Scanning the genome for gene SNPs related to climate adaptation and estimating selection at the molecular level in boreal black spruce

Abstract

Outlier detection methods were used to scan the genome of the boreal conifer black spruce (Picea mariana [Mill.] B.S.P.) for gene single-nucleotide polymorphisms (SNPs) potentially involved in adaptations to temperature and precipitation variations. The scan involved 583 SNPs from 313 genes potentially playing adaptive roles. Differentiation estimates among population groups defined following variation in temperature and precipitation were moderately high for adaptive quantitative characters such as the timing of budset or tree height (Q(ST) = 0.189-0.314). Average differentiation estimates for gene SNPs were null, with F(ST) values of 0.005 and 0.006, respectively, among temperature and precipitation population groups. Using two detection approaches, a total of 26 SNPs from 25 genes distributed among 11 of the 12 linkage groups of black spruce were detected as outliers with F(ST) as high as 0.078. Nearly half of the outlier SNPs were located in exons and half of those were nonsynonymous. The functional annotations of genes carrying outlier SNPs and regression analyses between the frequencies of these SNPs and climatic variables supported their implication in adaptive processes. Several genes carrying outlier SNPs belonged to gene families previously found to harbour outlier SNPs in a reproductively isolated but largely sympatric congeneric species, suggesting differential subfunctionalization of gene duplicates. Selection coefficient estimates (S) were moderate but well above the magnitude of drift (>>1/N(e)), indicating that the signature of natural selection could be detected at the nucleotide level despite the recent establishment of these populations during the Holocene.

The challenge of separating signatures of local adaptation from those of isolation by distance and colonization history: The case of two white pines

“…In similar comparisons made between Picea mariana and P. glauca (divergence time >10 MYA), Prunier, Laroche, Beaulieu, and Bousquet (2011) found more adaptive similarities at the gene family level (paralogs) than at the gene level (orthologs). The redundancy of functions among recently duplicated genes in conifers could have offered the possibility for selection to act on paralogous genes in different species (Namroud et al., 2010).…”

Genome scanning for detecting adaptive genes along environmental gradients in the Japanese conifer, Cryptomeria japonica

“…Eckert et al (2010) identified 22 candidate loci (BF log 10 42.0) associated with climate variables from 1730 loci in 682 loblolly pine tree samples covering the full range of the species. Prunier et al (2011) also identified 10 candidate loci above 99% confidence interval in black spruce. The proportion of detected loci (1.3% and 1.7%, respectively) associated to the climate variables was very similar with our results.…”

“…Genome scanning is an effective and useful method for detecting genetic differentiation and candidate genes associated with specific phenotypes or environmental variables in forest tree species (Eveno et al, 2008;Namroud et al, 2008;Eckert et al, 2010;Holliday et al, 2010;Neale and Kremer, 2011;Prunier et al, 2011).…”

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…This trend indicates that larger sets of genes should be analyzed in conifers to get a more complete picture of LD of the gene space. The information obtained should contribute to build more efficient gene SNP arrays for use in association studies (González-Martínez et al, 2008) and for outlier detection among natural populations or environments (Namroud et al, 2008;Prunier et al, 2011). Accordingly, we sequenced a large number of genes in natural populations of white spruce to assess LD and its contributing factors more completely, and to compare with results obtained for other conifers.…”