GWAS and QTLanalysis for 124 individual traits

Investigating the genetic architecture of important agronomic traits in grapevine, like grape quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. Here, we developed a high-density 200K single nucleotide polymorphism array and validated its effectiveness by genotyping 471 accessions from three F1 breeding populations. We developed a high-throughput grape phenotyping tool that accurately captures berry color, shape and size. By integrating data from the two platforms, associated loci were identified over three growing seasons. Association mapping, and haplotype analysis identified novel loci and candidate genes for berry shape (bHLH017), soluble sugars (ACT) and organic acids (ALTM1 and FUSC2), as well as vine cold tolerance (NAC08), and fine mapped the flower sex determination locus. Furthermore, we validated the functional role of NAC08, demonstrating that it activated the expression of RFS6 to increase raffinose levels and confer co..., , , # GWAS and QTLanalysis for 124 individual traits

[https://doi.org/10.5061/dryad.02v6wwqcx](https://doi.org/10.5061/dryad.02v6wwqcx)

## Description of the data and file structure

HTP was carried out for three years (2020, 2021, and 2022) of berries produced by the BF × Y73 F1 population. We verified the distributions of all traits in the population and conducted genome wide association studies (GWAS) and quantitative trait locus (QTL) analysis for 124 individual traits related to berry morphometry and color, as well as 4 composite traits (Figures EV1 and EV2, Supporting Information). The Expanded Figure EV1 (Figure EV1) and Expanded Figure EV2 (Figure EV2) have been submitted.
### Files and variables

#### File: Expanded\_View\_Figure\_1.pdf

**Description:** GWAS results of 124 individual traits

#### File: Expanded\_View\_Figure\_2.pdf

**Description:** QTL results  of 124 individual traits
## Code/software

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