Genome-wide effects of selective breeding on adaptation of reforestation seedlots for future climates

I.R. MacLachlan, J. Tuytel, P. Smets, T. Wang, and S.N. Aitken

Climatic change is predicted to cause a lag in the productivity of western Canada’s forests that will have negative economic, ecological, and social impacts. Such a lag in productivity is caused by shifting climates that are expected disconnect locally adapted provenances from their established climatic optima. To assess the impacts of climate change on forests in British Columbia and Alberta, the AdapTree project is utilizing a combination of genomic and phenotypic approaches to quantify the genetic architecture of local adaptation to climate and to assess climate-based seed transfer approaches.

The component of AdapTree described here will investigate the effects of selection in tree breeding programs on adaptive diversity and climate-related phenotypic traits in the economically and ecologically important species lodgepole pine (Pinus contorta) and interior spruce (Picea glauca (Monech) Voss, P. engelmannii Parry ex Engelm. and their natural hybrids). In Western Canada the use of reforestation seedlots from advanced generation selective breeding programs is increasing rapidly and accounts for a majority of reforestation. The genetic effects of selective breeding on long-domesticated crops species are well documented, but the genomic consequences of selective breeding on adaptive forest diversity and divergence, as well as the suitability of reforestation seedlots to future climates remain unclear. We are evaluating how selective breeding affects the adaptive phenotypic and genomic architecture of reforestation seedlots. The primary questions that guide this research are: 1) How much do climatically-linked phenotypic traits differ between natural and seed orchard populations; 2) Do correlated responses to phenotypic selection exist between height as the primary artificial selection trait and other phenotypic traits of importance to local adaptation; 3) What are the effects of selective tree breeding on adaptive genetic diversity in reforestation seedlots; and 4) How much molecular genomic divergence exists among natural and seed orchard populations from the same geographic areas, and does the amount of adaptive genomic divergence reflect phenotypic divergence?

A combination of analysis techniques that dissect the effects of selective breeding on adaptive phenotypic and genomic diversity and divergence in both species are being applied. Seedlots have been sampled across British Columbia and Alberta to obtain representative natural (>250 seedlots per species) and selectively bred reforestation seedlots (~20 orchard lots per species. Seedling common gardens containing >2,500 individuals per species have been established at UBC and at a field site in the central interior of BC. Phenotypic data is being collected on several climatically relevant phenological and growth traits. All trees will be genotyped for a suite of ~25,000 to 50,000 candidate adaptive SNPs being identified through exome capture and re-sequencing, and analyses including associations with provenance climate or phenotypes and outlier tests in other activities within AdapTree.

This research will allow evaluation of current provincial reforestation seedlot diversity standards in the context of adaptive rather than neutral genetic variation, and prediction of future climatic seedlot transfer ranges. This will contribute vital information to developing provincial policies on assisted genotype migration that aim to maintain forest productivity in British Columbia and Alberta under a changing climate.