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.

RNA测序实验与高密度连锁图谱相结合，旨在发现梭形锈病抗性QTL。对来自两种塔柏（Pinus taeda L.）全同胞群体的针叶组织的大量样本进行了单独测序。采用PacBio ISOseq技术对每个家系进行单独测序，从而产生了两个家系特有的参考转录组。同时，从同一家系中制备了Illumina文库，使用患病和非患病个体的混合样本。将2x50bp的配对末端读段与PacBio参考转录组进行比对，以调用SNP。通过在少量被注释为NLR型抗性基因的PacBio连续片段上进行的读段计数数据的混合分离分析，发现了SNP与疾病表型之间的显著关联。