University of Oulu

Tyrmi, J. S., Vuosku, J., Acosta, J. J., Li, Z., Sterck, L., Cervera, M. T., Savolainen, O., & Pyhäjärvi, T. (2020). Genomics of Clinal Local Adaptation in Pinus sylvestris Under Continuous Environmental and Spatial Genetic Setting. G3: Genes|Genomes|Genetics, 10(8), 2683–2696. https://doi.org/10.1534/g3.120.401285

Genomics of clinal local adaptation in Pinus sylvestris under continuous environmental and spatial genetic setting

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Author: Tyrmi, Jaakko S.1,2; Vuosku, Jaana1; Acosta, Juan J.3;
Organizations: 1Department of Ecology and Genetics, University of Oulu, FI-90014 Oulu, Finland
2Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
3Camcore, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC
4Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
5VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
6Centro de Investigación Forestal (CIFOR), Instituto Nacional de Investigaciones Agrarias (INIA), 28040 Madrid, Spain
Format: article
Version: published version
Access: open
Online Access: PDF Full Text (PDF, 1.8 MB)
Persistent link: http://urn.fi/urn:nbn:fi-fe2020091069218
Language: English
Published: Genetics Society of America, 2020
Publish Date: 2020-09-10
Description:

Abstract

Understanding the consequences of local adaptation at the genomic diversity is a central goal in evolutionary genetics of natural populations. In species with large continuous geographical distributions the phenotypic signal of local adaptation is frequently clear, but the genetic basis often remains elusive. We examined the patterns of genetic diversity in Pinus sylvestris, a keystone species in many Eurasian ecosystems with a huge distribution range and decades of forestry research showing that it is locally adapted to the vast range of environmental conditions. Making P. sylvestris an even more attractive subject of local adaptation study, population structure has been shown to be weak previously and in this study. However, little is known about the molecular genetic basis of adaptation, as the massive size of gymnosperm genomes has prevented large scale genomic surveys. We generated a both geographically and genomically extensive dataset using a targeted sequencing approach. By applying divergence-based and landscape genomics methods we identified several loci contributing to local adaptation, but only few with large allele frequency changes across latitude. We also discovered a very large (ca. 300 Mbp) putative inversion potentially under selection, which to our knowledge is the first such discovery in conifers. Our results call for more detailed analysis of structural variation in relation to genomic basis of local adaptation, emphasize the lack of large effect loci contributing to local adaptation in the coding regions and thus point out the need for more attention toward multi-locus analysis of polygenic adaptation.

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Series: G3. Genes, genomes, genetics
ISSN: 2160-1836
ISSN-E: 2160-1836
ISSN-L: 2160-1836
Volume: 10
Issue: 8
Pages: 2683 - 2696
DOI: 10.1534/g3.120.401285
OADOI: https://oadoi.org/10.1534/g3.120.401285
Type of Publication: A1 Journal article – refereed
Field of Science: 1181 Ecology, evolutionary biology
1184 Genetics, developmental biology, physiology
Subjects:
Funding: This work was supported by European Comission 7th Framework Programme project ProCoGen (289841) to O.S., Biocenter Oulu, Emil Aaltosen Säätiö (160284 O), Oulun Läänin Talousseuran Maataloussäätiö to JT, Academy of Finland (287431 and 293819) to T.P. Z.L. was funded by a postdoctoral fellowship from the Special Research Fund of Ghent University (BOFPDO2018001701).
EU Grant Number: (289841) PROCOGEN - Promoting a functional and comparative understanding of the conifer genome- implementing applied aspects for more productive and adapted forests.
Academy of Finland Grant Number: 287431
293819
Detailed Information: 287431 (Academy of Finland Funding decision)
293819 (Academy of Finland Funding decision)
Copyright information: © 2020 Tyrmi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
  https://creativecommons.org/licenses/by/4.0/