Candidate Transcriptomic Sources of Inbreeding Depression in Drosophila melanogaster

Abstract

The genomic causes of inbreeding depression are poorly known. Several studies have found widespread transcriptomic alterations in inbred organisms, but it remains unclear which of these alterations are causes of the depression and which are mere responses to the ensuing physiological stress induced by increased homozygosity due to inbreeding. Attempting to differentiate causes from responses, we made a c-DNA microarray analysis of inbreeding depression in Drosophila melanogaster. The rationale of the experiment was that, while depression is a general phenomenon involving reductions in fitness in different inbred lines, its first genetic causes would be different for each inbred line, as they are expected to be caused by the fixation of rare deleterious genes. We took four sets of inbred sublines, each set descending from a different founding pair obtained from a large outbred stock, and compared the expression of the three most depressed sublines and the three least depressed sublines from each set. Many changes in expression were common to all sets, but fourteen genes, grouped in four expression clusters, showed strong set-specific changes, and were therefore possible candidates to be sources of the inbreeding depression observed.

Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster

“…Finally, inbreeding has been shown to produce substantial changes in gene expression (Kristensen et al 2005; Ayroles et al 2009; Paige 2010; García et al 2012), which could modulate the rate of inbreeding depression. In fact, it has been shown that some changes of gene expression triggered by inbreeding may have a protective role against the negative effects of inbreeding, in the sense of restricting the amount of inbreeding depression for fitness (García et al 2012, 2013a, 2013b). Thus, it is possible that accelerated declines for fitness under inbreeding are a consequence of changes in expression across the genome.…”

Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation

“…Yet, the impact of these challenges on our patterns of parallelism seems to be modest since we detected many differences between ecotype pairs of a very recent origin within each locality, and still only a minor fraction of these differences were repeatable among localities. Moreover, expression measurements in different species did not reveal a consistent variation in signal intensity due to sequence mismatches 24 , 78 , since the expression of each gene is calculated as the average intensity for each probe set. Second, if divergent traits in Littorina (e.g.…”

Identification of genes involved in inbreeding depression of reproduction in Langshan chickens

“…Furthermore, most phenotypic differences are related to the regulation of gene expression even in the absence of genetic variation. Previous studies have shown that inbreeding causes changes in the expression of a large numbers of genes [ 8 ]. Several studies on Drosophila melanogaster suggested that some of the transcriptomic alterations in inbred individuals were due to inbreeding depression, whereas some have been reported as protective responses against inbreeding depression [ 8 , 9 ].…”

“…Previous studies have shown that inbreeding causes changes in the expression of a large numbers of genes [ 8 ]. Several studies on Drosophila melanogaster suggested that some of the transcriptomic alterations in inbred individuals were due to inbreeding depression, whereas some have been reported as protective responses against inbreeding depression [ 8 , 9 ]. Despite these studies, a detailed regulatory mechanism of transcriptomic alterations in inbreeding depression is not well understood.…”

“…Despite these studies, a detailed regulatory mechanism of transcriptomic alterations in inbreeding depression is not well understood. To the best of our knowledge, most previous studies on inbreeding depression were performed in plants [ 5 ] and some animal models such as Mus musculus [ 10 ], Drosophila melanogaster [ 6 , 8 ] and Argopecten irradians [ 11 ]. So far, studies on genome-wide changes in gene expression in inbred individuals and the molecular mechanisms of inbreeding depression at the transcriptome level in poultry are limited.…”