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Ginkgo biloba  L. is a well-known living gymnosperm fossil that has medicinal and ornamental value. In this study, a high density genetic map was constructed with megagametophytes of 94 seeds from a single  Ginkgo  tree by employing the specific-locus amplified fragment (SLAF) sequencing technique. The average sequencing depth was 11.20×, which yielded 538,031 high-quality SLAFs. Among these SLAFs, 204,361 were heterozygous in the maternal tree and segregated in the progeny. The established map contained 12,263 SLAFs that were assigned to 12 linkage groups (LGs). The number of LGs on this map equaled the number of chromosomes in  Ginkgo . The total map length was 1,671.77 cM, with an average distance of 0.89 cM between adjacent marker bins. Map evaluation based on the haplotype map and the heat map validated the high quality of the established map. Because  Ginkgo  is an economically and biologically important tree, strenuous efforts have been exerted to sequence its genome. This new map, built using sequence-based markers, will serve in the future as a fundamental platform for anchoring sequence assemblies along  Ginkgo  chromosomes. This map also provides a desirable platform for various genetic studies of  Ginkgo , including gene/quantitative trait locus mapping and marker-aided selection.

A Highly Dense Genetic Map for Ginkgo biloba Constructed Using Sequence-Based Markers