scholarly journals Conserved Expression Profiles of Circadian Clock-related Genes in Two Lemna Species Showing Long-day and Short-day Photoperiodic Flowering Responses

2006 ◽  
Vol 47 (5) ◽  
pp. 601-612 ◽  
Author(s):  
Kumiko Miwa ◽  
Masayuki Serikawa ◽  
Sayaka Suzuki ◽  
Takao Kondo ◽  
Tokitaka Oyama
Keyword(s):  
Circadian Clock ◽  
Expression Profiles ◽  
Short Day ◽  
Photoperiodic Flowering ◽  
Long Day

scholarly journals The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6626 ◽  
Author(s):  
Geoffrey Thomson ◽  
James Taylor ◽  
Joanna Putterill
Keyword(s):  
Flowering Time ◽  
Medicago Truncatula ◽  
Differential Expression Analysis ◽  
Potential Candidate ◽  
Diurnal Pattern ◽  
Transcriptomic Response ◽  
Short Day ◽  
Photoperiodic Flowering ◽  
Long Day ◽  
Young Leaves

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.

scholarly journals The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula

2018 ◽  
Author(s):  
Geoffrey Thomson ◽  
James Taylor ◽  
Joanna Putterill
Keyword(s):  
Flowering Time ◽  
Medicago Truncatula ◽  
Differential Expression Analysis ◽  
Potential Candidate ◽  
Diurnal Pattern ◽  
Transcriptomic Response ◽  
Short Day ◽  
Photoperiodic Flowering ◽  
Long Day ◽  
Young Leaves

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.

scholarly journals The Photoperiod Pathway in Fragaria (Rosaceae)

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 1010E-1011
Author(s):  
Philip J. Stewart ◽  
Ashley R. Winslow ◽  
Kevin M. Folta
Keyword(s):  
Cdna Libraries ◽  
Flowering Locus T ◽  
Degenerate Pcr ◽  
Short Day ◽  
Photoperiodic Flowering ◽  
Long Day ◽  
Important Pathway ◽  
Photoperiod Pathway ◽  
Flowering Control ◽  
Signal Transduction Systems

The transition from vegetative growth to reproductive growth is carefully controlled by a number of independent signal transduction systems, one of which interprets photoperiod. Photoperiodic control of flowering time has been well-described in Arabidopsis and rice, revealing the presence of a generally common network of regulatory proteins. Timely and appropriate progression to flowering is critical to profitable production of cultivated strawberry (Fragaria ×ananassa), a species that includes long-day, short-day, and day-neutral cultivars. In an effort to characterize the photoperiodic flowering control mechanism in strawberry, the Fragaria orthologs of the photoperiod pathway genes were cloned and sequenced. Strawberry versions of Constans, Constans-like, Leafy, Flowering Locus T, and Suppressor of Constans Overexpression 1 were identified by screening cDNA libraries and through degenerate PCR approaches. Expression of these transcripts in short-day and day-neutral cultivars was tested under long and short photoperiods. Functional complementation of Arabidopsis mutants was performed where appropriate, alleles were identified, genetic linkage was determined where possible, and relationships between the strawberry genes and homologs from other species were studied. These trials define the mechanistic elements of an agriculturally important pathway in this valuable crop, and lays the foundation for transgenic studies in strawberry to manipulate the floral transition.

scholarly journals The transcriptomic response to a short day to long day shift in leaves of the reference legume Medicago truncatula

2018 ◽  
Author(s):  
Geoffrey Thomson ◽  
James Taylor ◽  
Joanna Putterill
Keyword(s):  
Flowering Time ◽  
Medicago Truncatula ◽  
Differential Expression Analysis ◽  
Potential Candidate ◽  
Diurnal Pattern ◽  
Transcriptomic Response ◽  
Short Day ◽  
Photoperiodic Flowering ◽  
Long Day ◽  
Young Leaves

Photoperiodic flowering aligns plant reproduction to favourable seasons of the year to maximise successful production of seeds and grains. However understanding of this process in the temperate legumes of the Fabaceae family, which are important both agriculturally and ecologically, is incomplete. Previous work in the reference legume Medicago truncatula has shown that the FT-like gene MtFTa1 is a potent floral activator. While MtFTa1 is upregulated by long-day photoperiods (LD) and vernalisation, the molecular basis of this is unknown as functional homologues of key regulatory genes present in other species, notably CONSTANS in A. thaliana, have not been identified. In LD MtFTa1 maintains a near constant diurnal pattern of expression unlike its homologue FT in A. thaliana, which has a notable peak in expression at dusk. This suggests a different manner of regulation. Furthermore, M. truncatula possesses other FT-like genes such as two LD induced MtFTb genes which may also act in the regulation of flowering time. MtFTb genes have a diurnal pattern of expression with peaks at both four and sixteen hours after dawn. This study utilises RNA-Seq to analyse the transcriptome of M. truncatula leaves to identify genes which may regulate or be co-expressed with these FT-like genes following a shift from short-day photoperiods to inductive long-days. Specifically this study focuses on the first four hours of the day in the young leaves, which coincides with the first diurnal peak of the FTb genes. Following differential expression analysis at each timepoint, genes which alter their pattern of expression are distinguished from those which just alter their magnitude of expression (and those that do neither). It goes on to categorise these genes into groups with similar patterns of expression using c-means clustering and identifies a number of potential candidate photoperiod flowering time genes for future studies to consider.

scholarly journals Transcriptomal dissection of soybean circadian rhythmicity in two geographically, phenotypically and genetically distinct cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yanlei Yue ◽  
Ze Jiang ◽  
Enoch Sapey ◽  
Tingting Wu ◽  
Shi Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Chromosome Structure ◽  
Clock Genes ◽  
Expression Profiles ◽  
Circadian Rhythmicity ◽  
Rna Seq ◽  
Night Time ◽  
Time Points ◽  
Circadian Clock Genes

Abstract Background In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear. Results We used two geographically, phenotypically and genetically distinct cultivars, conventional juvenile Zhonghuang 24 (with functional J/GmELF3a, a homolog of the circadian clock indispensable component EARLY FLOWERING 3) and long juvenile Huaxia 3 (with dysfunctional j/Gmelf3a) to dissect the soybean circadian clock with time-series transcriptomal RNA-Seq analysis of unifoliate leaves on a day scale. The results showed that several known circadian clock components, including RVE1, GI, LUX and TOC1, phase differently in soybean than in Arabidopsis, demonstrating that the soybean circadian clock is obviously different from the canonical model in Arabidopsis. In contrast to the observation that ELF3 dysfunction results in clock arrhythmia in Arabidopsis, the circadian clock is conserved in soybean regardless of the functional status of J/GmELF3a. Soybean exhibits a circadian rhythmicity in both gene expression and alternative splicing. Genes can be grouped into six clusters, C1-C6, with different expression profiles. Many more genes are grouped into the night clusters (C4-C6) than in the day cluster (C2), showing that night is essential for gene expression and regulation. Moreover, soybean chromosomes are activated with a circadian rhythmicity, indicating that high-order chromosome structure might impact circadian rhythmicity. Interestingly, night time points were clustered in one group, while day time points were separated into two groups, morning and afternoon, demonstrating that morning and afternoon are representative of different environments for soybean growth and development. However, no genes were consistently differentially expressed over different time-points, indicating that it is necessary to perform a circadian rhythmicity analysis to more thoroughly dissect the function of a gene. Moreover, the analysis of the circadian rhythmicity of the GmFT family showed that GmELF3a might phase- and amplitude-modulate the GmFT family to regulate the juvenility and maturity traits of soybean. Conclusions These results and the resultant RNA-seq data should be helpful in understanding the soybean circadian clock and elucidating the connection between the circadian clock and soybean maturity.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

Control of torpor and body weight patterns by a seasonal timer in Siberian hamsters

1989 ◽  
Vol 257 (1) ◽  
pp. R142-R149 ◽  
Author(s):  
T. J. Bartness ◽  
J. A. Elliott ◽  
B. D. Goldman
Keyword(s):  
Body Weight ◽  
Food Intake ◽  
Implant Removal ◽  
Daily Torpor ◽  
Short Day ◽  
Siberian Hamsters ◽  
Long Day ◽  
Preparatory Phase ◽  
Pelage Color ◽  
Seasonal Responses

Two experiments were designed to assess whether the short-day-induced patterns of shallow daily torpor, body weight, and other seasonal responses (food intake and pelage pigmentation) exhibited by Siberian hamsters (Phodopus sungorus sungorus) are under the control of a "seasonal timekeeping mechanism" that is independent of reproductive status [testosterone, (T)]. We examined whether the patterning and expression of these seasonal responses were altered by decreases in serum T that accompany gonadal regression during the first 8 wk of short-day exposure (i.e., the "preparatory phase" of the torpor season) or by experimental increases in serum T after this phase. Short-day-housed, castrated hamsters bearing T implants had long-day levels of the hormone and did not exhibit torpor. Appropriate seasonal patterns and levels of torpor, body weight, pelage color stage, and food intake were exhibited after T implant removal although serum T was clamped to long-day levels during the preparatory phase. In animals that were gonad intact during the preparatory phase and were subsequently castrated and given T implants, torpor did not occur as long as the implants were in place. However, the patterns and levels of daily torpor, food intake, and body weight rapidly returned to appropriate seasonal values compared with the castrated, blank-implanted controls on T implant removal; these effects occurred whether the T implants were removed when torpor frequency was increasing, at its peak, or decreasing across the torpor season. T did not affect pelage color stage under any condition.(ABSTRACT TRUNCATED AT 250 WORDS)

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