Whole genome scanning of a Mediterranean basin hotspot collection provide new insights into olive tree biodiversity and biology.

Abstract

Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. Τhe availability of whole genome assemblies and annotations of olive tree cultivars and oleasters have contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources with olive tree populations that span across the entire Mediterranean region. This study has developed the most complete genomic variation map and comprehensive catalogue/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree "Throuba Naxos" was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes, known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by selective sweep scan to be under selection pressure on all olive tree chromosomes. To exploit further the genomic and phenotypic resources obtained from the current work, Genome Wide Association Analyses were performed for twenty-three morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of the olive tree biology.