Development of Genomic Tools for Comparative Mapping and QTL Studies in Northern Red Oak (<i>Quercus rubra</i> L.)

<p>Oaks (<i>Quercus spp</i>.) 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). <i>Quercus rubra</i> is the most wide-ranging species in <i>Quercus</i> section <i>Lobatae</i>, the oak section native only in the Americas. Despite the huge ecological and economic importance of <i>Q. rubra</i>, 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 <i>Q. rubra</i>, 40 EST-SSR previously mapped in European pedunculate oak <i>Q. robur </i>L.<i> </i>(<i>Quercus</i> section <i>Quercus</i>) and one EST-SSR marker from <i>Castanea mollissima </i>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 <i>Q. robur</i> 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 <i>Quercus</i>.</p><p>Finally we located genomic regions associated with spring bud burst in <i>Q. rubra</i> using an interval mapping and Random Forest approach. We hypothesized that the genome architecture of bud burst QTL would be similar to that of <i>Q. robur</i>. Our results indicate the presence of major bud burst QTL on linkage group 2, in agreement with the LG2 region found in <i>Q. robur.</i> 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 <i>Q. rubra</i>.</p>