The identification of markers that can serve as predictors of egg quality and for diagnosing problems with embryo development would benefit production efficiency in fish hatcheries. Since mRNA transcription is arrested in the late-stage oocyte 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 has therefore been targeted to identify informative markers and levels of specific transcripts have been shown to be associated with various measures of egg quality. However, these differentially expressed genes (DEGs) have not been consistent among studies. As a start to determining factors that contribute to disparate results among studies, we compared expression of 65 select transcripts previously reported to be potential markers of egg quality in rainbow trout, between unfertilized eggs that yielded high and low eyeing rates, among three populations using an assay based on the nCounter analysis data system (Nanostrings Technologies; Seattle, WA). The pattern of transcripts differentially expressed with egg quality remain consistent among year classes of the same line supporting value to line specific DEG discovery efforts. On the other hand, less similarity in dysregulated transcripts among lines than within year classes of the same line suggest patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were confirmed, there is considerable variability in transcript abundance among eggs of similar quality for each of the genes and low correlations between transcript abundance and eyeing rate. These factors make it difficult to predict the quality of a single batch of eggs based on transcript abundance of just a few genes.
To further characterize the association of maternal transcript profiles with egg quality, we used poly(A) inclusive RNA isoform sequencing (PAIso-seq) to investigate the effects of oocyte ageing on mRNA transcript abundance profiles and poly(A) tail length distributions. Maternal transcripts stored in the egg have short poly(A) tails that must be elongated to allow translation, which takes place for some transcripts before ovulation. We first compared transcript tail-lengths between freshly ovulated oocytes and embryos at 24 hours post fertilization in high quality eggs, and then in unfertilized oocytes in response to in vivo postovulatory ageing up to 14 days.