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.

1115 RESEARCH G enetic tests are designed to provide phenotypic information for estimation of genetic parameters such as variance components, heritability, genetic correlations, and breeding values. In breeding, this information is used for the selection of elite parents, families, and individuals for commercial production and subsequent generations of genetic improvement. For traits with complex inheritance, breeding values (BVs) are typically estimated with best linear unbiased prediction (BLUP) and used to rank the population for selection (Piepho et al., 2008). Best linear unbiased predictions are based on the theory of resemblance between relatives due to genetic factors (Lynch and Walsh, 1998), which are almost always derived from the pedigree (Mrode, 2005). Consequently, when the pedigree information is accurate better estimates of genetic parameters are obtained. Unfortunately, pedigree errors are common in

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Summary• Sequencing of the Populus trichocarpa genome creates an opportunity to describe the transcriptome of a woody perennial species and establish an atlas of gene expression. A comparison with the transcriptomes of other species can also define genes that are conserved or diverging in plant species.• Here, the transcriptome in vegetative organs of the P. trichocarpa reference genotype Nisqually-1 was characterized. A comparison with Arabidopsis thaliana orthologs was used to distinguish gene functional categories that may be evolving differently in a woody perennial and an annual herbaceous species.• A core set of genes expressed in common among vegetative organs was detected, as well as organ-specific genes. Statistical tests identified chromatin domains, where adjacent genes were expressed more frequently than expected by chance. Extensive divergence was detected in the expression patterns of A. thaliana and P. trichocarpa orthologs, but transcription of a small number of genes appeared to have remained conserved in the two species.• Despite separation of lineages for over 100 million yr, these results suggest that selection has limited transcriptional divergence of genes associated with some essential functions in A. thaliana and P. trichocarpa. However, extensive remodeling of transcriptional networks indicates that expression regulation may be a key determinant of plant diversity.

A primary goal of evolutionary genetics is to discover and explain the genetic basis of fitness-related traits and how this genetic basis evolves within natural populations. Unprecedented technological advances have fueled the discovery of genetic variants associated with ecologically relevant phenotypes in many different life forms, as well as the ability to scan genomes for deviations from selectively neutral models of evolution. Theoretically, the degree of overlap between lists of genomic regions identified using each approach is related to the genetic architecture of fitness-related traits and the strength and type of natural selection molding variation at these traits within natural populations. Here we address for the first time in a plant the degree of overlap between these lists, using patterns of nucleotide diversity and divergence for .7000 unique amplicons described from the extensive expressed sequence tag libraries generated for loblolly pine (Pinus taeda L.) in combination with the .1000 published genetic associations. We show that loci associated with phenotypic traits are distinct with regard to neutral expectations. Phenotypes measured at the whole plant level (e.g., disease resistance) exhibit an approximately twofold increase in the proportion of adaptive nonsynonymous substitutions over the genome-wide average. As expected for polygenic traits, these signals were apparent only when loci were considered at the level of functional sets. The ramifications of this result are discussed in light of the continued efforts to dissect the genetic basis of quantitative traits.A primary goal of population and quantitative genetics is to understand the genetic architecture of ecologically relevant traits (Stinchcombe and Hoekstra 2008; Barrett and Hoekstra 2011;Neale and Kremer 2011). A primary step on the path to this goal is to link genetic with phenotypic variation, either through linkage mapping of quantitative trait loci using pedigrees or through linkage disequilibrium mapping in natural populations (Lander and Schork 1994), with the latter currently being the most utilized. A multitude of studies ranging across a diverse set of taxa have discovered myriad genotype-phenotype correlations (Hindorff et al. 2009;Ingvarsson and Street 2011;Neale and Kremer 2011). Each discovered variant, however, often explains only a small fraction of the heritable phenotypic variance, thus being consistent with a polygenic model for the genetic architecture of complex traits (Lynch and Walsh 1998). Concomitant with the discovery of these associations are population genomic scans documenting deviations from expectations derived using the neutral theory (Nielsen 2005). Such scans have also discovered large numbers of loci putatively underlying phenotypic traits in many different taxa (e.g., Pollinger et al. 2005;Pritchard et al. 2010;Hufford et al. 2012), but in this case the link between genotype and phenotype is not explicit. A natural question thus arises about how much overlap exists between the lists gen...