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.

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

“…Functional studies in Arabidopsis have also implicated CCR in affecting cellulose MF orientation (Ruel et al 2009). Since that first study, association studies analyzing wood traits, adaptation to drought, cold, aridity, and disease resistance have been reported mainly in pines and poplars (Dillon et al 2010;Eckert et al 2009Eckert et al ,2010Gonzalez-Martinez et al 2007Ingvarsson et al 2008;Quesada et al 2010). Results from an expanded association study with hundreds of SNPs in about 100 cell wall genes has revealed several SNPs significantly associated with different wood quality traits in E. nitens (Southerton et al 2004;Thumma and Southerton unpublished).…”

Genetic Resistance to Fusiform Rust in Southern Pines and White Pine Blister Rust in White Pines—A Contrasting Tale of Two Rust Pathosystems—Current Status and Future Prospects

“…Fortunately, genetic resistance to these rusts has been discovered in all pines species studied [6][7][8][9][10][11][12][13][14][15]. Resistance breeding programs, begun over 50 years ago, continue to produce trees with resistance in the U.S. and Canada [9,16,17]. During this period, knowledge has been gained and progress made in developing resistant material for reforestation and restoration, but further work is needed to increase the levels of resistance and to ensure its durability in the face of evolving pathogen virulence.…”

Ecological and association genetics in two Mediterranean pine species

“…But notice that candidate-gene association mapping has proved effective to identify loci showing evidence of moderate to large effect on fitnessrelated traits in pines (e.g. González-Martínez et al 2007Quesada et al 2010;Eckert et al 2012;. …”

“…Heterozygote effects were computed using a Bayesian mixed linear model that imputes missing data and fits simultaneously additive SNP effects and population structure (Quesada et al 2010), as implemented in BAMD software v. 3.5 (Li et al 2012 Mediterranean) within the species range. In this case, the distributions of additive SNP effects were used to identify significant differences (i.e.…”

“…The main difference between them is that association mapping considers populations rather than pedigrees (Balding 2006 important advantages for complex trait dissection in conifers (see below) and it has proved effective to identify genes underlying adaptive traits in these species (e.g. for pines Quesada et al, 2010;Eckert et al, 2012;. However, both population and association genetics methods have rarely looked to polygenic adaptation in forest trees.…”