Arabidopsis Archives - Page 2 of 5

Arabidopsis Research Roundup: June 10th.

Categories: Aberdeen University, Arabidopsis, Cambridge University, CPIB, GARNet, Global, John Innes Centre, Sainsbury Lab

Tags: Arabidopsis, GARNet, John Innes Centre

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Published on: June 10, 2015

This weeks UK Arabidopsis Research Roundup features work from two members of the GARNet advisory board who are working on very different aspects of how plants response to external stimuli. In addition there is a genetic and biochemical dissection of primary cell wall formation as well as a comment piece that questions recent findings concerning the relationship between auxin, ABP1 and cortical microtubules.

Busoms S, Teres J, Huang X, Bomblies K, Danku J, Douglas A, Weigel D, Poschenrieder C, Salt DE (2015) Salinity is an agent of divergent selection driving local adaptation of Arabidopsis thaliana to coastal habitats Plant Physiology http://dx.doi.org/pp.00427.2015

Current GARNet Chairman David Salt from Aberdeen has collaborated with researchers from Spain, Germany and the USA in this study that looks at the drivers of adaptive evolution of Arabidopsis plants grown in saline conditions. Unusually this is a field-based study using Arabidopsis that naturally grow in coastal or inland areas of NE Span. Plants taken from coastal areas outperform inland plants when grown on highly saline soils, indicating local adaptation to salt tolerance. The authors conclude that the variation in sodium concentration is causing divergent selection between these two populations.

Monaghan J, Matschi S, Romeis T, Zipfel C (2015) The calcium-dependent protein kinase CPK28 negatively regulates the BIK1-mediated PAMP-induced calcium burst Plant Signaling and Behaviour June 2015 http://dx.doi.org/10.1080/15592324.2015.1018497

GARNet advisory board member Cyril Zipfel from the Sainsbury lab led this study looking at the role of the cytoplasmic kinase BIK1 in the plants response to microbial infection. In plants that are mutant for the Ca2+-dependent protein kinase CPK28, BIK1 accumulates, which leads to enhancing immune signaling. In this study the authors add to these previous finding from their lab by showing that CPK28 also contributes to a burst of Ca2+ production following exposure to pathogens.

Mortimer JC, Faria-Blanc N, Yu X, Tryfona T, Sorieul M, Ng YZ, Zhang Z, Stott K, Anders N, Dupree P (2015) An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14 Plant Journal http://dx.doi.org/10.1111/tpj.12898

Paul Dupree from the Biochemistry department at the University of Cambridge led this work that investigated a newly characterised form of Xylan, a little studied component of the plant primary cell wall. Genetic analysis indicates that the IRX9L, IRX10L and IRX14 proteins are necessary for xylan backbone synthesis. Importantly this new xylan is contains GlcA side chains, whose addition only requires the glucuronyltransferase GUX3. This type of xylan has not been observed in secondary cell walls so the authors comment on how differences in xylan structure assist in the formation of primary vs secondary cell walls.

Taken from wikipedia.

T Baskin (2015) Auxin inhibits expansion rate independently of cortical microtubules. Trends in Plant Science http://dx.doi.org/10.1016/j.tplants.2015.05.008

Visiting scholar at CPIB in Nottingham, Tobias Baskin provides a short reply to a publication in Nature that claimed that the control of cell expansion by auxin is caused by reorientation of cortical microtubules. In this paper, Tobias provides evidence from both a simple experiment and from the literature that this might not be the paradigm-shifting observation that it initially appears.

Genome Resequencing for Mutant Identification

by Geraint

Categories: Arabidopsis, bioinformatics, GARNet

Tags: Arabidopsis, BBSRC, bioinformatics, GARNet, genomics, next generation sequencing

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Published on: June 8, 2015

As most biologists will be aware, the cost of DNA sequencing has been falling well in advance of the costs predicted by Moores law (although argued by Neil Hall a few years ago, this might not have been the best thing to happen, intellectually at least).

Instead of simply sequencing many genomes for the sake of it, this also offers opportunities for researchers to use this technology to ‘do-science’ that might previously have been prohibitively laborious or expensive. One such area where this is true is in the identification of novel mutations in plants, especially in Arabidopsis.

Classic approaches to identity the location of an EMS mutation involved mutant identification, backcrossing, selection, rough mapping by PCR or CAPS markers, probably more crossing and then a little guesswork toward the end..…..before using Sanger sequencing to identify what you hope is the causative mutation. Even with a strong following wind this process could take upwards of a year……. many a 1990s PhD thesis was written off the back of mutant identification. In contrast it is now relatively cheap to resequence the Arabidopsis genome so a lot of time can be taken out of this process. In addition, resequencing can remove some of the difficulty involved with selective of mutants that have a subtle phenotypes wherein inaccurate selection of putative mutants would significantly set back the process.

Back in 20111, Anthony Hall’s group in Liverpool University used resequencing in parallel with classic genetics to identify the lesion in the novel early bird1 gene (ebi1), which has a defect in function of the circadian clock. In this case ebi1, which was generated using EMS, was backcrossed 4 times to reduce the number of EMS-induced SNPs not associated with phenotype, and then sequenced alongside the original wildtype plant (from the WS ecotype). The critical part of the protocol came in the power of the software they used to detect homozygous SNPs in the ebi1 line. Indeed the researchers ran into some difficulties due to a high number of SNPs they initially identified. However, when they combined altering the stringency of SNP-calling together with classical rough mapping they were left with approximately 30 SNPs to finally assess. Using a priori knowledge of proposed gene function and by investigating expression changes in these candidates they ultimately identified a novel mutant. Although this process was ultimately successful, it took some extra time due to the difficulty of mutant selection, optimization of the SNP-calling software and subsequent analysis of gene expression.

A recent paper from the lab of Lucia Strader at Washington University in St Louis shows how powerful resequencing can be if you are using a robust method of mutant selection. In their case they isolated mutants with a defect in the root growth response to ABA, which is an unequivocal phenotype to score. They backcrossed their initial mutants, selected for ABA resistance in F2 generation before resequencing these resistant plants. Using this process the authors report that they narrowed their search to between 3-10 candidate genes and that they have subsequently identified novel (unpublished) genes using this method. In addition, as an exemplar of their protocol they used it to isolate novel alleles of known ABA-resistant mutants.

Schematic for mutant identification using NGS. Reproduced from Taylor and Francis PSB http://dx.doi.org/10.1080/15592324.2014.1000167

In parallel they used a similar protocol to the Hall lab where they resequenced non-backcrossed plants and then selected SNPs that only lay within exons.Using this approach they identified between 100-200 homozygous SNPs, a potentially fifty-fold increase compared to their other method. Therefore when you are working with a strong robust phenotype it is probably worth the extra time to obtain a back-crossed population in order to have greater confidence you are isolated your mutant of interest.

The authors importantly note that one limitation of this protocol is that by only selecting for exonic mutations, they are removing the possibility of identifying mutants with splicing or non-coding defects, which may in turn rule out a number of candidate genes.

For me the take-home message from this second study is that if you have a robust phenotype to select for and are confident that your mutation is novel then use of ever-improving NGS is now a time and cost effective way of mutant identification.

In fact this technology might inspire a return to the forward genetic screens of the 80s and 90s , with the aim of identifying novel genes involved in well characterised signaling pathways……..except that PhD students might now have to characterise 10 novel genes prior to graduation….

Arabidopsis Research Roundup: June 3rd 2015

by Geraint

Categories: Arabidopsis, GARNet, Global, John Innes Centre, Open Access

Tags: Arabidopsis, BBSRC, Cardiff, GARNet workshop, genetics, John Innes Centre, NRI, QMUL

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Published on: June 3, 2015

We are unashamedly biased in this weeks Arabidopsis Research Roundup which firstly features work from the group of GARNet PI Jim Murray about the genetic interactions that define growth of lateral organs. Elsewhere we highlight papers that investigate a different role for CYCD3 genes in vascular development, the role of TFL1 in the shoot meristem and the ability of Arabidopsis seedling to tolerant a high light environment during ontogenesis.

Randall RS, Sornay E, Dewitte W, Murray JA (2015) AINTEGUMENTA and the D-type cyclin CYCD3;1 independently contribute to petal size control in Arabidopsis: evidence for organ size compensation being an emergent rather than a determined property Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv200

Jim Murray and Walter Dewitte (Cardiff) lead this study that investigates the relationship between the AINTEGUMENTA (ANT) transcription factor and cyclin CYCD3;1 during lateral aerial organ (LAO) formation. LAO growth is determined by the both the number and size of cells that comprise the organ. During petal development, ant mutants have reduced cell number but increased cell size, demonstrating a ‘compensatory mechanism’ of growth. In contrast cycd3;1 mutants have increased cell size that results in larger petals, showing no compensatory mechanism. Interestingly ant cycd3;1 double mutants do show growth compensation in the same tissue. The authors propose that occurrence of the compensatory mechanism depends on at which time-point during distinct phases of cell division and cell expansion the growth defect occurs.

C Collins, Maruthi M.N and C Jahn (2015) CYCD3 D-type cyclins regulate cambial cell proliferation and secondary growth in Arabidopsis. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv218

Another study that investigates a different role of D-type cyclins is led by former Murray lab member, Carl Collins working at the Natural Resources Institute at the University of Greenwich. The factors that control cambial cell growth are poorly understood but the authors provide a link between the cell cycle and cambial differentiation by showing that CYCD3 subgroup of genes play a role in the process. Three CYCD3 genes are expressed in cambial tissue and the equivalent triple mutant has reduced hypocotyl and stem diameter, which is linked to a reduction in mitotic activity. Conversely, mutant xylem cells increased in size. This shows that CYCD3 genes provide a mechanism for controlling the correct proportions of cell growth during vascular development. This might provide a useful tool in the future study of this important process in woody plants.

Carvalho FE, Ware MA, Ruban AV (2015) Quantifying the dynamics of light tolerance in Arabidopsis plants during ontogenesis Plant Cell Environment http://dx.doi.org/10.1111/pce.12574

The group of Professor Alexander Ruban at Queen Marys University London utilise a novel methodology to measure the ‘intactness’ of photosystem II (PSII). In this paper they assess the amount of light required to inhibit PSII activity through the life cycle of Arabidopsis plants grown in short days. They show that maximum light tolerance occurs in 8-week old plants. Interestingly the light tolerance correlates with rates of electron transport yet did not coincide with the chlorophyll a/b ratios or anthocyanin content.

Baumann K, Venail J, Berbel A, Domenech MJ, Money T, Conti L, Hanzawa Y, Madueno F, Bradley D (2015) Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv247

The TFL1 gene is a repressor of flowering in the Arabidopsis shoot meristem. Researchers from the UK, USA, Spain and Italy, led by Desmond Bradley at the JIC show that ecoptocally expressed TFL1 can repress flowering outside of its normal expression domain. By comparing the expression of TFL1 with genes that determine floral identity (APETALA, LEAFY) the authors conclude that the shoot meristem is more sensitive to TFL1, allowing the maintenance of a vegetative state in this tissue.

Arabidopsis Research Roundup: May 27th

by Geraint

Categories: Arabidopsis, CPIB, GARNet, Global, James Hutton Institute, John Innes Centre, Sainsbury Lab

Tags: Arabidopsis, BBSRC, GARNet

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Published on: May 27, 2015

This weeks Arabidopsis Research Roundup sees a small number of high quality publications driven by UK-based researchers together with a couple of collaborative efforts that highlight the international aspect of research. Topics include two greatly different descriptions of how a plant responds to attack, an investigation into the intersection of vesicle and potassium transport as well as descriptions of auxin and sugar signaling.

Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB, Wirthmueller L, Menke FL, Sohn KH, Jones JD (2015) A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. Cell 161, p1089-1100 http://dx.doi.org/10.1016/j.cell.2015.04.024

Jonathan Jones at the Sainsbury lab collaborated with his ex-PhD student Kee Hoon Sohn (now at Massey University in NZ) to produce this high profile publication in Cell. Professor Jones’s group has been in the vanguard of research into the response to bacterial pathogens and this paper adds a further layer of understanding as they show that the plant uses a bacteria’s own ‘attack mechanism’ against itself. Many bacterial effector proteins target WRKY DNA-binding protein domains in order to interfere with transcription. This work shows that the plant defence factor RRS1 also contains a WRKY domain, enabling it to ‘sense’ when the bacteria is in the cell and act as a decoy that makes the bacteria subsequently open to attack.

Jaouannet M, Morris JA, Hedley PE, Bos JI (2015) Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance. PLos Pathogens 11: e1004918.

The group of Jorunn Bos at the James Hutton Institute in Dundee looked at a different aspect of the defence response whereby they investigated transcriptional responses to aphid predation on Arabidopsis. Host and non-host responses to aphids show a high degree of overlap in expression but interestingly the host response included repressive of genes involved in metabolism and oxidative response. This type of study will pave the way for the future development of aphid control strategies in crop plants and once again highlights the utility of Arabidopsis as a model system.

Zhang B, Karnik R, Wang Y, Wallmeroth N, Blatt MR, Grefen C (2015) The Arabidopsis R-SNARE VAMP721 Interacts with KAT1 and KC1 K+ Channels to Moderate K+ Current at the Plasma Membrane Plant Cell [Epub]

Control of potassium channels is the focus of this work from Mike Blatt’s lab at the University of Glasgow. They identify a subset of SNARE proteins (that are involved in vesicle trafficing) that control K+ channels, albeit in an unconventional manner. The vesicle-associated membrane proteins 721 (VAMP721) is able to target vesicles as well as supressing the actitivty of the K+ channels KAT1 and KC. This leads to a model whereby different subsets of SNARE proteins opposingly effect K+ channel activity alongside having an effect on vesicular transport.

Panoli A, Martin MV, Alandete-Saez M, Simon M, Neff C, Swarup R, Bellido A, Yuan L, Pagnussat GC, Sundaresan V. (2015) Auxin Import and Local Auxin Biosynthesis Are Required for Mitotic Divisions, Cell Expansion and Cell Specification during Female Gametophyte Development in Arabidopsis thaliana. PLoS One. 10:e0126164.

The primary interest of Ranjan Swarup’s group at the University of Nottingham is in hormone signalling and root development yet he is included as a collaborator in this publication led from UC-Davies that focusses on auxin signalling during female gametophyte development. The paper shows that the YUCCA family of the auxin biosynthetic genes are asymmetrically expressed during embryo sac development and that the AUX1 and LAX1 auxin influx carriers are expressed only at both the micropylar pole of the embryo sac and in adjacent cells of the ovule. In addition aux1lax1lax2 triple mutants show numerous gametophytic developmental defects. Given the importance of auxin in most aspects of plant development, this paper highlights the specific manner in which auxin is required for mitotic divisions, cell expansion and patterning during embryo sac development.

Zheng L, Shang L, Chen X, Zhang L, Xia Y, Smith C, Bevan MW, Li Y, Jing HC (2015) TANG, Encoding a Symplekin_C Domain-contained Protein, Influences Sugar Responses in Arabidopsis Plant Physiol [Epub]

Mike Bevan at the JIC is a collaborator on this Chinese driven project that investigates Arabidopsis tang1 mutants. These plants are hypersensitive to sugar amd following a classic map-based cloning approach, the TANG1 gene was found to encode a novel protein with a predicted Symplekin tight junction protein C-terminal. As TANG1 is ubquitiously expressed and has little effect on known sugar signalling pathways, the precise in vivo role of the protein remains somewhat opaque even though it is clearly an important player in the response to sugar in Arabidopsis.

Great British Success in ERA-CAPS

by Geraint

Categories: Arabidopsis, Brassica, Celebrating Basic Plant Science, epigenetics, funding, plant pathogens, UKPSF, Uncategorized

Tags: Arabidopsis, BBSRC, ERA-CAPS, funding, GARNet workshop, John Innes Centre, plant pathogens, UKPSF, wheat

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Published on: May 20, 2015

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:

Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

Arabidopsis Research Roundup

by Geraint

Categories: Arabidopsis, GARNet, Global, UKPSF

Tags: Arabidopsis, arabidopsis research round-up, CPIB, GARNet, John Innes Centre

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Published on: May 14, 2015

Your UK Arabidopsis Research Round-up this week contains studies that aim to define a network of lateral root formation, elucidate modes of calcium signaling, determine mechanisms of epigenetic memory and also the influence of exon-edge evolution in determining the extent of selective pressure.

Liu J, Whalley HJ, Knight MR. Combining modelling and experimental approaches to explain how calcium signatures are decoded by calmodulin-binding transcription activators (CAMTAs) to produce specific gene expression responses. New Phytologist. 2015 Apr 27. doi: 10.1111/nph.13428.

Marc Knight’s group at the University of Durham have attempted to decode the complex mechanism by which calcium controls changes in gene expression. They have developed an experimentally parameterized model that reveals calcium signals are amplified by the binding of calmodulin and calmodulin-binding transcription activators (CAMTAs). Interestingly, the model suggests that gene expression change in response to a calcium signature is defined by the previous history of that signal.

Lavenus J, Goh T, Guyomarc’h S, Hill K, Lucas M, Voß U, Kenobi K, Wilson MH, Farcot E, Hagen G, Guilfoyle TJ, Fukaki H, Laplaze L, Bennett MJ. Inference of the Arabidopsis Lateral Root Gene Regulatory Network Suggests a Bifurcation Mechanism That Defines Primordia Flanking and Central Zones. Plant Cell. 2015 May 5. pii: tpc.114.132993.

The biology of lateral root (LR) formation has been well researched over the past decade although a full robust regulatory network that controls this process has remained elusive. CPIB at the University of Nottingham, together with European collaborators have used a series of transcriptomic datasets to develop a time-delay correlation algorithm (TDCor) to infer the gene expression network (GRN) controlling LR initiation. The GRNs associated with AUXIN RESPONSE FACTOR7 and ARF5 predict a mutual inhibition and a patterning mechanism that controls flanking and central zone specification of LR primordia.

Berry S, Hartley M, Olsson TS, Dean C, Howard M Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. Elife. 2015 May 8;4. doi: 10.7554/eLife.07205.

Epigenetic ‘memory’ allows plant cells to retain a memory of past environmental or development events. One key regulator of this process is the Polycomb Repressive Complex2 (PRC2). Histone proteins that are modified by the PRC2 can be inherited through cell division. The groups of Mark Howard and Caroline Dean at the JIC investigated whether this inheritance directs long term memory in a cis or trans manner. Two copies of the Arabidopsis FLC gene, which is a target for PRC2, were monitored in the same plant. Interestingly they reveal that one FLC copy could be silenced but the other remained active, providing evidence that epigenetic memory, at least of FLC, is stored in trans but not in cis.

Bush SJ, Kover PX, Urrutia AO. Lineage-specific sequence evolution and exon edge conservation partially explain the relationship of evolutionary rate and expression level in A. thaliana. Mol Ecol. 2015 Apr 30. doi: 10.1111/mec.13221.

Alongside genetic changes in response to phenotypic adaptation, the elements of a genes DNA structure can also affect evolutionary rates. In Arabidopsis the ‘edge’ of exons, which flank introns and contain splice enhancers are known to have a higher degree of evolutionary conservation compared to coding regions. Dr Arazi Urrutia and collaborators from the University of Bath assessed selective pressure (measured by dN/dS) and showed that exon edge conservation partially explains the relationship between rates of protein evolution and expression level. Without any consideration of exon-edge conservation can potentially increase the number of genes designated as being under adaptive selection. Therefore the authors conclude that exon-edge conversation should be an important consideration when assessing overall dN/dS ratios.

Natural variation in Arabidopsis, the MAGIC way

by Charis Cook

Categories: Arabidopsis, Summary for non-specialists, systems biology

Tags: Arabidopsis, natural variation

Comments: No Comments

Published on: November 24, 2014

The research: Finding the causes of variation in seed size and number

In the Arabidopsis Research Round-up a few weeks ago, Lisa highlighted a paper from a team at the University of Bath about natural variation in Arabidopsis seeds. Lead author Paula Kover and her team investigated the genetic basis of variation in seed size and number.

All plants negotiate a trade-off between the number and size of their seeds, so it was a surprise to learn that of 9 QTL for seed number and 8 for seed size, there was only 1 overlapping QTL. The strong negative correlation seen in size and number is logically due to resource use efficiency, but these data suggest that this is not determined genetically.

There is enough of a positive correlation between seed number and fruit length that fruit length is sometimes used to estimate seed number – though the correlation is not strong. Here too there was only 1 QTL overlapping between the two traits, suggesting that any correlation is not inherent and may vary according to environmental or internal factors.

Based on QTL analysis, Kover et al. identify five potential genes that underlie quantitative variation in seed size and number: AAP1 (AT1G58360) and KLUH (AT1G13710) on chromosome 1; and JAGGED LATERAL ORGANS (AT4G00220), YABBY 3 (AT4G00180), and BEL1 (AT5G41410) on chromosomes 4 and 5.

The tool: MAGIC Arabidopsis lines

All the above work was carried out using Mulitparent Advanced Generation Inter-Cross (MAGIC) Arabidopsis lines. Kover and others developed these lines to improve methods of identifying natural allelic variation that underlies variable phenotypic traits. The lines are recombinant, inbred over 6 generations, that originate from an intermated hereogenous stock. This pedigree means they represent a large diversity of genes in mostly homozygous lines; ideal for accurate QTL mapping. The original MAGIC paper from 2009 paper states ‘MAGIC lines occupy an intermediate niche between naturally occurring accessions and existing synthetic populations.’

The MAGIC lines are an incredible open resource for studying natural variation in Arabidopsis: they enable a researcher to map a trait to within 300kb. All lines in the 2009 paper are available from NASC. A set of digital tools, hosted at the Wellcome Trust Centre for Human Genetics, contains the (open source) software needed to run the QTL analysis and the data files associated with the lines.

Highlighted paper: Gnan, Priest and Kover. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines. Genetics, 2014. 10.1534/genetics.114.170746

Also cited: Kover et al. A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLOS Genetics, 2009. DOI: 10.1371/journal.pgen.1000551

For a comparison of resources for studying natural variation, see Weigel, Plant Phys, 2012 158:2-22

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

Tags: Arabidopsis, arabidopsis research round-up, Edinburgh, Ferenc Nagy, Hungarian Academy of Sciences, research, round-up, SULSA, The Plant Cell, university of edinburgh

Comments: No Comments

Published on: November 5, 2014

Just one new paper to share with you this week!

Binkert M, Kozma-Bognar L, Terecskei K, de Veylder L, Nagy F and Ulm R. UV-B-responsive association of the Arabidopsis bZIP transcription factor ELONGATED HYPOCOTYL5 with target genes, including its own promoter. The Plant Cell, 28 October 2014. DOI: 10.1105/tpc.114.130716. [Open Access]

Though he has a joint appointment at the Hungarian Academy of Sciences, Ferenc Nagy is also SULSA Chair of Cell Biology at the University of Edinburgh. Working with Swiss, Hungarian and Belgian colleagues, this paper describes research to understand the transcription factors regulating plants’ protective responses to UV-B. It is shown that, in Arabidopsis, binding of the bZIP transcription factor ELONGATED HYPOCOTYL5 (HY5) to the promoters of UV-B-responsive genes is enhanced by UV-B independently of the UV-B photoreceptor UV RESISTANCE LOCUS8 (UVR8).

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