DNA Sequence Analysis of Microsatellite Markers Enhances Their Efficiency for Germplasm Management in an Italian Olive Collection

Abstract

<jats:p>Genetic diversity studies using microsatelite analysis were carried out in a set of 39 accessions of <jats:italic>Olea europaea</jats:italic> L., corresponding to the majority of the regional autochthon germplasm in Apulia. Samples of olive leaves were harvested from plants growing in the olive germplasm collection of the <jats:italic>Consiglio per la Ricerca e Sperimentazione in Agricoltura</jats:italic> (C.R.A.) - <jats:italic>Istituto Sperimentale per l'Olivicoltura</jats:italic> at Rende in Cosenza Italy. Herein, we evaluated the extent to which microsatellite analysis using electrophoresis was capable of identifying traditional olive cultivars. In addition, the DNA sequence of all amplicons was determined and the number of repeat units was established for each sample. Using five loci, electrophoretic analysis identified 24 genotype profiles, while DNA sequence analysis detected 28 different genotype profiles, identifying 54% of cultivars. The remaining 46% were composed of seven different accession groups containing genetically indistinguishable cultivars, which are presumably synonyms. This study demonstrates the utility of microsatellite markers for management of olive germplasm and points out the high level of polymorphisms in microsatellite repeats when coupled with DNA sequence analysis. The establishment of genetic relationships among cultivars in the Apulian germplasm collection allows for the construction of a molecular database that can be used to establish the genetic relationships between known and unknown cultivars.</jats:p>

SSR Marker-Based DNA Fingerprinting and Cultivar Identification of Olives (Olea europaea)

“…We obtained a higher average number of polymorphic alleles (4.6) than Noormohammadi et al (2009) and Cipriani et al (2002). Our results are also comparable to Carriero et al (2002), Belaj et al (2003), Sarri et al (2006), and Muzzalupo et al (2006). This high level of polymorphism in olives could be important for future breeding efforts in Turkey.…”

“…The number of polymorphic alleles ranged from 3 (DCA-04 and DCA-17) to 6 (DCA-11, DCA-16, GAPU-89), with an average of 4.6 fragments per primer, indicating that the primers DCA-11, DCA-16, and GAPU-89 were the most effective for discriminating among the cultivars analyzed here. The high level of polymorphism in olive cultivars revealed by SSR markers was evident (Carriero et al 2002;Sarri et al 2006;Muzzalupo et al 2006;Gomes et al 2009;Noormohammadi et al 2009). We obtained a higher average number of polymorphic alleles (4.6) than Noormohammadi et al (2009) and Cipriani et al (2002).…”

“…It has been reported that synonymous naming is also common in the olive germplasm in other olive-growing Mediterranean countries. For example, identification of synonymous cases in Italian and Portuguese olive germplasm has been reported using SSR and other molecular markers (Muzzalupo et al 2006;Gomes et al 2009). …”

Local old olive landrace varieties in Israel—Valuable plant genetic resources in olive cultivation

“…Isozymes (Ouazzani et al, 1993;Trujillo et al, 1995), random-amplified polymorphic DNA (RAPD) (Belaj et al, 2003b(Belaj et al, , 2003cKhadari et al, 2003), amplified fragment-length polymorphism (AFLP) (Montemurro et al, 2005;Owen et al, 2005), inter-simple sequence repeats (ISSRs), microsatellites (simple sequence repeats, SSRs) (Carriero et al, 2002;Essadki et al, 2006;Muzzalupo et al, 2006), and morphological and morphometric characters (IOC, 2007) have been used to reveal the relationships among them. Considerable research effort has been directed to the development of SSR and ISSR markers, mainly for the purpose of distinguishing between different cultivars (Carriero et al, 2002;Essadki et al, 2006;Muzzalupo et al, 2006). In some cases, these proved to be informative for genotypic differentiation as well (e.g., Cipriani et al, 2002;Essadki et al, 2006).…”

“…In some cases, these proved to be informative for genotypic differentiation as well (e.g., Cipriani et al, 2002;Essadki et al, 2006). Several studies have been aimed at characterizing olive germplasm (Belaj et al, 2002;Khadari et al, 2003;Lopes et al, 2004;La Mantia et al, 2005;Muzzalupo et al, 2006), and others at differentiating and/or studying relationships among cultivated varieties (Carriero et al, 2002;Cipriani et al, 2002;Belaj et al, 2004;Montemurro et al, 2005;Owen et al, 2005;Essadki et al, 2006). In a recent study, the combination of AFLP and SSR markers grouped 111 olive accessions belonging to 60 cultivars according to their type of use as oil, table, or dual-purpose olives (Montemurro et al, 2005).…”