Correction: Genotype-by-environment interactions affecting heterosis in maize.
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ABSTRACT:
SUBMITTER: Li Z
PROVIDER: S-EPMC6681948 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Correction: Genotype-by-environment interactions affecting heterosis in maize.
Li Zhi Z Coffey Lisa L Garfin Jacob J Miller Nathan D ND White Michael R MR Spalding Edgar P EP Leon Natalia de N Kaeppler Shawn M SM Schnable Patrick S PS Springer Nathan M NM Hirsch Candice N CN
PloS one 20190805 8
[This corrects the article DOI: 10.1371/journal.pone.0191321.]. ...[more]
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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.
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