Dissecting the complex genetic basis of pre- and post-harvest traits in Vitis vinifera L. using genome-wide association studies

Abstract

Addressing the pressing challenges in agriculture necessitates swift advancements in breeding programs, particularly for perennial crops like grapevines. Moving beyond the traditional biparental quantitative trait loci (QTL) mapping, we conducted a genome-wide association study (GWAS) encompassing 588 Vitis vinifera L. cultivars from a Chilean breeding program, spanning three seasons and testing 13 key yield-related traits. A strong candidate gene, Vitvi11g000454, located on chromosome 11 and related to plant response to biotic and abiotic stresses through jasmonic acid signaling, was associated with berry width and holds potential for enhancing berry size in grape breeding. We also mapped novel QTL associated with post-harvest traits across chromosomes 2, 4, 9, 11, 15, 18, and 19, broadening our grasp on the genetic intricacies dictating fruit post-harvest behavior, including decay, shriveling, and weight loss. Leveraging gene ontology annotations, we drew parallels between traits and scrutinized candidate genes, laying a robust groundwork for future trait-feature identification endeavors in plant breeding. We also highlighted the importance of carefully considering the choice of the response variable in GWAS analyses, as the use of best linear unbiased estimators (BLUEs) corrections in our study may have led to the suppression of some common QTL in grapevine traits. Our results underscore the imperative of pioneering non-destructive evaluation techniques for long-term conservation traits, offering grape breeders and cultivators insights to improve post-harvest table grape quality and minimize waste.

Acknowledgements

This project was funded by ANID FONDECYT under grant agreement No 11161044. P.B. and M.G.-R. received funding from CORFO INNOVA 09PMG-7229 and INIA/MINAGRI (code 500495-70). J.I.yS. was supported by the Beatriz Galindo Program (BEAGAL18/00115) from the Ministerio de Educación y Formación Profesional of Spain and the Severo Ochoa Program for Centres of Excellence in R&D from the “Agencia Estatal de Investigación” of Spain, grant SEV-2016- 0672 (2017-2021) to the CBGP. J.G.-A. is working under a UPM predoctoral grant as part of the program “Programa Propio I +D+i” financed by the Universidad Politécnica de Madrid. H.F.C. received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 818144. E.S. received funding from CORFO-UC Davis Chile Project 13CEI2-21852 and INIA/MINAGRI Conservation of Genetic Resources Program (Code 501453-70).

Author contribution

The study was conceived by J.I.yS. and P.B., who also obtained funding. J.G.-A. conducted statistical and a part of bioinformatics analysis, created the figures, and wrote a significant portion of the article. J.I.yS. also wrote a large part of the article. P.B. contributed experimental and genomic data. T.C. contributed to pre-data analysis. R.L. and H.F.C. performed bioinformatic analysis and genotyping; E.S. provided genetic resources and phenotypic data; and M.G.-R. collected phenotypic data. The manuscript was drafted by J.I.yS., J.G.-A., V.S.-Z., and P.B. All authors participated in the discussion of the results, reviewed the manuscript, and contributed to the article’s development. The submitted version of the article has been approved by all authors.

Data availability

The data underlying the findings presented in this article are available in the GitHub repository maintained by TheRocinante-lab at https://github.com/TheRocinante-lab/Publications/tree/main/2024/GarciaAbadilloEtAl_Dissecting. This repository contains all the data necessary to reproduce the results presented in this paper. Additionally, the repository is freely accessible to anyone who wishes to explore the data or use it for their own research purposes. We encourage interested researchers to take advantage of this resource and to contact us if they have any questions or would like more information about the data.

Conflict of interest statement

The authors declare no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research Journal online.

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