ORCID Profile
0000-0003-4306-9756
Current Organisation
University of Adelaide
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Research Topics
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Top 5 Research Topics
ANZSRC Field of Research (FoR)
Epigenetics (incl. Genome Methylation and Epigenomics) | Plant Developmental and Reproductive Biology | Genetics | Plant Biology | Plant Cell and Molecular Biology | Gene Expression (incl. Microarray and other genome-wide approaches) | Gene Expression | Crop and Pasture Improvement (Selection and Breeding) | Genetic Development (Incl. Sex Determination) | Animal Nutrition | Crop and Pasture Production | Crop and Pasture Biomass and Bioproducts | Molecular Evolution | Foetal Development and Medicine |
ANZSRC Socio-Economic Objective (SEO)
Expanding Knowledge in the Biological Sciences | Plant Production and Plant Primary Products not elsewhere classified | Primary products from plants | Barley | Primary products from animals | Environmental health | Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in the Medical and Health Sciences
Related Links
Publications
MicroRNAs in Honey Bee Caste Determination
Publisher: Springer Science and Business Media LLC
Date: 07-01-2016
DOI: 10.1038/SREP18794
Abstract: The cellular mechanisms employed by some organisms to produce contrasting morphological and reproductive phenotypes from the same genome remains one of the key unresolved issues in biology. Honeybees ( Apis mellifera ) use differential feeding and a haplodiploid sex determination system to generate three distinct organismal outcomes from the same genome. Here we investigate the honeybee female and male caste-specific microRNA and transcriptomic molecular signatures during a critical time of larval development. Both previously undetected and novel miRNAs have been discovered, expanding the inventory of these genomic regulators in invertebrates. We show significant differences in the microRNA and transcriptional profiles of diploid females relative to haploid drone males as well as between reproductively distinct females (queens and workers). Queens and drones show gene enrichment in physio-metabolic pathways, whereas workers show enrichment in processes associated with neuronal development, cell signalling and caste biased structural differences. Interestingly, predicted miRNA targets are primarily associated with non-physio-metabolic genes, especially neuronal targets, suggesting a mechanistic disjunction from DNA methylation that regulates physio-metabolic processes. Accordingly, miRNA targets are under-represented in methylated genes. Our data show how a common set of genetic elements are differentially harnessed by an organism, which may provide the remarkable level of developmental flexibility required.
Functional characterisation of HvCO1, the barley (Hordeum vulgare) flowering time ortholog of CONSTANS
Publisher: Wiley
Date: 10-01-2012
Randomly Amplified DNA Fingerprinting: A Culmination of DNA Marker Technologies Based on Arbitrarily-Primed PCR Amplification
Publisher: Hindawi Limited
Date: 2002
DOI: 10.1155/S1110724302206026
Abstract: Arbitrarily-primed DNA markers can be very useful for genetic fingerprinting and for facilitating positional cloning of genes. This class of technologies is particularly important for less studied species, for which genome sequence information is generally not known. The technologies include Randomly Amplified Polymorphic DNA (RAPD), DNA Amplification Fingerprinting (DAF), and Amplified Fragment Length Polymorphism (AFLP). We have modified the DAF protocol to produce a robust PCR-based DNA marker technology called Randomly Amplified DNA Fingerprinting (RAF). While the protocol most closely resembles DAF, it is much more robust and sensitive because licons are labelled with either radioactive 33 P or fluorescence in a 30-cycle PCR, and then separated and detected on large polyacrylamide sequencing gels. Highly reproducible RAF markers were readily lified from either purified DNA or alkali-treated intact leaf tissue. RAF markers typically display dominant inheritance. However, a small but significant portion of the RAF markers exhibit codominant inheritance and represent microsatellite loci. RAF compares favorably with AFLP for efficiency and reliability on many plant genomes, including the very large and complex genomes of sugarcane and wheat. While the two technologies detect about the same number of markers per large polyacrylamide gel, advantages of RAF over AFLP include: (i) no requirement for enzymatic template preparation, (ii) one instead of two PCRs, and (iii) overall cost. RAF and AFLP were shown to differ in the selective basis of lification of markers from genomes and could therefore be used in complementary fashion for some genetic studies.
A High Amylose Wheat Diet Improves Gastrointestinal Health Parameters and Gut Microbiota in Male and Female Mice
Publisher: MDPI AG
Date: 21-01-2021
Abstract: High amylose wheat (HAW) contains more resistant starch than standard amylose wheat (SAW) and may have beneficial effects on gastrointestinal health. However, it is currently unclear whether these effects differ according to the level of HAW included in the diet or between males and females. Male and female C57BL/6 mice (n = 8/group/sex) were fed SAW65 (65% SAW control), HAW35 (35% HAW), HAW50 (50% HAW) or HAW65 (65% HAW) diet for eight weeks. Female but not male, mice consuming any amount of HAW exhibited accelerated gastric emptying compared to SAW65 group. In both sexes, relative colon weights were higher in the HAW65 group compared to SAW65 group and in females, relative weights of the small intestine and cecum were also higher in the HAW65 group. In females only, colonic expression of Pyy and Ocln mRNAs were higher in the HAW65 group compared to HAW35 and HAW50 groups. In both sexes, mice consuming higher amounts of HAW (HAW50 or HAW65) had increased fecal bacterial load and relative abundance of Bacteroidetes phylum and reduced relative abundance of Firmicutes compared to SAW65 group. These data are consistent with a beneficial impact of HAW on gastrointestinal health and indicate dose-dependent and sex-specific effects of HAW consumption.
Complete Genome Sequence Data for the Grapevine Crown Gall–Inhibiting Bacteria Allorhizobium vitis F2/5
Publisher: Scientific Societies
Date: 02-2022
Nodulation factor receptor kinase 1α controls nodule organ number in soybean (Glycine max L. Merr)
Publisher: Wiley
Date: 10-11-2010
FT/FD-GRF5 repression loop directs growth to increase soybean yield
Publisher: Cold Spring Harbor Laboratory
Date: 07-10-2018
DOI: 10.1101/437053
Abstract: Major advances in crop yield are eternally needed to cope with population growth. To balance vegetative and reproductive growth plays an important role in agricultural yield. To extend vegetative phase can increase crop yield, however, this strategy risks loss of yield in the field as crops may not mature in time before winter come. Here, we identified a repression feedback loop between GmFTL / GmFDL and GmGRF5-1 ( Glycine-max-Flowering-Locus-T/Glycine-max-FDL and Glycine-max-GROWTH-REGULATING-FACTOR5-1 ), which functions as a pivotal regulator in balancing vegetative and reproductive phases in soybean. GmFTL / GmFDL and GmGRF5-1 directly repress gene expression each other. Additionally, GmGRF5-1 enhances vegetative growth by directly enhancing expression of photosynthesis- and auxin synthesis-related genes. To modulate the loop, such as fine-tuning GmFTL expression to trade-off vegetative and reproductive growth, increases substantially soybean yield in the field. Our findings not only uncover the mechanism balancing vegetative and reproductive growth, but open a new window to improve crop yield.
The root hair defective phenotype of Arabidopsis thaliana Pol IV subunit mutant nrpd1a-3 is associated with a deletion in RHD6
Publisher: microPublication Biology
Date: 2019
Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 13-07-2017
DOI: 10.1105/TPC.16.00828
Keeping it cool
Publisher: eLife Sciences Publications, Ltd
Date: 23-03-2023
DOI: 10.7554/ELIFE.86885
Abstract: A well-established model for how plants start the process of flowering in periods of cold weather may need revisiting.
Binuclear Metal Centers in Plant Purple Acid Phosphatases: Fe–Mn in Sweet Potato and Fe–Zn in Soybean
Publisher: Elsevier BV
Date: 10-1999
Genome‐wide analysis of epigenetic and transcriptional changes associated with heterosis in pigeonpea
Publisher: Wiley
Date: 03-02-2020
DOI: 10.1111/PBI.13333
Deciphering the epitranscriptome: A green perspective
Publisher: Wiley
Date: 20-06-2016
DOI: 10.1111/JIPB.12483
An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II
Publisher: Springer Science and Business Media LLC
Date: 14-12-2008
DOI: 10.1038/NSMB.1539
Abstract: Genetic evidence indicates that plant-specific homologs of DNA-dependent RNA polymerase (Pol) II large subunits form Pol IV and Pol V complexes involved in small interfering RNA production and RNA-directed DNA methylation. Here we describe evidence that Pol V contains subunits shared with Pol II, but that RNA polymerase II subunit (RPB)-4 is missing from Pol V and that RPB5 is present as a Pol V-specific isomer, RPB5b. Pol V also has other proteins that are not present in Pol II, consistent with a role of this complex as an effector of silencing.
Chromosome-level assembly of the common vetch reference genome (Vicia sativa)
Publisher: Cold Spring Harbor Laboratory
Date: 13-10-2021
DOI: 10.1101/2021.10.11.464017
Abstract: Vicia sativa L. (Common Vetch, n = 6) is an annual, herbaceous, climbing legume that is distributed in tropical, sub-tropical and temperate climates. Originating in the Fertile Crescent of the Middle East, V. sativa is now widespread and grows in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we here present a chromosome-level reference genome sequence for V. sativa . We applied a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis to construct a chromosome-level genome of V. sativa . The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.9 gigabases (Gb) with a median contig length of 684 kb. Benchmarking Universal Single-Copy Orthologs (BUSCO) of the assembly demonstrated a very high completeness of 98 % of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 58,415 protein-coding genes. The high-quality chromosome-level genome assembly of V. sativa will provide novel insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic ersity and for understanding adaption to erse arid environments.
Near-Complete Genome Assembly of the Grapevine Crown Gall Pathogen Allorhizobium vitis Strain K377
Publisher: American Society for Microbiology
Date: 30-09-2021
DOI: 10.1128/MRA.01359-20
Abstract: Here, we report the annotated, near-complete genome sequence of Allorhizobium vitis K377, a phytopathogenic Rhizobiales strain isolated from a grapevine in South Australia. The assembled genome sequence is 6.40 Mb long, with 5,855 predicted protein-coding sequences, 56 tRNAs, and 12 rRNAs, and contains ttuC (tartrate metabolism chromosomal) and nopaline synthesis, uptake, and catabolic genes (tumor-inducing plasmid-encoded).
Decision letter: Vernalization-triggered expression of the antisense transcript COOLAIR is mediated by CBF genes
Publisher: eLife Sciences Publications, Ltd
Date: 03-01-2023
Sexually dimorphic response of increasing dietary intake of high amylose wheat on metabolic and reproductive outcomes in male and female mice
Publisher: MDPI AG
Date: 25-12-2020
DOI: 10.3390/NU12010061
Abstract: High amylose wheat (HAW) has a higher resistant starch content and lower glycaemic index than standard amylose wheat (SAW), which may be associated with health benefits. This study aimed to determine the effects of replacing SAW with HAW on metabolic and reproductive parameters in male and female mice. Male and female C57BL/6 mice were randomly ided into groups (n = 8/group/sex) and fed either a SAW65 (65% SAW w/w control), HAW35 (35% HAW w/w), HAW50 (50% HAW w/w) or HAW65 (65% HAW w/w) diet for eight weeks. In male but not female, the HAW65 group had a lower abdominal circumference, relative total fat mass, relative gonadal fat mass and plasma leptin concentration compared to the HAW35 group. There were no differences in fasting blood glucose concentrations or plasma concentrations of cholesterol, triglycerides or non-esterified fatty acids between groups in either males or females. The HAW-fed males had a higher testicular weight and HAW-fed females spent less time in diestrus and a longer time in metestrus compared to the SAW-fed mice. Higher dietary intake of HAW appears to reduce abdominal fat deposition compared to the lower level of HAW in a sexually dimorphic manner. The impacts on reproductive parameters in the HAW-fed mice require further investigation.
Genome-wide identification of MicroRNAs in leaves and the developing head of four durum genotypes during water deficit stress
Publisher: Public Library of Science (PLoS)
Date: 12-11-2015
Two Nucleoporin98 homologous genes jointly participate in the regulation of starch degradation to repress senescence in Arabidopsis
Publisher: Springer Science and Business Media LLC
Date: 26-06-2020
DOI: 10.1186/S12870-020-02494-1
Abstract: Starch is synthesized during daylight for temporary storage in leaves and then degraded during the subsequent night to support plant growth and development. Impairment of starch degradation leads to stunted growth, even senescence and death. The nuclear pore complex is involved in many cellular processes, but its relationship with starch degradation has been unclear until now. We previously identified that two Nucleoporin98 genes ( Nup98a and Nup98b ) redundantly regulate flowering via the CONSTANS ( CO )-independent pathway in Arabidopsis thaliana . The double mutant also shows severe senescence phenotypes. We find that Nucleoporin 98 participates in the regulation of sugar metabolism in leaves and is also involved in senescence regulation in Arabidopsis . We show that Nup98a and Nup98b function redundantly at different stages of starch degradation. The nup98a-1 nup98b-1 double mutant accumulates more starch, showing a severe early senescence phenotype compared to wild type plants. The expression of marker genes related to starch degradation is impaired in the nup98a-1 nup98b-1 double mutant, and marker genes of carbon starvation and senescence express their products earlier and in higher abundance than in wild type plants, suggesting that abnormalities in energy metabolism are the main cause of senescence in the double mutant. Addition of sucrose to the growth medium rescues early senescence phenotypes of the nup98a-1 nup98b-1 mutant. Our results provide evidence for a novel role of the nuclear pore complex in energy metabolism related to growth and development, in which Nup98 functions in starch degradation to control growth regulation in Arabidopsis .
Significant cell differences in pod ventral suture in shatter‐resistant and shatter‐susceptible common vetch accessions
Publisher: Wiley
Date: 05-2021
DOI: 10.1002/CSC2.20427
Abstract: Common vetch ( Vicia sativa subsp. sativa L.) is a self‐pollinating annual forage legume with high nutritional value. However, pod shattering can cause severe yield loss at maturity and therefore is a significant trait for crop improvement. Our previous studies indicated that the ventral suture is critical to pod shattering in common vetch. To better understand the anatomy of the ventral suture, we evaluated eight shatter‐susceptible and 18 shatter‐resistant accessions for pod dehiscing characteristics over three consecutive years by comprehensively comparing the vascular bundle anatomical structure of the ventral suture. Four traits, specifically vascular bundle cell volume, bundle cap slope, single vascular bundle width, and external valve margin cells, were significantly different between the shatter‐susceptible and ‐resistant accessions. We found that the shatter‐resistant common vetches had a larger vascular bundle cell volume and bundle cap slope, an increased single vascular bundle width, and external valve margin cells that were significantly thicker than those of shatter‐susceptible accessions. All of the shatter‐susceptible pods had clear abscission layers. On the basis of these data, we propose a seesaw model of pod shattering in common vetch. Our morphological traits provide a novel insight into the pod shattering mechanism of common vetch, which will be valuable for breeding shatter‐resistant legumes.
Two SUMO Proteases SUMO PROTEASE RELATED TO FERTILITY1 and 2 Are Required for Fertility in Arabidopsis
Publisher: Oxford University Press (OUP)
Date: 24-10-2017
DOI: 10.1104/PP.17.00021
Inheritance and mapping of 11 avirulence genes in Phytophthora sojae
Publisher: Elsevier BV
Date: 10-2002
DOI: 10.1016/S1087-1845(02)00027-0
Abstract: Two new crosses involving four races (races 7, 16, 17, and 25) of the soybean root and stem rot pathogen Phytophthora sojae were established (7/16 cross 17/25 cross). An F2 population derived from each cross was used to determine the genetic basis of avirulence towards 11 different resistance genes in soybean. Avirulence was found to be dominant and determined by a single locus for Avr1b, 1d, 1k, 3b, 4, and 6, as expected for a simple gene-for-gene model. We also observed several cases of segregation, inconsistent with a single dominant gene being solely responsible for avirulence, which suggests that the genetic background of the different crosses can affect avirulence. Avr4 and 6 cosegregated in both the 7/16 and 17/25 crosses and, in the 7/16 cross, Avr1b and 1k were closely linked. Information from segregating RAPD, RFLP, and AFLP markers screened on F2 progeny from the two new crosses and two crosses described previously (a total of 212 F2 in iduals, 53 from each cross) were used to construct an integrated genetic linkage map of P. sojae. This revised genetic linkage map consists of 386 markers comprising 35 RFLP, 236 RAPD, and 105 AFLP markers, as well as 10 avirulence genes. The map is composed of 21 major linkage groups and seven minor linkage groups covering a total map distance of 1640.4cM.
Experimental reconstruction of double‐stranded break repair‐mediated plastid DNA insertion into the tobacco nucleus
Publisher: Wiley
Date: 16-12-2017
DOI: 10.1111/TPJ.13769
Abstract: The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-stranded DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-stranded DNA break repair. Microhomology-mediated linking of disparate segments of chloroplast DNA occurs frequently during healing of induced nuclear double-stranded breaks (DSB) but the resulting nuclear integrants are often immediately unstable. Non-Mendelian inheritance of a selectable marker (neo), used to identify plastid DNA transfer, was observed in the progeny of about 50% of lines emerging from the screen. The instability of these de novo nuclear insertions of plastid DNA (nupts) was shown to be associated with deletion not only of the nupt itself but also of flanking nuclear DNA within one generation of transfer. This deletion of pre-existing nuclear DNA suggests that the genetic impact of organellar DNA transfer to the nucleus is potentially far greater than previously thought.
Complete Genome Sequence of Allorhizobium vitis Strain K306, the Causal Agent of Grapevine Crown Gall
Publisher: American Society for Microbiology
Date: 16-07-2020
DOI: 10.1128/MRA.00565-20
Abstract: Here, we present the annotated complete genome sequence of Allorhizobium vitis K306, a phytopathogenic strain causing crown gall of grapevine. The A. vitis K306 genome is 5.79 Mb long with 5,199 predicted protein-coding genes and contains 2 circular chromosomes of 3.8 Mb and 1.1 Mb and 2 plasmids, namely, pTiK306 and pTrK306, that are 262 kb and 581 kb, respectively.
An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells inArabidopsis
Publisher: Oxford University Press (OUP)
Date: 05-2007
Abstract: The silencing phenotype in Arabidopsis thaliana lines with an inverted repeat transgene under the control of a phloem-specific promoter was manifested in regions around veins due to a mobile signal of silencing. Genetic analysis implicates RNA-DEPENDENT RNA POLYMERASE2 (RDR2) and an RNA polymerase IVa subunit gene (NRPD1a) in the signaling mechanism. We also identified an SNF2 domain–containing protein (CLASSY1) that acts together with RDR2 and NRPD1a in the spread of transgene silencing and in the production of endogenous 24-nucleotide short interfering RNAs (siRNAs). Cytochemical analysis indicates that CLASSY1 may act in the nucleus with NRPD1a and RDR2 in the upstream part of RNA silencing pathways that generate a double-stranded RNA substrate for Dicer-like (DCL) nucleases. DCL3 and ARGONAUTE4 act in a downstream part of the pathway, leading to endogenous 24-nucleotide siRNA production, but are not required for intercellular signaling. From genetic analysis, we conclude that another downstream part of the pathway associated with intercellular signaling requires DCL4 and at least one other protein required for 21-nucleotide trans-acting siRNAs. We interpret the effect of polymerase IVa and trans-acting siRNA pathway mutations in terms of a modular property of RNA silencing pathways.
Nitrate regulates floral induction in Arabidopsis, acting independently of light, gibberellin and autonomous pathways
Publisher: Springer Science and Business Media LLC
Date: 27-11-2010
Role of the Arabidopsis PIN6 Auxin Transporter in Auxin Homeostasis and Auxin-Mediated Development
Publisher: Public Library of Science (PLoS)
Date: 29-07-2013
Purification and Functional Analysis of Plant Long Noncoding RNAs (lncRNA)
Publisher: Springer New York
Date: 2019
DOI: 10.1007/978-1-4939-9045-0_7
Abstract: More than 70% of eukaryotic genomes are transcribed into RNA transcripts, the majority of these transcripts are noncoding protein, and their biological functions are largely unknown. Over the last decade, the application of high-throughput sequencing technologies has led to the description of almost all cellular coding and noncoding RNA transcripts except perhaps for those transcripts that are lowly abundant or those present only in specific cells that are underrepresented in s led tissue(s). An often underrepresented class of noncoding are long noncoding RNAs (lncRNAs), and these often play key regulatory functions for many biological processes such as cell identity and cell ision. However, the purification and functional characterization in vitro are still a challenge in both animal and plant experimental systems. Here, we describe in detail methodology for purification of specific cell types, bioinformatic annotation of lncRNAs, and investigation of biological function using the reference plant Arabidopsis thaliana.
Chromosome-level assembly of the common vetch (Vicia sativa) reference genome
Publisher: GigaScience Press
Date: 31-01-2022
DOI: 10.46471/GIGABYTE.38
Abstract: Vicia sativa L. (common vetch, n = 6) is an annual, herbaceous, climbing legume, originating in the Fertile Crescent of the Middle East and now widespread in the Mediterranean basin, West, Central and Eastern Asia, North and South America. V. sativa is of economic importance as a forage legume in countries such as Australia, China, and the USA, and contributes valuable nitrogen to agricultural rotation cropping systems. To accelerate precision genome breeding and genomics-based selection of this legume, we present a chromosome-level reference genome sequence for V. sativa, constructed using a combination of long-read Oxford Nanopore sequencing, short-read Illumina sequencing, and high-throughput chromosome conformation data (CHiCAGO and Hi-C) analysis. The chromosome-level assembly of six pseudo-chromosomes has a total genome length of 1.65 Gbp, with a median contig length of 684 Kbp. BUSCO analysis of the assembly demonstrated very high completeness of 98% of the dicotyledonous orthologs. RNA-seq analysis and gene modelling enabled the annotation of 53,218 protein-coding genes. This V. sativa assembly will provide insights into vetch genome evolution and be a valuable resource for genomic breeding, genetic ersity and for understanding adaption to erse arid environments.
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth
Publisher: Public Library of Science (PLoS)
Date: 22-11-2019
Origin and Functional Prediction of Pollen Allergens in Plants
Publisher: Oxford University Press (OUP)
Date: 19-07-2016
DOI: 10.1104/PP.16.00625
Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae
Publisher: Springer Science and Business Media LLC
Date: 14-08-2015
Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs
Publisher: Oxford University Press (OUP)
Date: 06-01-2017
DOI: 10.1105/TPC.16.00751
Induction of flowering by seasonal changes in photoperiod
Publisher: Wiley
Date: 04-03-2004
Mobile MicroRNAs Hit the Target
Publisher: Wiley
Date: 17-08-2011
DOI: 10.1111/J.1600-0854.2011.01253.X
Abstract: MicroRNAs (miRNAs) are negative regulators of gene expression in eukaryotic organisms, whereas small interfering RNAs (siRNAs) guide host-cell defence against viruses, transposons and transgenes. A key issue in plant biology is whether miRNAs act only in cells in which they are formed, or if, like siRNAs, they also function after passive diffusion or active transportation into other cells. Recent reports show that miRNAs are indeed able to move between plant cells to direct developmental programming of gene expression. In both leaf and root development, miRNAs establish intercellular gradients of gene expression that are essential for cell and tissue differentiation. Gradients in gene expression also play crucial roles in animal development, and there is strong evidence for intercellular movement of miRNAs in animals. Thus, intercellular movement of miRNAs may be crucial to animal developmental biology as well as plants.
Inactivation of Duplicated Nod Factor Receptor 5 (NFR5) Genes in Recessive Loss-of-Function Non-Nodulation Mutants of Allotetraploid Soybean (Glycine max L. Merr.)
Publisher: Oxford University Press (OUP)
Date: 09-12-2009
DOI: 10.1093/PCP/PCP178
Abstract: Chemically induced non-nodulating nod139 and nn5 mutants of soybean (Glycine max) show no visible symptoms in response to rhizobial inoculation. Both exhibit recessive Mendelian inheritance suggesting loss of function. By allele determination and genetic complementation in nod139 and nn5, two highly related lipo-oligochitin LysM-type receptor kinase genes in Glycine max were cloned they are presumed to be the critical nodulation-inducing (Nod) factor receptor similar to those of Lotus japonicus, pea and Medicago truncatula. These duplicated receptor genes were called GmNFR5alpha and GmNFR5beta. Nonsense mutations in GmNFR5alpha and GmNFR5beta were genetically complemented by both wild-type GmNFR5alpha and GmNFR5beta in transgenic roots, indicating that both genes are functional. Both genes lack introns. In cultivar Williams82 GmNFR5alpha is located in chromosome 11 and in tandem with GmLYK7 (a related LysM receptor kinase gene), while GmNFR5beta is in tandem with GmLYK4 in homologous chromosome 1, suggesting ancient synteny and regional segmental duplication. Both genes are wild type in G. soja CPI100070 and Harosoy63 however, a non-functional NFR5beta allele (NFR5beta*) was discovered in parental lines Bragg and Williams, which harbored an identical 1,407 bp retroelement-type insertion. This retroelement (GmRE-1) and related sequences are located in several soybean genome positions. Paradoxically, putatively unrelated soybean cultivars shared the same insertion, suggesting a smaller than anticipated genetic base in this crop. GmNFR5alpha but not GmNFR5beta* was expressed in inoculated and uninoculated tap and lateral root portions at about 10-25% of GmATS1 (ATP synthase subunit 1), but not in trifoliate leaves and shoot tips.
JMJ14, a JmjC domain protein, is required for RNA silencing and cell-to-cell movement of an RNA silencing signal in Arabidopsis
Publisher: Cold Spring Harbor Laboratory
Date: 15-05-2010
DOI: 10.1101/GAD.579910
Abstract: JMJ14 is a histone H3 Lys4 (H3K4) trimethyl demethylase that affects mobile RNA silencing in an Arabidopsis transgene system. It also influences CHH DNA methylation, abundance of endogenous transposon transcripts, and flowering time. JMJ14 acts at a point in RNA silencing pathways that is downstream from RNA-dependent RNA polymerase 2 (RDR2) and Argonaute 4 (AGO4). Our results illustrate a link between RNA silencing and demethylation of histone H3 trimethylysine. We propose that JMJ14 acts downstream from the Argonaute effector complex to demethylate histone H3K4 at the target of RNA silencing.
MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat
Publisher: American Association for the Advancement of Science (AAAS)
Date: 13-05-2022
Abstract: Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural ersity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 ( HB-2 ), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
Transcriptome and Coexpression Network Analyses Provide In-Sights into the Molecular Mechanisms of Hydrogen Cyanide Synthesis during Seed Development in Common Vetch (Vicia sativa L.)
Publisher: MDPI AG
Date: 18-02-2022
DOI: 10.3390/IJMS23042275
Abstract: The common vetch (Vicia sativa L.) seed is an ideal plant-based protein food for humans, but its edible value is mainly limited by the presence of cyanogenic glycosides that hydrolyze to produce toxic hydrogen cyanide (HCN), and the genes that regulate HCN synthesis in common vetch are unknown. In this study, seeds from common vetch at 5, 10, 15, 20, 25, 30, and 35 days after anthesis were s led, and the seven stages were further ided into five developmental stages, S1, S2, S3, S4, and S5, based on morphological and transcriptome analyses. A total of 16,403 differentially expressed genes were identified in the five developmental stages. The HCN contents of seeds in these five stages were determined by alkaline titration, and weighted gene coexpression network analysis was used to explain the molecular regulatory mechanism of HCN synthesis in common vetch seeds. Eighteen key regulatory genes for HCN synthesis were identified, including the VsGT2, VsGT17 and CYP71A genes, as well as the VsGT1 gene family. VsGT1, VsGT2, VsGT17 and CYP71A jointly promoted HCN synthesis, from 5 to 25 days after anthesis, with VsGT1-1, VsGT1-4, VsGT1-11 and VsGT1-14 playing major roles. The HCN synthesis was mainly regulated by VsGT1, from 25 to 35 days after anthesis. As the expression level of VsGT1 decreased, the HCN content no longer increased. In-depth elucidation of seed HCN synthesis lays the foundations for breeding common vetch with low HCN content.
Small RNAs hit the big time
Publisher: Wiley
Date: 17-04-2007
The clock primes defense at dawn.
Publisher: Wiley
Date: 19-04-2011
DOI: 10.1038/ICB.2011.30
Reviving grain quality in wheat through non‐destructive phenotyping techniques like hyperspectral imaging
Publisher: Wiley
Date: 09-2023
DOI: 10.1002/FES3.498
The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling inArabidopsis
Publisher: Cold Spring Harbor Laboratory
Date: 04-2006
DOI: 10.1101/GAD.373506
Abstract: Floral development at the Arabidopsis shoot apical meristem occurs in response to environmental cues that are perceived in different tissues. Photoperiod is detected in the vascular tissue of the leaf (phloem) and promotes production of a systemic signal that induces flowering at the meristem. Vernalization, the response to winter temperatures, overcomes a block on photoperiodic floral induction. In Arabidopsis , this block is caused by inhibitors of flowering that comprise several related MADS-box transcription factors, the most prominent of which is FLC. We show that FLC delays flowering by repressing production in the leaf of at least two systemic signals, one of which is controlled by the RAF kinase inhibitor-like protein FT. Reducing expression of these signals indirectly represses expression of genes involved in floral induction at the meristem. In addition, FLC expression in the meristem impairs response to the FT signal by directly repressing expression of the SOC1 MADS-box transcription factor and preventing up-regulation of the bZIP transcription factor FD. Repression of genes acting at multiple levels in this hierarchy is required for the extreme delay in flowering caused by FLC. An FLC:HA fusion protein binds directly in vivo to the promoter regions of FD and SOC1 and to the first intron of FT . Thus vernalization relieves transcriptional repression of key regulatory genes in both the leaf and meristem, allowing production of systemic signals in the leaves and conferring competence on the meristem to respond to these signals.
A rapid and versatile combined DNA/RNA extraction protocol and its application to the analysis of a novel DNA marker set polymorphic between Arabidopsis thaliana ecotypes Col-0 and Landsberg erecta
Publisher: Springer Science and Business Media LLC
Date: 23-08-2005
Abstract: Many established PCR-based approaches in plant molecular biology rely on lengthy and expensive methods for isolation of nucleic acids. Although several rapid DNA isolation protocols are available, they have not been tested for simultaneous RNA isolation for RT-PCR applications. In addition, traditional map-based cloning technologies often use ill-proportioned marker regions even when working with the model plant Arabidopsis thaliana , where the availability of the full genome sequence can now be exploited for the creation of a high-density marker systems. We designed a high-density polymorphic marker set between two frequently used ecotypes. This new polymorphic marker set allows size separation of PCR products on agarose gels and provides an initial resolution of 10 cM in linkage mapping experiments, facilitated by a rapid plant nucleic acid extraction protocol using minimal amounts of A. thaliana tissue. Using this extraction protocol, we have also characterized segregating T-DNA insertion mutations. In addition, we have shown that our rapid nucleic acid extraction protocol can also be used for monitoring transcript levels by RT-PCR lification. Finally we have demonstrated that our nucleic acid isolation method is also suitable for other plant species, such as tobacco and barley. To facilitate high-throughput linkage mapping and other genomic applications, our nucleic acid isolation protocol yields sufficient quality of DNA and RNA templates for PCR and RT-PCR reactions, respectively. This new technique requires considerably less time compared to other purification methods, and in combination with a new polymorphic PCR marker set dramatically reduces the workload required for linkage mapping of mutations in A. thaliana utilizing crosses between Col-0 and Landsberg erecta (L er ) ecotypes.
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