Genomic analysis of fruit size and shape traits in apple: unveiling candidate genes through GWAS analysis

Abstract

Genomic tools facilitate the efficient selection of improved genetic materials within a breeding program. Here, we focus on two apple fruit quality traits: shape and size. We utilized data from 11 fruit morphology parameters gathered across three years of harvest from 355 genotypes of the apple REFPOP collection, which serves as a representative sample of the genetic variability present in European-cultivated apples. The data were then employed for genome-wide association studies (GWAS) using the FarmCPU and the BLINK models. The analysis identified 59 SNPs associated with fruit size and shape traits (35 with FarmCPU and 45 with BLINK) responsible for 71 QTNs. These QTNs were distributed across all chromosomes except for chromosomes 10 and 15. Thirty-four QTNs, identified by 27 SNPs, were related for size traits, and 37 QTNs, identified by 26 SNPs, were related to shape attributes. The definition of the haploblocks containing the most relevant SNPs served to propose candidate genes, among them the genes of the ovate family protein MdOFP17 and MdOFP4 that were in a 9.7kb haploblock on Chromosome 11. RNA-seq data revealed low or null expression of these genes in the oblong cultivar “Skovfoged” and higher expression in the flat “Grand’mere.” The Gene Ontology enrichment analysis support a role of OFPs and hormones in shape regulation. In conclusion, this comprehensive GWAS analysis of the apple REFPOP collection has revealed promising genetic markers and candidate genes associated with apple fruit shape and size attributes, providing valuable insights that could enhance the efficiency of future breeding programs.

Acknowledgements

C.D. was supported by “DON CARLOS ANTONIO LOPEZ” Abroad Postgraduate Scholarship Program, BECAL-Paraguay. V.C.A. is a recipient of grant PRE2019-088780 funded by MCIN/AEI/10.13039/501100011033 and by “ESF Investing in your future.” This research was supported by project PID2021-128885OB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe.” This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 817970 (INVITE). We acknowledge support from the CERCA Programme (“Generalitat de Catalunya”), and the “Severo Ochoa Programme for Centres of Excellence in R&D” 2016-2019 (SEV-2015-0533) and 2020-2023 (CEX2019-000902-S) both funded by MCIN/AEI/10.13039/501100011033.

Author contributions

M.J.A. and C.D. contributed to the design and implementation of the research and to the analysis of the results. C.D. conducted the laboratory experiments. V.C.A. performed the whole-genome RNAseq and the GCN analysis. All authors contributed to the writing of the manuscript.

Data availability

Data are available in the Supplementary Data file.

Conflict of interest statement

None declared.

Supplementary data

Supplementary data are available at Horticulture Research online.

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