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Genetics, Vol. 168, 1413-1420, November 2004, Copyright © 2004
doi:10.1534/genetics.104.030973
Additivity and trans-acting Effects on Gene Expression in Male Drosophila simulans
M. L. Wayne*,1,
Y.-J. Pan
,
S. V. Nuzhdin
and
L. M. McIntyre
* Department of Zoology, University of Florida, Gainesville, Florida 32611
Computational Genomics, Department of Agronomy, Purdue University, West Lafayette, Indiana 47907
Section of Ecology and Evolution, University of California, Davis, California 95616
1 Corresponding author: Department of Zoology, University of Florida, Box 118525, Gainesville, FL 32611-8525.
E-mail: mlwayne{at}zoo.ufl.edu
Understanding how genetic variation is maintained begins with a comprehensive description of what types of genetic variation exist, the extent and magnitude of the variation, and patterns discernable in that variation. However, such studies have focused primarily on DNA sequence data and have ignored genetic variation at other hierarchical levels of genetic information. Microarray technology permits an examination of genetic variation at the level of mRNA abundance. Utilizing a round-robin design, we present a quantitative description of variation in mRNA abundance in terms of GCA (general combining ability or additive variance). We test whether genes significant for GCA are randomly distributed across chromosomes and use a nonparametric approach to demonstrate that the magnitude of the variation is not random for GCA. We find that there is a paucity of genes significant for GCA on the X relative to the autosomes. The overall magnitude of the effects for GCA on the X tends to be lower than that on the autosomes and is contributed by rare alleles of larger effect. Due to male hemizygosity, GCA for X-linked phenotypes must be due to trans-acting factors, while GCA for autosomal phenotypes may be due to cis- or trans-acting factors. The contrast in the amount of variation between the X and the autosomes suggests that both cis and trans factors contribute to variation for expression in D. simulans with the preponderance of effects being trans. This nonrandom patterning of genetic variation in gene expression data with respect to chromosomal context may be due to hemizygosity in the male.
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