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Full genome re-sequencing reveals a novel circadian clock mutationin Arabidopsis
School of Biological Sciences, University of Liverpool, Liverpool, UK.
Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).ORCID iD: 0000-0003-2038-4892
Applied Biosystems, part of Life Technologies, Warrington, UK.
School of Biological Sciences, University of Liverpool, Liverpool, UK.
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2011 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1465-6914, Vol. 12, R28- p.Article in journal (Refereed) Published
Abstract [en]

Background: Map based cloning in Arabidopsis thaliana can be a difficult and time-consuming process,specifically if the phenotype is subtle and scoring labour intensive. An alternative to map basedcloning would be to directly sequence the whole genome of a mutant to uncover the mutationresponsible for the phenotype.

Results: Here, we have re-sequenced the 120 Mb genome of a novel Arabidopsis clock mutant earlybird (ebi-1), using massively parallel sequencing by ligation. This process was further complicated by the fact that ebi-1 is in Wassilewskija (Ws-2), not the reference accession ofArabidopsis. The approach reveals evidence of DNA strand bias in the ethyl methanesulfonate(EMS) mutation process. We have demonstrated the utility of sequencing a backcrossed line andusing gene expression data to limit the number of SNP considered. Using new SNP informationwe have excluded a previously identified clock gene, PRR7. Finally, we have identified a SNPin the gene AtNFXL-2 as the likely cause of the ebi-1 phenotype and validated this bycharacterising a further allele.

Conclusion: In Arabidopsis, as in other organisms, the (EMS) mutation load can be high. Here wedescribe how sequencing a backcrossed line, using functional genomics and analysing new SNPinformation can be used to reduce the number EMS mutations for consideration. Moreover, theapproach we describe here does not require out-crossing and scoring F2 mapping populations, anapproach which can be compromised by background effects. The strategy has broad utility andwill be an extremely useful tool to identify causative SNP in other organisms.

Place, publisher, year, edition, pages
2011. Vol. 12, R28- p.
National Category
Biochemistry and Molecular Biology Botany
URN: urn:nbn:se:umu:diva-35864DOI: 10.1186/gb-2011-12-3-r28OAI: diva2:349778
Available from: 2010-09-08 Created: 2010-09-08 Last updated: 2014-11-17Bibliographically approved
In thesis
1. The circadian clock in annuals and perennials: coordination of Growth with Environmental Rhythms
Open this publication in new window or tab >>The circadian clock in annuals and perennials: coordination of Growth with Environmental Rhythms
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Since the first signs of life on planet earth, organisms have had to adapt to the daily changes between light and dark, and high and low temperatures. This has led to the evolution of an endogenous time keeper, known as the circadian clock. This biological timing system helps the organism to synchronize developmental and metabolic events to the most favorable time of the day. Such a mechanism is of considerable value to plants, since they in contrast to animals cannot change location when the environment becomes unfavorable. Thus is the ability to predict coming events of central importance in a plants life. This thesis is a study of the molecular machinery behind the clockwork in the small weed plant Arabidopsis thaliana as well as its close relative perennial; the woody species Populus. We have characterized a novel component of the circadian clock, EARLY BIRD (EBI). EBI is involved in transcriptional and translational regulation, via interaction with the known post-translational clock regulator ZEITLUPE (ZTL). In Populus, we describe the role of the circadian clock and its components with respect to entry and exit of dormancy and show that gene expression of the Populus LATE ELONATED HYPOCOTYL (LHY) genes are crucial importance for freezing tolerance and thereby survival at high latitudes. Furthermore, the input to the Populus clock is mediated via the phytochrome A (phyA) photoreceptor.

Abstract [sv]

Liv på jorden har alltid behövt anpassa sig till de dagliga växlingarna mellan främst ljus och mörker. Detta har lett till evolutionen av en intern, biologisk klocka, känd som den circadianska klockan, efter latinets ”circa diem”, som betyder ”ungefär en dag”. Denna inre klocka hjälper organismer att styra biologiska processer till den tid på dygnet som är mest gynnsam för deras utveckling och överlevnad. Denna mekanism är av stort värde för växter, eftersom de inte kan söka skydd på mera lämpliga platser om de blir utsatta för olika former av stress. Det gör att förmågan att förutse kommande händelser är av yttersta vikt för växter. Denna avhandling är en studie av det molekylära nätverk som styr denna biologiska klocka i den lilla örtplantan Arabidopsis thaliana (backtrav), och den besläktade träd-arten Populus (hybrid-asp). Vi har karaktäriserat en ny komponent i den circadianska klockan i Arabidopsis, EARLY BIRD (EBI). EBI är involverad i transkriptionell och translationell reglering av klockan, via interaktion med den kända post-translationella klock-regulatorn ZEITLUPE (ZTL). I Populus har vi beskrivit den interna klockan och dess roll i processer som invintring, vinterdvala och återstart av tillväxt. LATE ELONATED HYPOCOTYL (LHY) generna i Populus är avgörande för förvärv av köld-tolerans och således överlevnad på högre latituder. Dessutom har vi visat att signaler till den circadianska klockan i Populus är medierade via fotoreceptorn phytochrome A (phyA).

Place, publisher, year, edition, pages
Umeå: Umeå Universitet, Institutionen för fysiologisk botanik, 2010. 61 p.
circadian clock, arabidopsis, populus
National Category
Biochemistry and Molecular Biology Plant Biotechnology Botany
Research subject
Molecular Biology
urn:nbn:se:umu:diva-35870 (URN)978-91-7459-062-3 (ISBN)
Public defence
2010-10-01, KB3B1, KBC-huset, Umeå universitet, Umeå, 10:00 (English)
Available from: 2010-09-10 Created: 2010-09-08 Last updated: 2010-09-10Bibliographically approved

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Eriksson, Maria EJohansson, Mikael
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Department of Plant PhysiologyUmeå Plant Science Centre (UPSC)
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