Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss

Abstract

Background Maternal 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. The maternal mRNAs have short poly(A) tails after undergoing post-transcriptional processing necessary for stabilizing them for storage. The transcripts undergo cytoplasmic polyadenylation when they are to be translated. Transcriptome analyses comparing total mRNA and elongated poly(A) mRNA content among eggs of different quality can provide insight into molecular mechanisms affecting egg developmental competence in rainbow trout. The present study used RNA-seq to compare transcriptomes of unfertilized eggs of rainbow trout females yielding different eyeing rates, following rRNA removal and poly(A) retention for construction of the libraries. Results The percentage of embryos to reach the 32-cell stage at 24 h post fertilization was significantly correlated to family eyeing rate, indicating that inviable embryos were developmentally compromised before zygotic genome activation. RNA sequencing identified 2 differentially expressed transcripts (DETs) from total mRNA sequencing comparing females with low-quality (< 5% eyeing), medium-quality (30–50% eyeing), and high-quality (> 80% eyeing) eggs. In contrast, RNA sequencing from poly(A) captured transcripts 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 of mitochondrial genes were enriched with polyadenylated transcript sequencing and they were significantly 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 ribosomal and mitochondrial functions. Other modules involved transcription, translation, cell division, apoptosis, and immune responses. Conclusions Our results indicate that differences in egg quality may be derived from differences in maternal nuclear transcript activation and cytoplasmic polyadenylation before ovulation, as opposed to accumulation and storage of maternal nuclear transcripts during oogenesis. Transcriptome comparisons suggest low-quality eggs suffered from impaired oxidative phosphorylation and translation. The DETs identified in this study provide insight into developmental competence in rainbow trout eggs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5690-5) contains supplementary material, which is available to authorized users.

Domestication modulates the expression of genes involved in neurogenesis in high‐quality eggs of Sander lucioperca

“…The developmental competence of eggs until maternal‐to‐zygotic transition exclusively relies on maternally derived biomolecules, such as proteins and messenger RNAs (mRNAs; Cheung et al, 2019; Ma, Martin, Dixon, Hernandez, & Weber, 2019). The composition and profile of these molecules, deposited in the eggs during the oogenesis and final oocyte maturation (FOM; Bobe & Labbé, 2010), can be considered as a reflection of the direct response of the female to particular conditions, suggesting potential “molecular programming” of the eggs being adjustable by husbandry practices (Sullivan, Chapman, Reading, & Anderson, 2015).…”

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

“…Previous studies have characterized early mortality in line A. We characterized mortality in the 20 families from population A1 when used in our previous analysis of transcript abundance (Ma et al 2019). In these 20 families almost all the mortality observed by eyeing, took place between the 8-and 32-cell stages.…”

“…In addition to mRNAs, pro les of microRNAs and mitochondrial genome-encoded small RNAs were related to egg deterioration caused by post-ovulatory aging in rainbow trout (Ma et al 2015;2016). Recently, we identi ed over 1000 differentially expressed transcripts or genes (DEGs) associated with eyeing rate in unfertilized rainbow trout eggs (Ma et al 2019). However, these differences were only found when the libraries used for sequencing were prepared following polyadenylation capture and not rRNAremoval, suggesting differences in egg quality may derive in part from differences in maternal transcript activation and cytoplasmic polyadenylation before ovulation.…”

“…To meet this aim we designed an assay based on the nCounter analysis data system (Nanostrings Technologies; Seattle, WA) to compare expression of 65 mRNAs previously identi ed as being differentially expressed with egg quality (Additional le 1: Table S1). Most of the genes incorporated in the assay are DEGs from our previous transcriptome analysis of egg viability in rainbow trout using RNA-Seq, (Ma et al 2019), but also includes 10 additional transcripts reported as dysregulated in poor quality eggs in rainbow trout Bonnet et al 2007b), and also igf-3 since many IGF-system genes were already in the assay. The genes from Ma et al 2019 were selected for the assay primarily based on magnitude of statistical differences and fold-change.…”

“…Three populations of broodstock were compared including two different year classes from a commercial line and females from the 2015 year-class at the National Center for Cool and Cold Water Aquaculture (NCCCWA). One of the year classes from the commercial line included eggs from the same females used in our RNA-Seq study (Ma et al 2019). In all 152 families were included in the study.…”