Genomic Selection in Forest Trees: Beyond Proof of Concept

RNAseq experiments were performed in conjunction with high-density linkage mapping for the discovery of fusiform rust resistance QTL. Bulked samples from needle tissue from two full-sib populations of Pinus taeda L. were sequenced separately. PacBio ISOseq was used to sequence each family separately, resulting in two family-specific reference transcriptomes. Illumina libraries were also prepared from the same families, using bulks of diseased and non-diseased individuals. 2x50bp paired-end reads were aligned to the PacBio reference transcriptomes to call SNP. Significant associations between SNP and the disease phenotype were discovered using bulked segregant analysis of read count data on a small number of PacBio contigs annotated as NLR-type resistance genes.