Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding

Abstract

Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

“…These data are needed for larger scale studies addressing the many diversity issues raised by their combined economic, ecological and conservation interests (Cavender-Bares 2016; Fetter et al 2017;Holliday et al 2017). However, recent achievements and data availability from the Q. robur genome sequence project (Plomion et al 2018) opens a large range of applications in many related temperate and tropical Fagaceae species due to their conserved synteny (Cannon et al 2018).…”

“…High-throughput (HT) techniques of the next-generation sequencing (NGS) era and increased genome sequencing efforts in the last decade have greatly improved access to genomic resources in non-model forest tree species, but these have only been applied recently to largescale ecological and population genomics research Kremer 2011, Neale et al 2013;Plomion et al 2016, Holliday et al 2017. One notable exception are studies undertaken in the model genus Populus (e.g.…”

Interspecies gene flow is a key evolutionary process for the adaptation of long-lived species to new environmental conditions

“…Gray (black cottonwood) and the simultaneous expression of the corresponding adaptive traits in the latter species . Moreover, J. Degner presented the results from a recent study of genomic clines in a mosaic hybrid zone between Picea engelmannii Parry and P. glauca (Moench) Voss in Western Canada (Holliday et al (2017). Disproportionate introgression of single nucleotide polymorphism markers (SNPs) related to climate variables were found in hybrid individuals and, in a given environment, these hybrids possessed disproportionately introgressed alleles from the parental species that best matched their habitat.…”

The Evolution of Tree Diversity: Proceedings of the 2016 IUFRO Genomics and Forest Tree Genetics Conference, Phylogenetics and Genomic Evolution Session, Arcachon, France

“…A motif woven through most of these papers-and indeed, through the conference as a whole (Holliday et al 2017)-is the importance of genome-scale data and explicit model-based hypothesis testing to addressing even basic questions in the evolution of tree diversity. Analyses based on a handful of loci and summary statistics will probably always play an important role in rangewide surveys of genetic diversity, identification of hybrid individuals, broad-scale or initial phylogenetic surveys, and the characterization of phylogenetic and genetic diversity of communities.…”

“…While we know much about the impact of tree diversity on ecosystem services (Cavender-Bares 2016;Liang et al 2016) and the assembly and maintenance of tree diversity at community and regional scales (e.g., Mason et al 2012;Dryflor et al 2016), we know less about the evolutionary forces shaping the origins and maintenance of tree diversity. The Phylogenetics and Genomic Evolution Session of the 2016 IUFRO Genomics and Forest Tree Genetics Conference was convened in Arcachon, France, in May 2016 (Holliday et al 2017) to bring together researchers addressing evolutionary relationships within and among tree species. The papers in the current issue sample from the topics covered in this session and address three overarching subjects in the evolution of tree diversity.…”