scholarly journals Phenotypic and transcriptomic responses to stress differ according to population geography in an invasive species

2020 ◽  
Author(s):  
Pierre Marin ◽  
Angelo Jaquet ◽  
Justine Picarle ◽  
Marie Fablet ◽  
Vincent Merel ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Invasive Species ◽  
Genotype By Environment Interaction ◽  
Differentially Expressed ◽  
Short Time Scale ◽  
Environment Interaction ◽  
Rapid Adaptation ◽  
Non Invasive ◽  
Genotype By Environment ◽  
The Impact

AbstractBackgroundAdaptation to rapid environmental changes must occur within a short time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and successfully adapted to novel environmental conditions. Here we investigated how invasive and non-invasive populations of D. suzukii deal with an oxidative stress at both the phenotypic and molecular level. We also investigated the impact of transposable element insertions on the differential gene expression between genotypes in response to oxidative stress.ResultsInvasive populations lived longer in the untreated condition than non-invasive Japanese populations. As expected, lifespan was greatly reduced following exposure to paraquat, but this reduction varied among genotypes (a genotype by environment interaction, GEI) with invasive genotypes appearing more affected by exposure than non-invasive genotypes. We also performed transcriptomic sequencing of selected genotypes upon and without paraquat and detected a large number of genes differentially expressed, distinguishing the genotypes in the untreated environment. While a small core set of genes were differentially expressed by all genotypes following paraquat exposure, much of the response of each population was unique. Interestingly, we identified a set of genes presenting genotype by environment interaction (GEI). Many of these differences may reflect signatures of history of past adaptation. Transposable elements (TEs) were not activated after oxidative stress and differentially expressed (DE) genes were significantly depleted of TEs.ConclusionIn the decade since the invasion from the south of Asia, invasive populations of D. suzukii have diverged from populations in the native area regarding their genetic response to oxidative stress. This suggests that such transcriptomic changes could be involved in the rapid adaptation to local environments.

scholarly journals Phenotypic and Transcriptomic Responses to Stress Differ According to Population Geography in an Invasive Species

2021 ◽  
Vol 13 (9) ◽  
Author(s):  
Pierre Marin ◽  
Angelo Jaquet ◽  
Justine Picarle ◽  
Marie Fablet ◽  
Vincent Merel ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
United States ◽  
Invasive Species ◽  
Environmental Changes ◽  
The United States ◽  
Short Time Scale ◽  
Environment Interaction ◽  
Rapid Adaptation ◽  
Drosophila Suzukii ◽  
The Impact

Abstract Adaptation to rapid environmental changes must occur within a short-time scale. In this context, studies of invasive species may provide insights into the underlying mechanisms of rapid adaptation as these species have repeatedly encountered and adapted to novel environmental conditions. We investigated how invasive and noninvasive genotypes of Drosophila suzukii deal with oxidative stress at the phenotypic and molecular levels. We also studied the impact of transposable element (TE) insertions on the gene expression in response to stress. Our results show that flies from invasive areas (France and the United States) live longer in natural conditions than the ones from native Japanese areas. As expected, lifespan for all genotypes was significantly reduced following exposure to paraquat, but this reduction varied among genotypes (genotype-by-environment interaction) with invasive genotypes appearing more affected by exposure than noninvasive ones. A transcriptomic analysis of genotypes upon paraquat treatment detected many genes differentially expressed (DE). Although a small core set of genes were DE in all genotypes following paraquat exposure, much of the response of each genotype was unique. Moreover, we showed that TEs were not activated after oxidative stress and DE genes were significantly depleted of TEs. In conclusion, it is likely that transcriptomic changes are involved in the rapid adaptation to local environments. We provide new evidence that in the decade since the invasion from Asia, the sampled genotypes in Europe and the United States of D. suzukii diverged from the ones from the native area regarding their phenotypic and genomic response to oxidative stress.

Simultaneously accounting for population structure, genotype by environment interaction, and spatial variation in marker–trait associations in sugarcaneThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽  
2010 ◽  
Vol 53 (11) ◽  
pp. 973-981 ◽  
Author(s):  
Xianming Wei ◽  
Phillip A. Jackson ◽  
Scott Hermann ◽  
Andrzej Kilian ◽  
Katarzyna Heller-Uszynska ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Mapping ◽  
Spatial Variation ◽  
Sugar Content ◽  
Genotype By Environment Interaction ◽  
Cane Yield ◽  
Type I ◽  
Environment Interaction ◽  
Genotype By Environment ◽  
The Impact

Few association mapping studies have simultaneously accounted for population structure, genotype by environment interaction (GEI), and spatial variation. In this sugarcane association mapping study we tested models accounting for these factors and identified the impact that each model component had on the list of markers declared as being significantly associated with traits. About 480 genotypes were evaluated for cane yield and sugar content at three sites and scored with DArT markers. A mixed model was applied in analysis of the data to simultaneously account for the impacts of population structure, GEI, and spatial variation within a trial. Two forms of the DArT marker data were used in the analysis: the standard discrete data (0, 1) and a continuous DArT score, which is related to the marker dosage. A large number of markers were significantly associated with cane yield and sugar content. However, failure to account for population structure, GEI, and (or) spatial variation produced both type I and type II errors, which on the one hand substantially inflated the number of significant markers identified (especially true for failing to account for GEI) and on the other hand resulted in failure to detect markers that could be associated with cane yield or sugar content (especially when failing to account for population structure). We concluded that association mapping based on trials from one site or analysis that failed to account for GEI would produce many trial-specific associated markers that would have low value in breeding programs.

scholarly journals Among-environment heteroscedasticity and genetic autocorrelation: implications for the study of phenotypic plasticity.

Genetics ◽  
1995 ◽  
Vol 139 (4) ◽  
pp. 1815-1829
Author(s):  
P Dutilleul ◽  
C Potvin
Keyword(s):  
Phenotypic Plasticity ◽  
Variance Component ◽  
Statistical Tests ◽  
Statistical Significance ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Data Set ◽  
Genotype By Environment ◽  
Sample Covariance ◽  
The Impact

Abstract The impact of among-environment heteroscedasticity and genetic autocorrelation on the analysis of phenotypic plasticity is examined. Among-environment heteroscedasticity occurs when genotypic variances differ among environments. Genetic autocorrelation arises whenever the responses of a genotype to different environments are more or less similar than expected for observations randomly associated. In a multivariate analysis-of-variance model, three transformations of genotypic profiles (reaction norms), which apply to the residuals of the model while preserving the mean responses within environments, are derived. The transformations remove either among-environment heteroscedasticity, genetic autocorrelation or both. When both nuisances are not removed, statistical tests are corrected in a modified univariate approach using the sample covariance matrix of the genotypic profiles. Methods are illustrated on a Chlamydomonas reinhardtii data set. When heteroscedasticity was removed, the variance component associated with the genotype-by-environment interaction increased proportionally to the genotype variance component. As a result, the genetic correlation rg was altered. Genetic autocorrelation was responsible for statistical significance of the genotype-by-environment interaction and genotype main effects on raw data. When autocorrelation was removed, the ranking of genotypes according to their stability index dramatically changed. Evolutionary implications of our methods and results are discussed.

scholarly journals Association between lactoferrin single nucleotide polymorphisms and milk production traits in Polish Holstein cattle

2014 ◽  
Vol 57 (1) ◽  
pp. 1-12
Author(s):  
Adrianna Pawlik ◽  
Grazyna Sender ◽  
Magdalena Sobczynska ◽  
Agnieszka Korwin-Kossakowska ◽  
Jolanta Oprzadek ◽  
...  
Keyword(s):  
Genotype By Environment Interaction ◽  
Bovine Lactoferrin ◽  
Environment Interaction ◽  
Production Traits ◽  
Breeding Values ◽  
Genotype By Environment ◽  
Lactoferrin Gene ◽  
Milk Performance ◽  
Estimated Breeding Values ◽  
The Impact

Abstract. Bovine lactoferrin exhibits strong potential for further applications as a mastitis resistance marker. Since selection for mastitis resistance should not interfere with dairy performance, we investigated the association between bovine lactoferrin gene polymorphism and production traits in Polish Holsteins. The associations between four SNPs, localized in the 5’-flanking region and in exons 4 and 9 of the lactoferrin gene, and dairy performance were examined. SNPs were associated with almost all test-day milk performance traits. Significant associations were found between lactoferrin genotypes and the estimated breeding values for those traits. To find out whether the discrepancies between the lactoferrin gene SNP’s influence on phenotype (test-day milk performance) and on estimated breeding values originate from the impact of other factors, we explored the genotype by environment interaction. Substantial impacts of SCC, lactation stage and parity were found. This paper suggests that the genotype by environment interaction may significantly change associations between genes and traits. It is important to include similar analyses to the studies on disease markers before using them in the selection.

scholarly journals 210 Genotype by environment interaction for pre-weaning survival in commercial crossbred pigs

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 40-41
Author(s):  
Francesco Tiezzi ◽  
Justin Fix ◽  
Clint Schwab
Keyword(s):  
Fixed Effects ◽  
Genotype By Environment Interaction ◽  
Single Step ◽  
Random Regression ◽  
Residual Variance ◽  
Phenotypic Variance ◽  
Environment Interaction ◽  
Genomic Breeding ◽  
Genotype By Environment ◽  
The Impact

Abstract Pre-weaning survival (PWS) is a trait of major importance in swine productions systems. Selection is made difficult by the low heritability of the trait(s) and genotype by environment interaction (GxE) could be present. In addition to that, given the binary nature of the trait, phenotypic variance is virtually null in contemporary group where PWS is large. The objective of this study was to assess the impact of heterogeneous phenotypic variance and GxE on PWS. We used survival to day 5 as a trait of interest, available for 574,828 crossbred piglets raised in a commercial environment. Piglets were progeny of 559 sires (450 genotyped with 60k SNP chip) and raised into 242 contemporary groups (CG). In estimating GxE, the E component was represented by fourth-order Legendre polynomials built on the CG solutions. A Single-Step random-regression sire model with heterogeneous residuals (10 classes) was used, once the CG solutions were obtained by a similar model that neglected GxE. Other (fixed) effects in the models were sow parity, litter size, litter transfer of the piglet, gender of the piglet, dam genetic line and litter (random). Results show an increase in phenotypic and residual variance as PWS decreased, which is expected given the nature of the binary trait. Genetic variance increased following the same trend, which made heritability to be constant (~2%). Genomic breeding values for most represented sires were plotted as a function of CG survival. While no variation among the sires can be found in CG with full survival, larger variance is shown as PWS decreases. Re-ranking among the sires is present as CG change. Results suggest that modeling PWS should account for the heterogeneous variance among CG. A moderate GxE in PWS at day 5 is also suggested.

Using AMMI approach to delineate genotype by environment interaction and stability of barley (Hordeum vulgare L.) genotypes under northern Indian shivalik hill conditions

2020 ◽  
Vol 80 (03) ◽  
Author(s):  
Om Prakash Yadav ◽  
A. K. Razdan ◽  
Bupesh Kumar ◽  
Praveen Singh ◽  
Anjani K. Singh
Keyword(s):  
Hordeum Vulgare ◽  
Grain Yield ◽  
Principal Component ◽  
Genotype By Environment Interaction ◽  
Environment Interaction ◽  
Hordeum Vulgare L ◽  
Genotype By Environment ◽  
Biplot Analysis ◽  
Principal Component Axis ◽  
Ammi Analysis

Genotype by environment interaction (GEI) of 18 barley varieties was assessed during two successive rabi crop seasons so as to identify high yielding and stable barley varieties. AMMI analysis showed that genotypes (G), environment (E) and GEI accounted for 1672.35, 78.25 and 20.51 of total variance, respectively. Partitioning of sum of squares due to GEI revealed significance of interaction principal component axis IPCA1 only On the basis of AMMI biplot analysis DWRB 137 (41.03qha–1), RD 2715 (32.54qha–1), BH 902 (37.53qha–1) and RD 2907 (33.29qha–1) exhibited grain yield superiority of 64.45, 30.42, 50.42 and 33.42 per cent, respectively over farmers’ recycled variety (24.43qha–1).

Sign in / Sign up

Export Citation Format

Share Document