Genetic mosaic of the Mediterranean fig: comprehensive genomic insights from a gene bank collection

Author:

Bazakos Christos123ORCID,Michailidis Michail24,Tourvas Nikolaos5,Alexiou Konstantinos G.67,Mellidou Ifigeneia12,Polychroniadou Chrysanthi28,Boutsika Anastasia1,Xanthopoulou Aliki12,Moysiadis Theodoros189,Skodra Christina4,Kollaros Marios‐Georgios4,Glavakis Evangelos10,Stournaras Vasileios1112,Karagiannis Evangelos13,Aravanopoulos Filippos5,Molassiotis Athanassios4ORCID,Tanou Georgia28ORCID,Ganopoulos Ioannis12

Affiliation:

1. Institute of Plant Breeding and Genetic Resources, ELGO DIMITRA Thermi Greece

2. Joint Laboratory of Horticulture, ELGO DIMITRA Thermi Greece

3. Max Planck Institute for Plant Breeding Research Department of Comparative Development and Genetics Cologne Germany

4. Laboratory of Pomology, Department of Horticulture Aristotle University of Thessaloniki Thermi Greece

5. Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment Aristotle University of Thessaloniki Thessaloniki Greece

6. Centre for Research in Agricultural Genomics, CSIC‐IRTA‐UAB‐UB Barcelona Spain

7. Institut de Recerca i Tecnologia Agroalimentàries Barcelona Spain

8. Institute of Soil and Water Resources, ELGO‐DIMITRA Thermi Greece

9. Department of Computer Science, School of Sciences and Engineering University of Nicosia Nicosia Cyprus

10. Glavakis Fruit Trees Greece

11. Institute of Olive Tree, Subtropical Crops and Viticulture, ELGO‐DIMITRA, Department of Olive and Horticultural Crops Kalamata Greece

12. Department of Agriculture University of Ioannina Arta Greece

13. Department of Agriculture University of Western Macedonia Florina Greece

Abstract

AbstractHigh‐depth whole‐genome resequencing of 53 diverse fig tree genotypes yielded a rich dataset of genetic variants. We successfully identified 5,501,460 single‐nucleotide polymorphisms (SNPs) and 1,228,537 insertions and deletions (InDels), providing a high‐density and excellent‐quality genetic map of the fig tree. We also performed a detailed population structure analysis, dividing the 53 genotypes into three geographical groups and assessing their genetic diversity and divergence. Analysis of structural variants (SVs) and copy number variations (CNVs) revealed their potential functional impact, particularly in plant‐pathogen interaction and secondary metabolism. Metabolomic fingerprinting of fig genotypes uncovered extensive variation in primary metabolites and polyphenolic compounds, highlighting the influence of genotype on fruit quality traits such as nutritional content and bioactive compound composition. The genome‐wide association study (GWAS) identified critical SNPs associated with fruit quality and morphological features. The discovery of significant candidate genes, such as AGL62, GDSL, and COBRA‐like protein 4 genes, offers promising targets for marker‐assisted selection and genome editing approaches to improve fig fruit morphological and quality traits. This extensive genomic analysis of fig trees enhances our understanding of the genetic basis of important agronomic traits and provides a rich resource for future research in this economically and nutritionally significant fruit.

Publisher

Wiley

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