scholarly journals Multiple layers of cryptic genetic variation underlie a yeast complex trait

2018 ◽  
Author(s):  
Jonathan T Lee ◽  
Alessandro L V Coradini ◽  
Amy Shen ◽  
Ian M Ehrenreich

Cryptic genetic variation may be an important contributor to heritable traits, but its extent and regulation are not fully understood. Here, we investigate the cryptic genetic variation underlying a Saccharomyces cerevisiae colony phenotype that is typically suppressed in a cross of the lab strain BY4716 (BY) and a derivative of the clinical isolate 322134S (3S). To do this, we comprehensively map the trait's genetic basis in the BYx3S cross in the presence of three different genetic perturbations that enable its expression. This allows us to detect and compare the specific loci harboring cryptic genetic variants that interact with each perturbation. In total, we identify 21 loci, all but one of which interacts with just a subset of the perturbations. Beyond impacting which loci contribute to the trait, the genetic perturbations also influence the extent of additivity, epistasis, and genotype-environment interaction among the detected loci. Additionally, we show that the single locus interacting with all three perturbations corresponds to the coding region of the cell surface gene FLO11. Nearly all of the other loci influence FLO11 transcription in cis or trans. However, the perturbations reveal cryptic genetic variation in different pathways and sub-pathways upstream of FLO11, suggesting that multiple layers of cryptic genetic variation with highly contextual effects underlie the trait. Our work demonstrates an abundance of cryptic genetic variation in transcriptional regulation and illustrates how this cryptic genetic variation complicates efforts to study the relationship between genotype and phenotype.

Genetics ◽  
2019 ◽  
Vol 211 (4) ◽  
pp. 1469-1482 ◽  
Author(s):  
Jonathan T. Lee ◽  
Alessandro L. V. Coradini ◽  
Amy Shen ◽  
Ian M. Ehrenreich

2020 ◽  
Vol 7 (3) ◽  
pp. 191720 ◽  
Author(s):  
Kristen Côté ◽  
Andrew M. Simons

High levels of genetic variation are often observed in natural populations, suggesting the action of processes such as frequency-dependent selection, heterozygote advantage and variable selection. However, the maintenance of genetic variation in fitness-related traits remains incompletely explained. The extent of genetic variation in obligately self-fertilizing populations of Lobelia inflata (Campanulaceae L.) strongly implies balancing selection. Lobelia inflata thus offers an exceptional opportunity for an empirical test of genotype-environment interaction (G × E) as a variance-maintaining mechanism under fluctuating selection: L. inflata is monocarpic and reproduces only by seed, facilitating assessment of lifetime fitness; genome-wide homozygosity precludes some mechanisms of balancing selection, and microsatellites are, in effect, genotypic lineage markers. Here, we find support for the temporal G × E hypothesis using a manipulated space-for-time approach across four environments: a field environment, an outdoor experimental plot and two differing growth-chamber environments. High genetic variance was confirmed: 83 field-collected individuals consisted of 45 distinct microsatellite lineages with, on average, 4.5 alleles per locus. Rank-order fitness, measured as lifetime fruit production in 16 replicated multilocus genotypes, changed significantly across environments. Phenotypic differences among microsatellite lineages were detected. Results thus support the G × E hypothesis in principle. However, the evaluation of the effect size of this mechanism and fitness effects of life-history traits will require a long-term study of fluctuating selection on labelled genotypes in the field.


1984 ◽  
Vol 103 (3) ◽  
pp. 543-547 ◽  
Author(s):  
S. Singh ◽  
M. S. Dahiya

SummaryThe data obtained from 360 progeny families produced by crossing 40 F2 plants from each of three wheat crosses HD 2009 × HD 1949, Raj 821 × WH 147 and NP 876 × HD 1949, to three testers (the testers being the two parents of each original cross and their F1 in each case) were subjected to triple test cross analysis for detecting and estimating additive, dominance and epistatic components of genetic variation and interaction of these components with environment for plant height, spike length, number of tillers per plant, number of spikelets per spike, number of grains per spike, 1000-grain weight, number of days from sowing to heading and to maturity, grain yield per plant and grain yield/above ground dry matter ratio (harvest index). Epistasis was an important element for plant height, number of tillers per plant, number of grains per spike and grain yield per plant in all three crosses. Both the i type and j and l type epistasis were equally important. In general, the magnitude of additive component was larger than that of dominance component. The additive gene effects were more sensitive to environmental change than the dominance gene effects. Similarly, j and l type epistasis was relatively more sensitive to environment than the i type epistasis.


1992 ◽  
Vol 41 (4) ◽  
pp. 335-352 ◽  
Author(s):  
J. Ando

AbstractThe present study compared two different types of English-language teaching approaches, the grammatical approach (GA) and the communicative approach (CA), by the cotwin control method. This study has two purposes: to study the effects of teaching approaches and to estimate genetic influences upon learning aptitudes. Seven pairs of identical twins (MZ) and 4 pairs of fraternal twins (DZ) participated in the experiment along with 68 other nontwin fifth graders. Each cotwin was assigned to the GA and CA respectively and received 20 hours of lessons over a 10-day period. The behavioral similarities between MZ cotwins were statistically and descriptively depicted. No major effect of either teaching approach was noted, but the genetic influence upon individual differences of learning achievement was obvious. Furthermore, an interesting interaction between the teaching approaches and intelligence was found, that is, that the GA capitalises on and CA compensates for intelligence. This interactional pattern could be interpreted as an example of genotype-environment interaction. The relationship between genetic factors and learning aptitudes is discussed.


Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1233-1244 ◽  
Author(s):  
Juha Merilä ◽  
James D Fry

Abstract In several studies of natural populations of birds, the heritability of body size estimated by parent-offspring regression has been lower when offspring have developed in poor feeding regimens than when they developed in good feeding regimens. This has led to the suggestion that adaptation under poor regimens may be constrained by lack of genetic variation. We examined the influence of environmental conditions on expression of genetic variation in body size of nestling blue tits (Parus caeruleus) by raising full sibs in artificially reduced and enlarged broods, corresponding to good and poor feeding regimens, respectively. Individuals grown in the poor regimen attained smaller body size than their sibs grown in the good regimen. However, there was among-family variation in response to the treatments—i.e., genotype-environment interactions (GEIs). Partitioning the GEI variance into contributions attributable to (1) differences in the among-family genetic variance between the treatments and (2) imperfect correlation of genotypic values across treatments identified the latter as the main cause of the GEI. Parent-offspring regressions were not significantly different when offspring were reared in the good environment (h2 = 0.75) vs. when they were reared in the poor environment (h2 = 0.63). Thus, there was little evidence that genetic variance in body size was lower under the poor conditions than under the good conditions. These results do not support the view that the genetic potential for adaptation to poor feeding conditions is less than that for adaptation to good conditions, but they do suggest that different genotypes may be favored under the different conditions.


2015 ◽  
Vol 282 (1819) ◽  
pp. 20152041 ◽  
Author(s):  
Robert Peuß ◽  
Hendrik Eggert ◽  
Sophie A. O. Armitage ◽  
Joachim Kurtz

The relationship between robustness and evolvability is a long-standing question in evolution. Heat shock protein 90 (HSP90), a molecular chaperone, has been identified as a potential capacitor for evolution, since it allows for the accumulation and release of cryptic genetic variation, and also for the regulation of novel genetic variation through transposon activity. However, to date, it is unknown whether Hsp90 expression is regulated upon demand (i.e. when the release of cryptic genetic variation is most needed). Here, we show that Hsp90 has reduced transcription under conditions where the mobilization of genetic variation could be advantageous. We designed a situation that indicates a stressful environment but avoids the direct effects of stress, by placing untreated (focal) red flour beetles, Tribolium castaneum , into groups together with wounded conspecifics, and found a consistent reduction in expression of two Hsp90 genes ( Hsp83 and Hsp90 ) in focal beetles. We moreover observed a social transfer of immunity in this non-eusocial insect: there was increased activity of the phenoloxidase enzyme and downregulation of the immune regulator, imd . Our study poses the exciting question of whether evolvability might be regulated through the use of information derived from the social environment.


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