University of Oulu

Pyhäjärvi, T, Kujala, ST, Savolainen, O. 275 years of forestry meets genomics in Pinus sylvestris. Evol Appl. 2019; 13: 11– 30. https://doi.org/10.1111/eva.12809

275 years of forestry meets genomics in Pinus sylvestris

Saved in:
Author: Pyhäjärvi, Tanja1,2; Kujala, Sonja T3; Savolainen, Outi1,2
Organizations: 1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
2Biocenter Oulu, University of Oulu, Oulu, Finland
3Natural Resources Institute Finland, Luke, Oulu, Finland
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.1 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe202003107776
Language: English
Published: John Wiley & Sons, 2020
Publish Date: 2020-03-10
Description:

Abstract

Pinus sylvestris has a long history of basic and applied research that is relevant for both forestry and evolutionary studies. Its patterns of adaptive variation and role in forest economic and ecological systems have been studied extensively for nearly 275 years, detailed demography for a 100 years and mating system more than 50 years. However, its reference genome sequence is not yet available and genomic studies have been lagging compared to, for example, Pinus taeda and Picea abies, two other economically important conifers. Despite the lack of reference genome, many modern genomic methods are applicable for a more detailed look at its biological characteristics. For example, RNA‐seq has revealed a complex transcriptional landscape and targeted DNA sequencing displays an excess of rare variants and geographically homogenously distributed molecular genetic diversity. Current DNA and RNA resources can be used as a reference for gene expression studies, SNP discovery, and further targeted sequencing. In the future, specific consequences of the large genome size, such as functional effects of regulatory open chromatin regions and transposable elements, should be investigated more carefully. For forest breeding and long‐term management purposes, genomic data can help in assessing the genetic basis of inbreeding depression and the application of genomic tools for genomic prediction and relatedness estimates. Given the challenges of breeding (long generation time, no easy vegetative propagation) and the economic importance, application of genomic tools has a potential to have a considerable impact. Here, we explore how genomic characteristics of P. sylvestris, such as rare alleles and the low extent of linkage disequilibrium, impact the applicability and power of the tools.

see all

Series: Evolutionary applications
ISSN: 1752-4563
ISSN-E: 1752-4571
ISSN-L: 1752-4563
Volume: 13
Issue: 1; SI
DOI: 10.1111/eva.12809
OADOI: https://oadoi.org/10.1111/eva.12809
Type of Publication: A2 Review article in a scientific journal
Field of Science: 1184 Genetics, developmental biology, physiology
Subjects:
Funding: The work was funded by Academy of Finland (287431 and 293819 to TP, 309978 to STK, and 307582 GENOWOOD to OS) and European Union’s Horizon 2020 research and innovation programme under grant agreement No 773383 (B4EST).
Academy of Finland Grant Number: 287431
293819
Detailed Information: 287431 (Academy of Finland Funding decision)
293819 (Academy of Finland Funding decision)
Copyright information: © 2019 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
  https://creativecommons.org/licenses/by/4.0/