Identification of cold-hardiness related genes in coastal Douglas fir (Pseudotsuga menziesii)

Abstract

We here apply a candidate gene-based approach by screening 228 single-nucleotide polymorphisms (SNPs) located in 117 genes along cold-hardiness related environmental gradients. Genes have been selected a priori based on existing databases and relevant metabolic pathways in other species. To explore patterns of adaptive variation along these gradients we used three different approaches: a Bayesian outlier detection method, a multinomial logistic regression and a Bayesian environmental analysis. These methods differ in the extent to which they implement information on genetic population structure and the environment. A total of 33 genotype-environment associations could be detected in 24 distinct genes. Results of the outlier analysis corroborated those of the logistic regression. In contrast, results of the Bayesian environmental analysis were incongruent with those of the regression model and identified almost exclusively a non-overlapping set of putative selective genes.