275 years of forestry meets genomics in Pinus sylvestris
|Author:||Pyhäjärvi, Tanja1,2; Kujala, Sonja T3; Savolainen, Outi1,2|
1Department of Ecology and Genetics, University of Oulu, Oulu, Finland
2Biocenter Oulu, University of Oulu, Oulu, Finland
3Natural Resources Institute Finland, Luke, Oulu, Finland
|Online Access:||PDF Full Text (PDF, 1.1 MB)|
|Persistent link:|| http://urn.fi/urn:nbn:fi-fe202003107776
John Wiley & Sons,
|Publish Date:|| 2020-03-10
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.
|Type of Publication:||
A1 Journal article – refereed
|Field of Science:||
1184 Genetics, developmental biology, physiology
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).
|EU Grant Number:||
(773383) B4EST - Adaptive BREEDING for productive, sustainable and resilient FORESTs under climate change
|Academy of Finland Grant Number:||
287431 (Academy of Finland Funding decision)
293819 (Academy of Finland Funding decision)
309978 (Academy of Finland Funding decision)
307582 (Academy of Finland Funding decision)
© 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.