PacBio IsoSeq reference transcriptomes for Pinus taeda L.

Fusiform rust disease, caused by the endemic fungus Cronartium quercuum f.
sp. fusiforme, is the most damaging disease affecting economically
important pine species in the southeast United States. In this report, we
detail the genomic localization and sequence-level discovery of candidate
race-nonspecific broad-spectrum fusiform rust resistance genes in Pinus
taeda L. Two full-sib families, each with ~1000 progeny, were challenged
with a complex inoculum consisting of over 150 pathogen isolates.
High-density linkage mapping revealed three QTL distributed on two linkage
groups. The two QTL on linkage group 2 were additive with respect to their
effects on the probability of disease outcome. All three QTL were
validated using a population of 2057 cloned pine genotypes in a
six-year-old multi-environmental field trial. As a complement to the QTL
mapping approach, bulked  segregant RNAseq analysis revealed a
small number of candidate nucleotide binding leucine rich repeat genes
harboring SNP significantly associated with disease resistance. The
results of this study demonstrate that single qualitative resistance genes
can confer effective resistance against genetically diverse mixtures of an
endemic pathogen.