scholarly journals Plasticity of maternal environment dependent expression-QTLs of tomato seeds

2021 ◽  
Author(s):  
Mark G. Sterken ◽  
Harm Nijveen ◽  
Martijn van Zanten ◽  
Jose Jimenez-Gomez ◽  
Nafiseh Geshnizjani ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Seed Quality ◽  
Maternal Environment ◽  
Natural Genetic Variation ◽  
Knowledge Based ◽  
Environmental Responsiveness ◽  
Germination Ability ◽  
Genetic Landscape ◽  
Nutrient Environment

Seeds are essential for plant reproduction, survival, and dispersal. Germination ability and successful establishment of young seedlings strongly depends on seed quality and on environmental factors such as nutrient availability. In tomato (Solanum lycopersicum) and many other species, seed quality and seedling establishment characteristics are determined by genetic variation, as well as the maternal environment in which the seeds develop and mature. The genetic contribution to variation in seed and seedling quality traits and environmental responsiveness can be estimated at transcriptome level in the dry seed by mapping genomic loci that affect gene expression (expression QTLs) in contrasting maternal environments. In this study, we applied RNA-sequencing to measure gene expression of seeds of a tomato RIL population derived from a cross between S. lycopersicum (cv. Moneymaker) and S. pimpinellifolium (G1.1554). The seeds matured on plants cultivated under different nutritional environments; i.e. on high phosphorus or low nitrogen. The obtained SNPs were subsequently used to construct a high-density genetic map. We show how the genetic landscape of plasticity in gene regulation in dry seeds is affected by the maternal nutrient environment. The combined information on natural genetic variation mediating (variation in) responsiveness to the environment may contribute to knowledge-based breeding programs aiming to develop crop cultivars that are resilient to stressful environments.

scholarly journals Translating natural genetic variation to gene expression in a computational model of the Drosophila gap gene regulatory network

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184657 ◽  
Author(s):  
Vitaly V. Gursky ◽  
Konstantin N. Kozlov ◽  
Ivan V. Kulakovskiy ◽  
Asif Zubair ◽  
Paul Marjoram ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Computational Model ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Natural Genetic Variation ◽  
Gap Gene ◽  
Gene Regulatory

scholarly journals Natural genetic variation profoundly regulates gene expression in immune cells and dictates susceptibility to CNS autoimmunity

2016 ◽  
Vol 17 (7) ◽  
pp. 386-395 ◽  
Author(s):  
F Bearoff ◽  
R del Rio ◽  
L K Case ◽  
J A Dragon ◽  
T Nguyen-Vu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Immune Cells ◽  
Natural Genetic Variation ◽  
Cns Autoimmunity

scholarly journals Natural genetic variation alters Alzheimer’s‐related gene expression modules in mice

2020 ◽  
Vol 16 (S2) ◽  
Author(s):  
Ann E. Wells ◽  
Narayanan Raghupathy ◽  
Raymond F. Robledo ◽  
Daniel M. Gatti ◽  
Steven C. Munger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Related Gene ◽  
Natural Genetic Variation

scholarly journals Impact of Natural Genetic Variation on Gene Expression Dynamics

PLoS Genetics ◽  
2013 ◽  
Vol 9 (6) ◽  
pp. e1003514 ◽  
Author(s):  
Marit Ackermann ◽  
Weronika Sikora-Wohlfeld ◽  
Andreas Beyer
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Natural Genetic Variation ◽  
Gene Expression Dynamics

scholarly journals Natural genetic variation affecting transcription factor spacing at regulatory regions is generally well tolerated

2020 ◽  
Author(s):  
Zeyang Shen ◽  
Jenhan Tao ◽  
Gregory J. Fonseca ◽  
Christopher K. Glass
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Binding Sites ◽  
Regulation Of Gene Expression ◽  
Regulatory Elements ◽  
Nucleotide Polymorphisms ◽  
Enhancer Activity ◽  
Single Nucleotide ◽  
Natural Genetic Variation ◽  
Influence Gene Expression

AbstractRegulation of gene expression requires the combinatorial binding of sequence-specific transcription factors (TFs) at promoters and enhancers. Single nucleotide polymorphisms (SNPs) and short insertions and deletions (InDels) can influence gene expression by altering the sequences of TF binding sites. Prior studies also showed that alterations in the spacing between TF binding sites can influence promoter and enhancer activity. However, the relative importance of altered TF spacing has not been systematically analyzed in the context of natural genetic variation. Here, we exploit millions of InDels provided by five diverse strains of mice to globally investigate the effects of altered spacing on TF binding and local histone acetylation in macrophages. We find that spacing alterations resulting from InDels are generally well tolerated in comparison to genetic variants that directly alter TF binding sites. These findings have implications for interpretation of non-coding genetic variation and comparative analysis of regulatory elements across species.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. VI. Environmental Constraints on Adaptation and Divergence

Genetics ◽  
1997 ◽  
Vol 146 (2) ◽  
pp. 471-479 ◽  
Author(s):  
Michael Travisano
Keyword(s):  
Escherichia Coli ◽  
Genetic Variation ◽  
Experimental Evolution ◽  
Population Genetic ◽  
Environmental Constraints ◽  
Asymmetric Pattern ◽  
Nutrient Environment ◽  
Mean Fitness ◽  
Population Genetic Variation

The effect of environment on adaptation and divergence was examined in two sets of populations of Escherichia coli selected for 1000 generations in either maltose- or glucose-limited media. Twelve replicate populations selected in maltose-limited medium improved in fitness in the selected environment, by an average of 22.5%. Statistically significant among-population genetic variation for fitness was observed during the course of the propagation, but this variation was small relative to the fitness improvement. Mean fitness in a novel nutrient environment, glucose-limited medium, improved to the same extent as in the selected environment, with no statistically significant among-population genetic variation. In contrast, 12 replicate populations previously selected for 1000 generations in glucose-limited medium showed no improvement, as a group, in fitness in maltose-limited medium and substantial genetic variation. This asymmetric pattern of correlated responses suggests that small changes in the environment can have profound effects on adaptation and divergence.

scholarly journals Inherited Differences in Crossing Over and Gene Conversion Frequencies Between Wild Strains of Sordaria fimicola From “Evolution Canyon”

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1573-1593
Author(s):  
Muhammad Saleem ◽  
Bernard C Lamb ◽  
Eviatar Nevo
Keyword(s):  
Genetic Variation ◽  
Gene Conversion ◽  
Spontaneous Mutation ◽  
Crossing Over ◽  
Natural Genetic Variation ◽  
Evolution Canyon ◽  
Wild Strains ◽  
Sordaria Fimicola ◽  
First And Second Generation ◽  
Consistent Direction

Abstract Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in “Evolution Canyon,” Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II.

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