SNPs in a Large Genomic Scaffold Are Strongly Associated with Cr1(R), Major Gene for Resistance to White Pine Blister Rust in Range-Wide Samples of Sugar Pine (Pinus lambertiana)

Sugar pine, Pinus lambertiana Douglas, is a keystone species of montane forests from Baja California to southern Oregon. Like other North American white pines, populations of sugar pine have been greatly reduced by the disease white pine blister rust (WPBR) caused by a fungal pathogen, Cronartium ribicola, that was introduced into North America early in the twentieth century. Major gene resistance to WPBR segregating in natural populations has been documented in sugar pine. Indeed, the dominant resistance gene in this species, Cr1, was genetically mapped, although not precisely. Genomic single nucleotide polymorphisms (SNPs) placed in a large scaffold were reported to be associated with the allele for this major gene resistance (Cr1(R)). Forest restoration efforts often include sugar pine seed derived from the rare resistant individuals (typically Cr1(R)/Cr1(r)) identified through an expensive 2-year phenotypic testing program. To validate and geographically characterize the variation in this association and investigate its potential to expedite genetic improvement in forest restoration, we developed a simple PCR-based, diploid genotyping of DNA from needle tissue. By applying this to range-wide samples of susceptible and resistant (Cr1(R)) trees, we show that the SNPs exhibit a strong, though not complete, association with Cr1(R). Paralleling earlier studies of the geographic distribution of Cr1(R) and the inferred demographic history of sugar pine, the resistance-associated SNPs are marginally more common in southern populations, as is the frequency of Cr1(R). Although the strength of the association of the SNPs with Cr1(R) and thus, their predictive value, also varies with geography, the potential value of this new tool in quickly and efficiently identifying candidate WPBR-resistant seed trees is clear.