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Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up

Tags: Arabidopsis, arabidopsis thaliana, GARNet committee, genetics, genome research, John Innes Centre, Jonathan Jones, Nicholas Harberd, Paula Kover, PLOS Pathogens, The Sainsbury Laboratory, university of bath, University of Oxford

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Published on: October 23, 2014

There are three new and exciting Arabidopsis papers from the UK research community this week. The University of Bath makes two appearances, once with a Genetics paper, and once in collaboration with the University of Oxford in Genome Research. Representing Norwich this week, Jonathan Jones heads up a Sainsbury Lab/John Innes Centre collaboration to investigate simultaneous changes in gene expression between Arabidopsis and a pathogen.

Gnan S, Priest A and Kover PX. The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thalianaMAGIC lines. Genetics, 13 October 2014. DOI: 10.1534/genetics.114.170746.

This team from the University of Bath explored the natural variation in genes affecting seed size and seed number in Arabidopsis. Both seed size and seed number were found to be affected by non-overlapping QTLs, therefore suggesting these two traits can evolve independently of each other. Trade-off between these two traits in terms of fecundity and yield is dependent upon life history traits.

Jiang C, Mithani A, Belfield EJ, Mott R, Hurst LD and Harberd NP. Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations. Genome Research, 14 October 2014. DOI: 10.1101/gr.177659.114. [Open Access]

GARNet committee member Nick Harberd led on this Genome Research paper, along with co-corresponding author Caifu Jiang from China, and colleagues from theUniversity of Bath and Pakistan. In animal cells, repeated or prolonged presentation of a stressor often leads to increased mutations, which can increase the risk of cancer. Being sessile, plants do not get cancer in the same way that humans do, but do they acquire more mutations? Does stress – here the example of high soil salinity is used – drive the evolution of plants through increased phenotypic diversity? Yes, it seems so.

Asai S, Rallapalli G, Piquerez SJM, Caillaud M-C, Furzer OJ, Ishaque N, Wirthmueller L, Fabro G, Shirasu K and Jones JDG. Expression profiling during Arabidopsis/downy mildew interaction reveals a highly expressed effector that attenuates responses to salicylic acid. PLOS Pathogens, 16 October 2014. DOI: 10.1371/journal.ppat.1004443. [Open Access]

Led by Jonathan Jones, scientists from The Sainsbury Laboratory in Norwich worked with Lennart Wirthmueller from the John Innes Centre, and two Japanese collaborators, to produce this PLOS Genetics paper. Though gene expression patterns have been studied independently in the pathogen Hyaloperenospora arabidopsidis, and in its host Arabidopsis thaliana, they have not been compared simultaneously. Using a high-throughput cDNA tag sequencing method, this paper describes simultaneous changes in gene expression profiles in both host and pathogen.

Arabidopsis Research Round-up

by Guest Blogger

Categories: Arabidopsis, Global, Round-up

Tags: AIP, andrew millar, Arabidopsis, arabidopsis research round-up, blog, david salt, GARNet, John Innes Centre, karen halliday, kim findlay, research, research round-up, rod scott, round-up, university of aberdeen, university of bath, university of edinburgh

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Published on: October 2, 2014

Apologies there hasn’t been an Arabidopsis Research Round-up for a few weeks, I’ve been on annual leave getting married! Here’s a catch up of the newest Arabidopsis research papers from the UK community over the last month, including one from a GARNet committee member, and one from a former GARNet PI.

Schatlowski N, Wolff P, Santos-González J, Schoft V, Siretskiy A, Scott R, Tamaru H and Köhler C. Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis. The Plant Cell, 1 September 2014. DOI: 10.1105/tpc.114.130120.

Rod Scott from the University of Bath was involved on this Plant Cell paper. With Swedish, Austrian and Swiss colleagues, it was identified that, through the suppression of expressed imprinted genes, hypomethylation can occur in pollen that alters the epigenetic control of the ‘interploidy hybridization barrier’. Based on these findings, the researchers here present a novel method for the generation of viable triploid Arabidopsis plants, which could have significant impact for plant breeding.

Chew YH, Wenden B, Flis A, et al. Multiscale digital Arabidopsis predicts individual organ and whole-organism growth. Proceedings of the National Academy of Sciences of the United States of America, 2 September 2014. DOI: 10.1073/pnas.1410238111. [Open Access]

You can tell former GARNet PI Andrew Millar from the University of Edinburgh led this paper – it’s all about linking the Arabidopsis research community! Quantitative modeling is undeniably an important tool in modern predictive biology, but understanding plants at a molecular level doesn’t necessarily help us to ‘bridge the genotype to phenotype gap’ and predict how molecular changes affect the whole organism, or vice versa. Linking together several models across multiple scales, Millar and colleagues here present a validated multiscale model of Arabidopsis rosette growth, enabling prediction of how genetic regulation and biochemical dynamics may affect organ and whole-plant growth.

Chao D-Y, Baraniecka P, Danku J, Koprivova A, Lahner B, Luo H, Yakubova E, Dilkes BP, Kopriva S and Salt DE. Variation in sulfur and selenium accumulation is controlled by naturally occurring isoforms of the key sulfur assimilation enzyme APR2 across the Arabidopsis thaliana species range. Plant Physiology, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

GARNet committee member and ‘Mr Ionomics’ David Salt, from the University of Aberdeen, was the lead on this new paper in Plant Physiology, working with colleagues from the John Innes Centre, Purdue, Cologne and Shanghai. This study used linkage mapping in synthetic F2 populations to investigate the natural variation in total leaf sulphur and selenium levels across a wide range of Arabidopsis thaliana accessions. Though the significance is not yet understood, it was found that the catalytic capacity of APR2, an enzyme important in allowing the accumulation of sulphur and selenium in leaves, varied by four orders of magnitude.

Fujikura U, Elsaesser L, Breuninger H, Sanchez-Rodriguez C, Ivakov A, Laux T, Findlay K, Persson S and Lenhard M. Atkinesin-13A modulates cell wall synthesis and cell expansion in Arabidopsis thaliana via the THESEUS1 pathway. PLOS Genetics, 18 September 2014. DOI: 10.1104/pp.114.247825. [Open Access]

For plants to grow they need to not only proliferate their cells, but expand the size of the cells too. Since plant cells are encased in a rigid cell wall, the cell wall structure must be temporarily loosened to allow expansion and the deposition of additional cell wall materials. Working with a German-led team and colleagues in Australia, Kim Findlay from the John Innes Centre contributed to this paper, which discusses the roles of AtKINESIN-13-A and its homologue AtKINESIN-13B in limiting cell expansion and size in Arabidopsis thaliana.

Johansson H, Jones HJ, Foreman J, Hemsted JR, Stewart K, Grima R and Halliday KJ. Arabidopsis cell expansion is controlled by a photothermal switch.Nature Communications, 26 September 2014. DOI: 10.1038/ncomms5848. [Open Access]

A second appearance in today’s Round-up for the University of Edinburgh’s Karen Halliday, and another paper discussing cell expansion. This time, this Nature Communications paper explores the finding that phytochrome B-controlled growth in the Arabidopsis hypocotyl is strictly regulated by temperature: a shift in temperature induces a dramatic reversal of response from inhibition to promotion of hypocotyl elongation by light.

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