MircroRNA Profiles of Early Rice Inflorescence Revealed a Specific miRNA5506 Regulating Development of Floral Organs and Female Megagametophyte in Rice

The developmental process of inflorescence and gametophytes is vital for sexual reproduction in rice. Multiple genes and conserved miRNAs have been characterized to regulate the process. The changes of miRNAs expression during the early development of rice inflorescence remain unknown. In this study, the analysis of miRNAs profiles in the early stage of rice inflorescence development identified 671 miRNAs, including 67 known and 44 novel differentially expressed miRNAs (DEMs). Six distinct clusters of miRNAs expression patterns were detected, and Cluster 5 comprised 110 DEMs, including unconserved, rice-specific osa-miR5506. Overexpression of osa-miR5506 caused pleiotropic abnormalities, including over- or under-developed palea, various numbers of floral organs and spikelet indeterminacy. In addition, the defects of ovaries development were frequently characterized by multiple megasporocytes, ovule-free ovary, megasporocyte degenerated and embryo sac degenerated in the transgenic lines. osa-miR5506 targeted REM transcription factor LOC_Os03g11370. Summarily, these results demonstrated that rice-specific osa-miR5506 plays an essential role in the regulation of floral organ number, spikelet determinacy and female gametophyte development in rice.

Download Full-text

Transcript Profiling of MIKCc MADS-Box Genes Reveals Conserved and Novel Roles in Barley Inflorescence Development

Frontiers in Plant Science ◽

10.3389/fpls.2021.705286 ◽

2021 ◽

Vol 12 ◽

Author(s):

Hendrik N. J. Kuijer ◽

Neil J. Shirley ◽

Shi F. Khor ◽

Jin Shi ◽

Julian Schwerdt ◽

...

Keyword(s):

Expression Patterns ◽

Floral Organ ◽

Transcript Analysis ◽

Mads Box ◽

Mads Box Genes ◽

Inflorescence Development ◽

Abcde Model ◽

Wide Range ◽

Dicotyledonous Plants ◽

Range Of Functions

MADS-box genes have a wide range of functions in plant reproductive development and grain production. The ABCDE model of floral organ development shows that MADS-box genes are central players in these events in dicotyledonous plants but the applicability of this model remains largely unknown in many grass crops. Here, we show that transcript analysis of all MIKCc MADS-box genes through barley (Hordeum vulgare L.) inflorescence development reveals co-expression groups that can be linked to developmental events. Thirty-four MIKCc MADS-box genes were identified in the barley genome and single-nucleotide polymorphism (SNP) scanning of 22,626 barley varieties revealed that the natural variation in the coding regions of these genes is low and the sequences have been extremely conserved during barley domestication. More detailed transcript analysis showed that MADS-box genes are generally expressed at key inflorescence developmental phases and across various floral organs in barley, as predicted by the ABCDE model. However, expression patterns of some MADS genes, for example HvMADS58 (AGAMOUS subfamily) and HvMADS34 (SEPALLATA subfamily), clearly deviate from predicted patterns. This places them outside the scope of the classical ABCDE model of floral development and demonstrates that the central tenet of antagonism between A- and C-class gene expression in the ABC model of other plants does not occur in barley. Co-expression across three correlation sets showed that specifically grouped members of the barley MIKCc MADS-box genes are likely to be involved in developmental events driving inflorescence meristem initiation, floral meristem identity and floral organ determination. Based on these observations, we propose a potential floral ABCDE working model in barley, where the classic model is generally upheld, but that also provides new insights into the role of MIKCc MADS-box genes in the developing barley inflorescence.

Download Full-text

Arabidopsis QWRF1 and QWRF2 Redundantly Modulate Cortical Microtubule Arrangement in Floral Organ Growth and Fertility

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.634218 ◽

2021 ◽

Vol 9 ◽

Author(s):

Huifang Ma ◽

Liyuan Xu ◽

Ying Fu ◽

Lei Zhu

Keyword(s):

Cell Expansion ◽

Expression Patterns ◽

Cortical Microtubule ◽

Floral Organ ◽

Organ Development ◽

Cortical Microtubules ◽

Organ Growth ◽

Floral Organ Development ◽

Floral Organs ◽

Organ Identity

Floral organ development is fundamental to sexual reproduction in angiosperms. Many key floral regulators (most of which are transcription factors) have been identified and shown to modulate floral meristem determinacy and floral organ identity, but not much is known about the regulation of floral organ growth, which is a critical process by which organs to achieve appropriate morphologies and fulfill their functions. Spatial and temporal control of anisotropic cell expansion following initial cell proliferation is important for organ growth. Cortical microtubules are well known to have important roles in plant cell polar growth/expansion and have been reported to guide the growth and shape of sepals and petals. In this study, we identified two homolog proteins, QWRF1 and QWRF2, which are essential for floral organ growth and plant fertility. We found severely deformed morphologies and symmetries of various floral organs as well as a significant reduction in the seed setting rate in the qwrf1qwrf2 double mutant, although few flower development defects were seen in qwrf1 or qwrf2 single mutants. QWRF1 and QWRF2 display similar expression patterns and are both localized to microtubules in vitro and in vivo. Furthermore, we found altered cortical microtubule organization and arrangements in qwrf1qwrf2 cells, consistent with abnormal cell expansion in different floral organs, which eventually led to poor fertility. Our results suggest that QWRF1 and QWRF2 are likely microtubule-associated proteins with functional redundancy in fertility and floral organ development, which probably exert their effects via regulation of cortical microtubules and anisotropic cell expansion.

Download Full-text

A Genetic Screen for Modifiers of UFO Meristem Activity Identifies Three Novel FUSED FLORAL ORGANS Genes Required for Early Flower Development in Arabidopsis

Genetics ◽

10.1093/genetics/149.2.579 ◽

1998 ◽

Vol 149 (2) ◽

pp. 579-595

Author(s):

Joshua Z Levin ◽

Jennifer C Fletcher ◽

Xuemei Chen ◽

Elliot M Meyerowitz

Keyword(s):

Flower Development ◽

Control Cell ◽

Floral Organ ◽

Genetic Screen ◽

Inflorescence Development ◽

Cauline Leaf ◽

Floral Organs ◽

Complementation Groups ◽

Control Organ ◽

Early Flower

Abstract In a screen to identify novel genes required for early Arabidopsis flower development, we isolated four independent mutations that enhance the Ufo phenotype toward the production of filamentous structures in place of flowers. The mutants fall into three complementation groups, which we have termed FUSED FLORAL ORGANS (FFO) loci. ffo mutants have specific defects in floral organ separation and/or positioning; thus, the FFO genes identify components of a boundary formation mechanism(s)acting between developing floral organ primordia. FFO1 and FFO3 have specific functions in cauline leaf/stem separation and in first- and third-whorl floral organ separation, with FFO3 likely acting to establish and FFO1 to maintain floral organ boundaries. FFO2 acts at early floral stages to regulate floral organ number and positioning and to control organ separation within and between whorls. Plants doubly mutant for two ffo alleles display additive phenotypes, indicating that the FFO genes may act in separate pathways. Plants doubly mutant for an ffo gene and for ufo, lfy, or clv3 reveal that the FFO genes play roles related to those of UFO and LFY in floral meristem initiation and that FFO2 and FFO3 may act to control cell proliferation late in inflorescence development.

Download Full-text

Identification of the Role of SOX2 During Early Embryogenesis in Pigs

10.21203/rs.3.rs-104075/v1 ◽

2020 ◽

Author(s):

Mingyun Lee ◽

Jong-Nam Oh ◽

Seung-Hun Kim ◽

Kwang-Hwan Choi ◽

Dong-Kyung Lee ◽

...

Keyword(s):

Late Stage ◽

Developmental Process ◽

Early Stage ◽

Expression Patterns ◽

Cell Number ◽

Early Embryogenesis ◽

Human Embryos ◽

Pcr Analysis ◽

Lineage Specification ◽

Model Animal

Abstract BackgroundThe lineage specification of mammalian embryos during preimplantation development has been studied for a long time but is still unclear. To understand the developmental process, many studies have examined lineage markers and mechanisms focusing on mouse embryos, but there are differences from human embryos. Pigs have been studied extensively in the field of disease model animals and xenotransplantation because of their physiological similarity with humans. Therefore, it is necessary to analyze gene expression patterns and lineage specification markers during early embryogenesis in pigs, a model animal similar to humans.ResultsAnalysis of the expression pattern of the core pluripotent factors (OCT4, SOX2 and NANOG) of preimplantation porcine embryos showed that SOX2 was only expressed in some cells from the early stage, so SOX2 was selected as an ICM inducible factor candidate. Next, transcript and protein expression patterns were estimated at the early stage (Day 5) and late stage (Day 7) of blastocysts injected with the CRISPR Cas9 system selected through gRNA validation. An ICC assay revealed that the expression of ICM-related genes (SOX2, NANOG and SOX17), except OCT4, was suppressed, and the total cell number was also decreased. Likewise, according to real-time PCR analysis, pluripotency-related genes (NANOG, SOX17 and SMAD7), excluding OCT4, and proliferation-related genes (KDM8 and DDB1) were decreased in SOX2-targeted blastocysts, which showed more differences in late-stage blastocyst than in early-stage blastocyst. Last, in SOX2-overexpressing embryos, the total blastocyst cell number was greatly increased, but the ICM/TE ratio decreased.ConclusionsTaken together, our results demonstrated SOX2 is essential for ICM formation and cell proliferation in porcine early stage embryogenesis. These findings will help to elucidate gene regulation related to lineage specification during porcine early development.

Download Full-text

Identification of Differentially Expressed Genes Using cDNA-AFLP During Six Days In Vitro Tuberization of Potato

Zuriat ◽

10.24198/zuriat.v14i1.6751 ◽

2015 ◽

Vol 14 (1) ◽

Author(s):

Nono Carsono ◽

Christian Bachem

Keyword(s):

Gene Expression ◽

Developmental Process ◽

Expression Patterns ◽

Induction Medium ◽

In Vitro Tuberization ◽

Storage Organ ◽

Developmentally Regulated ◽

Study Gene Expression ◽

Differential Pattern

Tuberization in potato is a complex developmental process resulting in the differentiation of stolon into the storage organ, tuber. During tuberization, change in gene expression has been known to occur. To study gene expression during tuberization over the time, in vitro tuberization system provides a suitable tool, due to its synchronous in tuber formation. An early six days axillary bud growing on tuber induction medium is a crucial development since a large number of genes change in their expression patterns during this period. In order to identify, isolate and sequencing the genes which displaying differential pattern between tuberizing and non-tuberizing potato explants during six days in vitro tuberization, cDNA-AFLP fingerprint, method for the visualization of gene expression using cDNA as template which is amplified to generate an RNA-fingerprinting, was used in this experiment. Seventeen primer combinations were chosen based on their expression profile from cDNA-AFLP fingerprint. Forty five TDFs (transcript derived fragment), which displayed differential expressions, were obtained. Tuberizing explants had much more TDFs, which developmentally regulated, than those from non tuberizing explants. Seven TDFs were isolated, cloned and then sequenced. One TDF did not find similarity in the current databases. The nucleotide sequence of TDF F showed best similarity to invertase ezymes from the databases. The homology of six TDFs with known sequences is discussed in this paper.

Download Full-text

The mac1 Gene: Controlling the Commitment to the Meiotic Pathway in Maize

Genetics ◽

10.1093/genetics/142.3.1009 ◽

1996 ◽

Vol 142 (3) ◽

pp. 1009-1020 ◽

Cited By ~ 3

Author(s):

William F Sheridan ◽

Nadezhda A Avalkina ◽

Ivan I Shamrov ◽

Tatyana B Batyea ◽

Inna N Golubovskaya

Keyword(s):

Female Gametophyte ◽

Embryo Sac ◽

Flowering Plants ◽

Normal Female ◽

Ovule Development ◽

Partial Sterility ◽

Embryo Sac Formation ◽

Female Gametophyte Development ◽

Normal Meiosis ◽

Pleiotropic Mutation

Abstract The switch from the vegetative to the reproductive pathway of development in flowering plants requires the commitment of the subepidermal cells of the ovules and anthers to enter the meiotic pathway. These cells, the hypodermal cells, either directly or indirectly form the archesporial cells that, in turn, differentiate into the megasporocytes and microsporocytes. We have isolated a recessive pleiotropic mutation that we have termed multiple archesporial cells1 (macl) and located it to the short arm of chromosome 10. Its cytological phenotype suggests that this locus plays an important role in the switch of the hypodermal cells from the vegetative to the meiotic (sporogenous) pathway in maize ovules. During normal ovule development in maize, only a single hypodermal cell develops into an archesporial cell and this differentiates into the single megasporocyte. In macl mutant ovules several hypodermal cells develop into archesporial cells, and the resulting megasporocytes undergo a normal meiosis. More than one megaspore survives in the tetrad and more than one embryo sac is formed in each ovule. Ears on mutant plants show partial sterility resulting from abnormalities in megaspore differentiation and embryo sac formation. The sporophytic expression of this gene is therefore also important for normal female gametophyte development.

Download Full-text

Development of extracellular vesicles-based classifier for detection of early-stage bladder, ovarian, and pancreatic cancer.

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.15_suppl.3048 ◽

2021 ◽

Vol 39 (15_suppl) ◽

pp. 3048-3048

Author(s):

Juan Pablo Hinestrosa ◽

Razelle Kurzrock ◽

Jean Lewis ◽

Nick Schork ◽

Ashish M. Kamat ◽

...

Keyword(s):

Pancreatic Cancer ◽

Confidence Interval ◽

Extracellular Vesicles ◽

Metastatic Disease ◽

Cancer Detection ◽

Early Stage ◽

Expression Patterns ◽

Stepwise Logistic Regression ◽

Liquid Biopsies ◽

Cancer Early Detection

3048 Background: Many cancers are lethal because they present with metastatic disease. Because localized/resectable tumors produce vague symptoms, diagnosis is delayed. In pancreatic cancer, only ̃10% of patients survive five years, and it will soon become the second leading cause of cancer-related deaths in the USA. For patients with metastatic disease, the 2- and 5-year survival is < 10% and ̃3%, respectively. For the few patients with local disease, 5-year survival is ̃40%. Many other cancers have comparable differences between early- and late-stage disease. It is apparent a diagnostic assay for early-stage cancers would transform the field by minimizing the need for aggressive surgeries and other harsh interventions, and by its potential to increase survival. Identifying cancer-specific aberrations in blood-based “liquid” biopsies offers a prospect for a non-invasive cancer detection tool. In the bloodstream, there are extracellular vesicles (EVs) with cargoes including membrane and cytosolic proteins, as well as RNA and lipids derived from their parent cells. Methods: We used an alternating current electrokinetics (ACE) microarray to isolate EVs from the plasma of stage I and II bladder (N = 48), ovarian (N = 42), and pancreatic cancer patients (N = 44), and healthy volunteers (N = 110). EVs were analyzed using multiplex protein immunoassays for 54 cancer-related proteins. EV protein expression patterns were analyzed using stepwise logistic regression followed by a split between training and test sets (67%/33% respectively). This process enabled biomarker selection and generation of a classifier to discriminate between cancer and healthy donors. Results: The EV protein-based classifier had an overall area under curve (AUC) of 0.95 with a sensitivity of 71.2% (69.4% – 73.0%, at 95% confidence interval) at > 99% specificity. The classifier’s performance for the pancreatic cancer cohort was very strong, with overall sensitivity of 95.7% (94.6% – 96.9%, at 95% confidence interval) at > 99% specificity. Conclusions: EV-associated proteins may enable early cancer detection where surgical resection is most likely to improve outcomes. The classifier’s performance for the initial three cancers studied showed encouraging results. Future efforts will include examining additional cancer types and evaluating the classifier performance using samples from donors with related benign conditions with the aim of a pan-cancer early detection assay.

Download Full-text

The PINHEAD/ZWILLE gene acts pleiotropically in Arabidopsis development and has overlapping functions with the ARGONAUTE1 gene

Development ◽

10.1242/dev.126.3.469 ◽

1999 ◽

Vol 126 (3) ◽

pp. 469-481 ◽

Cited By ~ 24

Author(s):

K. Lynn ◽

A. Fernandez ◽

M. Aida ◽

J. Sedbrook ◽

M. Tasaka ◽

...

Keyword(s):

Expression Patterns ◽

Bilateral Symmetry ◽

Floral Organ ◽

Axillary Shoot ◽

Apical Meristems ◽

Shoot Apical Meristems ◽

Positional Identity ◽

Competence Factor ◽

High Level

Several lines of evidence indicate that the adaxial leaf domain possesses a unique competence to form shoot apical meristems. Factors required for this competence are expected to cause a defect in shoot apical meristem formation when inactivated and to be expressed or active preferentially in the adaxial leaf domain. PINHEAD, a member of a family of proteins that includes the translation factor eIF2C, is required for reliable formation of primary and axillary shoot apical meristems. In addition to high-level expression in the vasculature, we find that low-level PINHEAD expression defines a novel domain of positional identity in the plant. This domain consists of adaxial leaf primordia and the meristem. These findings suggest that the PINHEAD gene product may be a component of a hypothetical meristem forming competence factor. We also describe defects in floral organ number and shape, as well as aberrant embryo and ovule development associated with pinhead mutants, thus elaborating on the role of PINHEAD in Arabidopsis development. In addition, we find that embryos doubly mutant for PINHEAD and ARGONAUTE1, a related, ubiquitously expressed family member, fail to progress to bilateral symmetry and do not accumulate the SHOOT MERISTEMLESS protein. Therefore PINHEAD and ARGONAUTE1 together act to allow wild-type growth and gene expression patterns during embryogenesis.

Download Full-text

pha-4 is Ce-fkh-1, a fork head/HNF-3alpha, beta, gamma homolog that functions in organogenesis of the C. elegans pharynx

Development ◽

10.1242/dev.125.12.2171 ◽

1998 ◽

Vol 125 (12) ◽

pp. 2171-2180 ◽

Cited By ~ 4

Author(s):

J.M. Kalb ◽

K.K. Lau ◽

B. Goszczynski ◽

T. Fukushige ◽

D. Moons ◽

...

Keyword(s):

Early Stage ◽

Sequence Similarity ◽

Expression Patterns ◽

Ectopic Expression ◽

Specific Gene ◽

Gata Factor ◽

Enhancer Element ◽

C Elegans ◽

Fork Head ◽

Organ Identity

The C. elegans Ce-fkh-1 gene has been cloned on the basis of its sequence similarity to the winged-helix DNA binding domain of the Drosophila fork head and mammalian HNF-3alpha, beta, gamma genes, and mutations in the zygotically active pha-4 gene have been shown to block formation of the pharynx (and rectum) at an early stage in embryogenesis. In the present paper, we show that Ce-fkh-1 and pha-4 are the same gene. We show that PHA-4 protein is present in nuclei of essentially all pharyngeal cells, of all five cell types. PHA-4 protein first appears close to the point at which a cell lineage will produce only pharyngeal cells, independently of cell type. We show that PHA-4 binds directly to a ‘pan-pharyngeal enhancer element’ previously identified in the promoter of the pharyngeal myosin myo-2 gene; in transgenic embryos, ectopic PHA-4 activates ectopic myo-2 expression. We also show that ectopic PHA-4 can activate ectopic expression of the ceh-22 gene, a pharyngeal-specific NK-2-type homeodomain protein previously shown to bind a muscle-specific enhancer near the PHA-4 binding site in the myo-2 promoter. We propose that it is the combination of pha-4 and regulatory molecules such as ceh-22 that produces the specific gene expression patterns during pharynx development. Overall, pha-4 can be described as an ‘organ identity factor’, completely necessary for organ formation, present in all cells of the organ from the earliest stages, capable of integrating upstream developmental pathways (in this case, the two distinct pathways that produce the anterior and posterior pharynx) and participating directly in the transcriptional regulation of organ specific genes. Finally, we note that the distribution of PHA-4 protein in C. elegans embryos is remarkably similar to the distribution of the fork head protein in Drosophila embryos: high levels in the foregut/pharynx and hindgut/rectum; low levels in the gut proper. Moreover, we show that pha-4 expression in the C. elegans gut is regulated by elt-2, a C. elegans gut-specific GATA-factor and possible homolog of the Drosophila gene serpent, which influences fork head expression in the fly gut. Overall, our results provide evidence for a highly conserved pathway regulating formation of the digestive tract in all (triploblastic) metazoa.

Download Full-text