Abstract
BackgroundThe initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants. Such adaptive life-history traits often show strong local adaptation along environmental gradients but, despite their importance, the genetic architecture of these traits remains poorly understood.ResultsWe integrate whole genome re-sequencing with environmental and phenotypic data from common garden experiments to investigate the genomic basis of local adaptation across a latitudinal gradient in European aspen (Populus tremula). A single genomic region containing the PtFT2 gene mediates local adaptation in the timing of bud set and explains 65% of the observed genetic variation in bud set. This locus is the likely target of a recent selective sweep that originated right before or during colonization of northern Scandinavia following the last glaciation. Field and greenhouse experiments confirm that variation in PtFT2 gene expression affects the phenotypic variation in bud set that we observe in wild natural populations.ConclusionsOur results reveal a major effect locus that determines the timing of bud set and that has facilitated rapid adaptation to shorter growing seasons and colder climates in European aspen. The discovery of a single locus explaining a substantial fraction of the variation in a key life-history trait is remarkable, given that such traits are generally considered to be highly polygenic. These findings provide a dramatic illustration of how loci of large-effect for adaptive traits can arise and be maintained over large geographical scales in natural populations.
Highlights
The initiation of growth cessation and dormancy represent critical life-history trade-offs between survival and growth and have important fitness effects in perennial plants
After stringent variant calling and filtering, we identified a total of 4,425,109 high-quality single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) > 5%
Swedish populations of P. tremula have gone through a recent admixture of divergent post-glacial lineages following the Last Glacial Maximum (LGM) [14] and it is possible that this is capable of generating a genome-wide pattern of clinal variation
Summary
Sample collection and sequencing We collected material from all available trees in the Swedish Aspen (SwAsp), which consists of 116 individuals collected from 12 different locations spanning the distribution range in Sweden [12] (Fig. 1a). Leaf material was sampled from one clonal replicate of each individual growing at a common garden experiment located in Sävar, northern Sweden. Whole genome sequencing and base calling were performed on the Illumina HiSeq 2000 platform for all individuals to a mean, per-sample depth of approximately 30× at the Science for Life Laboratory, Stockholm, Sweden. Read mapping, and post-mapping filtering A total of 103 SwAsp individuals were successfully sequenced. We used Trimmomatic v0.30 to trim bases from both ends of the reads if their qualities were < 20.
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