Transcriptome analysis of egg viability in rainbow trout (Oncorhynchus mykiss)

Authors: Ma, Hao; MARTIN, KYLE - Troutlodge, Inc; DIXON III, DOUG - Troutlodge, Inc; HERNANDEZ, ALVARO - University Of Illinois; Weber, Gregory - Greg

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2019
Publication Date: 4/27/2019
Citation: Ma, H., Martin, K., Dixon III, D., Hernandez, A.G., Weber, G.M. 2019. Transcriptome analysis of egg viability in rainbow trout (Oncorhynchus mykiss). Biomed Central (BMC) Genomics. 20:319. https://doi.org/10.1186/s12864-019-5690-5.
DOI: https://doi.org/10.1186/s12864-019-5690-5

Interpretive Summary: Fertility is high in the rainbow trout industry when fish are maintained under optimal conditions. Nevertheless, quality of the eggs can be affected by many factors. Understanding mechanisms by which egg quality becomes compromised in response to suboptimal genetics, management, nutrition, and environmental conditions is critical to optimizing hatchery productivity. The egg and early embryo are not capable of making mRNA and therefore mRNA must be stored in the egg for making the proteins required during early development. These mRNAs are stored with short poly(A) tails which is a string of adenine nucleotides on the tail-end of the mRNA. When the mRNA is to be used for translation to make proteins, the tail is elongated. We compared the transcriptomes of high- and low-quality eggs, looking at both total mRNAs, and also the activated mRNAs with long poly(A) tails. There was little difference in the transcriptomes of high-quality and low-quality eggs when we looked at total mRNA levels. This suggests that the eggs started with the same amount of the mRNAs. However, there were differences in the levels of over 900 mRNAs that had long poly(A) tails suggesting differences in egg quality may derive in part from differences in the activation of stored mRNAs. Many of the mRNAs that differed with egg quality were involved with the function of mitochondria and ribosomes which are important for energy production and translation. The differentially expressed transcripts identified in this study provide insight into developmental competence in rainbow trout eggs.

Technical Abstract: Background: Maternal mRNA transcripts are accumulated in the oocyte during oogenesis to provide for protein synthesis from oocyte maturation through early embryonic development, when nuclear transcription is silenced. These maternal transcripts have short poly(A) tails after undergoing post-transcriptional processing necessary for stabilizing the transcripts for storage. The transcripts undergo cytoplasmic polyadenylation when the transcripts are to be translated. Transcriptome analyses comparing total mRNA content and content of elongated poly(A) mRNAs among eggs of different quality can provide insight into molecular mechanism affecting developmental competence of the egg. The present study used RNA-seq to compare transcriptomes of unfertilized eggs of rainbow trout families yielding different eyeing rates, following rRNA-removal and poly(A) capture for construction of the libraries. Results: The percentage of embryos to reach the 32-cell stage at 24 hours post-fertilization was significantly correlated to family eyeing rate, supporting the embryos were developmentally compromised before zygote genome activation. RNA sequencing identified 2 differentially expressed transcripts (DETs) from total mRNA sequencing comparing families with low quality (<5% eyeing), medium quality (30%-50% eyeing), and high quality (>80% eyeing) eggs. In contrast, RNA sequencing from poly(A) capture transcript sequencing identified 945 DETs between low and high-quality eggs, 1012 between low and medium quality eggs, and only 2 between medium and high-quality eggs. The transcripts encoded by mitochondrial genes were enriched in the polyadenylated transcript sequencing and reduced in low quality eggs. Similarly, mitochondrial DNA was reduced in low quality eggs compared with medium and high-quality eggs. The functional gene analysis classified the 945 DETs between low and high-quality eggs into 31 functional modules, many of which were related to ribosome and mitochondrion. The other modules were involved in transcription, translation, cell division, apoptosis, and immune responses. Conclusions: Our results support differences in egg quality deriving from differences in mitochondrial function and maternal nuclear transcript activation and polyadenylation before ovulation, as opposed to accumulation and storage of maternal nuclear transcripts during oogenesis. Transcriptome comparisons support low-quality eggs suffered from inadequacies for oxidative phosphorylation and translation. The differentially expressed transcripts identified in this study provide insight into developmental competence in rainbow trout eggs.