**5. Conclusions**

Nowadays, the olive industry requires certified olive cultivars with elite agronomic characteristics and adapted to modern intensive mechanized orchards (Hatzopoulos et al., 2002). Very few cultivars are grown commercially in more than one region or country, while most of them have a local diffusion. The cases of cultivars homonyms and synonyms associated with high genetic diversity makes the olive tree germplasm very difficult to characterize. The PCR-based markers opened the possibility to develop, over the last two decades, new molecular techniques for cultivar identification and further certification purposes in order to certify the propagated material. It is essential to study the genetic base of olive germplasm in order to characterize and compare with other genetic, phenotypic and agronomic data. Different molecular markers have been used in genetic diversity studies which give us information about the relationships between cultivars and the olive domestication process.

The choice on which molecular technique would be the most suitable for olive genetic resource characterization depend on a number of factors as the level of variability of the species, and the resources available (Belaj et al., 2006). Technological advancement has contributed to the development, in every aspect, of molecular genetic markers, making them technically simpler, efficient, cost-effective, and faster than the classic methods.

However, molecular approaches (nuclear and cytoplasmic) should not be considered alone or as substitutes of morphological characterization but as complementary tools, more complete and effective, for olive genetic resources studies. The several molecular markers used for germplasm variability studies may play a major role in olive tree breeding programs when using marker assisted selection for biotic and abiotic stress tolerance, olive fruits and oil quality traits.

However, there are still aspects of cultivars synonymous that still needed to be addressed in order to develop a complete database, in order to have an overview of the genetic variability available. As soon as the recent olive genome sequence is released new strategies may be taken in order olive germplasm management, breeding strategies and certification issues.

#### **6. References**

22 Genetic Diversity in Plants

The sequence characterized amplified region (SCAR) have been widely developed for plant breeding studies in several species such as wheat (Hernández et al., 1999), grapevine (Vidal et al., 2000), tomato (Zhang & Stommel, 2001), and pear (Lee et al., 2004; Marieschi et al., 2011). In olive, this type of marker has also been applied for olive germplasm evaluation and mapping (Bautista et al., 2003; Busconi et al., 2006; Hernández et al., 2001a), and for analysis

The development of sequence characterized amplified region (SCAR) involves cloning of the amplified product, and then sequencing the two ends of the cloned product that appeared to be specific. The SCAR has the advantage of being inherited in a codominant fashion in contrast to RAPD which are inherited in a dominant manner (Mohan et al., 1997). Bautista et al. (2003) used this technology to develop specific markers useful for olive cultivar identification and mapping. They demonstrated that the use of SCAR markers is enough to provide a simple, cheap, and reliable procedure to identify geographically related olive cultivars. The development of SCAR markers by directly sequencing olive RAPD bands was reported by Hernández et al. (2001a) and they demonstrated that the generated markers were useful for the marker assisted selection of the high flesh/stone ratio. This type of marker has also been applied for olive germplasm evaluation and mapping (Bautista et al., 2003; Busconi et al., 2006). Wu et al. (2004) combined RAPD, SCAR and SSR markers to construct a linkage map

The single nucleotide polymorphisms are a marker system that can differentiate individuals based on variations detected at the level of a single nucleotide base in the genome. Such variations are present in large abundance in the genomes of higher organisms including plants (Agarwal et al., 2008). The SNP-based markers have been used in many plant species. In olive, due to olive unknown genome, this technique has not been widely applied. Reale et al. (2006) used SNP markers to genotype 65 olive samples obtained from Europe and Australia, and observed that 77% of the cultivars were clearly discriminate. However, the authors developed SNP markers from olive gene sequences available in the GenBank database and from arbitrary sampling using the sequence-related amplification

Nowadays, the olive industry requires certified olive cultivars with elite agronomic characteristics and adapted to modern intensive mechanized orchards (Hatzopoulos et al., 2002). Very few cultivars are grown commercially in more than one region or country, while most of them have a local diffusion. The cases of cultivars homonyms and synonyms associated with high genetic diversity makes the olive tree germplasm very difficult to characterize. The PCR-based markers opened the possibility to develop, over the last two decades, new molecular techniques for cultivar identification and further certification purposes in order to certify the propagated material. It is essential to study the genetic base of olive germplasm in order to characterize and compare with other genetic, phenotypic and agronomic data. Different molecular markers have been used in genetic diversity studies which give us information about the relationships between cultivars and the olive

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**4.6 Single Nucleotide Polymorphisms (SNP)** 

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**5. Conclusions** 

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