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To assay differences in transcript abundance levels between genotypes and between sexes, total transcript level was assayed using the 3′ expression module (Affymetrix Drosophila 2.0 PM probe sets).
Such interactions may be obtained in a case-only design if independence between genotypes and between genotypes and environment exposure is assumed.
Phenotypic differences have been described between genotypes and between individual strains, most notably an E1 mutation among some ECSA strains, which facilitates replication in Aedes albopictus mosquitoes (3 ).
Mapped reads were provided as an input to Cufflinks (version 2.1.1) for transcript assembly, and then, differential expression of genes between genotypes and between treatments were analyzed by CuffDiff [ 36].
For these reasons, each quarter of the dataset constituting one genotype in one season was centered, which removed differences in mean level of expression between genotypes and between seasons.
One of the limitations of the case-only design is that, in order to obtain gene-gene and gene-environment interactions, independence between genotypes and between genotypes and environment exposure must be assumed.
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In D. melanogaster, genetic variation in female mating preferences between genotypes, and across varying outcomes of interactions between males, may have implications for the maintenance of variation in territoriality and sexual signalling, even in apparently homogenous environments.
Below ground biomass allocation differed by up to 10% between genotypes and 94% between sites.
There were statistically significant differences in FHB Type II disease severity between genotypes and also between the seasons (Table S1).
Interactions between genotypes and genotypes or between genotypes and environmental factors were also estimated by using conditional logistic regression.
Further analysis of tumors showed that there was no difference in relative tumor size between genotypes and no correlation between tumor onset and size (Supplementary Figure S1d).
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