e. pyridoxal 5ʹ-phosphate binding lysine) ( Supplemental Fig. 4), suggesting that it is a pyridoxal 5ʹ-phosphate-dependent enzyme. The availability of molecular tests for egg quality as predictors of developmental

success would benefit Atlantic cod aquaculture. Therefore, we aimed to use functional genomics tools and techniques to study the cod egg transcriptome and identify candidate molecular biomarkers of egg quality. While some maternal transcripts included in our qPCR studies were associated with extremes in egg quality (e.g. Nutlin-3a datasheet acy3 expression was lowest in the highest quality fertilized and unfertilized eggs), there was little correlation between egg quality and transcript expression when all females were considered. Further, although one gene (cth) was negatively correlated

with egg quality, it had an extremely narrow range of expression among egg batches. Thus, these data suggest that none of the genes studied by qPCR are suitable single biomarkers of cod egg quality. Still, we provide new information on the cod maternal transcriptome, and report that several of the names of genes that were previously reported to be highly expressed in Atlantic cod eggs [e.g. ribonucleoside diphosphate reductase subunit M2, cyclin A1, claudin-like protein ZF-A89, ubiquitin, and calmodulin in Lanes et al. (2013); cytochrome c oxidase subunit I in Kleppe et al. (2012)] were found in our “highly expressed in eggs regardless of egg C646 supplier quality” gene list ( Supplemental Table 8). These functional genomics studies provide valuable resources for future research on

the genes and pathways involved in egg and early embryonic development of Atlantic cod. While the majority of the genes selected for qPCR with fertilized egg templates had microarray and qPCR MEK inhibitor data that agreed in direction of change, 4 of the 12 genes (33%; usp14, cth, trappc3, and cnih) had microarray and qPCR fold-change values in opposite directions ( Table 1 and Table 2). This is similar to the results of Morais et al. (2012), who found that 4 out of 11 genes (36%) identified in a 16 K cod microarray experiment had microarray and qPCR fold-changes in opposite directions. As noted by Booman et al. (2011) and Liu et al. (2013), possible explanations for why microarray and qPCR results may differ include: 1) microarray probes and qPCR amplicons mapping to different regions of the transcript; and 2) the influence of paralogues (gene duplicates) or other related transcripts on microarray hybridization results, but not gene-specific qPCR assays. The remainder of the discussion is focused on the 5 microarray-identified genes that were qPCR confirmed as > 2-fold differentially expressed in fertilized eggs from the highest quality female versus both of the lowest quality females (dcbld1, ddc, acy3, kpna7, and hacd1) and the 3 IFN pathway genes (irf7, ifngr1, and ifrd1) that were also shown to be maternally expressed in cod.