Quantitative analysis of lateral root development with time-lapse imaging and deep neural network

During lateral root (LR) development, morphological alteration of the developing single LR primordium occurs continuously. Precise observation of this continuous alteration is important for understanding the mechanism involved in single LR development. Recently, we reported that very long-chain fatty acids are important signalling molecules that regulate LR development. In the study, we developed an efficient method to quantify the transition of single LR developmental stages using time-lapse imaging followed by a deep neural network (DNN) analysis. In this ‘insight’ paper, we discuss our DNN method and the importance of time-lapse imaging in studies on plant development. Integrating DNN analysis and imaging is a powerful technique for the quantification of the timing of the transition of organ morphology; it can become an important method to elucidate spatiotemporal molecular mechanisms in plant development

MYB30 regulates root cell elongation under abscisic acid signaling

Reactive oxygen species (ROS) and plant hormones play important roles in regulating plant growth and stress responses as signaling molecules. Abscisic acid (ABA) is known as the key regulator of both abiotic and biotic stress responses. During stress responses, ABA is known to regulate ROS production, indicating that important crosstalk occurs between ROS and ABA signaling. We recently reported that MYB30, an MYB-type transcription factor, regulates root cell elongation under ROS signaling. In this study, we analyzed the molecular interaction between ROS and ABA signal during for root development, which is mediated through MYB30 transcriptional regulation. We showed that MYB30-regulated root cell elongation was mediated by ROS production under ABA signaling. Our findings will provide one piece of evidence of the complex cross talk between ROS and hormone signaling that regulates root development

The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots[W][OA]

Iron deficiency induces a range of physiological responses that are controlled by transcriptional alterations concentrated in the root pericycle. The transcriptional regulator POPEYE regulates many of these responses possibly through interaction with iron deficiency response protein ILR3 and the putative E3 ligase protein BRUTUS

RNA-Seq Analysis of the Response of the Halophyte, <i>Mesembryanthemum crystallinum</i> (Ice Plant) to High Salinity

<div><p>Understanding the molecular mechanisms that convey salt tolerance in plants is a crucial issue for increasing crop yield. The ice plant (<i>Mesembryanthemum crystallinum</i>) is a halophyte that is capable of growing under high salt conditions. For example, the roots of ice plant seedlings continue to grow in 140 mM NaCl, a salt concentration that completely inhibits <i>Arabidopsis thaliana</i> root growth. Identifying the molecular mechanisms responsible for this high level of salt tolerance in a halophyte has the potential of revealing tolerance mechanisms that have been evolutionarily successful. In the present study, deep sequencing (RNAseq) was used to examine gene expression in ice plant roots treated with various concentrations of NaCl. Sequencing resulted in the identification of 53,516 contigs, 10,818 of which were orthologs of <i>Arabidopsis</i> genes. In addition to the expression analysis, a web-based ice plant database was constructed that allows broad public access to the data. The results obtained from an analysis of the RNAseq data were confirmed by RT-qPCR. Novel patterns of gene expression in response to high salinity within 24 hours were identified in the ice plant when the RNAseq data from the ice plant was compared to gene expression data obtained from <i>Arabidopsis</i> plants exposed to high salt. Although ABA responsive genes and a sodium transporter protein (HKT1), are up-regulated and down-regulated respectively in both <i>Arabidopsis</i> and the ice plant; peroxidase genes exhibit opposite responses. The results of this study provide an important first step towards analyzing environmental tolerance mechanisms in a non-model organism and provide a useful dataset for predicting novel gene functions.</p></div

Comparison of gene expression data obtained by RNAseq and by RT-qPCR.

<p>Expression level of selected genes in whole roots of ice plant subjected to 0 mM, 140 mM, 250 mM, or 500 mM NaCl treatment for 24 h as measured by RT-qPCR (white boxes). Gene expression was normalized against the housekeeping gene, <i>PolyUBQ10</i>. (n = 3, ±S.D.; **and * indicate <i>p</i><0.001 and <i>p</i><0.05 by Student’s <i>t</i>-test, respectively, the comparison is between 0 mM NaCl and the remaining NaCl concentrations). Gray boxes (NGS) indicate the level of gene expression obtained from RNAseq data. The RNAseq data are shown as the level of expression relative to 0 mM NaCl treatment which was set at a value of 1.</p