Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability

Authors: Weber, Gregory - Greg; Birkett, Jill; MARTIN, KYLE - Troutlodge, Inc; DIXON, II, DOUG - Troutlodge, Inc; Gao, Guangtu; Leeds, Timothy - Tim; Vallejo, Roger; Ma, Hao

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/3/2021
Publication Date: 6/15/2021
Citation: Weber, G.M., Birkett, J.E., Martin, K., Dixon, II, D., Gao, G., Leeds, T.D., Vallejo, R.L., Ma, H. 2021. Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability. Biomed Central (BMC) Genomics. 22. Article 448. https://doi.org/10.1186/s12864-021-07773-1.
DOI: https://doi.org/10.1186/s12864-021-07773-1

Interpretive Summary: Egg quality is an important production trait in aquaculture, but what makes an egg developmentally competent to be fertilized and develop into a normal embryo is poorly understood. Development of the egg and early embryo is almost completely reliant on messenger RNA derived from the dam, so understanding this maternal transcriptome may enable scientists to better predict egg quality and understand factors that cause poor egg quality. This study compared expression levels of 65 maternal transcripts in eggs of different qualities in multiple rainbow trout populations. Although the assay is sufficient to predict low egg quality, refinement of transcripts included in the assay will be required to diagnose the causes of the problems with egg quality.

Technical Abstract: Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by hatcheries. Expression levels of specific transcripts have been shown to associate with measures of egg quality in fishes. Nevertheless, these differentially expressed genes (DEGs) have not been consistent among studies, including those of rainbow trout. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among three study groups. Two of the groups are different year classes of the same population (Group A1 and Group A2), and the third is a different population from a different hatchery (Group B). The study used a Nanostrings Technologies nCounter analysis data systems assay comprised of 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Most of the transcripts, 54, were selected for the assay after being identified as DEGs in a previous study using a sub-set of egg samples from Group A1. There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Low read counts limited the detection of differences in 12 transcripts. Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same population. Greater similarity in dysregulated transcripts within year classes of the same population than among populations suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes.