Identification and validation of novel EST-SSR markers in olives

Abstract

The olive (Olea europaea L.) is a leading oil crop in the Mediterranean area. Limited information on the inheritance of agronomic significant traits hinders progress in olive breeding programs, which encourages the development of markers linked to the traits. In this study, we report on the development of 46 olive simple sequence repeat (SSR) markers, obtained from 577,025 expressed sequence tags (ESTs) in developing olive fruits generated in the framework of the Slovenian national olive transcriptome project. Sequences were de novo assembled into 98,924 unigenes, which were then used as a source for microsatellites searching. We identified 923 unigenes that contained 984 SSRs among which dinucleotide SSRs (36 %) were the most abundant, followed by tri-(33 %) and hexa-(21 %) nucleotides. Microsatellite repeat motif GA (37 %) was the most common among dinucleotides, while microsatellite repeat motif GAA was the most abundant trinucleotide SSR motif (16 %). Gene ontology annotations could be assigned to 27 % of the unigenes. A hundred and ten expressed sequence tag-derived-simple sequence repeats (EST-SSRs) with annotated genes were selected for primer designing and finally, 46 (42 %) polymorphic EST-SSRs were successfully amplified and used to validate genetic diversity among 24 olive varieties. The average number of alleles per locus, observed heterozygosity, expected heterozygosity, and polymorphic information content were 4.5, 0.649, 0.604 and 0.539, respectively. Twenty-seven EST-SSRs showed good diversity properties and were recommended for further olive genome investigation.

Assessment of morphological and genetic variability through genic microsatellite markers for essential oil in Sandalwood (Santalum album L.)

“…The oil concentration of the trees in Karnataka and Kerala was more similar despite the being more genetically similar to Telangana populations. Likewise, the average number of effective alleles per locus was ranged between 3.13 in 24 varieties of olives by 46 genic SSR markers (Arbeiter et al 2017).…”

Paternity tests support a diallelic self‐incompatibility system in a wild olive (Olea europaea subsp. laperrinei, Oleaceae)

“…Sixteen microsatellite loci (Arbeiter, Hladnik, Jakše, & Bandelj, ; Carriero, Fontanazza, Cellini, & Giorio, ; Salmona et al, ; Sefc et al, ; Table ; Data ) were used to characterize 71 mature diploid/triploid individuals of the CEFE collection (subspp. europaea , laperrinei , cuspidata, and hybrids) plus 32 embryos of Laperrine's olive and the 46 embryos of Mediterranean olive.…”

EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives

“…Sequences related to expressed tags such as the long core repeat of EST-SSRs [40][41][42], developed from transcript collections, might contribute to start the study of gene differences between olive subspecies, highlighting the possible functional effect of polymorphisms between olive genotypes [42]. In the last years, special attention was paid to the development and use of SNP markers in olive [43][44][45][46][47] and, thanks to a wide set of EST-SNPs recently developed [48], the study of functional polymorphisms in olive is finally having a boost.…”