Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits

Abstract

In sweet cherry (Prunus avium L.), large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2–6 years, and characterized using a genotyping-by-sequencing approach. The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes. We identified numerous SNP–trait associations for global fruit size (weight, width, and thickness), fruit cracking, fruit firmness, and stone size, and we pinpointed several candidate genes involved in phytohormone, calcium, and cell wall metabolisms. Finally, we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker–trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality, and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Acknowledgements

We thank the Prunus/Juglans Biological Resources Center managed by the INRAE Fruit Tree Experimental Unit for performing part of the phenotyping and for maintenance of the collection. This work was supported by the Région Nouvelle-Aquitaine with the project CerGEn reference 2018-1R20203, which funded the postdoctoral fellowship for A.S.L.D.

Author contributions

E.D., T.B. and J.Q.G. designed the research. E.D. coordinated the research. H.B. and T.B. managed and performed the phenotyping. M.F. prepared the samples for GBS. A.S.L.D. performed bioinfor-matics analyses for GBS data. A.S.L.D. and A.B. performed GWAS and genomic analyses with the help of L.L.D. and B.W. T.B., J.Q.G. and ED worked on the interpretation of results. A.S.L.D. and A.B. wrote the manuscript. All coauthors revised and validated the manuscript.

Data availability

The complete raw dataset can be freely and openly accessed in the ‘Recherche Data Gouv’ repository, via the identifier ‘GWAS on fruit quality traits using INRAE sweet cherry (P. avium) germplasm collection’ and at https://doi.org/10.57745/WVMJOV. The dataset consists of the list of plant material, genotyping resources, and phenotyping dataset.

Conflict of interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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