Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.)

Abstract

Genetic resistance to disease incited by necrotrophic pathogens is not well understood in plants. Whereas resistance is often quantitative, there is limited information on the genes that underpin quantitative variation in disease resistance. We used a population genomic approach to identify genes in loblolly pine (Pinus taeda) that are associated with resistance to pitch canker, a disease incited by the necrotrophic pathogen Fusarium circinatum. A set of 498 largely unrelated, clonally propagated genotypes were inoculated with F. circinatum microconidia and lesion length, a measure of disease resistance, data were collected 4, 8, and 12 weeks after inoculation. Best linear unbiased prediction was used to adjust for imbalance in number of observations and to identify highly susceptible and highly resistant genotypes ("tails"). The tails were reinoculated to validate the results of the full population screen. Significant associations were detected in 10 single nucleotide polymorphisms (SNPs) (out of 3938 tested). As hypothesized for genes involved in quantitative resistance, the 10 SNPs had small effects and proposed roles in basal resistance, direct defense, and signal transduction. We also discovered associated genes with unknown function, which would have remained undetected in a candidate gene approach constrained by annotation for disease resistance or stress response.

Figure 1.—

Geographical distribution of loblolly pine accessions sampled for this study. Size of the dots denotes the number of accessions collected in a particular county, as follows: •, 1–5; •, 6–10; , 11–15; ○, 16+ accessions. Bar, 200 km.

Figure 2.—

Distribution of BLUP clonal estimates for pitch canker lesion length (log transformed), highlighting the 50 most resistant and susceptible clones. Inserts show phenotypes of resistant and susceptible genotypes.