Correction: Genotype-by-environment interactions affecting heterosis in maize.
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ABSTRACT:
SUBMITTER: Li Z
PROVIDER: S-EPMC6681948 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The environment can influence heterosis, the phenomena in which the offspring of two inbred parents exhibits phenotypic performance beyond the inbred parents for specific traits. In this study we measured 25 traits in a set of 47 maize hybrids and their inbred parents grown in 16 different environments with varying levels of average productivity. By quantifying 25 vegetative and reproductive traits across the life cycle we were able to analyze interactions between the environment and multiple distinct instances of heterosis. The magnitude and rank among hybrids for better-parent heterosis (BPH) varied for the different traits and environments. Across the traits, a higher within plot variance was observed for inbred lines compared to hybrids. However, for most traits, variance across environments was not significantly different for inbred lines compared to hybrids. Further, for many traits the correlations of BPH to hybrid performance and BPH to better parent performance were of comparable magnitude. These results indicate that inbred lines and hybrids show similar trends in environmental response and both are contributing to observed genotype-by-environment interactions for heterosis. This study highlights the degree of heterosis is not an inherent trait of a specific hybrid, but varies depending on the trait measured and the environment where that trait is measured. Studies that attempt to correlate molecular processes with heterosis are hindered by the fact that heterosis is not a consistent attribute of a specific hybrid.
| S-EPMC5771596 | biostudies-literature
Project description:Background: Cases where genotype-phenotype relationships depend on environmental factors have been quantified for many complex diseases. Such genotype-environment interactions (GEI or GxE) may also affect expression Quantitative Trait Loci (eQTL) present in tissues critical for the manifestation of disease. To assess this hypothesis, we performed an analysis of eQTL-GEI resulting from an individual's smoking environment in the lung small airway epithelium (SAE). While the SAE is challenging to sample, this is the cell population that shows the first signs of smoking related stress and gene expression in the SAE appears to play a role in mediating smoking effects on lung disease. Results: We used expression microarrays to assay the SAE transcriptome for a small sample of African-American individuals and we analyzed SNPs genotyped genome-wide to identify GEI affecting eQTL. While a genome-wide trans- analysis identified few instances of GEI after a multiple test correction, an analysis of cis-genotypes identified a small but significant number of GEI affecting lung SAE gene expression. We determined that significant cases of eQTL-GEI were not driven by outliers and we were also able to find corroborative evidence for a few of these eQTL-GEI in a small, independent sample of individuals of European ancestry. Conclusion: Given that the power of GEI tests is low compared to tests of genotype association and that the total sample size of our study was small, including only 61 African American individuals in our focal population, the identification of significant GEI in our study implies that there may be considerable genotype-specific effects on eQTL due to smoking environment. We discuss individual cases of GEI of interest for lung disease, such as SDC1 and ZAK, as well as the broader implications of our results for the analysis of eQTL and for genome-wide association analysis of complex diseases.
2024-06-05 | GSE23087 | GEO
Project description:As one of the keys to healthy performance, robustness of farm animals is gaining importance, and with this comes increasing interest in genetic dissection of genotype-by-environment interactions (G×E). Changes in gene expression are among the most sensitive responses conveying adaptation to environmental stimuli. Environmentally responsive regulatory variation thus likely plays a central role in G×E. In the present study, we set out to detect action of environmentally responsive cis-regulatory variation by the analysis of condition-dependent allele specific expression (cd-ASE) in porcine immune cells. For this, we harnessed mRNA-sequencing data of peripheral blood mononuclear cells (PBMCs) stimulated in vitro with lipopolysaccharide, dexamethasone, or their combination. These treatments mimic common challenges such as bacterial infection or stress, and induce vast transcriptome changes. About two thirds of the examined loci showed significant ASE in at least one treatment, and out of those about ten percent exhibited cd-ASE. Most of the ASE variants were not yet reported in the PigGTEx Atlas. Genes showing cd-ASE were enriched in cytokine signaling in immune system and include several key candidates for animal health. In contrast, genes showing no ASE featured cell-cycle related functions. We confirmed LPS-dependent ASE for one of the top candidates, SOD2, which ranks among the major response genes in LPS-stimulated monocytes. The results of the present study demonstrate the potential of in vitro cell models coupled with cd-ASE analysis for the investigation of G×E in farm animals. The identified loci may benefit efforts to unravel the genetic basis of robustness and improvement of health and welfare in pigs.
| S-EPMC10061014 | biostudies-literature
Project description:High-throughput, field-based characterization of root systems for hundreds of genotypes in thousands of plots is necessary for breeding and identifying loci underlying variation in root traits and their plasticity. We designed a large-scale sampling of root pulling force, the vertical force required to extract the root system from the soil, in a maize diversity panel under differing irrigation levels for two growing seasons. We then characterized the root system architecture of the extracted root crowns. We found consistent patterns of phenotypic plasticity for root pulling force for a subset of genotypes under differential irrigation, suggesting that root plasticity is predictable. Using genome-wide association analysis, we identified 54 SNPs as statistically significant for six independent root pulling force measurements across two irrigation levels and four developmental timepoints. For every significant GWAS SNP for any trait in any treatment and timepoint we conducted post hoc tests for genotype-by-environment interaction, using a mixed model ANOVA. We found that 8 of the 54 SNPs showed significant GxE. Candidate genes underlying variation in root pulling force included those involved in nutrient transport. Although they are often treated separately, variation in the ability of plant roots to sense and respond to variation in environmental resources including water and nutrients may be linked by the genes and pathways underlying this variation. While functional validation of the identified genes is needed, our results expand the current knowledge of root phenotypic plasticity at the whole plant and gene levels, and further elucidate the complex genetic architecture of maize root systems.
| S-EPMC9051544 | biostudies-literature
Project description:[This corrects the article DOI: 10.1371/journal.pgen.1007019.].
| S-EPMC8478179 | biostudies-literature
Project description:Plant growth and productivity are greatly affected by drought, which is likely to become more threatening with the predicted global temperature increase. Understanding the genetic architecture of complex quantitative traits and their interaction with water availability may lead to improved crop adaptation to a wide range of environments. Here, the genetic basis of 20 physiological and morphological traits is explored by describing plant performance and growth in a Brassica rapa recombinant inbred line (RIL) population grown on a sandy substrate supplemented with nutrient solution, under control and drought conditions. Altogether, 54 quantitative trait loci (QTL) were identified, of which many colocated in 11 QTL clusters. Seventeen QTL showed significant QTL-environment interaction (Q×E), indicating genetic variation for phenotypic plasticity. Of the measured traits, only hypocotyl length did not show significant genotype-environment interaction (G×E) in both environments in all experiments. Correlation analysis showed that, in the control environment, stomatal conductance was positively correlated with total leaf dry weight (DW) and aboveground DW, whereas in the drought environment, stomatal conductance showed a significant negative correlation with total leaf DW and aboveground DW. This correlation was explained by antagonistic fitness effects in the drought environment, controlled by a QTL cluster on chromosome A7. These results demonstrate that Q×E is an important component of the genetic variance and can play a great role in improving drought tolerance in future breeding programmes.
| S-EPMC3904722 | biostudies-literature
Project description:Hybrids account for nearly all commercially planted varieties of maize and many other crop plants because crosses between inbred lines of these species produce first-generation [F1] offspring that greatly outperform their parents. The mechanisms underlying this phenomenon, called heterosis or hybrid vigor, are not well understood despite over a century of intensive research. The leading hypotheses-which focus on quantitative genetic mechanisms (dominance, overdominance, and epistasis) and molecular mechanisms (gene dosage and transcriptional regulation)-have been able to explain some but not all of the observed patterns of heterosis. Abiotic stressors are known to impact the expression of heterosis; however, the potential role of microbes in heterosis has largely been ignored. Here, we show that heterosis of root biomass and other traits in maize is strongly dependent on the belowground microbial environment. We found that, in some cases, inbred lines perform as well by these criteria as their F1 offspring under sterile conditions but that heterosis can be restored by inoculation with a simple community of seven bacterial strains. We observed the same pattern for seedlings inoculated with autoclaved versus live soil slurries in a growth chamber and for plants grown in steamed or fumigated versus untreated soil in the field. In a different field site, however, soil steaming increased rather than decreased heterosis, indicating that the direction of the effect depends on community composition, environment, or both. Together, our results demonstrate an ecological phenomenon whereby soil microbes differentially impact the early growth of inbred and hybrid maize.
| S-EPMC8325155 | biostudies-literature
Project description:Sugar beet, an important sugar crop, contributes significantly to the world's sugar production. However, genotype-environment interactions (GEI) often affect the quality characteristics of sugar beet. Hence, understanding the effects of GEI on sugar beet quality can aid in identifying high-quality genotypes that can adapt to different environments. Traditional variance analysis can only be used to examine the yield of a variety and not its specific adaptability to specific conditions. Therefore, more comprehensive analytical methods are required to evaluate the characteristics of the variety under specific environments. Additive main effects and multiplicative interaction (AMMI) and genotype main effect and genotype × environment interaction (GGE) biplot models can be employed to comprehensively evaluate different varieties and address the drawbacks associated with a single evaluation method. Moreover, these models also allow us to explore new varieties more objectively and comprehensively. In this study, the adaptability and stability of 16 sugar beet varieties, in terms of yield and sugar content, were evaluated using AMMI and GGE biplot analysis in seven pilot projects undertaken in 2022. In the assessment of a small but significant proportion of the total GEI variance for the two qualitative traits (yield and sugar content), 80.58% of the variance was explained by the cumulative contribution of IPC1, IPC2, and IPC3. AMMI and GGE biplots clearly highlighted that KWS4207 (G3) exhibited high and stable quality. They also demonstrated that the experiments in Jalaid Banner (Inner Mongolia) (E7) were the most representative. Together, the results suggested that the comprehensive application of AMMI and GGE biplot analysis allowed for a more comprehensive, scientific, and effective evaluation of sugar beet varieties across different regions. The findings offer a theoretical basis for sugar beet breeding and could guide the rational design of experiments for testing new varieties of sugar beet.
| S-EPMC10894595 | biostudies-literature
Project description:To assess plasticity in genetic regulation of gene expression in Arabidopsis thaliana, genome wide gene expression variation was analyzed in a Ler/Cvi recombinant inbred line (RIL) population treated with low-light. The variation in expression could be explained for many genes by expression quantitative trait loci (eQTLs), which were compared to a previous genetical genomics study in the same untreated population. Please note Characteristics[StrainOrLine] is the population of 162 recombinant inbred lines between the accessions Ler x Cvi. Ler and Cvi are the names of the parental accessions.
2013-03-01 | E-MTAB-1357 | biostudies-arrayexpress