Exploiting the genetic diversity of the fig tree to discover molecular markers associated with morphological and abiotic stress-related traits

Identifying and characterizing variants implicated in desirable traits holds the potential for advancing plant breeding efforts. Despite the promising commercial prospects of the fig tree (Ficus carica L.), owing to the nutritional richness of its fruits and the plant's good adaptability to harsh conditions, elucidating the genetic foundations of these traits remains a critical challenge. To date, there is a lack of in-depth studies on the genetic basis of morphological and abiotic stress-related traits. In this sense, this research aims to valorize and characterize the fig tree biodiversity in the Mediterranean basin and discover genes involved in these important traits. To assess genetic variability, 286 fig varieties were genotyped using a reference fig genome. In detail, 61 varieties were located from Spain, 110 from Tunisia, and 115 from Turkey. After whole genome sequencing and application of a variant calling pipeline, we identified 1,374,111 SNPs and 2,448,766 indels. Additionally, structural variation analysis identified 218 CNVs and 1363 SVs overlapping 1,833 genes involved in stress response, transport, metabolism, transcriptional regulation, and disease resistance. Population structure analysis revealed three distinct clusters corresponding to the geographical origin of genotypes, supported by principal component analysis, analysis of population structure, and phylogenetic tree construction. Interestingly, certain genotypes showed genetic relatedness across different clusters and countries, indicating potential synonymies or cryptic relatedness. Genome-wide association studies (GWAS) identified significant marker-trait associations for productive type and fruit traits, including fruit weight, fruit length, fruit width, total soluble solid content, titratable acidity, and firmness, as well as for traits involved in drought and salt stress response. Among the most notable results, the discovery of significant candidate genes, such as FMO1, LIMYB, CYP, ROS1, MYB, ABC transporter, WAK, CLM22, ERD6-like 5, HRGP, GA2OX8 and PP2C, were linked to fruit quality and development, offering targets for marker-assisted breeding strategies and genome editing to enhance yield, quality and environmental adaptation. For drought stress, GWAS identified SNPs associated with leaf temperature, relative water content, number of leaves, and plant height. Candidate genes such as BTB/POZ, BON1, GALT6, and GDP-L-fucose suggest involvement in key drought-response mechanisms. The GWAS on salt stress tolerance revealed SNPs associated with leaf temperature and relative water content. Notably, PEX7 was identified as a candidate gene linked to metabolism and abiotic stress response, while a strong peak on chromosome 3 revealed promising candidate genes, including Late Embryogenesis Abundant (LEA) Protein, Serine/Threonine Protein Kinases, and cysteine synthase, all known for their roles in salt stress tolerance. These findings provide the most comprehensive genome-wide insights into fig morphology and stress adaptation, offering valuable resources for future breeding programs.