Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program

Borrelli, C.; Prado, E.; Dumas, V.; Arnold, G.; Onimus, C.; Butterlin, G.; Jaegli, N.; Wiedemann-Merdinoglu, S.; Lacombe, M.-C.; Dorne, M.-A.; Umar-Faruk, A.; Chaumonnot, S.; Valentin, S.; Ley, L.; Reynard, J.-S.; Spring, J.-L.; Duchene, E.; Schneider, C.; Merdinoglu, D.; Avia, K.

doi:10.1101/2025.10.05.680539

Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.10.05.680539

Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program

View original source ↗Export metadata ↓

Abstract

Breeding disease-resistant grapevines that retain agronomic performance under variable climates requires loci and predictions that transfer across related hybrid families. We analyzed 1,081 genotypes from 95 crosses within the French INRAE-ResDur breeding program for 13 phenology, yield and berry-composition traits evaluated at five sites from 2006 to 2024. We integrated within-family QTL mapping, kinship- and population-adjusted multiple-population QTL mapping in 772 progeny, and structure-aware GWAS in 899-968 individuals, depending on the trait, together with cross-environment, cross-trait and local genomic estimated breeding-value analyses. Genetic and phenotypic differentiation among families strongly affected locus detection. Of 76 family-QTL intervals, seven, representing six trait-region hypotheses, were locally concordant across all three mapping frameworks. The strongest recurrent evidence involved a chromosome-16 region for veraison and harvest date, where a localGEBV block at 14.69 Mb ranked first for veraison and second for harvest; chromosome-14 cluster traits and chromosome-1 compactness emerged as additional validation priorities. Cross-environment meta-analysis detected no common fixed-effect association at 5% FDR but revealed extensive heterogeneous evidence. Cross-trait analysis grouped 270 significant marker tests into 54 candidate multi-trait regions, without establishing biological pleiotropy. Population-adjusted localGEBV yielded a mean leave-one-population-out correlation of 0.470 between phenotypic BLUPs and genomic scores across traits. These results distinguish compact haplotype-validation targets from background- and environment-dependent signals, supporting a staged strategy that combines marker- assisted selection for validated recurrent regions with externally validated multi-trait, multi- environment genomic prediction for polygenic traits.

Explore related subjects

genetics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Borrelli, C., Prado, E., Dumas, V., Arnold, G., Onimus, C., Butterlin, G., Jaegli, N., Wiedemann-Merdinoglu, S., Lacombe, M.-C., Dorne, M.-A., Umar-Faruk, A., Chaumonnot, S., Valentin, S., Ley, L., Reynard, J.-S., Spring, J.-L., Duchene, E., Schneider, C., Merdinoglu, D., Avia, K.. 2025-10-06. Uncovering the genetic basis of agronomic traits in over 1,000 grapevine genotypes derived from a disease resistance breeding program. https://doi.org/10.1101/2025.10.05.680539

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Generation of a transgenic cephalopod

Coleoid cephalopods (cuttlefish, octopus, and squid) are marine mollusks with elaborate nervous systems that support a diverse repertoire of complex behaviors. These include the neural control of the color, pattern, and texture of the skin, facilitating both adaptive camouflage and innate patterning that may reflect internal state. The development of transgenic cephalopods expressing fluorescent proteins, optogenetic actuators, and reporters of neural activity would contribute a new and important technology to cephalopod biology. The generation of transgenic cephalopods, however, has remained a major challenge. Here, we report the development of stable transgenic dwarf cuttlefish (Ascarosepion bandense) expressing ubiquitous nuclear-localized mScarlet, a red fluorescent protein. We evaluated multiple strategies for transgenesis, and established cuttlefish lines using both CRISPR and the transposons Sleeping Beauty and Minos. The stable expression of transgenes enabled live imaging of cell dynamics during embryonic development. The Minos transposon emerged as the most efficient transgenesis strategy and is adaptable to promoters and transgenes of choice. These strategies now enable the generation of diverse genetic tools for mechanistic studies of cephalopod biology.

genetics↗

bioRxiv2026

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗

bioRxiv2026

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗