2.4. Developing new markers for GWAS and varietal identification

Currently the most widely used molecular markers for varietal identification in olive are microsatellites, owing to their high polymorphism and the extensive availability of published data, which enables comparison of molecular profiles across collections. In fact, most international germplasm collections have been characterised with these markers. However, more recently, witht the development of high-throughput genotyping platforms and techniques (e.g. GBS, SPET), panels of single nucleotide polymorphisms (SNPs) are being produced. Thanks to which, their high reproducibility and abundance, SNPs, are particularly well suited for varietal for and intra-varietal identification purposes. The availability of resequenced genomes is also facilitating to the identification of a range of genomic mutations  — including (SNPs, copy number variations (CNVs), insertions and deletions (indels), and genic deletions and duplications  —) which will not only consolidate the varietal identification process but also clarify the evolutionary history of the species, improve the understanding of the genetic structure of olive germplasm, and help identify selection markers and/or markers with functional significance. 

Currently, some markers have already been identified that are significantly associated with phenotypic traits of major agronomic importance, such as drupe shape and oil quality. The identification of the molecular genetic determinants responsible for phenotypic variation will open new perspectives for the assisted selection breeding in olive, as well as for the application of gene editing technologies.