Journal Article

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

Fujii, Hiroaki, Blomster, Tiina, Poczai, Péter, Paulin, Lars, Department of Ecology and Genetics [Uppsala] (EBC) ; Uppsala University, Macpherson, Lee, Kammonen, Juhana, Viikki Plant Science Centre (ViPS) ; Faculty of Biological and Environmental Sciences [Helsinki] ; Helsingin yliopisto = Helsingfors universitet = University of Helsinki-Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Elomaa, Paula, Department of Biological Sciences [Buffalo] ; University at Buffalo [SUNY] (SUNY Buffalo) ; State University of New York (SUNY)-State University of New York (SUNY), Cui, Fuqiang, Salojärvi, Jarkko, Hagqvist, Risto, Punkkinen, Matleena, University of Turku, Possen, Boy, Natural Resources Institute Finland (LUKE), Helariutta, Ykä, Kelleher, Colin, Blokhina, Olga, Oksanen, Elina, Estonian University of Life Sciences (EMU), Kauppinen, Leila, Kovalchuk, Andriy, Palva, E Tapio, University of Oulu [Finland] = Oulun yliopisto [Suomi] = Université d'Oulu [Finlande], Mikola, Juha, Tervahauta, Arja, Lan, Tianying, Smolander, Olli-Pekk

2017

Overview

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.

• Publisher: Nature Publishing Group,CCSD,Nature Publishing Group US
• Subject: 45 / 45/77 / 45/91 / 631/208/212 / 631/208/2491 / 631/208/457 / Adaptation / Adaptation, Biological - genetics / Agriculture / Animal Genetics and Genomics / Betula - genetics / Betula - physiology / Betula pendula / Biomedicine / Biotechnology / Birch trees / Birches / Cancer Research / Chromosomes / Climate change / Coding / Colleges & universities / Correlation / Crashes / Enrichment / Environmental science / Finland / Gene Duplication / Gene expression / Gene Function / Gene regulation / Gene sequencing / Genes / Genetic aspects / Genetics / Genetics, Population / Genome, Plant / Genomes / Genomic analysis / Genotypes / Germplasm / Human Genetics / Identification and classification / Inbreeding / Laboratories / Latitude / Life cycle engineering / Life cycles / Life Sciences / Light effects / Longitude / Mathematical models / Natural resources / Phylogeny / Physiology / Plant biology / Plant Proteins - genetics / Plant sciences / Plants genetics / Polymorphism, Single Nucleotide / Polyploidy / Population / Population Density / Population number / Populations and Evolution / Temperature effects / Time measurement / Transcription