scholarly journals Genome-Wide Analysis of CCT Transcript Factors to Identify Genes Contributing to Photoperiodic Flowering in Oryza rufipogon

2021 ◽  
Vol 12 ◽  
Author(s):  
Xin Peng ◽  
Win Tun ◽  
Shuang-feng Dai ◽  
Jia-yue Li ◽  
Qun-jie Zhang ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Functional Characterization ◽  
Oryza Rufipogon ◽  
Developmental Expression ◽  
Cultivated Rice ◽  
Functional Roles ◽  
Rhythmic Expression ◽  
Photoperiodic Flowering ◽  
In The Wild ◽  
Functional Alleles

Photoperiod sensitivity is a dominant determinant for the phase transition in cereal crops. CCT (CONSTANS, CO-like, and TOC1) transcription factors (TFs) are involved in many physiological functions including the regulation of the photoperiodic flowering. However, the functional roles of CCT TFs have not been elucidated in the wild progenitors of crops. In this study, we identified 41 CCT TFs, including 19 CMF, 17 COL, and five PRR TFs in Oryza rufipogon, the presumed wild ancestor of Asian cultivated rice. There are thirty-eight orthologous CCT genes in Oryza sativa, of which ten pairs of duplicated CCT TFs are shared with O. rufipogon. We investigated daily expression patterns, showing that 36 OrCCT genes exhibited circadian rhythmic expression. A total of thirteen OrCCT genes were identified as putative flowering suppressors in O. rufipogon based on rhythmic and developmental expression patterns and transgenic phenotypes. We propose that OrCCT08, OrCCT24, and OrCCT26 are the strong functional alleles of rice DTH2, Ghd7, and OsPRR37, respectively. The SD treatment at 80 DAG stimulated flowering of the LD-grown O. rufipogon plants. Our results further showed that the nine OrCCT genes were significantly downregulated under the treatment. Our findings would provide valuable information for the construction of photoperiodic flowering regulatory network and functional characterization of the CCT TFs in both O. rufipogon and O. sativa.

The role of wild rice (Oryza rufipogon) awns in seed dispersal

2020 ◽  
Vol 30 (4) ◽  
pp. 319-324
Author(s):  
Yaddehige P.J. Amarasinghe ◽  
Mitsuharu Otsuka ◽  
Sathya Lim ◽  
Ryo Ishikawa ◽  
Takashige Ishii
Keyword(s):  
Seed Dispersal ◽  
Wild Rice ◽  
Oryza Rufipogon ◽  
Cultivated Rice ◽  
Natural Conditions ◽  
Horizontal Movement ◽  
Vertical Orientation ◽  
Initial Seed ◽  
Functional Alleles

AbstractCultivated rice (Oryza sativa L.) was domesticated from the Asian wild species O. rufipogon. Compared with cultivated rice, wild rice has spikelets/seeds with long barbed awns. In order to evaluate the role of awns in wild rice, four seed groups with different awn lengths (full, half, quarter and no awns) were prepared, and the following seed dispersal movements were investigated under simulated natural conditions as observed in the tropical Asian habitat: (1) seed detachment from the parent plant; (2) falling angle of mature seed; (3) ability to slip into small spaces; (4) horizontal movement on the ground and (5) horizontal movement in water. As a result, awns were found to enhance the detachment of matured seeds from the panicles in the initial seed dispersal step. They regulated vertical orientation in the air, and the vertical form may enable seeds to squeeze to the ground. The awned seeds also showed advantages in horizontal movements on the ground and in the water. In most of the experiments, seeds with full awns showed the best performance for seed dispersal, suggesting that wild rice keeps long awns to survive under natural conditions. Since seed awning is dominantly controlled by wild functional alleles at several loci, wild rice may be able to prevent a drastic reduction of awn length.

scholarly journals Identification of phosphorus stress related proteins in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.) using label-free quantitative proteomic analysis

2020 ◽  
Author(s):  
Qianwen Deng ◽  
Liweidan Bai ◽  
Liangfang Dai ◽  
Yaling Chen ◽  
Jun Fang ◽  
...  
Keyword(s):  
Wild Rice ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Oryza Rufipogon ◽  
Available Phosphorus ◽  
Label Free ◽  
Response Mechanism ◽  
Cultivated Rice ◽  
P Deficiency ◽  
Dongxiang Wild Rice

Abstract Background: The lack of available phosphorus (P) in soil is one of the important factors restricting rice growth. Previous studies indicated that Dongxiang wild rice (DXWR, O. rufipogon Griff.) was resistant to low-P stress. So far, the research of resistance mechanism in DXWR was very limited.Results: The results showed that 3589 significant differential accumulation proteins were identified between low P and the normal P treated root samples. 60 up-regulated and 15 down-regulated proteins were identified with ≥ 1.5-fold changes as an additional standard. Furthermore, among 75 significantly different expression proteins (SDEPs), 24 proteins also detected in previous transcriptome dataset verified by qRT-PCR, including OsPT2, OsPT8, OsPAP10c, OsPAP10a and OsPHF1. Through comprehensive analysis, it was found that DXWR could increase PAPs, membrane location of PTs, rhizosphere area, alternative splicing and decrease ROS activity to deal with low-P stress. Moreover, among the genes corresponding to 75 SDEPs, 7 uncharacterized genes were located in previous P related QTL intervals, of which two genes (LOC_Os12g09620 and LOC_Os03g40670) have been detected at both transcriptome and proteome levels. In addition, the expression patterns of OsPHR1, OsPHR2, OsPHO1 and NAT-OsPHO1 in DXWR were different in cultivated rice, suggesting that the response mechanism of some low-P tolerance in DXWR might be different from that in cultivated rice.Conclusions: This study screened out some candidate genes for low-P resistance and preliminarily verified that there might be a different low-P response mechanism in DXWR than in cultivated rice, which would provide insights in cloning the P-deficiency genes from wild rice, as well as elucidating the molecular mechanism of low-P resistance in DXWR.

scholarly journals A Rice Ancestral Genetic Resource Conferring Ideal Plant Shapes for Vegetative Growth and Weed Suppression

2021 ◽  
Vol 12 ◽  
Author(s):  
Noritoshi Inagaki ◽  
Hidenori Asami ◽  
Hideyuki Hirabayashi ◽  
Akira Uchino ◽  
Toshiyuki Imaizumi ◽  
...  
Keyword(s):  
Vegetative Growth ◽  
Incident Light ◽  
Rice Chromosome ◽  
Oryza Rufipogon ◽  
Weed Suppression ◽  
Chromosome Segment ◽  
Recurrent Parent ◽  
Cultivated Rice ◽  
In The Wild ◽  
Grain Yield And Quality

To maximize crop growth, crops need to capture sunlight efficiently. This property is primarily influenced by the shape of the crops such as the angle, area, and arrangement of leaves. We constructed a rice (Oryza sativa L.) inbred line that displayed an ideal transition of plant shapes in terms of sunlight receiving efficiency. During vegetative growth, this line exhibited tiller spreading with increased tiller number, which formed a parabolic antenna-like structure. The architecture probably improved light reception efficiency of individuals compared with the recurrent parent. The line achieved not only acceleration of the vegetative growth, but also significant suppression of weed growth under the canopy. The increased light reception efficiency of the line has consequently reduced the amount of incident light to the ground and supplied significant competitiveness against weeds. The spread tillers became erect from the entry of the reproductive growth phase, adaptively sustaining light reception efficiency in thicker stands. The line carries a small chromosomal segment from Oryza rufipogon Griff., a putative progenitor of Asian cultivated rice. The introduced chromosome segment had little effect on grain yield and quality. Our results shed light on potentials hidden in the wild rice chromosome segment to achieve the valuable traits.

scholarly journals Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.)

2016 ◽  
Author(s):  
Peter Civáň ◽  
Terence A. Brown
Keyword(s):  
Haplotype Diversity ◽  
Oryza Rufipogon ◽  
Gene Pools ◽  
Aromatic Rice ◽  
Cultivated Rice ◽  
Ecological Requirements ◽  
Asian Rice ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Taxonomic Groups

AbstractCultivated Asian rice (O. sativa L.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies of O. sativa – indica and japonica – have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups – aus and aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240 aus and 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes of japonica and indica, and reveal unique profiles of chloroplast diversity in aus and aromatic rice. Our results indicate that the latter two groups are not simple derivatives of indica and japonica, respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication of indica, japonica, aus and aromatic rice operated on genetically different gene pools and followed different dynamics.

scholarly journals Map-Based Cloning and Functional Analysis of YE1 in Rice, Which Is Involved in Light-Dependent Chlorophyll Biogenesis and Photoperiodic Flowering Pathway

2019 ◽  
Vol 20 (3) ◽  
pp. 758 ◽  
Author(s):  
Youlin Peng ◽  
Ting Zou ◽  
Lamei Li ◽  
Shiwen Tang ◽  
Qiao Li ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Early Flowering ◽  
Yellow Leaf ◽  
Rhythmic Expression ◽  
Rice Mutant ◽  
Photoperiodic Flowering ◽  
Cloning Method ◽  
Flowering Pathway ◽  
Photoperiod Sensitive ◽  
Chlorophyll Biogenesis

Light is one of the most important environmental factors that affect many aspects of plant growth, including chlorophyll (Chl) synthesis and flowering time. Here, we identified a rice mutant, yellow leaf and early flowering (ye1), and characterized the gene YE1 by using a map-based cloning method. YE1 encodes a heme oxygenase, which is localized to the chloroplasts. YE1 is expressed in various green tissues, especially in leaves, with a diurnal-rhythmic expression pattern, and its transcripts is also induced by light during leaf-greening. The mutant displays decreased Chl contents with less and disorderly thylakoid lamellar layers in chloroplasts, which reduced the photosynthesis rate. The early flowering phenotype of ye1 was not photoperiod-sensitive. Furthermore, the expression levels of Chl biosynthetic genes were downregulated in ye1 seedlings during de-etiolation responses to light. We also found that rhythmic expression patterns of genes involved in photoperiodic flowering were altered in the mutant. Based on these results, we infer that YE1 plays an important role in light-dependent Chl biogenesis as well as photoperiodic flowering pathway in rice.

scholarly journals SOS2 Comes to the Fore: Differential Functionalities in Physiology and Pathology

2021 ◽  
Vol 22 (12) ◽  
pp. 6613
Author(s):  
Fernando C. Baltanás ◽  
Rósula García-Navas ◽  
Eugenio Santos
Keyword(s):  
Expression Patterns ◽  
Critical Role ◽  
Ras Signaling ◽  
Epidermal Stem Cell ◽  
Functional Specificity ◽  
Functional Roles ◽  
Signaling Axis ◽  
Therapy Target ◽  
External Stimuli

The SOS family of Ras-GEFs encompasses two highly homologous and widely expressed members, SOS1 and SOS2. Despite their similar structures and expression patterns, early studies of constitutive KO mice showing that SOS1-KO mutants were embryonic lethal while SOS2-KO mice were viable led to initially viewing SOS1 as the main Ras-GEF linking external stimuli to downstream RAS signaling, while obviating the functional significance of SOS2. Subsequently, different genetic and/or pharmacological ablation tools defined more precisely the functional specificity/redundancy of the SOS1/2 GEFs. Interestingly, the defective phenotypes observed in concomitantly ablated SOS1/2-DKO contexts are frequently much stronger than in single SOS1-KO scenarios and undetectable in single SOS2-KO cells, demonstrating functional redundancy between them and suggesting an ancillary role of SOS2 in the absence of SOS1. Preferential SOS1 role was also demonstrated in different RASopathies and tumors. Conversely, specific SOS2 functions, including a critical role in regulation of the RAS–PI3K/AKT signaling axis in keratinocytes and KRAS-driven tumor lines or in control of epidermal stem cell homeostasis, were also reported. Specific SOS2 mutations were also identified in some RASopathies and cancer forms. The relevance/specificity of the newly uncovered functional roles suggests that SOS2 should join SOS1 for consideration as a relevant biomarker/therapy target.

Stability of the Synechococcus elongatus PCC 7942 circadian clock under directed anti-phase expression of the kai genes

Microbiology ◽  
2005 ◽  
Vol 151 (8) ◽  
pp. 2605-2613 ◽  
Author(s):  
Jayna L. Ditty ◽  
Shannon R. Canales ◽  
Breanne E. Anderson ◽  
Stanly B. Williams ◽  
Susan S. Golden
Keyword(s):  
Circadian Clock ◽  
Expression Patterns ◽  
Phase Relationship ◽  
Synechococcus Elongatus ◽  
Cycle Period ◽  
Rhythmic Expression ◽  
Core Components ◽  
Synechococcus Elongatus Pcc 7942 ◽  
Time Required ◽  
Pcc 7942

The kaiA, kaiB and kaiC genes encode the core components of the cyanobacterial circadian clock in Synechococcus elongatus PCC 7942. Rhythmic expression patterns of kaiA and of the kaiBC operon normally peak in synchrony. In some mutants the relative timing of peaks (phase relationship) between these transcription units is altered, but circadian rhythms persist robustly. In this study, the importance of the transcriptional timing of kai genes was examined. Expressing either kaiA or kaiBC from a heterologous promoter whose peak expression occurs 12 h out of phase from the norm, and thus 12 h out of phase from the other kai locus, did not affect the time required for one cycle (period) or phase of the circadian rhythm, as measured by bioluminescence reporters. Furthermore, the data confirm that specific cis elements within the promoters of the kai genes are not necessary to sustain clock function.

scholarly journals Comparison of gene expression in fresh and frozen–thawed human preimplantation embryos

Reproduction ◽  
2012 ◽  
Vol 144 (5) ◽  
pp. 569-582 ◽  
Author(s):  
Lisa Shaw ◽  
Sharon F Sneddon ◽  
Daniel R Brison ◽  
Susan J Kimber
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Developmental Expression ◽  
Preimplantation Embryos ◽  
Human Embryos ◽  
Molecular Events ◽  
Reliable Source ◽  
Human Preimplantation Embryos ◽  
Early Human

Identification and characterisation of differentially regulated genes in preimplantation human embryonic development are required to improve embryo quality and pregnancy rates in IVF. In this study, we examined expression of a number of genes known to be critical for early development and compared expression profiles in individual preimplantation human embryos to establish any differences in gene expression in fresh compared to frozen–thawed embryos used routinely in IVF. We analysed expression of 19 genes by cDNA amplification followed by quantitative real-time PCR in a panel of 44 fresh and frozen–thawed human preimplantation embryos. Fresh embryos were obtained from surplus early cleavage stage embryos and frozen–thawed embryos from cryopreserved 2PN embryos. Our aim was to determine differences in gene expression between fresh and frozen–thawed human embryos, but we also identified differences in developmental expression patterns for particular genes. We show that overall gene expression among embryos of the same stage is highly variable and our results indicate that expression levels between groups did differ and differences in expression of individual genes was detected. Our results show that gene expression from frozen–thawed embryos is more consistent when compared with fresh, suggesting that cryopreserved embryos may represent a reliable source for studying the molecular events underpinning early human embryo development.

scholarly journals Carotenoid Cleavage Dioxygenases: Identification, Expression, and Evolutionary Analysis of This Gene Family in Tobacco

2019 ◽  
Vol 20 (22) ◽  
pp. 5796
Author(s):  
Qianqian Zhou ◽  
Qingchang Li ◽  
Peng Li ◽  
Songtao Zhang ◽  
Che Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Physiological Stress ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Hormone Treatment ◽  
Nicotiana Sylvestris ◽  
Regulatory Elements ◽  
Evolutionary Analysis ◽  
Comprehensive Overview ◽  
Carotenoid Cleavage Dioxygenases

Carotenoid cleavage dioxygenases (CCDs) selectively catalyze carotenoids, forming smaller apocarotenoids that are essential for the synthesis of apocarotenoid flavor, aroma volatiles, and phytohormone ABA/SLs, as well as responses to abiotic stresses. Here, 19, 11, and 10 CCD genes were identified in Nicotiana tabacum, Nicotiana tomentosiformis, and Nicotiana sylvestris, respectively. For this family, we systematically analyzed phylogeny, gene structure, conserved motifs, gene duplications, cis-elements, subcellular and chromosomal localization, miRNA-target sites, expression patterns with different treatments, and molecular evolution. CCD genes were classified into two subfamilies and nine groups. Gene structures, motifs, and tertiary structures showed similarities within the same groups. Subcellular localization analysis predicted that CCD family genes are cytoplasmic and plastid-localized, which was confirmed experimentally. Evolutionary analysis showed that purifying selection dominated the evolution of these genes. Meanwhile, seven positive sites were identified on the ancestor branch of the tobacco CCD subfamily. Cis-regulatory elements of the CCD promoters were mainly involved in light-responsiveness, hormone treatment, and physiological stress. Different CCD family genes were predominantly expressed separately in roots, flowers, seeds, and leaves and exhibited divergent expression patterns with different hormones (ABA, MeJA, IAA, SA) and abiotic (drought, cold, heat) stresses. This study provides a comprehensive overview of the NtCCD gene family and a foundation for future functional characterization of individual genes.

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