Single nucleotide polymorphism (SNP) diversity in an olive germplasm collection

In contrast to other fruit crops, olive (Olea europaea) production is based mainly on traditional, locally selected cultivars. The world olive germplasm contains more than 2600 different cultivars, but olive genetic resources are poorly exploited and studied. Increasing our knowledge on olive tree genetics is a crucial step for breeding purposes and represents the future of olive growing. In the present work, we used the genotyping-by-sequencing (GBS) approach for genome-wide identification of single nucleotide polymorphisms (SNPs) to assess the level of genetic diversity in a collection of 78 olive cultivars. GBS analysis generated 37,792 high-quality SNPs, using an Olea europaea whole-genome sequence as reference. We were able to distinguish between SNPs located in intergenic regions (71.2%) and SNPs that overlap genes (28.8%), of which 2690 SNPs fell within annotated exons, affecting a total of 1302 genes. SNP markers developed by GBS and information on genetic diversity that emerged in this work will support genome-wide association mapping studies and breeding programs in olive.