Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris

Abstract

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12-15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; pi was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.

Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

“…This is very consistent with the unique function of phyA among the five Arabidopsis phytochromes (Figure 1) and with the fact that phyB mediates responses that apparently were established very early in the history of land plants, such as R-induced, FR-reversible germination (Mathews, 2006). It is also consistent with the low levels of nucleotide diversity that have been observed at PHYB in Arabidopsis and C. nipponica (Filiault et al, 2008;Mathews and McBreen, 2008;Ikeda et al, 2009), at PHYP in P. sylvestris (García-Gil et al, 2003), and with the relatively short branches in the PHYB clade (Figure 2), data which suggest that evolution at PHYB is relatively constrained. Previous tests for selection in phytochrome gene trees relied on subsets of the seed plant phylogeny or the genes (Yang and Nielsen, 2002; (A) Summary seed plant phytochrome tree.…”

Joint analysis of spatial genetic structure and inbreeding in a managed population of Scots pine

“…Together with a predominant random mating system (Koski, 1970), these features contribute to little or no genetic structure being found in undisturbed pine forests: both in large (Gullberg et al, 1985;Karhu et al, 1996;Dvornyk et al, 2002;García-Gil et al, 2003) and in fine geographic scales (Knowles, 1991;Xie and Knowles, 1991;Parker et al, 2001;Uchiyama et al, 2006;Marquardt et al, 2007). On the other hand, fragmentation and bottlenecks may cause a genetic structure because of selffertilization and mating among genetically related individuals (Vogl et al, 2002;Robledo-Arnuncio et al, 2004;Boys et al, 2005).…”

Comparing Bayesian estimates of genetic differentiation of molecular markers and quantitative traits: an application to Pinus sylvestris

“…However, when trying to estimate Q ST of the bud set data from P. sylvestris, the MCMC-chains produced a bimodal posterior of Q ST . The evident reason for the bimodality is that the family variances differed considerably between the two clusters because of the strong cline within the northern cluster (García-Gil et al, 2003). An earlier study has found that microsatellites and other molecular markers are hardly differentiated at all, whereas timing of bud set is very different between the original populations of the northern cluster (Karhu et al, 1996).…”

“…Quantitative and molecular data from P. sylvestris Seedlings of P. sylvestris were grown in a common garden experiment as described by García-Gil et al (2003). The experiment consisted of five populations along a latitudinal cline (67-401N).…”