High-Density SNP Based Genetic Map of an Interspecific Backcross Pedigree of Eucalyptus grandis x E. urophylla

Next-generation DNA sequencing technologies along with high-throughput SNP genotyping platforms offer new opportunities for genetic dissection in forest trees. Here we report a high-density SNP genetic linkage map constructed for an F₂ interspecific backcross of Eucalyptus grandis x E. urophylla. The backcross family consists of 295 individuals derived from backcrossing an F₁ hybrid (E. grandis x E. urophylla) clone as pollen parent with an unrelated E. urophylla individual (seed parent). The parents and backcross progeny were genotyped using the Illumina Infinium II platform using a 60K SNP array (Geneseek, Lincoln, NE). Of the 64,639 SNPs assayed, 19,182 (29.7%) were polymorphic and informative in the backcross. A framework of 3,454 non-redundant markers was selected for even genome coverage and used for linkage map construction. Parental linkage maps were constructed using the “cross-pollinator” mapping strategy in JoinMap 4.1. The E. urophylla map contains 1109 markers spread over 11 linkage groups spanning 1124.7 cM with an average interval of 1.0 cM, while the F₁ hybrid map spanning 1021 cM contain 1316 markers at 0.8 cM spacing. Comparison of the genetic distances and marker orders to the corresponding locations in the E. grandis genome (Phytozome) revealed several possible inconsistencies in the predicted physical positions of SNP markers. Besides their value for refining the Eucalyptus reference genome assembly and for comparative genomics in Eucalyptus, the linkage maps reported here will be useful for genetic dissection of growth and wood property traits segregating in the F₁ hybrid of E. grandis x E. urophylla.