Evidence map›Paper›PMID 41353497›Full record

ArticleScientific reports2025

Leveraging foundation models to dissect the genetic basis of cluster compactness and yield in grapevine.

Sadikshya Sharma, Jose R Munoz, Efrain Torres-Lomas, Jerry Lin, Hollywood Banayad, Yaniv Lupo, Veronica Nunez, Ana Gaspar, Dario Cantu, Luis Diaz-Garcia

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Sadikshya Sharma *Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Jose R Munoz *Department of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Efrain Torres-LomasDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Jerry LinDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Hollywood BanayadDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Yaniv LupoDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Veronica NunezDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Ana GasparDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Dario CantuDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA.
Luis Diaz-GarciaDepartment of Viticulture and Enology, University of California Davis, Davis, CA, 95616, USA. diazgarcia@ucdavis.edu.

Funding

American Vineyard Foundation 2023-2781California Grape Rootstock Improvement Commission A24-0828National Institute of Food and Agriculture 2022-51181-38240USDA-NIFA Specialty Crop Research Initiative 2022-51181-38240
6 · The paper itself

Abstract

Grape cluster compactness is a key trait that influences fruit quality, yield, and disease susceptibility. Understanding the genetic basis of this trait is essential for optimizing vineyard management and improving grapevine cultivars. In this study, we performed quantitative trait locus (QTL) mapping to identify genomic regions associated with cluster architecture and yield components in a bi-parental population derived from Vitis vinifera cv. Riesling × Cabernet Sauvignon. A total of 138 full-sibling progeny were evaluated over two growing seasons at Oakville, Napa Valley, California. Traditional yield-related traits were measured, including cluster number, total cluster weight, and average cluster weight. Additionally, an image-based phenotyping pipeline leveraging the foundation model Segment Anything Model (SAM) was employed to segment individual berries, measure their size and shape, and compute cluster compactness with minimal manual intervention. Trait correlations revealed that compact clusters tended to have a higher berry count but smaller berry size, highlighting the role of compactness in modulating cluster structure. Heritability estimates varied across traits, with berry dimensions and compactness displaying moderate to high heritability, indicating strong genetic control. Two parental linkage maps were constructed using a pseudo-test cross strategy. QTL mapping identified multiple loci associated with cluster architecture and yield components, with several stable QTLs detected across both years, with marker effects ranging from 7.6% to 22.1%. Notably, a QTL for cluster compactness was found in both seasons on chromosome 1 in Cabernet Sauvignon. Other stable QTLs were associated with berry size (chromosomes 6 and 17) and berry count (chromosome 5 in Cabernet Sauvignon and chromosome 7 in Riesling). Additional QTLs were detected in a single year, reflecting the influence of environmental variation. Our findings provide valuable insights into the application of foundation models requiring no prior training and minimal intervention for high-quality segmentation and enhance our understanding of the genetic architecture of cluster compactness and yield traits. The genomic regions identified in this study offer promising targets for breeding programs aimed at improving grape quality and disease resistance.

Indexed as

FruitQuantitative Trait LociVitisChromosome MappingModels, GeneticPhenotypeQuantitative Trait, HeritableCluster compactnessImage analysisQTLSegment anything modelVitis viniferaYield components

Identifiers

PMID41353497
PMCPMC12795812

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.