The development of Vitis × Muscadinia (V x M) wide hybrids, combining the disease resistance of muscadines (M. rotundifolia) with the berry quality attributes of V. vinifera grapes has be en a longstanding ambition of breeders. Stenospermocarpic seedless muscadine hybrids and wine grapes carrying powdery and downy mildew resistance introgressed from muscadines have been developed using classical techniques without the assistance of molecular tools through sustained effort over a century. However, progress has been impeded by differences in chromosome number (Vitis=38 chromosomes and Muscadinia=40 chromosomes) and genetic distance between the subgenera. A major objective of the new Vitis x Muscadinia Specialty Crop Research Initiative project is to develop and deploy new genotyping platforms and chromosome painting visualization tools to help grape and muscadine breeders track introgressed chromosomal regions in wide hybrids and accelerate trait discovery and cultivar development in new V x M hybrids. In order to develop a chromosome-painting visualization tool for V x M hybrids, we first conducted a large-scale population diversity analysis using historical data from the rhAmpSeq Vitis core panel. Structure analysis was performed to identify individuals belonging to Muscadinia and five additional subpopulations within subgenus Vitis. Approximately 33,000 marker haplotypes were identified as unique to Muscadinia and 671,000 haplotypes were identified as present only in Vitis. This haplotype information was used to create automated chromosome painting visualizations of introgressed segments in historical and modern V x M hybrids. These visualizations allow us to identify which Vitis-type hybrids carry muscadine introgressions in known resistance loci on chromosomes 12 (Run1/Rpv1), 18 (Run2/Rpv2), and 14 (Ren5) and which Muscadinia-type hybrids have introgressions associated with stenospermocarpy and other fruit-quality alleles from Vitis. This information will assist grape and muscadine breeders in planning crosses and discovering new disease resistance and fruit quality alleles. In the coming months, we intend to extend this strategy to a new low-cost DArTag genotyping panel that has been designed to amplify polymorphic markers in both subgenera. Breeders will then be able to rapidly assess which chromosomal regions and major-effect fruit quality and disease resistance alleles are present in a homozygous or heterozygous state in all new V × M hybrids.
