A Comprehensive High-Density Genetic Linkage Map For Loblolly Pine (Pinus taeda L.)

High-density genetic maps will be used to complete genome assembly of Pinus taeda, Pinus lambertiana and Pseudotsuga menziesii. In loblolly pine (Pinus taeda) genetics maps are available and currently housed in the TreeGenes database and navigated with the Comparative Map Viewer (cMap) interface. A new consensus high-density map of P. taeda has been developed based on two three-generation outbred pedigrees (base and qtl pedigree). Both populations were obtained by crossing the improved genotypes 20-1010 and 11-1060 from the North Carolina State University Cooperative Tree Improvement Program. Around 600 individuals for each population were genotyped with ≈2500 different markers (RFLPs, EST, SSR, SNPs). The grouping, ordering and spacing of the markers on each linkage group were performed and verified with different software as Record, OneMap, R/qtl and JoinMap^®4. A minimum LOD of 3.0 and a maximum recombination fraction of 0.45 were used as thresholds. Segregation distortion was tested using the chi-square goodness-of-fit test (p>0.05). Recombination fractions were converted to map distances in centimorgans (cM) using the Kosambi mapping function. Once both maps were obtained, the Combine Groups for Map Integration function from the JoinMap^®4 menu was used. This new consensus reference map will provide a solid framework to improve the genome assembly quality.