GARNet Research Roundup: November 1st 2019

This edition of the GARNet Research Roundup begins with a pan-UK study that has identified a gene involved in starch granule formation in polyploid wheat. Second is a study from Canterbury that identifies Arabidopsis QTLs involved in alternative splicing. Third is research from Cambridge that investigates the role of the nuclear circadian oscillator on sub-cellular calcium fluctuations. The fourth paper describes the development of a computer-vision tool designed for automated measurements of wheat spikes in the field. The fifth paper is a Korean-led study that has identified a transcription factor involved in pollen development and includes co-authors from Leicester. Last is a study from the University of Warwick that has looked into light-regulated gene expression during bulb initiation in onion.

Chia T, Chirico M, King R, Ramirez-Gonzalez R, Saccomanno B, Seung D, Simmonds J, Trick M, Uauy C, Verhoeven T, Trafford K (2019) A carbohydrate-binding protein, B-GRANULE CONTENT 1, influences starch granule size distribution in a dose-dependent manner in polyploid wheat. J Exp Bot. doi: 10.1093/jxb/erz405
Open Access

Tansy Chia is lead author on this study that brings together three of the UKs major plant breeding research centres; NIAB, Rothamsted and the JIC. They take advantage of the new genomic tools and mutant populations available in wheat to characterize the complex role of the BGC1 (B-GRANULE CONTENT 1) gene during formation of B-type starch granules.

Khokhar W, Hassan MA, Reddy ASN, Chaudhary S, Jabre I, Byrne LJ, Syed NH (2019) Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana Front Plant Sci. doi: 10.3389/fpls.2019.01160
Open Access

This work from Canterbury Christ Church University is led by Waqas Khokhar and Naeem Syed. They analysed 666 diverse Arabidopsis ecotypes to look for splicing quantitative trait loci (sQTLs)] that alter rates of alternative splicing. They identified a number of trans-sQTLs hotspots that align with known functional SNPs. This study provides the first sQTL resource across diverse ecotypes that can be used to compliment other available genome and transcriptome datasets.

Martí Ruiz MC, Jung HJ, Webb AAR (2019) Circadian gating of dark-induced increases in chloroplast- and cytosolic-free calcium in Arabidopsis. New Phytol. doi: 10.1111/nph.16280

María Carmen Martí Ruiz is lead author on this research undertaken in Alex Webb’s lab in Cambridge. They have looked at the role of the circadian clock in the control of calcium fluctuations in both cytoplasm and chloroplast stroma. They show the extent these changes are dependent on a nuclear-encoded circadian oscillator, adding a new role in sub-cellular Ca2+ signaling to the circadian machinery.

Sadeghi-Tehran P, Virlet N, Ampe EM, Reyns P, Hawkesford MJ (2019) DeepCount: In-Field Automatic Quantification of Wheat Spikes Using Simple Linear Iterative Clustering and Deep Convolutional Neural Networks. Front Plant Sci. doi: 10.3389/fpls.2019.01176
Open Access

Pouria Sadeghi-Tehran leads this theorectical study from Rothamsted Research that has developed an automated ‘DeepCount’ system for quantifying wheat spikes in the field. They use a deep convolutional neural network to test their program on field images and compare this method to other automated systems based on edge detection techniques and morphological analysis. Overall they show that this method has potential toward development of a portable and smartphone-assisted wheat-ear counting systems, that will have the associated benefits of counting accuracy and reduced labour.

Oh SA, Hoai TNT, Park HJ, Zhao M, Twell D, Honys D, Park SK (2019) MYB81, a microspore-specific GAMYB transcription factor, promotes pollen mitosis I and cell lineage formation in Arabidopsis. Plant J. doi: 10.1111/tpj.14564

Mingmin Zhao and David Twell are co-authors on this project led by Sung‐Aeong Oh and Korean colleagues. After screening pollen cell patterning mutants they have identified a role for the GAMYB transcription factor MYB81 during a narrow window prior to pollen mitosis I. They demonstrate that this protein is essential for establishing the male cell lineage in Arabidopsis pollen.

Rashid MHA, Cheng W, Thomas B (2019) Temporal and Spatial Expression of Arabidopsis Gene Homologs Control Daylength Adaptation and Bulb Formation in Onion (Allium cepa L.). Sci Rep. doi: 10.1038/s41598-019-51262-1 Open Access

This collaboration between the University of Warwick and Bangladesh Agricultural University is led by Harun Ar Rashid. They look at genetic regulation of light-dependent onion bulb initiation by growing plants under short and long days and testing the expression of known regulators of flowering time; AcFT, Ac LFY and AcGA3ox1. They also performed tissue-specific analysis to demonstrate differences in expression patterns that begin to suggest how these genes are involved in bulb initiation.

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