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Nat Genet. 2017 Jun;49(6):904-912. doi: 10.1038/ng.3862. Epub 2017 May 8.

Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch.

Author information

1
Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.
2
Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
3
Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
4
Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland.
5
Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA.
6
Department of Zoology, University of Cambridge, Cambridge, UK.
7
Green Technology, Natural Resources Institute Finland (Luke), Haapastensyrjä, Läyliäinen, Finland.
8
Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.
9
Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
10
Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland.
11
Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
12
Institute of Technology, University of Tartu, Tartu, Estonia.
13
Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearnysville, West Virginia, USA.
14
Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden.
15
Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland.
16
Department of Biosciences, University of Helsinki, Helsinki, Finland.
17
DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin, Ireland.
18
Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.
19
Department of Haemato-oncology, King's College London, London, UK.
20
Department of Environmental Sciences, University of Helsinki, Helsinki, Finland.
21
Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia.
22
Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland.
23
Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Helsinki, Finland.
24
Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway.
25
Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia.
26
Genetics and Physiology Unit, University of Oulu, Oulu, Finland.
27
Forest Research Institute Karelian Research Centre Russian Academy of Sciences, Petrozavodsk, Russia.
28
Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
29
Sainsbury Laboratory, University of Cambridge, Cambridge, UK.

Abstract

Silver birch (Betula pendula) is a pioneer boreal tree that can be induced to flower within 1 year. Its rapid life cycle, small (440-Mb) genome, and advanced germplasm resources make birch an attractive model for forest biotechnology. We assembled and chromosomally anchored the nuclear genome of an inbred B. pendula individual. Gene duplicates from the paleohexaploid event were enriched for transcriptional regulation, whereas tandem duplicates were overrepresented by environmental responses. Population resequencing of 80 individuals showed effective population size crashes at major points of climatic upheaval. Selective sweeps were enriched among polyploid duplicates encoding key developmental and physiological triggering functions, suggesting that local adaptation has tuned the timing of and cross-talk between fundamental plant processes. Variation around the tightly-linked light response genes PHYC and FRS10 correlated with latitude and longitude and temperature, and with precipitation for PHYC. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes KAK and MED5A.

PMID:
28481341
DOI:
10.1038/ng.3862
[Indexed for MEDLINE]

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