Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce

Abstract

Conifers are characterized by a large genome size and a rapid decay of linkage disequilibrium, most often within gene limits. Genome scans based on noncoding markers are less likely to detect molecular adaptation linked to genes in these species. In this study, we assessed the effectiveness of a genome-wide single nucleotide polymorphism (SNP) scan focused on expressed genes in detecting local adaptation in a conifer species. Samples were collected from six natural populations of white spruce (Picea glauca) moderately differentiated for several quantitative characters. A total of 534 SNPs representing 345 expressed genes were analysed. Genes potentially under natural selection were identified by estimating the differentiation in SNP frequencies among populations (F ST ) and identifying outliers, and by estimating local differentiation using a Bayesian approach. Both average expected heterozygosity and population differentiation estimates (H E = 0.270 and F ST = 0.006) were comparable to those obtained with other genetic markers. Of all genes, 5.5% were identified as outliers with F ST at the 95% confidence level, while 14% were identified as candidates for local adaptation with the Bayesian method. There was some overlap between the two gene sets. More than half of the candidate genes for local adaptation were specific to the warmest population, about 20% to the most arid population, and 15% to the coldest and most humid higher altitude population. These adaptive trends were consistent with the genes' putative functions and the divergence in quantitative traits noted among the populations. The results suggest that an approach separating the locus and population effects is useful to identify genes potentially under selection. These candidates are worth exploring in more details at the physiological and ecological levels.

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

“…Although overall structure is relatively weak in many forest trees (for example, Namroud et al, 2008), differentiation of populations from range-wide collections tends to be stronger than that of more local collections (Ingvarsson, 2005;Keller et al, 2010;Slavov et al, 2012;Cushman et al, 2014;Evans et al, 2014;Zhou et al, 2014). For instance, Heuertz et al (2006) found that across large geographic distances, Picea abies is strongly differentiated across large geographic barriers, with F ST estimates approaching those that we found among genetic groupings.…”

“…P. angustifolia is dioecious with putatively long-distance dispersal of pollen and seed, traits that are expected to minimize population structure (Hamrick and Godt, 1996), as has been shown in other species (for example, Namroud et al, 2008). Three factors could explain this result.…”

Accuracy of genomic selection models in a large population of open-pollinated families in white spruce

“…Weak population structure in white spruce from Québec has been reported in several studies using neutral genetic markers (Jaramillo-Correa et al, 2001;Namroud et al, 2008Namroud et al, , 2010 and was expected based on our previous analysis of a subset of the present discovery population . As a cautionary measure, we used the multidimensional scaling coefficients as population covariates for the GS analyses to control for any potential bias in prediction accuracy that could be brought about by such a population structure.…”

“…A population structure analysis was used to assess whether there were differences in allele frequencies among unobserved ancestral populations that could bias prediction accuracy estimates. Given the results obtained in previous studies conducted in the same area (JaramilloCorrea et al, 2001;Namroud et al, 2008Namroud et al, , 2010Beaulieu et al, 2011), we were expecting a weak or no population differentiation from SNPs. We used all available SNPs (m ¼ 6385) in multidimensional scaling and principal component analysis (Price et al, 2006) to estimate population covariates for each individual.…”

New evidence for habitat-specific selection in Wadden Sea Zostera marina populations revealed by genome scanning using SNP and microsatellite markers

“…In contrast, genelinked microsatellites are located close to a gene (often in the untranslated regions) and are typically derived from an EST (expressed sequence tag) library (Bouck and Vision 2007). In genome scans, gene-linked markers represent a very useful means to assign functional genes possibly responsible for the eVect seen at an outlier locus (Vasemagi et al 2005;Namroud et al 2008).…”