Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits

Abstract

Fruit quality traits are major breeding targets in cultivated strawberry ( Fragaria × ananassa ). Taking into account the requirements of both growers and consumers when selecting high-quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50 K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by genome-wide association studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition, and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new quantitative trait locus (QTL), demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf life. Moreover, major QTL for firmness, glossiness, skin resistance, and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness, and skin resistance. Overall, our study provides a potential avenue for extending shelf life without compromising flavor and color as well as the genetic markers needed to achieve this goal.

Acknowledgements

We thank Sarah Touzani and Eva Bouillon for their help in phenotyping. The project was funded by the Nouvelle-Aquitaine Region and the European Regional Development Fund (ERDF) (REGINA project no. 67822110; AgirClim project No. 2018-1R20202); and European Union Horizon 2020 research and innovation program (BreedingValue project No. 101000747; PRIMA-Partnership 2019-22 Med-Berry project). Al.P. was supported by the CIFRE (Convention Industrielle de Formation par la Recherche) contract between Invenio (SME, Bordeaux, France) and the INRAE BAP department.

Author’s contributions

B.D. and Al.P. conceived and designed the experiments. Al.P. conducted hands-on experiments and data collection. Au.P., Jo.P., and Ju.P. contributed to data collection. Al.P., P.R.S., B.D., and C.R. analyzed the data. Al.P., B.D., and C.R. wrote the original draft. All authors read and approved the final manuscript.

Data availability

All relevant data generated or analyzed are included in the manuscript and the supporting materials.

Conflict of interest statement

The authors declare that there are no conflicts of interest.

Supplementary Data

Supplementary data is available at Horticulture Research online.

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