ASHS 2025 Conference

Combining muscadine (M. rotundifolia) with bunch grapes (V. vinifera) addresses the challenges faced by each species. Muscadines provide strong disease resistance and adaptability to the southeastern U.S climate but lack key fruit quality traits such as seedlessness and crisp texture. In contrast, V. vinifera, produces high-quality fruit but is highly susceptible to diseases like Pierce’s disease and powdery mildew. Hybridization between the two aims to retain the desirable fruit characteristics of V. vinifera while incorporating the resilience of muscadines. Understanding the genetic basis of key agronomic traits in Vitis × Muscadinia (V × M) hybrids is essential for introgressing valuable traits such as seedlessness, disease resistance, and flavor into breeding populations. This study aimed to develop a high-density genetic linkage map to investigate the inheritance of seedlessness, sterility, and recombination patterns in wide hybrids. The mapping population was derived from a cross between AM-116, a seeded Muscadinia rotundifolia selection, and JB15-43-N0-25, a seedless V × M hybrid. Phenotypic evaluations of traits such as flower sex, winter injury, berry size, berry, color, yield, seedlessness, cluster architecture, and vigor were collected and integrated with genotypic data to create a linkage map and identify quantitative trait loci for these traits. RhAmpSeq genotyping was initially used as the primary method to genotype the population and assess recombination frequency across homeologous and homologous chromosome regions. However, because rhAmpSeq markers were designed using Vitis genomes without incorporating Muscadinia, marker coverage in Muscadinia genomic regions was limited. To overcome this limitation, SkimSeq whole-genome sequencing was later employed to construct a high-density linkage map. Principal Component Analysis (PCA) of genomic data revealed that individuals positioned closer to the V × M parent (JB15-43-N0-25) had a higher proportion of Vitis ancestry and an increased number of homeologous chromosomes. This pattern suggests that structural genomic incompatibilities affecting segregation distortion and recombination rates may result in reduced recombination in homeologous regions in V × M hybrids. These findings provide new insights into the genetic mechanisms governing sterility, recombination, and trait introgression in Vitis × Muscadinia hybrids, contributing to the development of breeding strategies aimed at integrating desirable traits across subgenera. Understanding these factors is crucial for overcoming genetic barriers in interspecific breeding and optimizing hybrid vigor for commercial muscadine grape production.