Forest‐tree population genomics and adaptive evolution

Abstract

SummaryForest trees have gained much attention in recent years as nonclassical model eukaryotes for population, evolutionary and ecological genomic studies. Because of low domestication, large open-pollinated native populations, and high levels of both genetic and phenotypic variation, they are ideal organisms to unveil the molecular basis of population adaptive divergence in nature. Population genomics, in its broadsense definition, is an emerging discipline that combines genome-wide sampling with traditional population genetic approaches to understanding evolution. Here we briefly review traditional methods of studying adaptive genetic variation in forest trees, and describe a new, integrated population genomics approach. First, alleles (haplotypes) at candidate genes for adaptive traits and their effects on phenotypes need to be characterized via sequencing and association mapping. At this stage, functional genomics can assist in understanding gene action and regulation by providing detailed transcriptional profiles. Second, frequencies of alleles in native populations for causative single-nucleotide polymorphisms are estimated to identify patterns of adaptive variation across heterogeneous environments. Population genomics, through deciphering allelic effects on phenotypes and identifying patterns of adaptive variation at the landscape level, will in the future constitute a useful tool, if cost-effective, to design conservation strategies for forest trees.

Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) as in ours Diversity of candidate genes for bud burst in oaks J Derory et al (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al (2005); 5.51 Â 10 À3 in Eveno et al (2008)) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002) or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than in earlier reports on pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al (2009); p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al (2008)).…”

Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) than in ours (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al, 2005;5.51 Â 10 À3 in Eveno et al, 2008) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002), or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when the comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than earlier reports in pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al, 2009; p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al, 2008) Although the number of genes is still low, our results confirm earlier findings obtained with other marker systems, suggesting that oak is highly variable species (Kremer and Petit, 1993;Mariette et al, 2002).…”

Hybridization in contact zone between temperate European pine species

“…These taxa differ from each other in phenotype, geographical distribution, and ecology, in particular for traits related to dehydrative stress and temperature (Critchfield and Little 1966). Pinus sylvestris is the most widespread and economically important forest tree species in Europe and Asia and shows adaptive variation in response to environmental gradients, e.g., in timing of bud set and cold hardiness (González-Martínez et al 2006;Hurme et al 2000). Pinus mugo is an endemic species typical of the mountainous regions of Europe (Critchfield and Little 1966).…”