GARNet Research Roundup: March 7th 2019


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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.

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

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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