GARNet Research Roundup: April 27th

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This weeks GARNet research roundup features four papers that include Malcolm Bennett (University of Nottingham) as an author. The first three are linked manuscripts that investigate the role of auxin on root hair development that is controlled by varying phosphate levels. Ranjan Swarup provides an audio summary of two of these papers on the GARNet YouTube and podcast feeds.

The fourth paper from Nottingham is a collaboration with GARNet PI Jim Murray (Cardiff University) that characterises the STM gene network and its influence on meristem development.

The fifth paper from the lab of Paul Dupree in Cambridge characterises the stem transcriptome whilst the next paper from Iain Johnston and George Bassel (University of Birmingham) identifies a bet-hedging network that influences seed germination. The final paper features Seth Davies (University of York) as a co-author and investigates the impact of changes in circadian rhythms on short architecture.


Researchers at the University of Nottingham are involved in three back-to-back papers that add a mechanistic framework to the relationship between phosphate and auxin signaling in root hairs.

Bhosale R, Giri J, Pandey BK, Giehl RFH, Hartmann A, Traini R, Truskina J, Leftley N, Hanlon M, Swarup K, Rashed A, Voß U, Alonso J, Stepanova A, Yun J, Ljung K, Brown KM, Lynch JP, Dolan L, Vernoux T, Bishopp A, Wells D, von Wirén N, Bennett MJ, Swarup R (2018) A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate. Nat Commun. 9(1):1409. doi: 10.1038/s41467-018-03851-3

Open Access

The first paper is led by Ranjan Swarup and defines components of auxin biosynthetic, transport and signaling pathways that are involved in the change root hair development in response to different phosphate concentrations in Arabidopsis. Ranjan discusses this paper on YouTube.

Giri J, Bhosale R, Huang G, Pandey BK, Parker H, Zappala S, Yang J, Dievart A, Bureau C, Ljung K, Price A, Rose T, Larrieu A, Mairhofer S, Sturrock CJ, White P, Dupuy L, Hawkesford M, Perin C, Liang W, Peret B, Hodgman CT, Lynch J, Wissuwa M, Zhang D, Pridmore T, Mooney SJ, Guiderdoni E, Swarup R, Bennett MJ (2018). Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate. Nat Commun. 9(1):1408. doi: 10.1038/s41467-018-03850-4

Open Access

This paper led by Malcolm Bennett uses a rice model to investigate the relationship between auxin and root hair elongation in response to low concentrations of phosphate. They show rice aux1 mutants have significant changes in root architecture.

Dindas J, Scherzer S, Roelfsema MRG, von Meyer K, Müller HM, Al-Rasheid KAS, Palme K, Dietrich P, Becker D, Bennett MJ, Hedrich R (2018) AUX1-mediated root hair auxin influx governs SCF(TIR1/AFB)-type Ca(2+) signaling. Nat Commun. 9(1):1174. doi: 10.1038/s41467-018-03582-5

Open Access

The third paper includes Malcolm Bennett as a co-author and investigates how the auxin transport and signaling pathways stimulate calcium signaling during root hair elongation.


Scofield S, Murison A, Jones A, Fozard J, Aida M, Band LR, Bennett M, Murray JAH (2018) Coordination of meristem and boundary functions by transcription factors in the SHOOT MERISTEMLESS regulatory network. Development pii: dev.157081. doi: 10.1242/dev.157081

Open Access
GARNet PI Jim Murray is the corresponding author on this manuscript that is led by Dr Simon Scofield and includes collaborators from the University of Nottingham. They have explored the gene regulatory network that is regulated by the key meristem identity gene SHOOT MERISTEMLESS (STM). This network includes an over-representation of transcription factor families, each of which have distinct roles in meristem development. They use in planta experimentation and in silico modeling to investigate the relationship between STM and CUC1 in more detail. Overall this study confirms that STM is a central regulator of shoot meristem function.


Faria-Blanc N, Mortimer JC, Dupree P (2018) A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis. Front Plant Sci. 9:384. doi: 10.3389/fpls.2018.00384

Open Access

Paul Dupree (University of Cambridge) is the corresponding author of this study that uses a range of Arabidopsis cell wall mutants to investigate the stem transcriptome. In plants with defects in xylan synthesis the authors found surprisingly few transcriptional changes. This indicates that once plants have committed to a terminal secondary cell wall program there is little need for transcriptional changes even after cell wall damage.


Johnston IG, Bassel GW (2018) Identification of a bet-hedging network motif generating noise in hormone concentrations and germination propensity in Arabidopsis. J R Soc Interface. 15(141). pii: 20180042. doi: 10.1098/rsif.2018.0042.

Open Access
Iain Johnston (University of Birmingham) leads this study that has identified a bet-hedging network that links hormone signaling during Arabidopsis germination. This type of network allows plants to more easily adapt to varying environmental conditions but can preclude maximum growth. In this system the network is based upon the regulation of ABA synthesis, activity and degradation, which is maintained at a constant mean level even though it exhibits significant noise. They investigate the parameters that might be tweaked to reduce variation in germination rate and therefore might be targets for modification in order to maximise responses under particular environmental conditions.

George Bassel who is a co-author on this paper will be speaking at the GARNet2018 Meeting in York in September.


Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C (2018) Circadian rhythms are associated with shoot architecture in natural settings. New Phytol. doi: 10.1111/nph.15162.

Seth Davies (University of York) is a co-author on this study that assesses the effect of circadian rhythms on aerial phenotypes that lead to fruit production in field grown Arabidopsis. This was assessed over two growing seasons and they show that variation in clock function significantly impacts shoot architecture.

The post GARNet Research Roundup: April 27th appeared first on Weeding the Gems.