scholarly journals Wheat EARLY FLOWERING3 is a dawn-expressed circadian oscillator component that regulates heading date

2021 ◽  
Author(s):  
Lukas Wittern ◽  
Gareth Steed ◽  
Laura J Taylor ◽  
Andy Greenland ◽  
Keith Gardner ◽  
...  
Keyword(s):  
Circadian Rhythms ◽  
Heading Date ◽  
Allelic Diversity ◽  
Circadian Oscillator ◽  
Loss Of Function ◽  
Coding Region ◽  
D Genome ◽  
Wheat Varieties ◽  
Causal Polymorphism ◽  
Night And Day

Optimising the seasonal control of flowering in the major crops is an important component of breeding to match crop adaptation to the target environment. Using an eight parent Multiparent Advanced Generation Inter-Cross (MAGIC) population we investigated the contribution of variation at circadian clock-associated genes to the regulation of heading date (flowering) in UK and European winter wheat varieties. We identified homoeologues of EARLY FLOWERING 3 (ELF3) as candidate genes for the Earliness per se (Eps) D1 and B1 loci in field conditions. We confirmed that a SNP within the coding region of TaELF3-B1 is the likely causal polymorphism underlying the Eps-B1 locus. We also identified that a reported deletion at the Eps-D1 locus encompassing TaELF3-D1, is in fact a novel allele that lies within an introgression region that contains an inversion relative to the Chinese Spring D genome. Our findings that ELF3 might be associated with the regulation of heading date prompted us to investigate whether ELF3 is a circadian oscillator gene in wheat, as it is in Arabidopsis. Using T. turgidum cv. Kronos carrying loss of function alleles for both copies of TtELF3 we found that circadian rhythms were severely disrupted. Furthermore, in T. aestivum, we found that loss of functional LUX ARRHYTHMO (LUX), an orthologue of the protein partner of ELF3 in Arabidopsis, also severely disrupted circadian rhythms. Whilst these data suggest a function for both ELF3 and LUX in the wheat circadian oscillator, that oscillator might be structured differently to that of Arabidopsis because wheat ELF3 and LUX transcripts are maximal at the end of the night and day respectively, rather than co-expressed at dusk as they are in Arabidopsis. We conclude that there is sufficient allelic diversity within the three wheat ELF3 homoeologues for selection to delay or advance heading, and that this can be achieved without pleiotropic deleterious alterations to circadian rhythms.

A Mathematical Model of a Retinal Oscillator

2000 ◽  
Author(s):  
Richard H. Rand ◽  
Erika T. Wirkus ◽  
Tong Li ◽  
Howard C. Howland
Keyword(s):  
Mathematical Model ◽  
Circadian Rhythms ◽  
Light Intensity ◽  
Circadian Oscillator ◽  
Diurnal Rhythms ◽  
Descriptive Model ◽  
Light Levels ◽  
Visual Systems ◽  
Night And Day

Abstract Circadian rhythms in vertebrates (including man) have been conjectured to help control changes in sensitivity of visual systems (which must operate over some 10 orders of magnitude in the course of night and day), by anticipating the changes in light intensity which occur at dusk and dawn (Cahill and Besharse, 1995). Diurnal rhythms in melatonin and dopamine in the retina have been shown to be affected both by a circadian oscillator as well as by changes in local light levels (Cahill and Besharse, 1995). In an experiment conducted in the laboratory of one of the authors (HCH), the growth of the eyes of baby chicks in their first two weeks of life has been shown to be strongly affected by exposure to 20 hours or more of light per day (Li et al., 2000). A descriptive model of the nature of the biochemistry of retinal dynamics has been presented (Morgan and Boelen, 1996). In this work we offer a mathematical model of the retinal oscillator based on the descriptive model given in (Morgan and Boelen, 1996). Using this model we simulate the experiment described in (Li et al., 2000).

scholarly journals Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms

2021 ◽  
Author(s):  
Caroline F. Wright ◽  
Nicholas M. Quaife ◽  
Laura Ramos-Hernández ◽  
Petr Danecek ◽  
Matteo P. Ferla ◽  
...  
Keyword(s):  
Developmental Disorder ◽  
Loss Of Function ◽  
Coding Region

scholarly journals OsPRR37 Alternatively Promotes Heading Date Through Suppressing the Expression of Ghd7 in the Japonica Variety Zhonghua 11 under Natural Long-Day Conditions

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yong Hu ◽  
Xin Zhou ◽  
Bo Zhang ◽  
Shuangle Li ◽  
Xiaowei Fan ◽  
...  
Keyword(s):  
Functional Divergence ◽  
Heading Date ◽  
Transcriptional Analysis ◽  
Dependent Manner ◽  
Coding Region ◽  
Japonica Variety ◽  
Long Day ◽  
Nucleotide Mutation ◽  
Alternative Function ◽  
Pr Domain

AbstractHeading date is an important agronomic trait of rice (Oryza sativa L.) and is regulated by numerous genes, some of which exhibit functional divergence in a genetic background-dependent manner. Here, we identified a late heading date 7 (lhd7) mutant that flowered later than wild-type Zhonghua 11 (ZH11) under natural long-day (NLD) conditions. Map-based cloning facilitated by the MutMap strategy revealed that LHD7 was on the same locus as OsPRR37 but exhibited a novel function as a promoter of heading date. A single-nucleotide mutation of G-to-A in the coding region caused a substitution of aspartic acid for glycine at site 159 within the pseudo-receiver (PR) domain of OsPRR37. Transcriptional analysis revealed that OsPRR37 suppressed Ghd7 expression in both ZH11 background under NLD conditions and the Zhenshan 97 background under natural short-day conditions. Consistently, the expression of Ehd1, Hd3a and RFT1 was enhanced by OsPRR37 in the ZH11 background. Genetic analysis indicated that the promotion of heading date and reduction in grain yield by OsPRR37 were partially dependent on Ghd7. Further investigation showed that the alternative function of OsPRR37 required an intact Ghd7-related regulatory pathway involving not only its upstream regulators OsGI and PhyB but also its interacting partner Hd1. Our study revealed the distinct role of OsPRR37 in the ZH11 background, which provides a more comprehensive understanding of OsPRR37 function and enriches the theoretical bases for improvement of rice heading date in the future.

scholarly journals Genomic patterns of introgression in interspecific populations created by crossing wheat with its wild relative

2019 ◽  
Author(s):  
Moses Nyine ◽  
Elina Adhikari ◽  
Marshall Clinesmith ◽  
Katherine W. Jordan ◽  
Allan K. Fritz ◽  
...  
Keyword(s):  
Aegilops Tauschii ◽  
Allelic Diversity ◽  
Sequence Divergence ◽  
Snp Markers ◽  
D Genome ◽  
Entire Genome ◽  
Wild Allele ◽  
Negative Epistasis ◽  
The Hill ◽  
Genomic Patterns

AbstractIntrogression from wild relatives is a valuable source of novel allelic diversity for breeding. We investigated the genomic patterns of introgression from Aegilops tauschii, the diploid ancestor of the wheat D genome, into winter wheat (Triticum aestivum) cultivars. The population of 351 BC1F3:5 lines was selected based on phenology from crosses between six hexaploid wheat lines and 21 wheat-Ae. tauschii octoploids. SNP markers developed for this population and a diverse panel of 116 Ae. tauschii accessions by complexity-reduced genome sequencing were used to detect introgression based on the identity-by-descent analysis. Overall, introgression frequency positively correlated with recombination rate, with a high incidence of introgression at the ends of chromosomes and low in the pericentromeric regions, and was negatively related to sequence divergence between the parental genomes. Reduced introgression in the pericentromeric low-recombining regions spans nearly 2/3 of each chromosome arm, suggestive of the polygenic nature of introgression barriers that could be associated with multilocus negative epistasis between the alleles of wild and cultivated wheat. On the contrary, negative selection against the wild allele of Tg, controlling free-threshing trait and located in the high-recombining chromosomal region, led to reduced introgression only within ∼10 Mbp region around Tg. These results are consistent with the effect of selection on linked variation described by the Hill-Robertson effect, and offer insights into the introgression population development for crop imrpovement to ensure retention of introgressed diversity across entire genome.

How to tell the time: the regulation of phosphoenolpyruvate carboxylase in Crassulacean acid metabolism (CAM) plants

2003 ◽  
Vol 31 (3) ◽  
pp. 728-730 ◽  
Author(s):  
H.G. Nimmo
Keyword(s):  
Circadian Rhythms ◽  
Phosphoenolpyruvate Carboxylase ◽  
Crassulacean Acid Metabolism ◽  
Acid Metabolism ◽  
Circadian Oscillator ◽  
Cam Plants ◽  
Reversible Phosphorylation ◽  
Circadian Expression ◽  
Phosphoenolpyruvate Carboxylase Kinase ◽  
Co2 Metabolism

Crassulacean acid metabolism (CAM) plants exhibit persistent circadian rhythms of CO2 metabolism. These rhythms are driven by changes in the flux through phosphoenolpyruvate carboxylase, which is regulated by reversible phosphorylation in response to a circadian oscillator. This article reviews progress in our understanding of the circadian expression of phosphoenolpyruvate carboxylase kinase.

scholarly journals Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene

2020 ◽  
Author(s):  
Flora Doffe ◽  
Vincent Carbonnier ◽  
Manon Tissier ◽  
Bernard Leroy ◽  
Isabelle Martins ◽  
...  
Keyword(s):  
Ethnic Diversity ◽  
Functional Characterization ◽  
Variant Calling ◽  
Asian Population ◽  
Tp53 Gene ◽  
Loss Of Function ◽  
Coding Region ◽  
Multiple Datasets ◽  
Novel Variants ◽  
Rare Genetic Variants

AbstractInfrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.

scholarly journals SPLICING ABNORMALITIES IN MYOTONIC DYSTROPHIES

2014 ◽  
pp. 9-23
Author(s):  
Denis Furling
Keyword(s):  
Clinical Features ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Cardiac Conduction ◽  
Nuclear Accumulation ◽  
Common Mechanism ◽  
Inherited Disease ◽  
Loss Of Function ◽  
Coding Region ◽  
Membrane Structures

Myotonic dystrophy of type 1 (DM1) is one of the most common muscular dystrophy in adults characterized by progressive muscle wasting and weakness, myotonia, cardiac conduction defects, alteration in cognitive functions as well as several other multisystemic symptoms. DM1 is an autosomal dominant inherited disease caused by an unstable CTG expansion ranging from ~50 to more than 1,000 repeats in the 3’ non-coding region of the DMPK gene. Expression of DMPK RNAs with expanded CUG repeats supports a toxic RNA gain-of-function as a pathologic mechanism for DM1. A similar or common mechanism may also be involved in DM type 2 that is caused by CCTG expansion in the first intron of the CNP (ZNF9) gene and shares similar clinical features with DM1 disease. In both myotonic dystrophies, nuclear accumulation of pathogenic CUG/CCUGexp-RNAs alters the activities of the RNA binding proteins such as MBNL1 and CUG-BP1 that leads to alternative splicing mis-regulation of a numerous of transcripts in DM tissues and ultimately, to clinical features of the disease. An overview of the DM splicing mis-regulation will be presented, with focus on mis- regulation of the BIN1 mRNA. In muscle, BIN1 plays an important role in tubular invaginations of the plasma membrane and is required for biogenesis of T-tubules, which are specialized membrane structures essential for excitation-contraction coupling. BIN1 splicing mis-regulation in DM patients due to MBNL1 loss-of-function results in the expression of an inactive form of BIN1 deprived of phosphoinositide-binding and membrane-tubulating activities. Reproducing similar BIN1 mis-splicing defect in the muscles of wild type mice is sufficient to promote T-tubule alterations and muscle strength decrease, suggesting that alteration of BIN1 splicing may contributes to muscle weakness, a prominent feature in DM.

scholarly journals Identification of a Rare and Potential Pathogenic MC4R Variant in a Brazilian Patient With Adulthood-Onset Severe Obesity

2020 ◽  
Vol 11 ◽  
Author(s):  
Kaio Cezar Rodrigues Salum ◽  
Guilherme Orofino de Souza ◽  
Gabriella de Medeiros Abreu ◽  
Mário Campos Junior ◽  
Fabiana Barzotto Kohlrausch ◽  
...  
Keyword(s):  
Body Weight ◽  
Severe Obesity ◽  
Rare Variants ◽  
Dominant Negative ◽  
Dominant Negative Effect ◽  
Loss Of Function ◽  
Coding Region ◽  
Childhood Onset ◽  
Brazilian Patient ◽  
Onset Group

BackgroundThe melanocortinergic pathway orchestrates the energy homeostasis and impairments in this system often lead to an increase in body weight. Rare variants in the melanocortin 4 receptor (MC4R) gene resulting in partial or complete loss of function have been described with autosomal co-dominant inheritance. These mutations are the most common cause of non-syndromic monogenic obesity. In this context, this study aimed to sequence the MC4R gene in a Brazilian cohort of adults with severe obesity.MethodsThis study included 163 unrelated probands with Body Mass Index (BMI) ≥ 35 kg/m2, stratified into three groups, according to the period of obesity onset. From the total sample, 25 patients were enrolled in the childhood-onset group (0–11 years), 19 patients in the adolescence/youth-onset group (12–21 years), and 119 patients in the adult-onset group (>21 years). Blood pressure, anthropometric and biochemical characteristics were obtained, and the MC4R coding region of each subject’s DNA was assessed using automated Sanger sequencing.ResultsSignificant anthropometric differences between the groups were observed. Higher body weight and BMI medians were found in patients with childhood-onset or adolescence/youth-onset when compared to the adulthood-onset obesity group. A total of five mutations were identified, including four missense variants: p.Ser36Thr, p.Val103Ile, p.Ala175Thr, and p.Ile251Leu. Additionally, we observed one synonymous variant (p.Ile198=). The p.Ala175Thr variant was identified in a female case with severe obesity and adulthood-onset. This variant was previously described as a partial loss-of-function mutation, in which the minor allele poses dominant-negative effect, probably resulting in reduced cAMP activity.ConclusionThis study showed a prevalence of common and rare variants in a cohort of Brazilian adults with severe obesity and candidates to bariatric surgery. We have identified a rare potentially pathogenic MC4R variant in a Brazilian patient with severe and adulthood-onset obesity.

Classification of wheat PPO genes and effect of non-synonymous cSNP on kernel PPO activity

2008 ◽  
Vol 5 (1) ◽  
pp. 81-86 ◽  
Author(s):  
Wang Xiao-Bo ◽  
Ma Chuan-Xi ◽  
Si Hong-Qi ◽  
He Xian-Fang
Keyword(s):  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Chain Reaction ◽  
Wheat Varieties ◽  
Single Nucleotide ◽  
Pcr Product ◽  
Dnaman Software ◽  
Dna Fragment ◽  
Polymerase Chain

AbstractPolyphenol oxidase (PPO) activity is highly related to the undesirable browning of wheat-based end products. In this study, wheat PPO sequences (mRNA) were searched/BLASTed in the NCBI database and aligned using DNAMAN software. The results showed that wheat PPO genes could be divided into two clusters (I and II) and that three genes (‘i’) of cluster II seemed not to be located on chromosomes 2A and 2D. Ninety-four single nucleotide polymorphisms (SNPs) were detected between two haplotypes of the PPO gene on chromosome 2D. Eighty of these were found in the coding region (coding (c) SNPs) and 36 were non-synonymous cSNPs, which could affect the PPO amino acid sequence. Primers (STS-H) were designed at some non-synonymous cSNPs sites and were used to investigate the correlations between allelic variants and PPO activity of seeds – a total of 130 common wheat varieties were evaluated in 2 years. The results showed that STS-H could amplify a 460 bp DNA fragment in most cultivars with high PPO activity, while no PCR product was detected in most cultivars with low PPO activity. To improve the selection efficiency of a single dominance molecular marker, the multiplex polymerase chain reaction (PCR) system of STS-H and STS01 markers was also studied, based on the complementary between them.

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