deficiency. , 1996 .

[11]  G. Dorado,et al.  Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.) , 2000, Theoretical and Applied Genetics.

[12]  M. Morgante,et al.  PCR-amplified microsatellites as markers in plant genetics. , 1993, The Plant journal : for cell and molecular biology.

[13]  K. M. Sefc,et al.  Genetic evidence of intra-cultivar variability within Iberian olive cultivars , 2004 .

[14]  F. Balloux,et al.  Tackling the population genetics of clonal and partially clonal organisms. , 2005, Trends in ecology & evolution.

[15]  D. Hartl,et al.  DNA Fingerprinting , 2019, Definitions.

[16]  J. Brookfield.  A simple new method for estimating null allele frequency from heterozygote deficiency , 1996, Molecular ecology.

[17]  M. Deguilloux,et al.  Allozyme variation of oleaster populations (wild olive tree) (Olea europaea L.) in the Mediterranean Basin , 2004, Heredity.

[18]  Joseph I. Hoffman,et al.  Automated binning of microsatellite alleles: problems and solutions , 2006 .

[19]  G. Besnard,et al.  Genetic relationships in the olive (Olea europaea L.) reflect multilocal selection of cultivars , 2001, Theoretical and Applied Genetics.

[20]  P. Taberlet,et al.  Genotyping errors: causes, consequences and solutions , 2005, Nature Reviews Genetics.

[21]  B. Javornik,et al.  DNA Fingerprinting of Olive Varieties by Microsatellite Markers , 2002 .

[22]  R. Tenreiro,et al.  Genetic diversity in the Olive tree (Olea europaea L. subsp. europaea) cultivated in Portugal revealed by RAPD and ISSR markers , 2004, Genetic Resources and Crop Evolution.

[23]  T. Lacombe,et al.  Development of a standard set of microsatellite reference alleles for identification of grape cultivars , 2004, Theoretical and Applied Genetics.

[24]  J. Jakše,et al.  DNA fingerprinting of olive varieties in Istria (Croatia) by microsatellite markers , 2008 .

[25]  C. Penha-Gonçalves,et al.  Long perfect dinucleotide repeats are typical of vertebrates, show motif preferences and size convergence. , 2004, Molecular biology and evolution.

[26]  G. Besnard,et al.  High genetic diversity and clonal growth in relict populations of Olea europaea subsp. laperrinei (Oleaceae) from Hoggar, Algeria. , 2005, Annals of botany.

[27]  W. Amos,et al.  Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion , 2004, Molecular ecology.

[28]  R. Lumaret,et al.  Plant genetics: Ancient wild olives in Mediterranean forests , 2001, Nature.

[29]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[30]  A. Belaj,et al.  Using RAPD and AFLP markers to distinguish individuals obtained by clonal selection of 'Arbequina' and 'Manzanilla de Sevilla' olive , 2004 .

[31]  A. Belaj,et al.  Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. , 2006, Genome.

[32]  J. Doebley,et al.  Microsatellites in Zea – variability, patterns of mutations, and use for evolutionary studies , 2002, Theoretical and Applied Genetics.

[33]  D. Sargent,et al.  A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars , 2008, Molecular Breeding.

[34]  L. Suvanto,et al.  Clone identification and clonal structure of the European aspen (Populus tremula) , 2005, Molecular ecology.

[35]  C. Gessler,et al.  Transferability of olive microsatellite loci across the genus Olea , 2003, Theoretical and Applied Genetics.

[36]  O. Lain,et al.  DNA Extraction from Olive Oil and PCR Amplification of Microsatellite Markers , 2005 .

[37]  M. Ater,et al.  Substantial genetic diversity in cultivated Moroccan olive despite a single major cultivar: a paradoxical situation evidenced by the use of SSR loci , 2008, Tree Genetics & Genomes.

[38]  K. M. Sefc,et al.  Identification of microsatellite loci in olive (Olea europaea) and their characaterization in Italian and Iberian olive trees. , 2000, Molecular ecology.

[39]  T. Lacombe,et al.  Historical origins and genetic diversity of wine grapes. , 2006, Trends in genetics : TIG.

[40]  G. Besnard,et al.  Olea europaea (Oleaceae) phylogeography based on chloroplast DNA polymorphism , 2002, Theoretical and Applied Genetics.

[41]  R. Testolin,et al.  SSR-based DNA fingerprints reveal the genetic diversity of Sicilian olive (Olea europaea L.) germplasm , 2005 .

[42]  F. Bonhomme,et al.  Comparison between classical and Bayesian methods to investigate the history of olive cultivars using SSR-polymorphisms , 2008 .

[43]  A. Blanco,et al.  Genetic relationships and cultivar identification among 112 olive accessions using AFLP and SSR markers. , 2005 .

[44]  E. Nielsen,et al.  Stocking impact and temporal stability of genetic composition in a brackish northern pike population (Esox lucius L.), assessed using microsatellite DNA analysis of historical and contemporary samples , 2005, Heredity.

[45]  J. Ibáñez,et al.  Characterization of sequence polymorphisms from microsatellite flanking regions in Vitis spp , 2008, Molecular Breeding.

[46]  L. Poggio,et al.  Complex mutational patterns and size homoplasy at maize microsatellite loci , 2007, Theoretical and Applied Genetics.

[47]  Kenneth R. Tobutt,et al.  Isolation and characterization of polymorphic microsatellites in olive (Olea europaea L.) and their transferability to other genera in the Oleaceae , 2002 .

[48]  J. Butler,et al.  Genetics and Genomics of Core Short Tandem Repeat Loci Used in Human Identity Testing , 2006, Journal of forensic sciences.

[49]  E. Perri,et al.  Detection of DNA in virgin olive oils extracted from destoned fruits , 2007 .

[50]  C. Fogher,et al.  Development and characterization of microsatellite loci from Olea europaea , 2006 .

[51]  R. Testolin,et al.  A set of simple-sequence repeat (SSR) markers covering the Prunus genome , 2003, Theoretical and Applied Genetics.

[52]  J. Lacape,et al.  Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs , 2006, Molecular Breeding.

[53]  C. Gessler,et al.  Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.) , 2002, Molecular Breeding.

[54]  A. Díaz,et al.  Development, characterization and inheritance of new microsatellites in olive (Olea europaea L.) and evaluation of their usefulness in cultivar identification and genetic relationship studies , 2006, Tree Genetics & Genomes.

[55]  M. Mardi,et al.  Microsatellite markers based assessment of genetic diversity in Iranian olive (Olea europaea L.) collections , 2007 .

[56]  S. Kalinowski,et al.  Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment , 2007, Molecular ecology.

[57]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[58]  R. Testolin,et al.  Characterization and Identification of the Main Spanish and Italian Olive Cultivars by Simple-sequence-repeat Markers , 2004 .

[59]  R. Testolin,et al.  Microsatellite markers isolated in olive (Olea europaea L.) are suitable for individual fingerprinting and reveal polymorphism within ancient cultivars , 2002, Theoretical and Applied Genetics.

[60]  A. Belaj,et al.  Genetic structure of wild and cultivated olives in the central Mediterranean basin. , 2006, Annals of botany.

[61]  J. Saunders,et al.  Selection of international molecular standards for DNA fingerprinting of Theobroma cacao , 2004, Theoretical and Applied Genetics.

[62]  Ahmed Rebai,et al.  Characterization and Identification of Tunisian Olive Tree Varieties by Microsatellite Markers , 2008 .

[63]  D. Weeks,et al.  A tale of two genotypes: consistency between two high-throughput genotyping centers. , 2002, Genome research.

[64]  R. Testolin,et al.  Comparative study of the discriminating capacity of RAPD, AFLP and SSR markers and of their effectiveness in establishing genetic relationships in olive , 2003, Theoretical and Applied Genetics.

[65]  E. Perri,et al.  Molecular Characterization of Italian Olive Cultivars by Microsatellite Markers. , 2008 .

[66]  S. Andelinović,et al.  Forensic botany: potential usefulness of microsatellite-based genotyping of Croatian olive (Olea europaea L.) in forensic casework. , 2007, Croatian medical journal.