Functional and population genomics of cold acclimation
Genecological studies in widely distributed tree species have revealed steep genetic clines along environmental gradients for traits related to adaptation to local climate. In the face of a changing climate, the ecological and economic importance of conifers necessitates an appraisal of how molecular genetic variation shapes quantitative trait variation. I am combining transcript profiling with association mapping to better understand the genomic architecture of adaptation to local climate in conifers, using Sitka spruce as a model. A microarray study during the fall hardening period revealed wholesale remodeling of the transcriptome within a population originating in the centre of the species range, and substantial variation in the autumn transcriptome was observed in populations from the northern and southern limits. I selected a suite of candidate genes, which were screened for single nucleotide polymorphisms (SNPs) in a panel of 24 individuals. A diverse array of biological processes were represented, including stress response, carbohydrate, lipid and phenylpropanoid metabolism, light signal transduction, and transcriptional and post-transcriptional regulation. Nucleotide diversity was approximately average for a conifer and linkage disequilibrium decayed rapidly. Tests of selective neutrality suggest widespread purifying selection within these candidate genes, though evidence for positive selection was detected within a few. I observed evidence for diversifying selection in 8% of the studied genes, which exhibited high population differentiation relative to the genome-wide average FST of 0.12. To identify genetic determinants of phenotypic variation in locally adaptive traits, an Illumina GoldenGate assay was used to genotype 768 SNPs in a mapping population comprised of 410 individuals from 12 populations collected across the species range. After correcting for population structure and relative kinship, associations were detected in 28 of the candidate genes, which cumulatively explained 28% and 34% of the phenotypic variance in cold hardiness and budset, respectively. Most notable among these associations were five genes putatively involved in light signal transduction, the key pathway regulating autumn growth cessation in perennials. This study represents a significant step toward the goal of characterizing the genomic underpinnings of adaptation to local climate in conifers, and provides a substantial resource for breeding and conservation genetics.