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Tree Genetics & Genomes

, 14:53 | Cite as

Comparative assessment of genetic diversity in Albanian olive (Olea europaea L.) using SSRs from anonymous and transcribed genomic regions

  • Aida Dervishi
  • Jernej Jakše
  • Hairi Ismaili
  • Branka Javornik
  • Nataša Štajner
Original Article
  • 139 Downloads
Part of the following topical collections:
  1. Germplasm Diversity

Abstract

A total of 560,578 sequencing reads obtained from the de novo NGS transcriptome sequencing of Olea europaea were searched for the presence of tri- and tetra-nucleotide repeat motifs, which resulted in 375 tri-nucleotide microsatellites and 252 tetra-nucleotides. Twelve expressed sequence tags (EST)-derived SSRs that gave a reproducible pattern, enabling easy scoring and allele size determination, were further tested for polymorphism on 165 cultivars O. europaea subsp. sativa and on 18 oleasters (O. europaea subsp. sylvestris). The main diversity parameters of EST-SSRs were compared to the genomic SSRs that have been most frequently used so far in olive genotyping and mapping studies. Diversity parameters were also compared for different lengths of repeat motifs (di-nucleotide, tri-nucleotide, and tetra-nucleotide microsatellites). The occurrence of null alleles was only observed in anonymous SSRs, while their frequencies were negative for all EST-SSR loci. Eight out of 12 EST-SSRs were classified as highly informative, indicating their applicability in assessing molecular diversity and genetic relatedness in olive. The 12 novel EST-SSR markers selected as a subset of all identified loci containing SSR motifs showed their suitability for evaluation of genetic diversity and population structure and for genetic mapping. They were also linked to genes and, as shown by annotation analysis, four of them have potential for interpretation of allelic variability related to disease resistance and can be evaluated as a potential diagnostic marker for disease resistance. The development of new EST-SSRs provides a valuable tool in molecular breeding programs for both cultivated and wild olives.

Keywords

EST-SSR marker Genetic diversity Genotyping Functional annotation 

Notes

Author contributions

NŠ coordinated the study and BJ and JJ participated in its design. HI prepared the plant material. AD harvested and processed the samples. AD performed genotyping analyses together with NŠ and analyzed data together with NŠ and JJ. AD and NŠ interpreted the data and wrote the manuscript. All authors read and approved the manuscript.

Funding information

The research was funded by the Slovenian Research Agency through Grant P4-0077.

Supplementary material

11295_2018_1269_MOESM1_ESM.docx (139 kb)
ESM 1 (DOCX 139 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biotechnology, Faculty of Natural SciencesUniversity of TiranaTiranaAlbania
  2. 2.Centre for Plant Biotechnology and Breeding, Agronomy DepartmentUniversity of LjubljanaLjubljanaSlovenia
  3. 3.Gene BankUniversity of AgricultureTiranaAlbania

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