GARNet Research Roundup: March 7th 2019

This edition of the GARNet research roundup begins with a study into the genetic basis of fertility in barley led by Sarah McKim from Dundee. Second is a study from Oxford and Leicester that characterizes the proteolytic control of chloroplast import. The third paper from Levi Yant’s group at JIC and Nottingham that attempts to discover the influence of polyploidism on population genomic effects whilst the fourth paper from Juliet Coates’ lab in Birmingham uses the growth of Arabidopsis to assess the potential of algal biomass as a biofertiliser. The next two papers include co-authors from Oxford and Warwick respectively and investigate different factors that control seed viability in Arabidopsis and Brassica oleracea. The final paper includes Seth Davies from York as a co-author on a study that looks at control of the circadian clock in field-grown Arabidopsis.


Zwirek M, Waugh R, McKim SM (2019) Interaction between row-type genes in barley controls meristem determinacy and reveals novel routes to improved grain. New Phytol. doi: 10.1111/nph.15548

Open Access

Current GARNet committee members Sarah McKim is the leader of this study in which first author is Monica Zwirek. They investigate the mechanism through which the barley VRS genes contribute to spikelet fertility. They undercover the epistatic relationship between five VRS genes that explains how they contribute to controlling fertility of lateral spikelets. Importantly they demonstrate that various vrs mutant combinations improve fertility in a variety of ways, information that will be useful during the generation of new varieties of barley.

https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.15548

Ling Q, Broad W, Trösch R, Töpel M, Demiral Sert T, Lymperopoulos P, Baldwin A, Jarvis RP (2019) Ubiquitin-dependent chloroplast-associated protein degradation in plants. Science. doi: 10.1126/science.aav4467

Qihua Ling and William Broad are the first authors on this study from the Universities of Oxford and Leicester. They investigate the role of proteolysis in the functional control of chloroplast-envelope translocases, which are required for the transport of proteins from nucleus-encoded genes into the chloroplast. They identify two newly characterised proteins that function in the same pathway as the known ubiquitin E3 ligase SP1. These novel proteins, SP2 and CDC48, are both required for the movement of ubiquitinated proteins from the chloroplast outer envelope membrane (OEM) into the cytosol, where they are degraded by the proteolytic machinery. This process of chloroplast-associated protein degradation (CHLORAD) maintains tight control of the activity of OEM proteins and is essential for organelle function.

http://science.sciencemag.org/content/363/6429/eaav4467.long

Monnahan P, Kolář F, Baduel P, Sailer C, Koch J, Horvath R, Laenen B, Schmickl R, Paajanen P, Šrámková G, Bohutínská M, Arnold B, Weisman CM, Marhold K, Slotte T, Bomblies K, Yant L (2019) Pervasive population genomic consequences of genome duplication in Arabidopsis arenosa. Nat Ecol Evol. doi: 10.1038/s41559-019-0807-4.

Patrick Monnahan at the John Innes Centre is first author on this study from the Yant lab that has recently moved to the University of Nottingham. In this collaboration with colleagues in the US, Austria, Sweden, the Czech Republic and Slovakia, they have performed large scale sequencing on 39 populations of Arabidopsis arenosa. These plants have differing levels of ploidy and they are attempting to understand how ploidy effects population genomics. They demonstrate that the ploidy effects are subtle but significant and that masking of deleterious mutations, faster substitution rates and interploidy introgression will likely impact the evolution of populations where polyploidy is common.


Ghaderiardakani F, Collas E, Damiano DK, Tagg K, Graham NS, Coates J (2019) Effects of green seaweed extract on Arabidopsis early development suggest roles for hormone signalling in plant responses to algal fertilisers. Sci Rep. doi: 10.1038/s41598-018-38093-2

Open Access

This work from the Coates lab at the University of Birmingham is led by Fatemeh Ghaderiardakani and looked into the potential of algal extracts as biofertiliser. They showed that at >0.1%, extracts taken from the common green seaweed Ulva intestinalis inhibit Arabidopsis seed germination and root elongation. At lower concentrations primary root elongation was promoted albeit with a complete loss of lateral root formation. Elemental analysis allows the authors to suggest that this effect was mediated via a novel mechanism involving aluminium. Overall the authors caution against the use of algal biofertilisers due to potential unforeseen negative effects on plant growth.


Viñegra de la Torre N, Kaschani F, Kaiser M, van der Hoorn RAL, Soppe WJJ, Misas Villamil JC (2019) Dynamic hydrolase labelling as a marker for seed quality in Arabidopsis seeds. Biochem J. doi: 10.1042/BCJ20180911.

GARNet Committee member Renier van der Hoorn is a co-author on this German-led study that investigates how the activity of seed-localised proteases can affect Arabidopsis seed germination. This study has clear real-world application regarding the storage of economically important seed stocks. They show that vacuolar processing enzymes (VPEs) become more active during aging whilst the activity of serine hydrolases declines alongside seed quality. This information has allowed the authors to develop protease-activity-based markers that will provide information about seed quality.


Schausberger C, Roach T, Stöggl WM, Arc E, Finch-Savage WE, Kranner I (2019) Abscisic acid-determined seed vigour differences do not influence redox regulation during ageing. Biochem J. doi: 10.1042/BCJ20180903

William Finch-Savage from the University of Warwick is a co-author on this Austrian-led study that looks at the effect of aging on the quality of Brassica oleracea seeds stored at two oxygen concentrations. Higher O2 causes a more rapid decrease in seed quality through aging yet in contrast aging did not alter the impact of the hormone ABA on seed viability. This study enables the authors to uncover two mechanisms that control seed quality that appear to act through different mechanisms.


Rubin MJ, Brock MT, Davis SJ, Weinig C (2019) QTL Underlying Circadian Clock Parameters Under Seasonally Variable Field Settings in Arabidopsis thaliana G3 (Bethesda). doi: 10.1534/g3.118.200770

Open Access

Seth Davies from the University of York is a co-author on this study led by Matthew Rubin from the University of Wyoming. They looked at the growth of Arabidopsis thaliana recombinant inbred lines grown in field conditions and found an extremely nuanced relationship regarding how QTLs that influence the circadian clock respond to environmental conditions. For example the authors showed that plant growth in June, July and September is controlled by different QTL architecture, demonstrating the complex regulation of the circadian clock in these field growth plants.

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