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Evolution of breeding systems and phenology: evolutionary genomic analysis using Arabidopsis relatives

Applicant Shimizu Kentaro
Number 135717
Funding scheme Project funding (Div. I-III)
Research institution Institut für Evolutionsbiologie und Umweltwissenschaften Universität Zürich
Institution of higher education University of Zurich - ZH
Main discipline Botany
Start/End 01.04.2011 - 31.05.2012
Approved amount 138'678.00
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All Disciplines (2)

Discipline
Botany
Ecology

Keywords (5)

evolution; adaptation; mating system; phenology; Arabidopsis

Lay Summary (English)

Lead
Lay summary

Millions species are living on the earth with astonishing diversity. Darwin proposed the first conclusive theory to explain organismal diversity with two principles: adaptation by natural selection, and speciation. However, little is known about the molecular mechanisms responsible for the diversity. The key to interdisciplinary study of biodiversity is evolutionary genomics. The basic data of evolutionary genomics is genomic information of multiple individuals of a species. Using such information, evolutionary genomics integrates ecology and molecular genetics in both directions. First, ecologically relevant genes can be identified by association mapping, quantitative trait locus (QTL) mapping, microarray or comparative genomics. Second, the adaptive meaning of a trait in nature can be shown by population genomic analysis. Adaptive evolution is the change of genomic constitution of the next generation due to survival and reproduction, and it leaves the molecular signatures of natural selection. To address questions on adaptation and speciation, we will use the model plant Arabidopsis thaliana and its relatives, which has enormous amount of genomic and genetic information available, and its relatives. Our previous analysis supported Darwin’s reproductive assurance model stating that selfing may be advantageous when mates are scarce (Tsuchimatsu et al. Nature 464, 1342, 2010). This proposal will contribute to two fundamental and broad questions in evolutionary biology: which genes are responsible for adaptation and for speciation? What evolutionary processes affect allele frequency of these genes? Our website is: http://www.botinst.uzh.ch/research/genomics/shimizu.html

Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Quantified expression levels of genes in allopolyploid species. IPSJ SIG Technical Reports
Yamada Megumi, Shimizu-Inatsugi Rie, Shimizu Kentaro K, Sese Jun (2013), Quantified expression levels of genes in allopolyploid species. IPSJ SIG Technical Reports, in Information Processing Society of Japan, 28, 1-2.
Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica
Tsuchimatsu Takashi, Kaiser Paskal, Yew Chow-Lih, Bachelier Julien B., Shimizu Kentaro K. (2012), Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica, in PLoS Genetics, 8(7), e1002838-e1002838.
The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata.
de la Chaux Nicole, Tsuchimatsu Takashi, Shimizu Kentaro K, Wagner Andreas (2012), The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata., in Mobile DNA, 3(1), 2-2.
Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches.
Kawagoe Tetsuhiro, Shimizu Kentaro K, Kakutani Tetsuji, Kudoh Hiroshi (2011), Coexistence of trichome variation in a natural plant population: a combined study using ecological and candidate gene approaches., in PloS one, 6(7), 22184-22184.
Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology.
Shimizu Kentaro K, Kudoh Hiroshi, Kobayashi Masaki J (2011), Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology., in Annals of botany, 108(4), 777-87.

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
International Okazaki Biological Conference 8 on Speciation and adaptation 20.03.2012 Okazaki, Japan
The 53th Annual Meeting of the Japanese Society of Plant Physiologists 17.03.2012 Kyoto, Japan
"Understanding Phenotypes', Symposium of the Zurich-Basel Plant Science Center 04.11.2011 Zurich, Switzerland
The 75th Meeting of the Botanical Society of Japan 17.09.2011 Tokyo, Japan
Young Researchers Conference on Evolutionary Genomics 01.08.2011 Tokyo, Japan
Annual Meeting of the Society for Molecular Biology and Evolution 27.07.2011 Kyoto, Japan
XVIII International Botanical Congress 26.07.2011 Melbourne, Austraria


Communication with the public

Communication Title Media Place Year
Talks/events/exhibitions Public lecture by the Society for Evolutionary Studies, Japan International 31.07.2011

Awards

Title Year
Most Outstanding Poster Award of the Royal Society of London at the Joint meeting of ESJ and EAFES 2012

Associated projects

Number Title Start Funding scheme
140917 Recurrent patterns in molecular adaptation and speciation: evolutionary genomic analysis using Arabidopsis relatives 01.06.2012 Project funding (Div. I-III)
116376 Adaptation and speciation: evolutionary genomic analysis using arabidopsis relatives 01.04.2008 Project funding (Div. I-III)

Abstract

A central question in biology is the molecular basis of biodiversity. Rapid advances in genomics provide novel tools for addressing key ecological and evolutionary questions in integrated biological sciences. Still, the study of adaptive molecular variation has been mostly limited to well-defined traits in model species. Since the preceding project, we have used A. thaliana and its relatives to study adaptation and speciation, including the evolution of self-compatibility and speciation by genome duplication. This follow-up proposal will extend two of our recent publications (Tsuchimatsu et al. Nature 464:1342-6, 2010 and Aikawa et al. Proc Natl Acad Sci USA 107:11632-7, 2010). First, we have revealed that the evolution of self-compatibility of A. thaliana occurred by a mutation in the male specificity gene SCR, and supported its recent origin during glacial-interglacial cycles. In this study, we found that floral traits responsible for selfing syndrome, such as the timing of autopollination by the coordinated growth of pistil and stamen, are polymorphic among accessions of A. thaliana. Although floral morphology of selfing species has been a major topic in evolution and ecology, very little is known about the genes responsible for it. In this project, we plan to identify them using genome-wide association studies combined with microarray data. We will conduct functional and evolutionary analysis to test how rapidly floral traits evolved. Second, we have studied a perennial species A. halleri, and found that the expression of the FLC flowering time gene shows one-year cycle, corresponding its perennial phenology. The advantage of A. halleri is that it is a perennial species with established transgenic technique, and we have already constructed transgenic plants in which the FLC expression was reduced by RNAi. In this proposal, we will analyze its phenotype regarding meristem identity and floral reversion. We also conduct functional and evolutionary analysis of vernalization responsive element in the first intron of the FLC gene.This proposal will strengthen the message from our previous research to the society stating that climate changes such as glacial cycles may induce rapid evolution that would be difficult to revert.
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