Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch
| cam.issuedOnline | 2017-05-08 | |
| cam.orpheus.success | Thu Jan 30 13:00:45 GMT 2020 - The item has an open VoR version. | |
| dc.contributor.author | Ruonala, R | |
| dc.contributor.author | Rastas, P | |
| dc.contributor.author | Helariutta, YE | |
| dc.contributor.orcid | Helariutta, Yrjo [0000-0002-7287-8459] | |
| dc.date.accessioned | 2017-08-22T11:12:17Z | |
| dc.date.available | 2017-08-22T11:12:17Z | |
| dc.date.issued | 2017-06 | |
| dc.description.abstract | Silver birch ($\textit{Betula pendula}$) 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 $\textit{B. pendula}$ 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 $\textit{PHYC}$ and $\textit{FRS10}$ correlated with latitude and longitude and temperature, and with precipitation for $\textit{PHYC}$. Similar associations characterized the growth-promoting cytokinin response regulator ARR1, and the wood development genes $\textit{KAK}$ and $\textit{MED5A}$. | |
| dc.description.sponsorship | Birch sequencing was supported by a Finnish Technology Development Agency (TEKES) grant to J.K., Y.H., and P.A. J.K. and Y.H. were supported by the Finnish Centre of Excellence in Molecular Biology of Primary Producers (Academy of Finland CoE program 2014-2019, decision 271832). Y.H. was funded by the Gatsby Foundation and the European Research Council Advanced Investigator Grant SYMDEV. V.A.A. acknowledges support from the US National Science foundation (0922742 and 1442190). J.S. acknowledges a University of Helsinki 3-year grant. A.H.S. and J.T. acknowledge Academy of Finland decision (266430). EST libraries were created with TEKES funding to E.T.P. | |
| dc.identifier.doi | 10.17863/CAM.12789 | |
| dc.identifier.eissn | 1546-1718 | |
| dc.identifier.issn | 1061-4036 | |
| dc.identifier.uri | https://www.repository.cam.ac.uk/handle/1810/266714 | |
| dc.language.iso | eng | |
| dc.publisher | Nature Publishing Group | |
| dc.publisher.url | http://dx.doi.org/10.1038/ng.3862 | |
| dc.rights | Attribution 4.0 International | |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| dc.subject | genomics | |
| dc.subject | plant genetics | |
| dc.subject | population genetics | |
| dc.title | Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch | |
| dc.type | Article | |
| dcterms.dateAccepted | 2017-04-12 | |
| prism.endingPage | 912 | |
| prism.publicationName | Nature Genetics | |
| prism.startingPage | 904 | |
| prism.volume | 49 | |
| pubs.funder-project-id | Gatsby Charitable Foundation (GAT3395/PR3) | |
| pubs.funder-project-id | European Research Council (323052) | |
| rioxxterms.licenseref.startdate | 2017-04-12 | |
| rioxxterms.licenseref.uri | http://creativecommons.org/licenses/by/4.0/ | |
| rioxxterms.type | Journal Article/Review | |
| rioxxterms.version | VoR | |
| rioxxterms.versionofrecord | 10.1038/ng.3862 |
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