Abstract:Muscadinia rotundifolia, an American species related to the European grapevine Vitis vinifera, has a high level of resistance to grapevine diseases. Backcross-based introgression has been used in French breeding programmes to transfer resistance factors from M. rotundifolia into cultivated backgrounds while eliminating the unwanted cultural traits and off-flavours. However, crosses between the two species have a low success rate, most of the hybrids are sterile, and phenotypic abnormalities are common in the offspring. In this context, it is essential to identify the genomic features that impede crosses between the two species. To this end, three mapping populations were generated by pseudo-backcrosses using M. rotundifolia as the donor parent and several V. vinifera cultivars as the recurrent parents. Genotyping-by-sequencing was used to establish high-density genetic linkage maps and to determine the origin of each segment of the chromosomes. Several segregation distortion regions were identified. In these regions, M. rotundifolia alleles were either conserved either eliminated. In addition, a high level of macrosynteny was observed between the parents of the pseudo-backcross 1 population. In this population, recombination rate variations were similar along the genome of both parents except on chromosome 7 of V. vinifera which correspond to chromosomes 7 and 20 of M. rotundifolia. In following pseudo-backcrosses, recombination rate abnormalities were observed on chromosomes with homeologous regions, i.e. regions with one allele from M. rotundifolia and one allele from V. vinifera. On these chromosomes, recombinations concentrate in homologous regions, and few or no recombinations are observed in the homeologous regions. These results will help breeders to select a suitable breeding strategy. The dataset is provided in support of the data paper: “Understanding recombination distribution in Muscadinia rotundifolia x Vitis vinifera backcrosses to improve grapevine breeding strategies” by Delame M., Prado E., Blanc S., Robert G., Mestre P., Rustenholz C., Merdinoglu D. (in preparation).

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