Arabidopsis Research Articles

Progress on genic male sterility gene in soybean.

Male sterility refers to the phenomenon that stamens cannot grow normally and produce viable pollen grains in plants. Hybrid seed production by taking advantage of the trait of male sterility is an effective and quick strategy to increase crop yield. Up to date, the yield of rice (Oryza sativa L.), maize (Zea mays L.), wheat (Triticum aestivum L.) and other crops has been greatly increased based on hybrid vigor utilization. Soybean (Glycine max (L.) Merr.) is a self-pollination species, artificial emasculation is not only time-consuming, but also labor-intensive and economically impracticable. So far, large scale hybrid breeding has not been performed in soybean due to the shortage of male sterile lines suitable for hybrid production. Therefore, it is urgent to identify a stable male sterile system for the rapid utilization of heterosis in soybean. In this review, we summarize the progress on the discovery of soybean genic male sterility (GMS) mutants and GMS genes. Combining with the investigation of GMS genes in Arabidopsis, rice and maize, we provide important insights into the identification and potential utilization of GMS genes in soybean in the perspective of reverse genetics.

Quantitative Analysis of Chromosome Polytenization in Synthetic Autopolyploids of <i>Arabidopsis thaliana</i>

Quantitative Analysis of Chromosome Polytenization in Synthetic Autopolyploids of <i>Arabidopsis thaliana</i>

Building a text mining pipeline to retrieve literature to study stress response in Arabidopsis

Building a text mining pipeline to retrieve literature to study stress response in Arabidopsis

Gametophytic Abortion in Heterozygotes but Not in Homozygotes: Implied Chromosome Rearrangement during T-DNA Insertion at the ASF1 Locus in Arabidopsis.

T-DNA insertional mutations in Arabidopsis genes have conferred huge benefits to the research community, greatly facilitating gene function analyses. However, the insertion process can cause chromosomal rearrangements. Here, we show an example of a likely rearrangement following T-DNA insertion in the Anti-Silencing Function 1B (ASF1B) gene locus on Arabidopsis chromosome 5, so that the phenotype was not relevant to the gene of interest, ASF1B. ASF1 is a histone H3/H4 chaperone involved in chromatin remodeling in the sporophyte and during reproduction. Plants that were homozygous for mutant alleles asf1a or asf1b were developmentally normal. However, following self-fertilization of double heterozygotes (ASF1A/asf1a ASF1B/asf1b, hereafter AaBb), defects were visible in both male and female gametes. Half of the AaBb and aaBb ovules displayed arrested embryo sacs with functional megaspore identity. Similarly, half of the AaBb and aaBb pollen grains showed centromere defects, resulting in pollen abortion at the bi-cellular stage of the male gametophyte. However, inheritance of the mutant allele in a given gamete did not solely determine the abortion phenotype. Introducing functional ASF1B failed to rescue the AaBb- and aaBb- mediated abortion, suggesting that heterozygosity in the ASF1B gene causes gametophytic defects, rather than the loss of ASF1. The presence of reproductive defects in heterozygous mutants but not in homozygotes, and the characteristic all-or-nothing pollen viability within tetrads, were both indicative of commonly-observed T-DNA-mediated translocation activity for this allele. Our observations reinforce the importance of complementation tests in assigning gene function using reverse genetics.

Tissue-Specific Regulation of Plastid Protein Import via Transit-Peptide Motifs.

Plastids differentiate into various functional types (chloroplasts, leucoplasts, chromoplasts, etc.) that have distinct proteomes depending on the specific tissue. Most plastid proteins are encoded by the nuclear genome, synthesized as higher molecular mass preproteins with an N-terminal transit peptide, and then posttranslationally imported from the cytosol. Evidence for tissue-specific regulation of import into plastids, and subsequent modulation of plastid proteomes, has been lacking. We quantified protein import into isolated pea (Pisum sativum) leaf chloroplasts and root leucoplasts and identified two transit-peptide motifs that specifically enhance preprotein import into root leucoplasts. Using a plastid preprotein expressed in both leaves and roots of stable transgenic plants, we showed that losing one of the leucoplast motifs interfered with its function in root leucoplasts but had no effect on its function in leaf chloroplasts. We assembled a list of all Arabidopsis (Arabid opsis thaliana) plastid preproteins encoded by recently duplicated genes and show that, within a duplicated preprotein pair, the isoform bearing the leucoplast motif usually has greater root protein abundance. Our findings represent a clear demonstration of tissue-specific regulation of organelle protein import and suggest that it operates by selective evolutionary retention of transit-peptide motifs, which enhances import into specific plastid types.

CrABCA2 Facilitates Triacylglycerol Accumulation in Chlamydomonas reinhardtii under Nitrogen Starvation.

The microalga Chlamydomonas reinhardtii accumulates triacylglycerols (TAGs) in lipid droplets under stress conditions, such as nitrogen starvation. TAG biosynthesis occurs mainly at the endoplasmic reticulum (ER) and requires fatty acid (FA) substrates supplied from chloroplasts. How FAs are transferred from chloroplast to ER in microalgae was unknown. We previously reported that an Arabidopsis thaliana ATP-binding cassette (ABC) transporter, AtABCA9, facilitates FA transport at the ER during seed development. Here we identified a gene homologous to AtABCA9 in the C. reinhardtii genome, which we named CrABCA2. Under nitrogen deprivation conditions, CrABCA2 expression was upregulated, and the CrABCA2 protein level also increased. CrABCA2 knockdown lines accumulated less TAGs and CrABCA2 overexpression lines accumulated more TAGs than their untransformed parental lines. Transmission electron microscopy showed that CrABCA2 was localized in swollen ER. These results suggest that CrABCA2 transports substrates for TAG biosynthesis to the ER during nitrogen starvation. Our study provides a potential tool for increasing lipid production in microalgae.

The Arabidopsis AtGCD3 protein is a glucosylceramidase that preferentially hydrolyzes long-acyl-chain glucosylceramides

The Arabidopsis AtGCD3 protein is a glucosylceramidase that preferentially hydrolyzes long-acyl-chain glucosylceramides

Study on total artificial illumination cultivation conditions of Arabidopsis thaliana

Study on total artificial illumination cultivation conditions of Arabidopsis thaliana

The detection of differentially expressed gene and atlas construction of pre-mRNA alternative splicing during seed germination of Arabidopsis thaliana

Seed germination is the initial phase of life cycle for plants and plays a pivotal role in regeneration of plant population, continuation of plant species and crop yield. However, seed germination is an extremely complex biological process and its regulatory mechanisms remain unclear. It is well known that gene expression and pre-mRNA alternative splicing are vital to the central dogma. In Arabidopsis genome, ~60% multi-exon genes are alternatively spliced. Alternative splicing is involved in the response to environmental cues, including abiotic and biotic stresses, in the regulation of crucial developmental processes such as flowering, and in circadian timekeeping. The present paper studies the effect of gene expression and alternative splicing on seed germination in Arabidopsis . We constructed RNA-seq datasets from dry seeds, germinating seeds 1–3, Young seeds and Seeds in Arabidopsis and carried out quality control for the raw reads by using FastQC and Trimmomatic. StringTie estimated transcript and gene expression from a mapping to the Arabidopsis genome obtained from Hisat2. We next created the gene expression matrix for Arabidopsis , which includes 37336 genes along the rows and 12 samples along the columns, and employed DESeq2 to systematically identify differentially expressed genes between different stages during seed germination. To elucidate the biological functions of differentially expressed genes, we performed a functional enrichment analysis of these genes using clusterProfiler tool. The results showed that many genes involved in metabolic processes, such as glycolysis and DNA synthesis, were activated during the seed germination. It ensures the reactivation of metabolism and basic cellular activities of seeds. Some genes involved in environmental responses, such as oxidative stress, toxic substance, heat, and water, were inhibited. This is essential for seeds to be successfully activated from a dormant state. Furthermore, rMATS was utilized to detect the pre-mRNA alternative splicing events and differential alternative splicing events under different conditions. We constructed the atlas of pre-mRNA alternative splicing at different stages of seed germination and analyzed the distribution characteristics of alternative splicing patterns across every stage. Besides, we detected the differential alternative splicing events between different germination stages and analyzed the biological functions of differential alternative splicing events during seed germination using clusterProfiler. A total of 18 genes, in which differential retained intron events were identified between dry seeds and germinating seeds 3, were enriched on splicing process. By visualization of alternative splicing events in AT4G25500 , which was done by using the rmats2sashimiplot tool, the inclusion levels and functions of differential alternative splicing between different stages of seed germination were clearly illuminated. Overall, we investigated the dynamic changes of gene expressed levels and alternative splicing events during seed germination of Arabidopsis based on bioinformatics methods and dissected omics features and regulated mechanisms during seed germination from the perspective of gene expression and alternative splicing of pre-mRNA. This study is expected to be helpful for elucidating the regulated mechanisms of seed germination and to provide a guideline for relevant experimental works.

Arabidopsis Raf-Like Kinase Raf10 Is a Regulatory Component of Core ABA Signaling.

Abscisic acid (ABA) is a phytohormone essential for seed development and seedling growth under unfavorable environmental conditions. The signaling pathway leading to ABA response has been established, but relatively little is known about the functional regulation of the constituent signaling components. Here, we present several lines of evidence that Arabidopsis Raf-like kinase Raf10 modulates the core ABA signaling downstream of signal perception step. In particular, Raf10 phosphorylates subclass III SnRK2s (SnRK2.2, SnRK2.3, and SnRK2.6), which are key positive regulators, and our study focused on SnRK2.3 indicates that Raf10 enhances its kinase activity and may facilitate its release from negative regulators. Raf10 also phosphorylates transcription factors (ABI5, ABF2, and ABI3) critical for ABA-regulted gene expression. Furthermore, Raf10 was found to be essential for the in vivo functions of SnRK2s and ABI5. Collectively, our data demonstrate that Raf10 is a novel regulatory component of core ABA signaling.

Oomycetes Used in Arabidopsis Research.

Arabidopsis plants in their natural environment are susceptible to infection by oomycete pathogens, in particular to downy mildew and white rust diseases. These naturally occurring infectious agents have imposed evolutionary pressures on Arabidopsis populations and are therefore highly relevant for the study of host-pathogen co-evolution. In addition, the study of oomycete diseases, including infections caused by several Phytophthora species, has led to many scientific discoveries on Arabidopsis immunity and disease. Herein, we describe the major oomycete species used for experiments on Arabidopsis, and how these pathosystems have been used to provide significant insights into mechanistic and evolutionary aspects of plant-oomycete interactions. We also highlight understudied aspects of plant-oomycete interactions, as well as translational approaches, that can be productively addressed using the reference pathosystems described in this article.

Are drought resistance strategies associated with life history strategy? A commentary on: 'Arabidopsis species deploy distinct strategies to cope with drought stress'.

This article comments on: M. Bouzid, F. He, G. Schmitz, R. E. Häusler, A. P. M. Weber, T. Mettler-Altmann and J. de Meaux. 2019. Arabidopsis species deploy distinct strategies to cope with drought stress. Annals of Botany 124(1): 27–40.

Corrigendum: miR156/SPL10 Modulates Lateral Root Development, Branching and Leaf Morphology in Arabidopsis by Silencing AGAMOUS-LIKE 79

[This corrects the article DOI: 10.3389/fpls.2017.02226.].

Controlling floral transition

Plant Science For seed crops, such as maize and wheat, flowers need to develop at the right time to optimize harvest. Hormonal signals and metabolic status coordinate to set the transition from vegetative to reproductive growth. During acute nitrogen starvation, the plant flowers in a last-chance attempt to reproduce. Olas et al. studied what happens in the model plant Arabidopsis when nitrogen status is suboptimal, but not at starvation levels. MicroRNA regulators and nitrate-responsive gene promotor elements detect nitrogen status directly in the shoot apical meristem, from which flowers arise. With low nitrogen and short days, flowering depends more upon the availability of carbon in the form of sugar. With longer days, low nitrogen matters less. Thus, when faced with limited nitrogen supplies, the plant integrates photoperiod, hormonal, and metabolic signals to define the moment of flowering. New Phytol. 10.1111/nph.15812 (2019).

Preparation of SiW11 Incorporated SiO2 Nanofibers(SiW11/SiO2) and Its Application in the Analysis of Polyamines in Arabidopsis†

Preparation of SiW11 Incorporated SiO2 Nanofibers(SiW11/SiO2) and Its Application in the Analysis of Polyamines in Arabidopsis†

Evaluation of geo-climactic location-of-origin features for effects on phenotype prediction accuracy with ML models: A case study in Arabidopsis thaliana

Evaluation of geo-climactic location-of-origin features for effects on phenotype prediction accuracy with ML models: A case study in Arabidopsis thaliana

Analysis of potential substrate binding sites of PDAT in Arabidopsis thaliana and Saccharomyces cerevisiae

Analysis of potential substrate binding sites of PDAT in Arabidopsis thaliana and Saccharomyces cerevisiae

Involvement of Pyridoxine/Pyridoxamine 5'-Phosphate Oxidase (PDX3) in Ethylene-Induced Auxin Biosynthesis in the Arabidopsis Root.

As sessile organisms, plants have evolved to adjust their growth and development to environmental changes. It has been well documented that the crosstalk between different plant hormones plays important roles in the coordination of growth and development of the plant. Here, we describe a novel recessive mutant, mildly insensitive to ethylene (mine), which displayed insensitivity to the ethylene precursor, ACC (1-aminocyclopropane-1-carboxylic acid), in the root under the dark-grown conditions. By contrast, mine roots exhibited a normal growth response to exogenous IAA (indole-3-acetic acid). Thus, it appears that the growth responses of mine to ACC and IAA resemble those of weak ethylene insensitive (wei) mutants. To understand the molecular events underlying the crosstalk between ethylene and auxin in the root, we identified the MINE locus and found that the MINE gene encodes the pyridoxine 5′-phosphate (PNP)/pyridoxamine 5′-phosphate (PMP) oxidase, PDX3. Our results revealed that MINE/PDX3 likely plays a role in the conversion of the auxin precursor tryptophan to indole-3-pyruvic acid in the auxin biosynthesis pathway, in which TAA1 (TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1) and its related genes (TRYPTOPHAN AMINOTRANSFERASE RELATED 1 and 2; TAR1 and TAR2) are involved. Considering that TAA1 and TARs belong to a subgroup of PLP (pyridoxal-5′-phosphate)-dependent enzymes, we propose that PLP produced by MINE/PDX3 acts as a cofactor in TAA1/TAR-dependent auxin biosynthesis induced by ethylene, which in turn influences the crosstalk between ethylene and auxin in the Arabidopsis root.

Arabidopsis ACC Oxidase 1 Coordinated by Multiple Signals Mediates Ethylene Biosynthesis and Is Involved in Root Development.

Ethylene regulates numerous aspects of plant growth and development. Multiple external and internal factors coordinate ethylene production in plant tissues. Transcriptional and post-translational regulations of ACC synthases (ACSs), which are key enzymes mediating a rate-limiting step in ethylene biosynthesis have been well characterized. However, the regulation and physiological roles of ACC oxidases (ACOs) that catalyze the final step of ethylene biosynthesis are largely unknown in Arabidopsis. Here, we show that Arabidopsis ACO1 exhibits a tissue-specific expression pattern that is regulated by multiple signals, and plays roles in the lateral root development in Arabidopsis. Histochemical analysis of the ACO1 promoter indicated that ACO1 expression was largely modulated by light and plant hormones in a tissue-specific manner. We demonstrated that point mutations in two E-box motifs on the ACO1 promoter reduce the light-regulated expression patterns of ACO1. The aco1-1 mutant showed reduced ethylene production in root tips compared to wild-type. In addition, aco1-1 displayed altered lateral root formation. Our results suggest that Arabidopsis ACO1 integrates various signals into the ethylene biosynthesis that is required for ACO1’s intrinsic roles in root physiology.

Correction: The TIE1 transcriptional repressor controls shoot branching by directly repressing BRANCHED1 in Arabidopsis.

[This corrects the article DOI: 10.1371/journal.pgen.1007296.].