The collective results of the present study supply powerful evidence that the ovary transcriptome may be a dominant factor contributing to quality. These findings also provide the first panoptic linkage of the various cell cycle regulatory components underpinning egg quality and, therefore, female reproductive fitness. Because the transcripts measured in ovary biopsy samples were taken prior to oocyte maturation and spawning, the observed transcriptomic differences were not a result of physical or physiological manifestations of embryo mortality but, rather, they are a feasible cause of these events. This mode of sampling offers the ability to select females a priori for breeding based on ovary gene expression profiles that are predictive of embryo developmental competency. Due to the evolutionary conservation of the gene pathways involved, their dysregulation may be an important molecular feature of reproductive failure in all vertebrates. Although the proximal cause of transcriptome defects associated with developmental incompetence remains unclear, pedigree is unlikely to have a major influence as natural selection would act to eliminate subfertile individuals and our limited survey of microsatellite loci did not reveal any association of genotype with transcriptome or fertility. We are presently replicating our experiments on additional groups of domesticated and wild striped bass employing direct sequencing, which will expand our coverage of the transcriptome while revealing a vast number of SNP’s embedded in the transcripts to better examine potential impacts of allelic variation. The genes related to transcription, translation, cell signaling and signal transduction are potential candidates for identification of such proximal causes as their rates of expression may be influenced under specific environmental conditions. Associated epigenetic modifications of the DNA could underpin the correlation between transcript profiles and fertility, but examining this hypothesis will require more genomic information on striped bass than is currently available. Application of our ANN approach to discover the relation between egg transcriptome and fertility in model species with more extensive genomic resources and knowledge of epigenetics, such as zebrafish, may be advantageous in this regard. Finally, our results suggest that caution be used when employing spawning stock biomass to indicate the reproductive health of commercially exploited fish stocks. The maturity schedule of females, upon which SSB computations are based, is usually estimated as the percentage of fish in each size or age class bearing growing or maturing oocytes or eggs, with the reproductive potential of such females being estimated based on their body mass. However, we observed large differences in egg quality and its unique transcriptomic fingerprint.