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Transcriptomic profiling of eggs of pikeperch, Sander lucioperca, obtained from wild and domesticated fish

ABSTRACT: Domestication of finfishes is a key element toward sustainable expansion of aquaculture sector. However, huge gap in knowledge on the mechanisms of adaptability of fish to the culture environment, being the first step toward successful domestication, exists. This affects the overall production capacity which is hindered, among others, by lowered reproductive capacity of domesticated stocks, including pikeperch – a highly valued commercial freshwater fish species. Transcriptomic profiling of embryos was found to be useful tool significantly contributing into understanding domestication process in aquaculture. Up to now there is no data on transcriptomic profiling of unfertilized eggs in any fish species as well as on pikeperch, in general. Using next generation sequencing the first complex transcriptome of pikeperch have been obtained (with 40,246 unique protein-coding genes). Next, specifically designed, pikeperch-specific microarrays (Agilent technologies) were developed (with 35,343 unique probes) and transcriptomic profiling of eggs coming from wild and domesticated populations (all characterized by high quality) was performed. From among 17,543 genes found to be expressed in eggs of pikeperch 710 were found to be differentially expressed. Functional, enrichment analysis revealed that the most enriched processes represented by the set of genes identified were developmental process, regulation of phosphorylation and nervous system development. The results of the present study provides a new insight into the processes being directly involved in the successful domestication of finfishes. It can be suggested that all the identified processes were pre-determined by the maternally derived set of genes contained already in the unfertilized eggs, what has never been reported to date. In addition to that, it has been shown for the first time that among the most important processes being affected by the domestication the post translation modifications of proteins along with development of the nervous system were identified. This allows to suggest that fish behavior should be considered as a very important trait for selection for aquaculture purposes in pikeperch.

ORGANISM(S): Sander lucioperca

PROVIDER: GSE142412 | GEO | 2020/06/30

REPOSITORIES: GEO

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Project description:The domestication is an evolutionary process during which individuals will progressively adapt to an environment controlled by humans. It is accompanied by epigenetic and genetic modifications potentially leading to modifications in the transcriptomic profile in various tissues. The reproduction process is among the biological functions highly affected whatever the species and/or the way of domestication. Indeed, the reproduction success often decreases in domesticated populations. For fish, the molecular content of the eggs is crucial for the proper embryogenesis. Among these molecules the mRNA content depends directly from the gene expression and thus may reflect the genetic modifications occurring during this process. Here, we investigated the transcriptomic profile of eggs coming from females of two populations (F1 and Fx) that were reared in the same conditions and were genetically close. Our main goal was thus to determine how the domestication process may affect the reproduction success in the Eurasian perch and if it was mediated by the regulation of the transcription in the eggs. A regular follow up of the oogenesis progression showed few differences of the hormonal production between the two populations. Nevertheless, the histological study showed that the F1 females were more developed by the end of the oogenesis induction than the domesticated ones and as a result, they spawned earlier than the domesticated ones. The study of the early developmental success revealed significant differences between the populations. The microarray analysis of unfertilized eggs presented more than 350 transcripts differently expressed between the two populations. Among them, some specific genes were drastically more expressed in the domesticated (mex3B, hace1 and an uncharacterized protein) or F1 (per) populations. Our data show that the F1 population is more sensitive to the environmental conditions to advance oogenesis and reach the spawning season earlier. The transcriptomic profiles in eggs coming from the two populations were different and may lead to developmental impairments having a potential link with the domestication process. Further analyses are needed to explain these differences.

Project description:Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates. Microarray analyses were performed on five individual rainbow trout per group of pure wild, pure domesticated, GH transgenic strain 1 in wild, GH transgenic strain 2 in wild, GH transgenic strain 1 in wild-domestic hybrid, and GH transgenic strain 2 in wild-domestic hybrid hybridized (one slide per individual) against a common wild-type RNA pool.

Project description:Gossypium barbadense is widely cultivated because of its extra-long staple cotton with superior luster, silkiness and high yield. These economically important traits were selected during initial domestication of an agronomically inferior wild ancestor, followed by millennia of human- mediated selection. To reveal the effects of this history on the cotton fiber transcriptome, we conducted comparative expression profiling on mechanically isolated fiber cells at three different stages encompassing early, mid, and late fiber elongation in wild (K101) and domesticated (Pima S-7) accessions, using a microarray platform that interrogates 42,429 unigenes. The distribution of differentially expressed genes across developmental stages was different in the two accessions, with a shift toward greater change earlier in cultivated than in wild G. barbadense. Approximately 4200 genes were differentially expressed between wild and domesticated accessions at one or more of the stages studied. Domestication appears to have led to enhanced modulation of cellular redox levels and the avoidance or delay of stress-like processes. Prolonged fiber growth in cultivated relative to wild G. barbadense is associated with upregulation of signal transduction and hormone signaling genes and down-regulation of cell wall maturation genes. Clues are provided into the processes and genes that may unwittingly have been selected by humans during domestication and development of modern elite lines. Several of the transcriptomic differences between wild and domesticated G. barbadense described here appear to have parallels in a second domesticated cotton species, Gossypium hirsutum, suggesting that replicated domestication of two different species has resulted in overlapping, parallel, metabolic transformations. Two accessions of G. barbadense were studied, the elite cultivar, Pima S-7, and a wild accession from Bolivia, K101. Seeds of both accessions were sown in sterilized potting mix in the Pohl Conservatory at Iowa State University, Ames, IA, and three biological replicates were grown for 3-5 months. Flowers were tagged at anthesis and harvested at three time points, 2, 10, and 20 days postanthesis. For each of three biological replicates, ovules were excised, frozen in liquid nitrogen, and stored at -80C.

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Transcriptomic profiling of eggs of pikeperch, Sander lucioperca, obtained from wild and domesticated fish

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