Major QTL confer race-nonspecific resistance in the co-evolved Cronartium quercuum f. sp. fusiforme-Pinus taeda pathosystem.

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. Unlike the major epidemics of agricultural crops, the co-evolved pine-rust pathosystem is characterized by steady-state dynamics and high levels of genetic diversity within environments. This poses a unique challenge and opportunity for the deployment of large-effect resistance genes. We used trait dissection to study the genetic architecture of disease resistance in two P. taeda parents that showed high resistance across multiple environments. Two mapping populations (full-sib families), each with ~1000 progeny, were challenged with a complex inoculum consisting of 150 pathogen isolates. High-density linkage mapping revealed three major-effect QTL distributed on two linkage groups. All three QTL were validated using a population of 2057 cloned pine genotypes in a 6-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 associated with disease resistance. The results of this study show that in P. taeda, a small number of major QTL can provide effective resistance against genetically diverse mixtures of an endemic pathogen. These QTL vary in their impact on disease liability and exhibit additivity in combination.