Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations

Abstract

Forest trees are dominant components of terrestrial ecosystems that have global ecological and economic importance. Despite distributions that span wide environmental gradients, many tree populations are locally adapted, and mechanisms underlying this adaptation are poorly understood. Here we use a combination of whole-genome selection scans and association analyses of 544 Populus trichocarpa trees to reveal genomic bases of adaptive variation across a wide latitudinal range. Three hundred ninety-seven genomic regions showed evidence of recent positive and/or divergent selection and enrichment for associations with adaptive traits that also displayed patterns consistent with natural selection. These regions also provide unexpected insights into the evolutionary dynamics of duplicated genes and their roles in adaptive trait variation.

Population genomics of the eastern cottonwood (Populus deltoides)

“…A better understanding of the genetic regulation of adaptation is fundamental for the development of adequate management and conservation strategies under a changing climate (Porth et al., 2015). In recent years, population genomics has been used to study tree populations, identifying genes under selection involved in local adaptation (Evans et al., 2014; Geraldes et al., 2014; Holliday et al., 2016; Zhou et al., 2014). The great advantage of population genomics studies over smaller‐scale population genetics studies is that the former allow identifying and correcting for genomewide demographic effects, increasing the power to detect locus‐specific effects (Stinchcombe & Hoekstra, 2008).…”

“…In spite of the concerns mentioned above, limited agreement between different methods is expected (Lotterhos & Whitlock, 2015). For example, a population genomics study based on whole‐genome resequencing of a natural P. trichocarpa population that analyzed a large number of polymorphisms and compared results between five different selection scans, found very little overlap between tests (Evans et al., 2014). This limited overlap can be explained by the ability of different methods to identify the effects of different models of selection, with outlier tests more suited to identify hard selective sweeps and EAA capable of detecting small changes in allele frequency due to selection acting on standing genetic variation (Evans et al., 2014; Sork et al., 2013).…”

“…The Populus trichocarpa genome, the first tree to be sequenced (Tuskan et al., 2006), created numerous opportunities for pioneering genomic studies in tree species. Several genomewide association, transcriptome, and population genomics studies have been reported for P. trichocarpa , contributing to the current knowledge about the species regulation of complex traits (McKown, Klápště, et al., 2014; Porth et al., 2013a, 2013b), extent of linkage disequilibrium (LD) and effective population size (Slavov et al., 2012; Zhou, Bawa, & Holliday, 2014), population structure (Geraldes et al., 2014; Slavov et al., 2012; Zhou et al., 2014), genetic diversity (Evans et al., 2014; Zhou et al., 2014), demographic history (Zhou et al., 2014), adaptation (Evans et al., 2014; Geraldes et al., 2014; Holliday, Zhou, Bawa, Zhang, & Oubida, 2016; Porth et al., 2015; Zhou et al., 2014), and sex determination (Geraldes et al., 2015). Studies in other poplar species (Stölting et al., 2013, 2015; Wang, Street, Scofield, & Ingvarsson, 2016a, 2016b) have significantly lagged behind.…”

“…Genetic structure is mainly driven by interspecific hybridization, isolation by distance, and natural selection (Evans et al., 2014; Geraldes et al., 2014; Slavov et al., 2012; Stölting et al., 2015; Wang et al., 2016b; Zhou et al., 2014). Adaptation has been shown to have a complex genetic architecture (Evans et al., 2014; Holliday et al., 2016; McKown, Guy, et al., 2014; McKown, Klápště, et al., 2014; Porth et al., 2015) and to be a driver of divergent evolution between species (Wang et al., 2016b). Contradictory estimates of LD decay have been reported for P. trichocarpa , with an early study on a reduced number of genes reporting fast LD decay below a threshold of 0.2 (200 bp, Wegrzyn et al., 2010).…”

Genetic architecture of wood properties based on association analysis and co‐expression networks in white spruce

“…However, the variation in quantitative traits explained by individual SNP markers is generally low and rarely exceeds 5% (Dillon et al ., 2010; Guerra et al ., 2013), consistent with multigenic control (Evans et al ., 2014) and the relatively shallow genomic sampling in most studies to date (< 1% and 10% of estimated gene coding loci per genome) (Nystedt et al ., 2013; Neale et al ., 2014). …”