Skip to main content
SpringerLink
Log in

Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.)

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Rapid and effective genotyping is an important goal to discriminate among the numerous olive cultivars and their wild related forms. The largely used di-nucleotide simple sequence repeat (SSR) markers show a high level of polymorphism and have strongly contributed to solve many inconsistencies in varietal identity, but many problems related to difficult discrimination of neighboring alleles and low comparability of data among different labs severely reduce their applicability for large-scale screening. The availability of numerous transcriptome libraries, which were developed from different tissues of several olive varieties, has allowed their intensive screening to search for polynucleotide microsatellite regions with long core repeats, potentially polymorphic among varieties. An accurate screening of all these polymorphisms has allowed to select a set of 25 trinucleotide and one tetranucleotide SSRs, showing a good level of discrimination power with a high allele pattern resolution and repeatability. They were preliminarily tested on a group of cultivated varieties then validated on a wider group of cultivated and wild plants, and related species and subspecies, demonstrating a good transferability within the entire Olea taxon. Furthermore, an in silico functional prediction has allowed to assign each transcribed sequence to their gene functions and biological process categories, highlighting their potential application of these new EST-SSRs as functional markers.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Acuna CV, Fernandez P, Villalba PV, García MN, Esteban Hopp H, Marcucci Poltri SN (2012) Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus. Tree Genet Genomes 8:289–301

    Article  Google Scholar 

  • Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372

    Article  CAS  PubMed  Google Scholar 

  • Alagna F, D’Agostino N, Torchia L, Servili M, Rao R, Pietrella M et al (2009) Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development. BMC Genomics 10:399

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Alagna F, Cirilli M, Galla G, Carbone F, Daddiego L, Facella P et al (2016) Transcript analysis and regulative events during flower development in olive (Olea europaea L.). PLoS One 11(4):e0152943

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Amos W, Hoffman JI, Frodsham A, Zhang L, Best S, Hill AVS (2007) Automated binning of microsatellite alleles: problems and solutions. Mol Ecol Notes 7:10–14

    Article  CAS  Google Scholar 

  • Asadi AA, Monfared SR (2014) Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Mol Gen Genomics 289(4):625–640

    Article  CAS  Google Scholar 

  • Atienza SG, de la Rosa R, Domínguez García MC, Martín A, Kilian A, Belaj A (2013) Use of DArT markers as a means of better management of the diversity of olive cultivars. Food Res Int 54:2045–2053

    Article  CAS  Google Scholar 

  • Baldoni L, Cultrera NGM, Mariotti R, Ricciolini C, Arcioni S, Vendramin GG et al (2009) A consensus list of microsatellite markers for olive genotyping. Mol Breed 24:213–231

    Article  CAS  Google Scholar 

  • Baldoni L, Belaj A (2010) Olive. In: Oil crop breeding. ed. J. Vollmann and I. Rajcan, Springer

  • Belaj A, del Carmen Dominguez-García M, Atienza SG, Urdíroz NM, De la Rosa R, Satovic Z et al (2012) Developing a core collection of olive (Olea europaea L.) based on molecular markers (DArTs, SSRs, SNPs) and agronomic traits. Tree Genet Genomes 8:365–378

    Article  Google Scholar 

  • Besnard G, El Bakkali A (2014) Sequence analysis of single-copy genes in two wild olive subspecies (Olea europaea L.): nucleotide diversity and potential use for testing admixture. Genome 57:145–153

    Article  CAS  PubMed  Google Scholar 

  • Besnard G, Hernández P, Khadari B, Dorado G, Savolainen V (2011) Genomic profiling of plastid DNA variation in the Mediterranean olive tree. BMC Plant Biol 11:80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Besnard G, Garcia-Verdugo C, De Casas RR, Treier UA, Galland N, Vargas P (2008) Polyploidy in the olive complex (Olea europaea): evidence from flow cytometry and nuclear microsatellite analyses. Ann Bot 101:25–30

    Article  CAS  PubMed  Google Scholar 

  • Biswas MK, Chai L, Mayer C, Xu Q, Guo W, Deng X (2012) Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus. Mol Biol Rep 39:5373–5386

    Article  CAS  PubMed  Google Scholar 

  • Biton I, Doron-Faigenboim A, Jamwal M, Mani Y, Eshed R, Rosen A et al (2015) Development of a large set of SNP markers for assessing phylogenetic relationships between the olive cultivars composing the Israeli olive germplasm collection. Mol Breed 35:1–14

    Article  Google Scholar 

  • Boccacci P, Beltramo C, Prando MS, Lembo A, Sartor C, Mehlenbacher SA et al (2015) In silico mining, characterization and cross-species transferability of EST-SSR markers for European hazelnut (Corylus avellana L.). Mol Breed 35:1–14

    Article  CAS  Google Scholar 

  • 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 35:449–462

    Article  CAS  Google Scholar 

  • Bradbury D, Smithson A, Krauss SL (2013) Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations. Mol Ecol 22:5112–5129

    Article  CAS  PubMed  Google Scholar 

  • Butler JM (2007) Short tandem repeat typing technologies used in human identity testing. BioTechniques 43:2–5

    Article  Google Scholar 

  • Cabezas JA, Ibanez J, Lijavetzky D, Velez D, Bravo G, Rodriguez V et al (2011) A 48 SNP set for grapevine cultivar identification. BMC Plant Biol 11:153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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

    Article  CAS  PubMed  Google Scholar 

  • Chankaew S, Isemura T, Isobe S, Kaga A, Tomooka N, Somta P et al (2014) Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (creole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis). PLoS One 9:e104990

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chapuis MP, Estoup A (2007) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24:621–631

    Article  CAS  PubMed  Google Scholar 

  • Chen M, Wu J, Wang L, Zhang X, Blair MW, Jia J, Wang S (2014) Development of mapped simple sequence repeat markers from common bean (Phaseolus vulgaris L.) based on genome sequences of a Chinese landrace and diversity evaluation. Mol Breed 33:489–496

    Article  CAS  Google Scholar 

  • Chiappetta A, Muto A, Bruno L, Woloszynska M, VanLijsebettens M, Bitonti MB (2015) A dehydrin gene isolated from feral olive enhances drought tolelance. Front Plant Sci 6:392

    Article  PubMed  PubMed Central  Google Scholar 

  • 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 104:223–228

    Article  CAS  PubMed  Google Scholar 

  • Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, Morgante M, Testolin R (2008) A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol 8:127

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S et al (2010) The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. Theor Appl Genet 121:1569–1585

    Article  PubMed  Google Scholar 

  • Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  CAS  PubMed  Google Scholar 

  • Corrado G, Alagna F, Rocco M, Renzone G, Varricchio P, Coppola V et al (2012) Molecular interactions between the olive and the fruit fly Bactrocera oleae. BMC Plant Biol 12:86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cubry P, Pujade-Renaud V, Garcia D, Espeout S, Le Guen V, Granet F, Seguin M (2014) Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.). Plant Breed 133:419–426

    Article  CAS  Google Scholar 

  • Dai F, Tang C, Wang Z, Luo G, He L, Yao L (2015) De novo assembly, gene annotation, and marker development of mulberry (Morus atropurpurea) transcriptome. Tree Genet Genomes 11:1–11

    Article  Google Scholar 

  • De Keyser E, De Riek J, Van Bockstaele E (2009) Discovery of species-wide EST-derived markers in Rhododendron by intron-flanking primer design. Mol Breed 23:171–178

    Article  CAS  Google Scholar 

  • De la Rosa R, James CM, Tobutt KR (2002) Isolation and characterization of polymorphic microsatellites in olive (Olea europaea L.) and their transferability to other genera in the Oleaceae. Mol Ecol Notes 2:265–267

    Article  CAS  Google Scholar 

  • De la Rosa R, Belaj A, Muñoz-Mérida A, Trelles O, Ortíz-Martín I, González-Plaza JJ et al (2013) Development of EST-derived SSR markers with long-core repeat in olive and their use for paternity testing. J Amer Soc Hort Sci 138:290–296

    CAS  Google Scholar 

  • Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B Stat Methodol:1–38

  • Diaz A, de la Rosa R, Martin A, Rallo P (2006) Development, characterization and inheritance of new microsatellites in olive (Olea europaea L.) and evaluation of their usefulness in cultivar identification and genetic relationship studies. Tree Genet Genomes 2:165–175

    Article  Google Scholar 

  • Díez CM, Imperato A, Rallo L, Barranco D, Trujillo I (2012) Worldwide core collection of olive cultivars based on simple sequence repeat and morphological markers. Crop Sci 52:211–221

    Article  Google Scholar 

  • Díez CM, Trujillo I, Martinez-Urdiroz N, Barranco D, Rallo L, Marfil P, Gaut BS (2014) Olive domestication and diversification in the Mediterranean Basin. New Phytol 206:436–447

    Article  PubMed  CAS  Google Scholar 

  • Dominguez-Garcia MDC, Belaj A, De la Rosa R, Satovic Z, Heller-Uszynska K, Kilian A (2012) Development of DArT markers in olive (Olea europaea L.) and usefulness in variability studies and genome mapping. Sci Hortic 136:50–60

    Article  CAS  Google Scholar 

  • Du FK, Xu F, Qu H, Feng S, Tang J, Wu R (2013) Exploiting the transcriptome of Euphrates poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database. PLoS One 8:e61337

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]. BMC Plant Biol 11:17

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Duran C, Singhania R, Raman H, Batley J, Edwards D (2013) Predicting polymorphic EST-SSRs in silico. Mol Ecol Resour 13:538–545

    Article  CAS  PubMed  Google Scholar 

  • El Bakkali A, Haouane H, Moukhli A, Costes E, Van Damme P, Khadari B (2013) Construction of core collections suitable for association mapping to optimize use of Mediterranean olive (Olea europaea L.) genetic resources. PLoS One 8(5):e61265

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445

    Article  CAS  PubMed  Google Scholar 

  • El-Rodeny W, Kimura M, Hirakawa H, Sabah A, Shirasawa K, Sato S et al (2014) Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba). Breed Sci 64:252

    Article  PubMed  PubMed Central  Google Scholar 

  • Emebiri LC (2010) An EST-SSR marker tightly linked to the barley male sterility gene (msg6) located on chromosome 6H. J Hered 101:769–774

    Article  CAS  PubMed  Google Scholar 

  • Essalouh L, El Aabidine AZ, Contreras S, Ben Sadok I, Santoni S, Khadari B, Jakse J, Bandelj D (2014) Genomic and EST microsatellite loci development and use in olive: molecular tools for genetic mapping and association studies. Acta Hortic 1057:543–549

    Article  Google Scholar 

  • Feng SP, Li WG, Huang HS, Wang JY, Wu YT (2009) Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Mol Breed 23:85–97

    Article  CAS  Google Scholar 

  • Ferrao LFV, Caixeta ET, Pena G, Zambolim EM, Cruz CD, Zambolim L (2015) New EST-SSR markers of Coffea arabica: transferability and application to studies of molecular characterization and genetic mapping. Mol Breed 35:1–5

    Article  CAS  Google Scholar 

  • Fu N, Wang Q, Shen HL (2013) De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PLoS One 8:e57686

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fungtammasan A, Ananda G, Hile SE, Su MSW, Sun C, Harris R et al (2015) Accurate typing of short tandem repeats from genome-wide sequencing data and its applications. Genome Res 25(5):736–749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Guo DL, Guo MX, Hou XG, Zhang GH (2014) Molecular diversity analysis of grape varieties based on iPBS markers. Biochem Sys Ecol 52:27–32

    Article  CAS  Google Scholar 

  • Haouane H, El Bakkali A, Moukhli A, Tollon C, Santoni S, Oukabli A, Modafar CE, Khadari B (2011) Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources. Genetica 139:1083–1094

    Article  PubMed  PubMed Central  Google Scholar 

  • Heesacker A, Kishore VK, Gao W, Tang S, Kolkman JM, Gingle A et al (2008) SSRs and INDELs mined from the sunflower EST database: abundance, polymorphisms, and cross-taxa utility. Theor Appl Genet 117:1021–1029

    Article  CAS  PubMed  Google Scholar 

  • Hinchliffe DJ, Turley RB, Naoumkina M, Kim HJ, Tang Y, Yeater KM, Li P, Fang DD (2011) A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). BMC Genomics 12:445

    Article  PubMed  PubMed Central  Google Scholar 

  • Hosseini-Mazinani M, Mariotti R, Torkzaban B, Sheikh-Hassani M, Ataei S, Cultrera NGM, Pandolfi S, Baldoni L (2014) High genetic diversity detected in olives beyond the boundaries of the Mediterranean Sea. PLoS One 9:e93146

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hu J, Wang L, Li J (2011) Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biol Plant 55:577–580

    Article  CAS  Google Scholar 

  • Huang H, Lu J, Ren Z, Hunter W, Dowd SE, Dang P (2011) Mining and validating grape (Vitis L.) ESTs to develop EST-SSR markers for genotyping and mapping. Mol Breed 28:241–254

    Article  CAS  PubMed  Google Scholar 

  • Jiao Y, Ma RJ, Shen ZJ, Yu ML (2014) Development of Ty1-copia retrotransposon-based SSAP molecular markers for the study of genetic diversity in peach. Biochem Sys Ecol 57:270–277

    Article  CAS  Google Scholar 

  • Kalia RK, Rai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334

    Article  CAS  Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  • Kaur S, Panesar PS, Bera MB, Kaur V (2015) Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review. Crc Cr Rev Anal Chem 55:41–49

    CAS  Google Scholar 

  • Kaya HB, Cetin O, Kaya H, Sahin M, Sefer F, Kahraman A, Tanyolac B (2013) SNP discovery by Illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers. PLoS One 8:e73674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kaya HB, Cetin O, Kaya HS, Sahin M, Sefer F, Tanyolac B (2016) Association mapping in Turkish olive cultivars revealed significant markers related to some important agronomic traits. Biochem Genet 54:506–533

    Article  CAS  PubMed  Google Scholar 

  • Khadari B, El Bakkali A, Zine El Aabidine A, Essalouh L, Contreras S, Sadok B, Costes E, Moukhli A (2014) How can we efficiently characterize genes of agronomic interest in olive: towards the genetic association studies? Acta Hortic 1057:551–558

    Article  Google Scholar 

  • King DG (2012) Evolution of simple sequence repeats as mutable sites. In: Tandem repeat polymorphisms: genetic plasticity, neural diversity and disease. Ed. A.J. Hannan, Landes Bioscience and Springer Science+Business Media

  • Leonarduzzi C, Spanu I, Labriola M, González-Martínez SC, Piotti A, Vendramin GG (2016) Development and characterization of three highly informative est-ssr multiplexes for Pinus halepensis Mill. and their transferability to other Mediterranean pines. Plant Mol Biol Rep 1–10

  • Li D, Deng Z, Qin B, Liu X, Men Z (2012) De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics 13:192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li S, Yin T, Wang M, Tuskan GA (2011) Characterization of microsatellites in the coding regions of the Populus genome. Mol Breed 27:59–66

    Article  CAS  Google Scholar 

  • Lima LS, Gramacho KP, Gesteira AS, Lopes UV, Gaiotto FA, Zaidan HA, Pires JL, Cascardo JCM, Micheli F (2008) Characterization of microsatellites from cacao—Moniliophthora perniciosa interaction expressed sequence tags. Mol Breed 22:315–318

    Article  CAS  Google Scholar 

  • Liu C, Yuan D, Lin Z (2014) Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. J Genet 93:689–697

    Article  CAS  PubMed  Google Scholar 

  • Long Y, Wang Y, Wu S, Wang J, Tian X, Pei X (2015) De novo assembly of transcriptome sequencing in Caragana korshinskii Kom. and characterization of EST-SSR markers. PLoS One 10(1):e0115805

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Loureiro J, Rodriguez E, Costa A, Santos C (2007) Nuclear DNA content estimations in wild olive (Olea europaea L. ssp. europaea var. sylvestris Brot.) and Portuguese cultivars of O. europaea using flow cytometry. Genet Res Crop Evol 54:21–25

    Article  CAS  Google Scholar 

  • Luro FL, Costantino G, Terol J, Argout X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008) Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ma JQ, Zhou YH, Ma CL, Yao MZ, Jin JQ, Wang XC, Chen L (2010) Identification and characterization of 74 novel polymorphic EST-SSR markers in the tea plant, Camellia sinensis (Theaceae). Am J Bot 97:e153–e156

    Article  CAS  PubMed  Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200

    Article  CAS  PubMed  Google Scholar 

  • Mousavi S, Mazinani MH, Arzani K, Ydollahi A, Pandolfi S, Baldoni L, Mariotti R (2014) Molecular and morphological characterization of Golestan (Iran) olive ecotypes provides evidence for the presence of promising genotypes. Genet Resour Crop Evol 61:775–785

    Article  Google Scholar 

  • Peakall R, Smouse P (2012) GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perrier X, Jacquemoud-Collet JP (2006) DARwin software. http://darwin.cirad.fr/darwin

  • Qi X, Cui F, Li Y, Ding A, Li J, Chen G, Wang H (2010) Molecular tagging wheat powdery mildew resistance gene pm21 by EST-SSR and STS markers. Mol Plant Breed 1

  • Qiu L, Yang C, Tian B, Yang JB, Liu A (2010) Exploiting EST databases for the development and characterization of EST-SSR markers in castor bean (Ricinus communis L.). BMC Plant Biol 10:278

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rallo P, Dorado G, Martín A (2000) Development of simple sequence repeats (SSRs) in olive tree (Olea europaea L.). Theor Appl Genet 101:984–989

    Article  CAS  Google Scholar 

  • Rallo P, Tenzer I, Gessler C, Baldoni L, Dorado G, Martin A (2003) Transferability of olive microsatellite loci across the genus Olea. Theor Appl Genet 107:940–946

    Article  CAS  PubMed  Google Scholar 

  • Ramchiary N, Nguyen VD, Li X, Hong CP, Dhandapani V, Choi SR, Yu G, Piao ZY, Lim YP (2011) Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives. DNA Res 18:305–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered 86:248–249

    Google Scholar 

  • Rousset F (2008) Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Sabino Gil F, Busconi M, da Câmara MA, Fogher C (2006) Development and characterization of microsatellite loci from Olea europaea. Mol Ecol Notes 6:1275–1277

    Article  CAS  Google Scholar 

  • Sarri V, Baldoni L, Porceddu A, Cultrera NGM, Contento A, Frediani M, Belaj A, Trujillo I, Cionini PG (2006) Microsatellite markers are powerful tools for discriminating among olive cultivars and assigning them to geographically defined populations. Genome 49:1606–1615

    Article  CAS  PubMed  Google Scholar 

  • Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • Sefc KM, Lopes MS, Mendonça D, Rodrigues dos Santos M, da Câmara Machado ML, da Câmara MA (2000) Identification of microsatellite loci in olive (Olea europaea) and their characterization in Italian and Iberian olive trees. Mol Ecol 9:1171–1173

    Article  CAS  PubMed  Google Scholar 

  • Shen D, Bo W, Xu F, Wu R (2014) Genetic diversity and population structure of the Tibetan poplar (Populus szechuanica var. tibetica) along an altitude gradient. BMC Genet 15(Suppl 1):S11

    Article  PubMed  PubMed Central  Google Scholar 

  • Shiferaw E, Pè ME, Porceddu E, Ponnaiah M (2012) Exploring the genetic diversity of Ethiopian grass pea (Lathyrus sativus L.) using EST-SSR markers. Mol Breed 30:789–797

    Article  CAS  PubMed  Google Scholar 

  • Shirasawa K, Oyama M, Hirakawa H, Sato S, Tabata S, Fujioka T et al (2011) An EST-SSR linkage map of Raphanus sativus and comparative genomics of the Brassicaceae. DNA Res 18:221–232

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sun J, Yin H, Li L, Song Y, Fan L, Zhang S, Wu J (2015) Evaluation of new IRAP markers of pear and their potential application in differentiating bud sports and other Rosaceae species. Tree Genet Genomes 11:1–13

    Article  Google Scholar 

  • Targońska M., Bolibok-Brągoszewska H., Rakoczy-Trojanowska M (2015) Assessment of genetic diversity in Secale cereale based on SSR markers. Plant Mol Biol Rep 1–15

  • This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L et al (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458

    Article  CAS  PubMed  Google Scholar 

  • Torkzaban B, Kayvanjoo AH, Ardalan A, Mousavi S, Mariotti R, Baldoni L et al (2015) Machine learning based classification of microsatellite variation: an effective approach for phylogeographic characterization of olive populations. PLoS One 10(11):e0143465

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res 10:967–981

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trujillo I, Ojeda MA, Urdiroz NM, Potter D, Barranco D, Rallo L, Diez CM (2014) Identification of the worldwide olive germplasm Bank of Cordoba (Spain) using SSR and morphological markers. Tree Genet Genomes 10:141–155

    Article  Google Scholar 

  • Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23(1):48–55

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Yan H, Fu X, Li X, Gao H (2013) Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.). Mol Biol Rep 40:3291–3298

    Article  CAS  PubMed  Google Scholar 

  • Weeks DE, Conley YP, Ferrell RE, Mah TS, Gorin MB (2002) A tale of two genotypes: consistency between two high-throughput genotyping centers. Genome Res 12:430–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie WG, Zhang XQ, Cai HW, Liu W, Peng Y (2010) Genetic diversity analysis and transferability of cereal EST-SSR markers to orchardgrass (Dactylis glomerata L.). Biochem Syst Ecol 38:740–749

    Article  CAS  Google Scholar 

  • Xu SC, Gong YM, Mao WH, Hu QZ, Zhang GW, Fu W, Xian QQ (2012) Development and characterization of 41 novel EST-SSR markers for Pisum sativum (Leguminosae). Am J Bot:e149–e153

  • Yang AH, Zhang JJ, Tian H, Yao XH (2012) Characterization of 39 novel EST-SSR markers for Liriodendron tulipifera and cross-species amplification in L. chinense (Magnoliaceae). Am J Bot e460-e464

  • Yao MZ, Ma CL, Qiao TT, Jin JQ, Chen L (2012) Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers. Tree Genet Genomes 8:205–220

    Article  Google Scholar 

  • You Y, Liu D, Liu H, Zheng X, Diao Y, Huang X, Hu Z (2015) Development and characterisation of EST-SSR markers by transcriptome sequencing in taro (Colocasia esculenta (L.) Schoot). Mol Breed 35:1–11

    Article  CAS  Google Scholar 

  • Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y (2010) Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) maxim. BMC Genomics 11:94

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang H, Wei L, Miao H, Zhang T, Wang C (2012) Development and validation of genic-SSR markers in sesame by RNA-seq. BMC Genomics 13:316

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang LY, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687

    Article  CAS  PubMed  Google Scholar 

  • Zhang M, Mao W, Zhang G, Wu F (2014) Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley. PLoS One 9:e94881

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhang L, Yuan M, Tao A, Xu J, Lin L, Fang P, Qi J (2015) Genetic structure and relationship analysis of an association population in jute (Corchorus spp.) evaluated by SSR markers. PLoS One 10:e0128195

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao Y, Williams R, Prakash CS, He G (2012) Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.). BMC Plant Biol 12:237

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhou C, He X, Li F, Weng Q, Yu X, Wang Y, Li M, Shi J, Gan S (2014) Development of 240 novel EST-SSRs in Eucalyptus L’Hérit. Mol Breed 33:221–225

    Article  Google Scholar 

  • Zhu H, Senalik D, McCown BH, Zeldin EL, Speers J, Hyman J et al (2012) Mining and validation of pyrosequenced simple sequence repeats (SSRs) from American cranberry (Vaccinium macrocarpon Ait.). Theor Appl Genet 124:87–96

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This research was supported by the Project “OLEA—Genomics and Breeding of Olive,” funded by the MIPAF, D.M. 27011/7643/10, and by the Project “BeFOre—Bioresources for Oliviculture,” 2015–2019, H2020-MSCA-RISE Marie Skłodowska-Curie Research and Innovation Staff Exchange, Grant Agreement No. 645595. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Author contributions

LB, RM, NC, and EA conceived and designed the experiments. RM, SM, NC, MR, and FB performed the experiments. FC, RM, MR, NC, FA, and FB analyzed the data. LB, GP, and EA contributed the reagents/materials/analysis tools. LB, RM, SM, MR, SM, FC, NC, and FB wrote the paper. LB and RM performed the maintenance of germplasm. GP and FC performed the assembly and mining of sequencing data. LB, RM, SM, MR, NC, FB, and EA reviewed the manuscript.

Author information

Authors and Affiliations

  1. CNR-Institute of Biosciences and Bioresources, Perugia, Italy

    R. Mariotti, N. G. M. Cultrera, F. Baglivo, M. Rossi & Luciana Baldoni

  2. CNR-Institute for Agricultural and Forest Systems in the Mediterranean, Perugia, Italy

    S. Mousavi

  3. Department of Agricultural, Food and Environmental Science, University of Perugia, Perugia, Italy

    E. Albertini

  4. CREA-Research Council for Agriculture and Agricultural Economy, Research Unit for Viticulture and Enology in Southern Italy, Turi, BA, Italy

    F. Alagna

  5. CREA-Research Council for Agriculture and Agricultural Economy, Olive Growing and Olive Oil Industry Research Centre, Rende, CS, Italy

    F. Carbone

  6. ENEA-Technical Unit for Technologies Development, Trisaia Research Centre, Rotondella, MT, Italy

    G. Perrotta

Authors
  1. R. Mariotti
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. G. M. Cultrera
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. Mousavi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. F. Baglivo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. M. Rossi
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. E. Albertini
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. F. Alagna
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. F. Carbone
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. G. Perrotta
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Luciana Baldoni
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Luciana Baldoni.

Ethics declarations

Competing interests

The authors declare that they have no competing interests.

Data archiving statement

The sequence data of EST-SSRs and predicted genes developed in the present work are available in GenBank EST and predicted gene databases (http://www.ncbi.nlm.nih.gov/genbank/) under the accession numbers reported in Table 4.

Additional information

Communicated by G. G. Vendramin

R. Mariotti and N. G. M. Cultrera are co-first authors, and they have contributed equally to this work.

Electronic supplementary material

ESM 1

(DOCX 23 kb)

Table S2

(XLSX 14 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mariotti, R., Cultrera, N.G.M., Mousavi, S. et al. Development, evaluation, and validation of new EST-SSR markers in olive (Olea europaea L.). Tree Genetics & Genomes 12, 120 (2016). https://doi.org/10.1007/s11295-016-1077-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-016-1077-9

Keywords

Search

Navigation