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Salvelinus Microarray experiment: selected line vs control line

ABSTRACT: Domestication has been practiced for centuries yet directed towards relatively few terrestrial crops and animals. While phenotypic and quantitative genetic changes associated with domestication have been amply documented, little is known about the molecular changes underlying the phenotypic evolution during the process. Here, we have investigated the brook charr (Salvelinus fontinalis) responses to artificial selection by means of transcriptional analysis of ~ 32 000 cDNA features performed in both a selected and control populations reared under identical environmental conditions during four generations. Our results indicate that selective breeding led to significant changes in the transcription of genes at the juvenile stage, where we observed 4.16% (156/3750) of differentially expressed genes between the two lines. No significant genes were revealed at the earlier life stage. Moreover, when comparing our results to those of previous studies on Atlantic salmon that compared lines that were selected for 5-7 generations for similar traits (e.g. growth), genes with similar biological functions were found to be under selection in both studies. These observations indicate that (1) four generations of selection caused substantial changes in regulation of gene transcription between selected and control populations and (2) selective breeding for improving the same phenotypic traits (e.g. rapid growth) in brook charr and Atlantic salmon tended to select for the same changes in transcription profiles as the expression of a small and similar set of genes were affected by selection.

ORGANISM(S): Salmo salar Salvelinus fontinalis

PROVIDER: GSE20490 | GEO | 2010/02/24

SECONDARY ACCESSION(S): PRJNA125183

REPOSITORIES: GEO

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Project description:We performed short-term bi-directional selective breeding for haloperidol-induced catalepsy, starting from three mouse populations of increasingly complex genetic structure: an F2 intercross, a heterogeneous stock (HS) formed by crossing four inbred strains (HS4) and a heterogeneous stock (HS-CC) formed from the inbred strain founders of the Collaborative Cross (CC). All three selections were successful, with large differences in haloperidol response emerging within three generations. Genome-wide analysis between the selected lines revealed post-selection loss of allelic diversity concurrent with significant genetic differences. In spite of large phenotypic differences, absolute gene-expression changes were modest and not concordant across selections. However, gene coexpression patterns changed significantly, as revealed by the weighted gene co-expression network analysis. In particular, we detected three modules (de novo subnetworks) that (a) were functionally enriched for neurobehavioral traits and (b) showed independently detectable changes in network connectivity across selections. By inferring strain contributions from the parental lines, we are able to identify significant differences in allelic content between the selected lines concurrent with large changes in transcript connectivity. Importantly, this observation implies that genetic polymorphisms can affect transcript and module connectivity without large changes in absolute expression levels. We conclude that, in this case, selective breeding acts at the subnetwork level, with the same modules but not the same transcripts affected across the three selections. Equal numbers of males and females (~200 total) from the founder populations (F2, HS4 and HS-CC) were phenotyped for haloperidol response using a two-step process that resulted in assigning animals to one of four groups; “1” was the least responsive, and “4” was the most responsive. Breeding pairs were selected from the most extreme response groups. The selection and breeding were continued for two additional generations; in the third generation, parents were bred for three rounds to produce progeny for gene expression. For each genetic background the submitted samples are labeled as either High or Low based on their response to haloperidol.

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Salvelinus Microarray experiment: selected line vs control line

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