Comparative assessment of genetic diversity in Albanian olive (Olea europaea L.) using SSRs from anonymous and transcribed genomic regions
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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.
KeywordsEST-SSR marker Genetic diversity Genotyping Functional annotation
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.
The research was funded by the Slovenian Research Agency through Grant P4-0077.
- Adawy SS, Mokhtar MM, Alsamman AM, Sakr MM (2015) Development of annotated EST-SSR database in olive (Olea europaea). Int J Sci Res 4:1063–1073Google Scholar
- Baldoni L, Cultrera NG, Mariotti R, Ricciolini C, Arcioni S, Vendramin GG, Buonamici A, Poceddu A, Sarri V, Ojeda MA, Trujillo I, Rallo L, Belaj A, Perri E, Salimonti A, Muzzalupo I, Casagrande A, Lain O, Messina R, Testolin R (2009) A consensus list of microsatellite markers for olive genotyping. Mol Breed 24:213–231CrossRefGoogle Scholar
- Belaj A, Cipriani G, Testolin R, Rallo L, Trujillo I (2004) Characterization and identification of main Spanish and Italian olive cultivars by simple-sequence-repeat markers. HortSci 39(7):1557–1561Google Scholar
- Choi H, Kim NH, Kim JH, Choi BS, Ahn I, Lee J, Yamg T (2011) Development of reproducible EST-derived SSR markers and assessment of genetic diversity in Panax ginseng cultivars and related species. J Ginseng Res 35(4):399–412. https://doi.org/10.5142/jgr.2011.35.4.399 CrossRefPubMedPubMedCentralGoogle Scholar
- Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S, Pezzotti M (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(8):1569–1585CrossRefPubMedGoogle Scholar
- Collani S, Galla G, Ramina A, Barcaccia G, Alagna F, Càceres EM, et al (2011) Self-incompatibility in olive: a new hypothesis on the S-locus genes controlling pollen-pistil interaction. In I workshop on floral biology and S-Incompatibility In Fruit Species. Acta Hortic 967:133–140Google Scholar
- De la Rosa R, Belaj A, Munoz-Merida A, Trelles O, Ortiz-Martin I, Gonzales-Plaza JJ, Valpuesta V, Beuzon CR (2013) Development of EST-derived SSR markers with long -core repeat in olive and their use for paternity testing. J Am Soc Hortic Sci 138(4):290–296Google Scholar
- Fendri M, Trujillo I, Trigui A, Rodriguez-Gracía MI, de Dioz Ramirez J (2010) Simple sequence repeat identification and endocarp characterization of olive tree accessions in Tunisian germplasm collection. HortSci 45(10):1429–1436Google Scholar
- Giampetruzzi A, Morelli M, Saponari M, Loconsole G, Chiumenti M, Boscia D, Savino VN, Martinelli GP, Saldarelli P (2016) Transcriptome profiling of two olive cultivars in response to infection by the CoDiRO strain of Xylella fastidiosa subsp. pauca. BMC Genomics 17(1):475CrossRefPubMedPubMedCentralGoogle Scholar
- Gomes S, Martins-Lopes P, Lopes L, Guedes-Pinto H (2009) Assessing genetic diversity in Olea europaea L, using ISSR and SSR markers. Plant Mol Biol Rep 123:82–89Google Scholar
- Hu J, Li J, Liang F, Liu L, Si S (2010) Genetic relationship of a cucumber germplasm collection revealed by newly developed EST-SSR marker. J Genet 89(2):28–32Google Scholar
- Lopes MS, Mendonça D, Sefc KM, Sabino-Gil F, de Camara-Machado A (2004) Genetic evidence of intra-cultivar variability with Iberian olive cultivars. HortSci 39(7):1562–1565Google Scholar
- Min XJ, Butler G, Storms R, Tsang A (2005) OrfPredictor: predicting protein-coding regions in EST-derived sequences. Nucleic Acids Res 1:33(Web Server Issue):W677–W680. (http://bioinformatics.ysu.edu/tools/OrfPredictor.html).
- 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. 1.5.d. Stanford University, StanfordGoogle Scholar
- Naga BLRI, Mangamoori LN, Subramanyam S (2012) Identification and characterization of EST-SSRs in finger millet (Eleusine coracana (L.) Gaertn.). J Crop Sci and Biotechnol 15(1): 9-16. https://doi.org/10.1007/s12892-011-0064-9
- Noormohammadi Z, Hosseini-Mazinani M, Trujillo I, Rallo L, Belaj A, Sadeghizadeh M (2007) Identification and classification of main Iranian olive cultivars using microsatellite markers. HortSci 42(7):1545–1550Google Scholar
- Rešetic T, Štajner N, Bandelj D, Javornik B, Jakše J (2013) Validation of candidate reference genes in RT-qPCR studies of developing olive fruit and expression analysis of four genes involved in fatty acids metabolism. Mol Breed 32:211. https://doi.org/10.1007/s11032-013-9863-7 CrossRefGoogle Scholar
- Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Misener S, Krawetz SA (eds) Methods in molecular biology, Bioinformatics methods and protocols, vol 132. Humana Press, Totowa, pp 365–386Google Scholar
- Tranbarger TJ, Kluabmongkol W, Sangsrakru D, Morcillo F, Tregear JW, Tragoonrung S, Billotte N (2012) SSR markers in transcripts of genes linked to post-transcriptional and transcriptional regulatory functions during vegetative and reproductive development of Elaeisguineensis. BMC Plant Biol 12:1. https://doi.org/10.1186/1471-2229-12-1 CrossRefPubMedPubMedCentralGoogle Scholar
- Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X (2011) Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 12:451. https://doi.org/10.1186/1471-2164-12-451 CrossRefPubMedPubMedCentralGoogle Scholar
- Weising K, Nybom H, Wolff K, Kahl G (2005) DNA fingerprinting in plants; principles, methods and applications, 2nd edn. CRC press Taylor and Francis Group, Boca Raton, pp 444Google Scholar