Genome Scan to Detect Genetic Structure and Adaptive Genes of Natural Populations of Cryptomeria japonica

Abstract

We investigated 29 natural populations of Cryptomeria japonica using 148 cleaved amplified polymorphic sequence markers to elucidate their genetic structure and identify candidate adaptive genes of this species. In accordance with the inferred evolutionary history of the species during and after the last glacial episode, the genetic diversity was higher in western populations than in northern populations. The results of phylogenetic and genetic structure analyses suggest that populations of the two main varieties of the species have clearly diverged from each other and that two of the examined loci are strongly associated with the differentiation between the two varieties. Using a coalescent simulation based on F ST and H e values, we detected five genes that had higher, and two that had lower, values than the respective 99% confidence intervals (C.I.s) that are theoretically expected intervals under a neutral infinite-island model. We also detected 13 outlier loci using a coalescent simulation based on the assumption that the 2 varieties originated from the splitting of an ancestral population. Four of these loci were detected by both methods, two of which were detected in a genetic structure analysis as loci associated with differentiation between the two varieties of the species, and are strong candidates for genes that have been subject to selection.

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

“…The R s values also varied, from 1.569 to 1.794 with an average of 1.721, and the H e values ranged from 0.292 to 0.320 with an average of 0.311 (Table 2). In contrast to findings from previous studies, these parameters do not reveal any clear geographical trends (Takahashi et al, 2005;Tsumura et al, 2007). The average F IS value for all loci was not significantly different from expectations under the Hardy-Weinberg equilibrium except for one locus, SNPg04215.…”

“…Hierarchical analysis indicated that genetic variation among varieties and populations accounted for 2.74% and 4.98% of the total variation, respectively. These results are similar to those from our previous study (Tsumura et al, 2007). While there was little genetic differentiation between variety groups, what differentiation there was pertained to genes related for local adaptation.…”

“…All trees sampled were growing in national forests that were candidates for in situ gene-conservation programs. The locations of the sampled populations covered most of the natural distribution of C. japonica (Figure 1, Tsumura et al, 2007).…”

“…The ura-sugi variety has slender branchlets with soft leaves, while the omote-sugi variety has rough branchlets with hard leaves (Yamazaki, 1995). A previous study focusing on 148 cleaved amplified polymorphic sequence loci revealed genetic differentiation between the two varieties, and four outlier loci were identified as potential local adaptation genes (Tsumura et al, 2007) that may be associated with the genetic differentiation between the varieties.…”

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

“…As a goal of this study, we assessed how 2 years of additional marker development would aVect the reliability of results collected with relatively few markers. Several genome scan studies have reanalysed existing data sets with diVerent outlier tests (Vitalis et al 2001;Beaumont and Balding 2004) or assessed the validity of outlier tests by using more than one test statistic (Vasemagi et al 2005;Kane and Rieseberg 2007;Tsumura et al 2007;Egan et al 2008;Mäkinen et al 2008). In contrast, extending a genome scan by doubling the number of markers has been done here for the Wrst time.…”