Genotype-environment interaction involving site differences in expression of genetic variation along with genotypic rank changes: simulations of economic significance

2018 ◽  
Vol 15 (1) ◽  
Author(s):  
Rowland D. Burdon ◽  
Yongjun Li
Keyword(s):  
Genetic Variation ◽  
Environment Interaction ◽  
Economic Significance ◽  
Genotype Environment Interaction

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
Keyword(s):  
Genetic Variation ◽  
Complex Trait ◽  
Environment Interaction ◽  
Coding Region ◽  
Cryptic Genetic Variation ◽  
Genotype Environment Interaction ◽  
Genetic Perturbations ◽  
In Cis ◽  
The Relationship ◽  
Surface Gene

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.

scholarly journals Genotype-environment interaction and the maintenance of genetic variation: an empirical study of Lobelia inflata (Campanulaceae)

2020 ◽  
Vol 7 (3) ◽  
pp. 191720 ◽  
Author(s):  
Kristen Côté ◽  
Andrew M. Simons
Keyword(s):  
Genetic Variation ◽  
Balancing Selection ◽  
Rank Order ◽  
Empirical Test ◽  
Heterozygote Advantage ◽  
Environment Interaction ◽  
Fluctuating Selection ◽  
Long Term Study ◽  
Genotype Environment Interaction ◽  
Lobelia Inflata

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.

Detection and estimation of components of genetic variation and genotype × environment interaction in three wheat crosses

1984 ◽  
Vol 103 (3) ◽  
pp. 543-547 ◽  
Author(s):  
S. Singh ◽  
M. S. Dahiya
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Plant Height ◽  
Environment Interaction ◽  
Gene Effects ◽  
Genotype Environment Interaction ◽  
Additive Component ◽  
Spike Number ◽  
Additive Gene ◽  
1000 Grain Weight

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.

Genetic Variation and Genotype × Environment Interaction for Yield and Other Agronomic Traits in Cassava in Nigeria

2007 ◽  
Vol 99 (4) ◽  
pp. 1137-1142 ◽  
Author(s):  
C. N. Egesi ◽  
P. Ilona ◽  
F. O. Ogbe ◽  
M. Akoroda ◽  
A. Dixon
Keyword(s):  
Genetic Variation ◽  
Agronomic Traits ◽  
Environment Interaction ◽  
Genotype Environment Interaction

Genetic Variation and Causes of Genotype-Environment Interaction in the Body Size of Blue Tit (Parus caeruleus)

Genetics ◽  
1998 ◽  
Vol 148 (3) ◽  
pp. 1233-1244 ◽  
Author(s):  
Juha Merilä ◽  
James D Fry
Keyword(s):  
Genetic Variation ◽  
Body Size ◽  
Genetic Variance ◽  
Natural Populations ◽  
The Body ◽  
Environment Interaction ◽  
Parus Caeruleus ◽  
Genotype Environment Interaction ◽  
The Poor ◽  
Good Environment

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.

Family variation in photosynthesis of 22-year-old black spruce: a test of two models of physiological response to water stress

1996 ◽  
Vol 26 (11) ◽  
pp. 1922-1933 ◽  
Author(s):  
John E. Major ◽  
Kurt H. Johnsen
Keyword(s):  
Genetic Variation ◽  
Soil Moisture ◽  
Water Potential ◽  
Black Spruce ◽  
Alternative Hypothesis ◽  
Genetic Differences ◽  
Environment Interaction ◽  
Physiological Measurement ◽  
Genotype Environment Interaction ◽  
Moisture Conditions

Gas exchange and water potential were measured in 22-year-old black spruce (Piceamariana (Mill.) BSP) trees from four full-sib families on two sites (one drier and one wetter) at the Petawawa National Forestry Institute, Ontario. Based on an observed genotype × environment interaction and earlier work with seedlings, a hypothesis was formed that at high soil moisture availability, no genetic differences in net photosynthesis (Pn) would exist and as soil moisture decreases, genetic differences in Pn would increase. From results of initial research with mature trees we formed an alternative hypothesis that genetic differences in Pn are constantly maintained under an array of soil moisture conditions. The two models were rigorously tested over a range of soil moisture conditions using two physiological measurement crews who switched sites throughout the day. Second-year foliage Pn of mature black spruce was more affected by nonstomatal limitations than by stomatal limitations. Progeny of one female had 12.5% and 7.4% higher Pn than progeny of another female on the dry and wet site, respectively. Genetic variation in Pn was consistent over a range of soil water potential. Thus, the first hypothesis was rejected in favor of the alternative hypothesis. Genetic variation in Pn appeared to be due to differential response to vapor pressure deficit. Suggestions as to how to reconcile the observed genotype × environment interaction in growth with the genetic differences in Pn are discussed.

Gas exchange of 20-year-old black spruce families displaying a genotype × environment interaction in growth rate

1995 ◽  
Vol 25 (3) ◽  
pp. 430-439 ◽  
Author(s):  
Kurt H. Johnsen ◽  
John E. Major
Keyword(s):  
Growth Rate ◽  
Genetic Variation ◽  
Gas Exchange ◽  
Water Potential ◽  
Black Spruce ◽  
Female Parent ◽  
First Year ◽  
Environment Interaction ◽  
Xylem Water Potential ◽  
Genotype Environment Interaction

Gas exchange and xylem water potential were measured on 20-year-old black spruce (Piceamariana (Mill.) B.S.P) trees from four full-sib families from a 7 × 7 diallel. These families constitute a 2 parent × 2 parent factorial breeding structure. One female parent (59) produced families that have displayed high productivity on three plantation sites, whereas the other female parent (63) produced families that had high growth rates on two of the sites but not on the third, least productive, site. In 1991 (a hot, dry year) measurements were obtained from trees at two sites; in 1992 (a cool, wet year) measurements were obtained from only one site. Gas exchange was measured on detached branches cut from the upper third of the crown; measurements were initiated within 2 min from cutting. In 1991, daytime xylem water potential, predawn xylem water potential, net photosynthesis (Pn), and needle conductance (gwv) were all lower in trees growing on the least productive site (2) than in trees growing on the most productive site (3), indicating that trees on site 2 were under greater water stress than those on site 3. Progeny of female 59 displayed higher Pn than progeny of female 63 over both years of contrasting rainfall and on both the wetter and drier sites during the first year. However, progeny of the two female parents did not differ with respect to gwv in either year nor on either site during the first year. The genetic variation in Pn/gwv, observed over sites and years, is positively related to growth rate only on the dry site. Thus, the genotype × environment interaction in growth appears to be due to relatively stable genetic differences in Pn. We hypothesize that water stress on the dry site reduces Pn below a threshold value at which point genetic variation in Pn impacts on productivity and results in genetic variation in growth rate. Furthermore, we hypothesize that on the wet site carbon gain per unit leaf area is not as limiting to growth rate; thus, the observed genetic differences in Pn do not influence genetic rankings in growth rate.

scholarly journals Genotype-Environment Interaction for Quantitative Trait Loci Affecting Life Span in Drosophila melanogaster

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 213-227 ◽  
Author(s):  
Cristina Vieira ◽  
Elena G Pasyukova ◽  
Zhao-Bang Zeng ◽  
J Brant Hackett ◽  
Richard F Lyman ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Quantitative Trait Loci ◽  
Life Span ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
Adult Life ◽  
Environment Interaction ◽  
Mapping Procedure ◽  
Genotype Environment Interaction ◽  
Trait Loci

Abstract The nature of genetic variation for Drosophila longevity in a population of recombinant inbred lines was investigated by estimating quantitative genetic parameters and mapping quantitative trait loci (QTL) for adult life span in five environments: standard culture conditions, high and low temperature, and heat-shock and starvation stress. There was highly significant genetic variation for life span within each sex and environment. In the analysis of variance of life span pooled over sexes and environments, however, the significant genetic variation appeared in the genotype × sex and genotype × environment interaction terms. The genetic correlation of longevity across the sexes and environments was not significantly different from zero in these lines. We estimated map positions and effects of QTL affecting life span by linkage to highly polymorphic roo transposable element markers, using a multiple-trait composite interval mapping procedure. A minimum of 17 QTL were detected; all were sex and/or environment-specific. Ten of the QTL had sexually antagonistic or antagonistic pleiotropic effects in different environments. These data provide support for the pleiotropy theory of senescence and the hypothesis that variation for longevity might be maintained by opposing selection pressures in males and females and variable environments. Further work is necessary to assess the generality of these results, using different strains, to determine heterozygous effects and to map the life span QTL to the level of genetic loci.

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