Dissecting the genetic basis of relevant fruit quality traits in interspecific grapevines (Vitis spp.)

Abstract

Understanding the genetic control of fruit composition traits in interspecific grapevines ( Vitis spp.) is crucial when breeding new cultivars with desirable fruit chemistry. To address this, a genome-wide association study (GWAS) was conducted using 587 genotypes derived from three elite selections. This study spanned 3 years (2020–2022) and with phenotyping conducted at three different timepoints within each season for a total of nine phenotyping events focused on nine fruit traits. Several strong and stable quantitative trait locus (QTL) associations were identified on chromosomes 6, 16, and 17 across multiple phenotyping events for most sugar- and acid-related traits. Notably, putative sugar transporter genes Vitvi16g00860 and Vitvi16g00861 on chromosome 16, which facilitate the movement of sugars and K ⁺ ions across membranes, were found to be associated with all sugar and acid traits studied. Additionally, several QTLs on chromosomes 1–5, 7, 14, and 18 were identified for various fruit quality traits across different phenotyping events. We determined functional connections between traits and scrutinized candidate genes by utilizing gene ontology annotations for genes located near significant SNPs. We also highlighted the effect of different forms of phenotype (best linear unbiased predictions and unmodified) in suppressing certain QTL associations. This GWAS study focused on fruit quality in grapes, establishing a necessary knowledge base regarding the genetic architecture of these traits to aid molecular breeders in further improving them.

Acknowledgements

Field planting and training of grapevine plants was conducted with support from R. Ibrahim, N. Theisen, M. Brooke, I. Tatar, S. Bogenrief, B. Rana, M. Mzumura, B. Köse, and numerous students of the High Value Crops research team. Genotype data for GBS was generated with logistical support from Justin Hegstad. GBS genotyping and phenotypic data collection were supported by the USDA Specialty Crop Block Grant award ‘Identification of Economically Important Fruit Quality Traits in Diverse Grapevine Genotypes for Elite Germplasm Development’, award #2019-NOGA19-438. rhAmpSeq marker development was done with the support of Vitisgen2. Funding for VitisGen ‘Accelerating grape cultivar improvement via phenotyping centers and next generation markers’ is provided by a Specialty Crop Research Initiative Competitive Grant, Award No. 2011-51181-38240, of the USDA National Institute of Food and Agriculture.

Author contributions

V.R.K. conducted the experiment, executed data analysis, and drafted the manuscript; J.S., A.S., and H.H.-V. conceived the study; H.H.V., X.L., and A.S. obtained funding; V.R.K., R.P., A.S., Z.W., and C.A. helped in data collection; X.L. prepared genotype data; 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 Figshare repository. The phenotype (https://doi.org/10.6084/m9.figshare.29299808.v1), genotype (https://doi.org/10.6084/m9.figshare.29300051.v1), and the QTL genetic map data files (http://doi.org/10.6084/m9.figshare.30494765.v1) can be accessed using assigned DOIs.

Conflicts of interest statement

The authors have no conflicts of interest to declare.

Supplementary material

Supplementary material is available at Horticulture Research online.

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