Development of durable resistance effective against a broad range of pathotypes is crucial for restoration of pathogen-damaged ecosystems. This study dissected the complex genetic architecture for limber pine quantitative disease resistance (QDR) to Cronartium ribicola using a genome-wide association study (GWAS). Eighteen-month-old seedlings were inoculated for resistance screening under controlled conditions. Disease development was quantitatively assessed for QDR-related traits over four years post inoculation. To reveal genomic architecture contributing to QDR-related traits, a set of genes related to disease resistance with genome-wide distribution was selected for targeted sequencing for genotyping of single-nucleotide polymorphisms (SNPs). GWAS revealed a set of SNPs significantly associated with quantitative traits for limber pine QDR to WPBR, including number of needle spots and stem cankers, as well as survival four years post-inoculation. The peaks of marker-trait associations displayed a polygenic pattern with genomic regions as potential resistant quantitative trait loci (QTLs), distributed over ten of the 12 linkage groups (LGs) of Pinus. None of them were linked to the Cr4-controlled major gene resistance (MGR) previously mapped on LG08. Both normal canker and bole infection were mapped on LG05, and the associated SNPs explained their phenotypic variance up to 52%, tagging a major resistant QTL. Candidate genes containing phenotypically associated SNPs encoded putative nucleotide-binding site leucine-rich repeat (NBS-LRR) proteins, LRR-receptor-like kinase (LRR-RLK), cytochrome P450 superfamily protein, heat shock cognate protein 70, glutamate receptor, RNA-binding family protein, and unknown protein. The confirmation of resistant QTLs broadens the genetic pool of limber pine resistance germplasm for resistance breeding.
Keywords: Antimicrobial or Fungicide Resistance.