scholarly journals Mutations in EID1 and LNK2 caused light-conditional clock deceleration during tomato domestication

2018 ◽  
Vol 115 (27) ◽  
pp. 7135-7140 ◽  
Author(s):  
Niels A. Müller ◽  
Lei Zhang ◽  
Maarten Koornneef ◽  
José M. Jiménez-Gómez
Keyword(s):  
Clock Gene ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Genomic Region ◽  
Circadian Period ◽  
Circadian Phase ◽  
Signatures Of Selection ◽  
Period Lengthening ◽  
Phytochrome B1 ◽  
Light Input

Circadian period and phase of cultivated tomato (Solanum lycopersicum) were changed during domestication, likely adapting the species to its new agricultural environments. Whereas the delayed circadian phase is mainly caused by allelic variation of EID1, the genetic basis of the long circadian period has remained elusive. Here we show that a partial deletion of the clock gene LNK2 is responsible for the period lengthening in cultivated tomatoes. We use resequencing data to phylogenetically classify hundreds of tomato accessions and investigate the evolution of the eid1 and lnk2 mutations along successive domestication steps. We reveal signatures of selection across the genomic region of LNK2 and different patterns of fixation of the mutant alleles. Strikingly, LNK2 and EID1 are both involved in light input to the circadian clock, indicating that domestication specifically targeted this input pathway. In line with this, we show that the clock deceleration in the cultivated tomato is light-dependent and requires the phytochrome B1 photoreceptor. Such conditional variation in circadian rhythms may be key for latitudinal adaptation in a variety of species, including crop plants and livestock.

Novel Loci Control Variation in Reproductive Timing inArabidopsis thalianain Natural Environments

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1875-1884 ◽  
Author(s):  
Cynthia Weinig ◽  
Mark C Ungerer ◽  
Lisa A Dorn ◽  
Nolan C Kane ◽  
Yuko Toyonaga ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Allelic Variation ◽  
Developmental Pathways ◽  
Natural Environments ◽  
Reproductive Timing ◽  
Controlled Environments ◽  
Photoperiod Pathway ◽  
Differential Involvement ◽  
Short Days ◽  
Transition To Flowering

AbstractMolecular biologists are rapidly characterizing the genetic basis of flowering in model species such as Arabidopsis thaliana. However, it is not clear how the developmental pathways identified in controlled environments contribute to variation in reproductive timing in natural ecological settings. Here we report the first study of quantitative trait loci (QTL) for date of bolting (the transition from vegetative to reproductive growth) in A. thaliana in natural seasonal field environments and compare the results with those obtained under typical growth-chamber conditions. Two QTL specific to long days in the chamber were expressed only in spring-germinating cohorts in the field, and two loci specific to short days in the chamber were expressed only in fall-germinating cohorts, suggesting differential involvement of the photoperiod pathway in different seasonal environments. However, several other photoperiod-specific QTL with large effects in controlled conditions were undetectable in natural environments, indicating that expression of allelic variation at these loci was overridden by environmental factors specific to the field. Moreover, a substantial number of QTL with major effects on bolting date in one or more field environments were undetectable under controlled environment conditions. These novel loci suggest the involvement of additional genes in the transition to flowering under ecologically relevant conditions.

scholarly journals Allelic variation in a single genomic region alters the hemolymph proteome in the snail Biomphalaria glabrata

2019 ◽  
Vol 88 ◽  
pp. 301-307 ◽  
Author(s):  
Euan R.O. Allan ◽  
Liping Yang ◽  
Jacob A. Tennessen ◽  
Michael S. Blouin
Keyword(s):  
Allelic Variation ◽  
Biomphalaria Glabrata ◽  
Genomic Region

scholarly journals Indirect genetic control of migration in a salmonid fish

2020 ◽  
Vol 16 (8) ◽  
pp. 20200299
Author(s):  
Suzanne J. Kelson ◽  
Stephanie M. Carlson ◽  
Michael R. Miller
Keyword(s):  
Growth Rate ◽  
Life History ◽  
Genetic Control ◽  
Early Life ◽  
Genetic Basis ◽  
Complex Trait ◽  
Genomic Region ◽  
Physiological Traits ◽  
Migratory Behaviour ◽  
Large Genomic Region

Migration is a complex trait that often has genetic underpinnings. However, it is unclear if migratory behaviour itself is inherited (direct genetic control), or if the decision to migrate is instead the outcome of a set of physiological traits (indirect genetic control). For steelhead/rainbow trout ( Oncorhynchus mykiss ), migration is strongly linked to a large genomic region across their range. Here, we demonstrate a shared allelic basis between early life growth rate and migratory behaviour. Next, we demonstrate that early life growth differs among resident/migratory genotypes in wild juveniles several months prior to migration, with resident genotypes achieving a larger size in their first few months of life than migratory genotypes. We suggest that the genetic basis of migration is likely indirect and mediated by physiological traits such as growth rate. Evolutionary benefits of this indirect genetic mechanism likely include flexibility among individuals and persistence of life-history diversity within and among populations.

scholarly journals 0433 Targeting Light Sensitivity Parameters to Optimize Circadian Phase Predictions

SLEEP ◽  
2020 ◽  
Vol 43 (Supplement_1) ◽  
pp. A166-A166
Author(s):  
J E Stone ◽  
E M McGlashan ◽  
S W Cain ◽  
A J Phillips
Keyword(s):  
Sensitivity Analysis ◽  
Circadian Clock ◽  
Mean Absolute Error ◽  
Light Response ◽  
Absolute Error ◽  
Light Sensitivity ◽  
Model Parameters ◽  
Circadian Period ◽  
Individual Level ◽  
Circadian Phase

Abstract Introduction Existing models of the human circadian clock accurately predict phase at group-level but not at individual-level. Interindividual variability in light sensitivity is not currently accounted for in these models and may be a practical approach to improving individual-level predictions. Using the gold-standard predictive model, we (i) identified whether varying light sensitivity parameters produces meaningful changes in predicted phase in field conditions; and (ii) tested whether optimizing parameters can significantly improve accuracy of circadian phase prediction. Methods Healthy participants (n=12, 7 women, aged 18-26) underwent continuous light and activity monitoring for 3 weeks (Actiwatch Spectrum). Salivary dim light melatonin onset (DLMO) was measured each week. A model of the human circadian clock and its response to light was used to predict the three weekly DLMO times using the individual’s light data. A sensitivity analysis was performed varying three model parameters within physiological ranges: (i) amplitude of the light response [p]; (ii) advance vs. delay bias of the light response [K]; and (iii) intrinsic circadian period [tau]. These parameters were then fitted using least squares estimation to obtain optimal predictions of DLMO for each individual. Accuracy was compared between optimized parameters and default parameters. Results The default model predicted DLMO with mean absolute error of 1.02h. Sensitivity analysis showed the average range of variation in predicted DLMOs across participants was 0.65h for p, 4.28h for K and 3.26h for tau. Fitting parameters independently, we found mean absolute error of 0.85h for p, 0.71h for K and 0.75h for tau. Fitting p and K together reduced mean absolute error to 0.57h. Conclusion Light sensitivity parameters capture similar or greater variability in phase as intrinsic circadian period, indicating they are a viable option for individualising circadian phase predictions. Future prospective work is needed using measures of light sensitivity to validate this approach. Support N/A

scholarly journals Circadian phase, circadian period and chronotype are reproducible over months

2017 ◽  
Vol 35 (2) ◽  
pp. 280-288 ◽  
Author(s):  
Thomas Kantermann ◽  
Charmane I Eastman
Keyword(s):  
Circadian Period ◽  
Circadian Phase

Genetic basis of Creutzfeldt-Jakob disease in the United Kingdom: a systematic analysis of predisposing mutations and allelic variation in the PRNP gene

1996 ◽  
Vol 98 (3) ◽  
pp. 259-264 ◽  
Author(s):  
O. Windl ◽  
Maureen Dempster ◽  
J. Peter Estibeiro ◽  
Richard Lathe ◽  
Rajith de Silva ◽  
...  
Keyword(s):  
United Kingdom ◽  
Genetic Basis ◽  
Allelic Variation ◽  
Prnp Gene ◽  
Systematic Analysis ◽  
The United Kingdom ◽  
Jakob Disease

scholarly journals Allelic Variation in a Willow Warbler Genomic Region Is Associated with Climate Clines

PLoS ONE ◽  
2014 ◽  
Vol 9 (5) ◽  
pp. e95252 ◽  
Author(s):  
Keith W. Larson ◽  
Miriam Liedvogel ◽  
BriAnne Addison ◽  
Oddmund Kleven ◽  
Terje Laskemoen ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Genomic Region ◽  
Willow Warbler

scholarly journals A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly

Genes ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1297
Author(s):  
Surabhi Ranavat ◽  
Hannes Becher ◽  
Mark F. Newman ◽  
Vinita Gowda ◽  
Alex D. Twyford
Keyword(s):  
Genetic Basis ◽  
De Novo ◽  
Draft Genome ◽  
Spatial Separation ◽  
Genomic Region ◽  
Alpinia Nigra ◽  
Floral Phenotype ◽  
Temporal And Spatial ◽  
Candidate Regions ◽  
High Depth

Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.

scholarly journals Development of SNP Markers for White Immature Fruit Skin Color in Cucumber (Cucumis sativus L.) Using QTL-seq and Marker Analyses

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2341
Author(s):  
D. S. Kishor ◽  
Hemasundar Alavilli ◽  
Sang-Choon Lee ◽  
Jeong-Gu Kim ◽  
Kihwan Song
Keyword(s):  
Skin Color ◽  
Genetic Basis ◽  
Recessive Gene ◽  
Genomic Region ◽  
Chromosome 3 ◽  
Missense Mutations ◽  
Cucumis Sativus L ◽  
Immature Fruit ◽  
Fruit Skin ◽  
Light Green

Despite various efforts in identifying the genes governing the white immature fruit skin color in cucumber, the genetic basis of the white immature fruit skin color is not well known. In the present study, genetic analysis showed that a recessive gene confers the white immature fruit skin-color phenotype over the light-green color of a Korean slicer cucumber. High-throughput QTL-seq combined with bulked segregation analysis of two pools with the extreme phenotypes (white and light-green fruit skin color) in an F2 population identified two significant genomic regions harboring QTLs for white fruit skin color within the genomic region between 34.1 and 41.67 Mb on chromosome 3, and the genomic region between 12.2 and 12.7 Mb on chromosome 5. Further, nonsynonymous SNPs were identified with a significance of p < 0.05 within the QTL regions, resulting in eight homozygous variants within the QTL region on chromosome 3. SNP marker analysis uncovered the novel missense mutations in Chr3CG52930 and Chr3CG53640 genes and showed consistent results with the phenotype of light-green and white fruit skin-colored F2 plants. These two genes were located 0.5 Mb apart on chromosome 3, which are considered strong candidate genes. Altogether, this study laid a solid foundation for understanding the genetic basis and marker-assisted breeding of immature fruit skin color in cucumber.

scholarly journals Neuron-specific knockouts indicate the importance of network communication to Drosophila rhythmicity

2019 ◽  
Author(s):  
M Schlichting ◽  
MM Diaz ◽  
J Xin ◽  
M Rosbash
Keyword(s):  
Gene Expression ◽  
Circadian Rhythms ◽  
Intercellular Communication ◽  
Clock Gene ◽  
Feedback Loops ◽  
Neuronal Firing ◽  
Network Communication ◽  
Constant Darkness ◽  
Circadian Period ◽  
Clock Gene Expression

AbstractAnimal circadian rhythms persist in constant darkness and are driven by intracellular transcription-translation feedback loops. Although these cellular oscillators communicate, isolated mammalian cellular clocks continue to tick away in darkness without intercellular communication. To investigate these issues in Drosophila, we assayed behavior as well as molecular rhythms within individual brain clock neurons while blocking communication within the ca. 150 neuron clock network. We also generated CRISPR-mediated neuron-specific circadian clock knockouts. The results point to two key clock neuron groups: loss of the clock within both regions but neither one alone has a strong behavioral phenotype in darkness; communication between these regions also contributes to circadian period determination. Under these dark conditions, the clock within one region persists without network communication. The clock within the famous PDF-expressing s-LNv neurons however was strongly dependent on network communication, likely because clock gene expression within these vulnerable sLNvs depends on neuronal firing or light.

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