Oaks (Quercus spp.) are ecologically significant components of hardwood forests in the northern hemisphere and are the most species-rich genus within the Fagaceae (oaks, chestnuts, and beeches). Quercus rubra is the most wide-ranging species in Quercus section Lobatae, the oak section native only in the Americas. Despite the huge ecological and economic importance of Q. rubra, a dominant species in the oak forests of Eastern North America, genetic studies were quite limited until recently. Using parentage analysis, we have identified 1048 full-sib progeny from a single seed and a single pollen parent. For framework map construction, 509 progeny were genotyped with 37 gSSR and 36 EST-SSR derived from Q. rubra, 40 EST-SSR previously mapped in European pedunculate oak Q. robur L. (Quercus section Quercus) and one EST-SSR marker from Castanea mollissima Blume. A subset of the full-sib family (217) was also genotyped with ddRADseq markers. Our current consensus map includes 108 gSSR and EST-SSR framework markers and 849 ddRADseq markers with an average distance between markers of ~1.06 cM. We have the expected number of linkage groups (12), each of which is tagged to the Q. robur linkage map using the 38 EST-SSR markers mapped in both species. Our map reveals a high degree of marker colinearity between northern red oak and pedunculate oak, suggesting that these two species share quite similar genome architecture. This map will serve as a basic foundation for the comparative study of the genetic architecture of adaptive traits and genome evolution in the genus Quercus.
Finally we located genomic regions associated with spring bud burst in Q. rubra using an interval mapping and Random Forest approach. We hypothesized that the genome architecture of bud burst QTL would be similar to that of Q. robur. Our results indicate the presence of major bud burst QTL on linkage group 2, in agreement with the LG2 region found in Q. robur. Additionally, we compared the nucleotide and amino acid sequence similarity of the markers identified as associated with bud bust on LG2 to identify potential candidate genes for this trait in Q. rubra.