The Alluring Simplicity and Complex Reality of Adaptation to Climate in Lodgepole Pine

Long-term provenance trials have revealed relatively strong patterns of local adaptation to climate in lodgepole pine (Pinus contorta). Population response functions suggest local populations will suffer growth reductions of 10 to 35% from climate change in the next century, but assisted gene flow could offset those losses. We are studying the genomic and phenotypic architecture of local adaptation in 279 lodgepole pine populations in the AdapTree project. Targeted sequence capture probes were designed by mapping the lodgepole pine transcriptome onto the loblolly pine genome to identify intron/exon boundaries, with very high success. About 15.9 million SNPs were discovered in 598 trees representing all populations, with 10.9 million genotyped in >10% of individuals. Of these, 3.2 milion SNPs with minor allele frequencies ≥0.05 were tested for associations with climatic variables, using Bayenv2, and with climate-related phenotypes (GWAS), using TASSEL. Population structure was accounted for using 240K non-coding SNPs.

Geospatial patterns of adaptation to climate are complex, involving many climatic variables and highly polygenic traits. Largely different subsets containing thousands of SNPs are associated with mean temperature, extreme temperature, and precipitation-related climatic variables. GWAS identified hundreds to thousands of candidate SNPs associated with growth, phenology and cold hardiness traits (p<0.0001). There was relatively little overlap between SNPs associated with climatic variables and those associated with phenotypes. Candidate adaptive SNPs have been selected for inclusion on a 50K SNP array for genotyping additional trees from these natural populations and from provincial breeding programs. Results will be used to design climate-based seed transfer systems that take the complexity of genetic and climatic landscapes into account.