Cork oak (Quercus suber L.) is an ecologically and economically important evergreen tree species native to the Mediterranean basin. Cork oak trees are found in a unique woodland ecosystem (known as ‘montado’ in Portugal and ‘dehesa’ in Spain), representing one of the most important agro-silvo-pastoral systems in the Mediterranean region, providing essential ecological, economic, and social benefits. These systems play a crucial role in biodiversity conservation, carbon sequestration, risk prevention, soil protection, and sustainable cork production. Cork oak has the ability to produce cork in a sustainable manner being the basis for a unique industry worldwide with a wide range of applications, harnessing its distinctive chemical and physical properties, and remaining one of the most non-wood forest products used worldwide.

Cork production is closely linked to the physical development of the cork oak, particularly trunk diameter, which determines when the tree is ready for the first harvest. The first extraction only occurs after approximately 19–25 years of growth, once the legally required diameter is reached, while subsequent extractions only occur every 9–12 years. This relationship allows phenotypic traits such as trunk diameter and height to be used as indicators of potential cork production. Hence, the integration of phenotypic data with high-throughput sequencing technologies allows genotype–phenotype association studies aimed at identifying molecular markers linked to desirable traits, with potential relevance for selection and improvement strategies. In this context, the aim of this study is to identify molecular markers associated with cork productivity.

In order to achieve this goal, the F1 cork oak population was selected as the genomic resource. This population is the only known cork oak population in which the progenitors of each offspring are identified, all originating from selected high-quality cork-producing parents. The F1 cork oak population is approximately 12 years old and has been phenotypically characterized during the last years, annually registering the height and diameter for each tree, traits directly associated with cork production. A subset of individuals from this population was selected, focusing on the five largest families. In total, 147 individuals were sampled and sequenced using whole-genome resequencing (WGRS), providing a high-resolution dataset. The collected phenotypic data and the genomic data are currently being analyzed, in order to identify molecular markers associated with cork production traits.

Through the use of the unique F1 cork oak population, this work provides a robust framework for studying trait inheritance while establishing a valuable foundation for future research into the resilience and sustainability of this species. Overall, this work is expected to contribute to the generation of genomic resources, providing valuable tools for future breeding and conservation programs of cork oak species.

Acknowledgments:

Work supported by Interreg Spain-Portugal (POCTEP) through FEDER under the project “SOS_PRODEHESAMONTADO (0086_SOS_PRODEHESAMONTADO_4_E). Authors acknowledge FCT for funding: LM (CEECINST/00131/2018), AU ( https://doi.org/10.54499/CEECINST/00100/2021/CP2774/CT0001), AF (UI/BD/153511/2022; https://doi.org/10.54499/UI/BD/153511/2022), the R&D unit MED (https://doi.org/10.54499/UID/05183/2025), and the Associate Laboratory CHANGE (https://doi.org/10.54499/LA/P/0121/2020).