Association of a novel Pinus monticola chitinase gene (PmCh4B) with quantitative resistance to Cronartium ribicola

Multiple families of pathogenesis-related (PR) proteins are believed to contribute to plant quantitative resistance to various pathogens. Along with other host PR proteins, PR3 chitinase is one protein component participating in genetic resistance of western white pine (Pinus monticola) to the white pine blister rust (WPBR) pathogen (Cronartium ribicola). In the present study, we characterized a novel P. monticola class IV chitinase gene (PmCh4B) and further analyzed its nucleotide variations in the open-pollinated seed families of diverse geographical distribution and variable levels of quantitative resistance to C. ribicola infection. PmCh4B showed high haplotype diversity (Hd=0.94) and nucleotide diversity (π=0.00965), similar to those of other conifer genes related to environmental stresses. A low level of intragenic linkage disequilibrium (LD) (but most of the levels with statistical significance) was found within a distance of ≈800 bp. Based on PmCh4B haplotype frequency, moderate to high levels of population structure were observed among P. monticola seed families currently used in breeding programs for WPBR resistance (average FST=0.163, P<0.001). Association analysis revealed that allelic variants and multiple single-nucleotide polymorphisms of PmCh4B were significantly associated with quantitative levels of P. monticola resistance against C. ribicola. This work represents the first association study for quantitative resistance in western white pine pathosystem and provides a potential for marker-assisted selection in white pine breeding.