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Comparison between two genotypes was made by one-way ANOVA.
For a given locus, the similarity index S xy between two genotypes was 1 when alleles were identical and 0 when alleles were different.
Determining conserved expression between two genotypes was based on the results of significance (binomial) tests, where more than 0.5% FDR indicated failure to reject the null hypothesis of similar expression.
Nevertheless, excepted pairs involving clementine and sweet orange combined with Willow leaf mandarin, sour orange and grapefruit, the percentage of heterozygous loci showing a same profile between two genotypes was very low near zero.
Therefore, the distance between two genotypes was calculated as: d i s t (x i − x j ) = ∑ k = 1 m log 2 (1 + w ′ k d a k ), where w k and da k are column vectors with typical elements equal to the information gain score and the number of different alleles, respectively, for each SNP in substring k.
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The corresponding nucleotide polymorphisms observed between two genotypes were also compiled an individual datasheets.
Combined effects between two genotypes were studied by creating different variables, each representing the combination of two genotypes, with the putative "low-risk" homozygous combination as reference category.
The distance between two genotypes is defined as the minimum number of changes in the number of repeats of any locus that converts one genotype to the other.
Between six and twelve genotypes were comparatively analyzed per marker.
One parameter that greatly differed between the two genotypes was, however, waking episode duration (Fig. S2).
In an independent experimental setting different swimming speed between the two genotypes was excluded (NEP knockout: 13.1±1.5 vs. wild-type: 14.4±1.2 m/min).
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