scholarly journals C. elegansharbors pervasive cryptic genetic variation for embryogenesis

2014 ◽  
Author(s):  
Annalise Paaby ◽  
Amelia White ◽  
David Riccardi ◽  
Kristin Gunsalus ◽  
Fabio Piano ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Networks ◽  
Genetic Basis ◽  
Disease Susceptibility ◽  
Disease Risk ◽  
Natural Populations ◽  
Cryptic Genetic Variation ◽  
Natural Genetic Variation ◽  
C Elegans ◽  
In The Wild

Conditionally functional mutations are an important class of natural genetic variation, yet little is known about their prevalence in natural populations or their contribution to disease risk. Here, we describe a vast reserve of cryptic genetic variation, alleles that are normally silent but which affect phenotype when the function of other genes is perturbed, in the gene networks ofC. elegansembryogenesis. We find evidence that cryptic-effect loci are ubiquitous and segregate at intermediate frequencies in the wild. The cryptic alleles demonstrate low developmental pleiotropy, in that specific, rather than general, perturbations are required to reveal them. Our findings underscore the importance of genetic background in characterizing gene function and provide a model for the expression of conditionally functional effects that may be fundamental in basic mechanisms of trait evolution and the genetic basis of disease susceptibility.

scholarly journals Wild worm embryogenesis harbors ubiquitous polygenic modifier variation

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Annalise B Paaby ◽  
Amelia G White ◽  
David D Riccardi ◽  
Kristin C Gunsalus ◽  
Fabio Piano ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Gene Function ◽  
Natural Populations ◽  
Complex Trait ◽  
Genetic Modifiers ◽  
Wild Type ◽  
Cryptic Genetic Variation ◽  
Quantitative Genetic ◽  
In The Wild

Embryogenesis is an essential and stereotypic process that nevertheless evolves among species. Its essentiality may favor the accumulation of cryptic genetic variation (CGV) that has no effect in the wild-type but that enhances or suppresses the effects of rare disruptions to gene function. Here, we adapted a classical modifier screen to interrogate the alleles segregating in natural populations of Caenorhabditis elegans: we induced gene knockdowns and used quantitative genetic methodology to examine how segregating variants modify the penetrance of embryonic lethality. Each perturbation revealed CGV, indicating that wild-type genomes harbor myriad genetic modifiers that may have little effect individually but which in aggregate can dramatically influence penetrance. Phenotypes were mediated by many modifiers, indicating high polygenicity, but the alleles tend to act very specifically, indicating low pleiotropy. Our findings demonstrate the extent of conditional functionality in complex trait architecture.

scholarly journals Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Basten L. Snoek ◽  
Mark G. Sterken ◽  
Roel P. J. Bevers ◽  
Rita J. M. Volkers ◽  
Arjen van’t Hof ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Cryptic Genetic Variation ◽  
C Elegans

scholarly journals Unexpected cell type-dependent effects of autophagy on polyglutamine aggregation revealed by natural genetic variation in C. elegans

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
J. Alexander-Floyd ◽  
S. Haroon ◽  
M. Ying ◽  
A. A. Entezari ◽  
C. Jaeger ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Cell Type ◽  
Natural Genetic Variation ◽  
C Elegans ◽  
Polyglutamine Aggregation

scholarly journals Cryptic Genetic Variation in Natural Populations: A Predictive Framework

2014 ◽  
Vol 54 (5) ◽  
pp. 783-793 ◽  
Author(s):  
C. C. Ledon-Rettig ◽  
D. W. Pfennig ◽  
A. J. Chunco ◽  
I. Dworkin
Keyword(s):  
Genetic Variation ◽  
Natural Populations ◽  
Cryptic Genetic Variation

scholarly journals Regional genetic diversity in circadian period in Boechera stricta populations is high relative to the global range of diversity in Arabidopsis

2021 ◽  
Author(s):  
Robby McMinn ◽  
Matti Salmela ◽  
Cynthia Weinig
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Significant Proportion ◽  
Natural Populations ◽  
Elevational Gradient ◽  
Environmental Data ◽  
Population Variation ◽  
Circadian Period ◽  
In The Wild ◽  
Boechera Stricta

Circadian clocks manifest adaptations to predictable 24-h fluctuations in the exogenous environment, but it has yet to be determined why the endogenous circadian period length in the wild varies genetically around the hypothesized optimum of 24 h. We quantified genetic variation in circadian period in leaf movement in 30 natural populations of the Arabidopsis relative Boechera stricta sampled within only 1° of latitude but across an elevational gradient spanning 2460−3300 m in the Rocky Mountains. Measuring over 3800 plants from 473 maternal families (7−20 per population), we found genetic variation that was of similar magnitude among vs. within populations, with population means varying between 21.9−24.9 h and maternal family means within populations varying by up to ~6 h. After statistically factoring out spatial autocorrelation at the habitat extremes, we found that elevation explained a significant proportion of genetic variation in circadian period such that higher-elevation populations had shorter mean period lengths and less within-population variation. Environmental data indicate that these spatial trends could be related to steep regional climatic gradients in temperature, precipitation, and their intra-annual variability. Our findings provide evidence that spatially fine-grained environmental heterogeneity contributes to naturally occurring genetic diversity in circadian traits in wild populations.

scholarly journals Heritable variation in resistance to the endonuclear parasite Holospora undulata across clades of Paramecium caudatum

2020 ◽  
Author(s):  
Jared Weiler ◽  
Giacomo Zilio ◽  
Nathalie Zeballos ◽  
Louise Noergaard ◽  
Winiffer D. Conce Alberto ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Natural Populations ◽  
Infection Prevalence ◽  
Post Inoculation ◽  
Paramecium Caudatum ◽  
Heritable Variation ◽  
Natural Genetic Variation ◽  
Geographical Scale ◽  
Neutral Marker ◽  
The Difference

AbstractResistance is a key determinant in interactions between hosts and their parasites. Understanding the amount and distribution of genetic variation in this trait can provide insights into (co)evolutionary processes and their potential to shape patterns of diversity in natural populations. Using controlled inoculation in experimental mass cultures, we investigated the quantitative genetic variation in resistance to the bacterial parasite Holospora undulata across a worldwide collection of strains of its ciliate host Paramecium caudatum. We combined the observed variation with available information on the phylogeny and biogeography of the strains. We found substantial variation in resistance among strains (with broad-sense heritability > 0.5), repeatable between laboratories and ranging from total resistance to near-complete susceptibility. Early (one week post inoculation) measurements provided higher estimates of resistance heritability than did later measurements (2-3 weeks), possibly due to diverging epidemiological dynamics in replicate cultures of the same strains. Genetic distance (based on a neutral marker) was positively correlated with the difference in resistance phenotype between strains (r = 0.45), essentially reflecting differences between highly divergent clades (haplogroups) within the host species. Haplogroup A strains, mostly European, were less resistant to the parasite (49% infection prevalence) than non-European haplogroup B strains (28%). At a smaller geographical scale (within Europe), strains that are geographically closer to the parasite origin (Southern Germany) were more susceptible to infection than those from further away. These patterns are consistent with a picture of local parasite adaptation. Our study demonstrates ample natural genetic variation in resistance on which selection can act and hints at symbiont adaptation producing signatures in geographic and lineage-specific patterns of resistance in this model system.

scholarly journals Natural Genetic Variation in a Multigenerational Phenotype in C. elegans

2018 ◽  
Vol 28 (16) ◽  
pp. 2588-2596.e8 ◽  
Author(s):  
Lise Frézal ◽  
Emilie Demoinet ◽  
Christian Braendle ◽  
Eric Miska ◽  
Marie-Anne Félix
Keyword(s):  
Genetic Variation ◽  
Natural Genetic Variation ◽  
C Elegans

scholarly journals Genetic Variation for Phenotypically Invariant Traits Detected in Teosinte: Implications for the Evolution of Novel Forms

Genetics ◽  
2002 ◽  
Vol 160 (1) ◽  
pp. 333-342
Author(s):  
Nick Lauter ◽  
John Doebley
Keyword(s):  
Genetic Variation ◽  
Single Gene ◽  
Phenotypic Expression ◽  
Natural Populations ◽  
Gene Mutations ◽  
Character State ◽  
Multiple Gene ◽  
Cryptic Genetic Variation ◽  
Mapping Strategy ◽  
Discrete Character

Abstract How new discrete states of morphological traits evolve is poorly understood. One possibility is that single-gene changes underlie the evolution of new discrete character states and that evolution is dependent on the occurrence of new single-gene mutations. Another possibility is that multiple-gene changes are required to elevate an individual or population above a threshold required to produce the new character state. A prediction of the latter model is that genetic variation for the traits should exist in natural populations in the absence of phenotypic variation. To test this idea, we studied traits that are phenotypically invariant within teosinte and for which teosinte is discretely different from its near relative, maize. By employing a QTL mapping strategy to analyze the progeny of a testcross between an F1 of two teosintes and a maize inbred line, we identified cryptic genetic variation in teosinte for traits that are invariant in teosinte. We argue that such cryptic genetic variation can contribute to the evolution of novelty when reconfigured to exceed the threshold necessary for phenotypic expression or by acting to modify or stabilize the effects of major mutations.

scholarly journals Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut

2021 ◽  
Author(s):  
Fan Zhang ◽  
Jessica L. Weckhorst ◽  
Adrien Assié ◽  
Ciara Hosea ◽  
Christopher A. Ayoub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Caenorhabditis Elegans ◽  
Signaling Pathways ◽  
Insulin Signaling ◽  
Natural Genetic Variation ◽  
Microbiome Composition ◽  
C Elegans ◽  
Free Living Nematode ◽  
Wild Strains ◽  
The Stability

Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans strains that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the phylogenetic and functional diversity naturally found in the C. elegans microbiome. Using this community, we show that C. elegans utilizes immune, xenobiotic and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with the enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of daf-2/IGFR and requires the insulin signaling transcription factors daf-16/FOXO and pqm-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum is correlated positively with host outcomes, as animals that develop faster are larger and have higher gut Ochrobactrum colonization as adults. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of microbiome composition in C. elegans.

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