The complete genome of the Italian olive varieties “Frantoio” and “Leccino” has been published for the first time: a step forward for the agriculture of the future

A step forward for olive tree research and the promotion of Italy's agricultural heritage: for the first time, the complete DNA sequencing of the Italian varieties “Frantoio” and “Leccino,” two of the most important Italian olive cultivars, has been completed and published.

The work, the result of collaboration between the Institute of Plant Production at the Sant'Anna School of Advanced Studies in Pisa, the King Abdullah University of Science & Technology, and the Arizona Genomics Institute, has just been published in the journal Scientific Data by the Springer-Nature group.

For the Frantoio variety, this is the first genome sequencing ever published worldwide. For Leccino, too, the data now available are more complete and accessible than previous studies, published only recently by foreign groups. Not only that: this is the first time that the genomes of these two Italian cultivars, which are particularly interesting for their differences in resistance to drought and salinity, have been compared in such detail.

A genetic heritage waiting to be discovered

The study made it possible to analyze and compare the genetic structures of the two varieties. In particular, it was possible to discover how the genomes of “Frantoio” (1.18 Gb) and ‘Leccino’ (1.43 Gb) are largely made up of repeated DNA sequences (~67.5% in ‘Frantoio’ and ~70.8% in ‘Leccino’) and, in particular, those known in the literature as ‘Long Terminal Repeats’ (LTRs). The structural differences between the two genomes are interesting, with 22,469 deletions, 21,218 insertions, and only 33 inversions in Frantoio compared to Leccino. By studying the genome in detail, 59,777 genes were identified in Frantoio. Of these, 47,201 were considered highly reliable and 37,061 genes were successfully annotated in terms of their function. In Leccino, 67,103 genes were identified, of which 53,302 were of high quality and 37,606 genes were annotated.

A tool to address the challenges of climate change

The study reveals the secrets of the genome of these ancient trees, opening new frontiers for their protection and improvement, especially in light of ongoing climate change. Despite the enormous environmental, cultural, and economic value of the olive tree, scientific knowledge of its genome has been surprisingly slow compared to other fruit trees, and information on the genomes of Italian cultivars has been lacking.

“The problem has always been the production of long, high-quality genomic sequences, a fundamental prerequisite for accurately assembling complex genomes such as those of the olive tree,” explains Luca Sebastiani, full professor of General Arboriculture and Tree Cultivation at the Sant'Anna School of Advanced Studies and coordinator of the study. “This detailed study will allow us to gain a deeper understanding of the evolution of the olive tree, to understand the process of domestication and to accelerate genetic improvement programs. The goal? To develop varieties that are more tolerant to environmental stress, resistant to disease and capable of producing higher quality and quantity of fruit. All this will ensure a more secure future for the cultivation of this species, which is a symbol of our land and our culture.”

The international research group and PNRR funding

The project was conducted by a team led by Luca Sebastiani and Andrea Zuccolo, with the participation of researchers Iqra Sarfraz and Alessandra Francini, PhD student and researcher at the Institute of Plant Production, respectively. Mirko Celii of KAUST and Rod A. Wing of the Arizona Genomics Institute also collaborated.

The work was funded by the National Agritech Center, as part of the PNRR – National Recovery and Resilience Plan, and through European funds for research on innovation and sustainability.