Multi-omics – enabled next-generation breeding in native American muscadine grapes: translational genomics for improved fruit quality and stress resilience

Abstract

Native American muscadine grape (Muscadinia rotundifolia) represents a strategically important reservoir of allelic diversity for grape improvement. This species combines exceptional nutraceutical value with inherent resilience to biotic and abiotic stressescommon in warm, humid production regions. As climate variability intensifies and disease and pest pressures evolve, muscadine-derived traits provide a complementary pathway to enhance the sustainability and stress tolerance of common grape (Vitis vinifera) while maintaining market standards for fruit and wine quality.

This presentation highlights how integrated multi-omics technologies enable a next-generation breeding framework that connectsgenetic variation to biochemical and physiological phenotypes with unprecedented resolution.

Genomic resources—including chromosome-scale reference assemblies, high-density SNP genotyping platforms, genome-wide association studies (GWAS), and structured breeding populations—are accelerating quantitative trait locus (QTL) discovery forcomplex traits related to fruit quality, stress adaptation, and reproductive development. These efforts are strengthened bytranscriptomic profiling, which elucidates gene regulatory networks across developmental stages and environmental conditions. Integrating expression dynamics with genetic mapping allows precise prioritization of candidate genes within QTL intervals, facilitating marker-assisted selection and genome-informed breeding.

Metabolomics further advances genotype-to-phenotype translation by quantifying dynamic changes in nutraceutical and stress-responsive metabolites that influence berry composition, ripening, antioxidant capacity, and environmental adaptation. When combinedwith genomics and transcriptomics, metabolomic datasets enable multilayered trait modeling and improve predictive accuracy for complex phenotypes. The addition of hormonomics introduces a regulatory dimension by linking hormone signaling networks todevelopmental and stress-response pathways.

To bridge discovery and deployment, gene-editing platforms validate high-confidence candidate genes identified through multi-omicsanalyses. Seedlessness serves as a case study within this pipeline, illustrating how QTL mapping and transcriptomic signaturesconverge on regulatory genes controlling seed and embryo development, followed by targeted CRISPR/Cas9-mediated editing to confirm causality and accelerate trait integration. This iterative discovery-to-validation framework reduces breeding cycle time and increases selection efficiency.

By USDAcharter, the Florida A&M University (FAMU) Viticulture Center maintains the public germplasm collection of Muscadiniaspecies and American native Pierce’s Disease–tolerant Vitis species and serves as one of five National Clean Plant Centers forGrapes. Implementation of an accelerated, omics-guided breeding pipeline has led to the release of three patented cultivars in the pastfive years: two muscadines—‘Floriana’ (red wine) and ‘Florida Onyx’ (fresh fruit)—and one Vitis hybrid cv. ‘Blanc du Soleil.’ We arenot only improving grapes—demonstrating that genomic discovery can translate directly into market-ready innovation.

Acknowledgements

USDA-NIFA 1890 Capacity Building Grant (CBG) Program, FL Specialty Crop Block Grant Program (FL SCBGP), Florida Wine (former Viticulture) Trust Fund.

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