From phenotype to gene during the oocyte-to-embryo transition: Integrating genetic and sequencing-based strategies to identify maternal-effect genes in zebrafish.

Identifying the genetic basis of phenotypes arising during early development remains a central challenge in biology. The oocyte-to-embryo transition (OET) and early embryogenesis are uniquely dependent on maternally supplied factors and tightly regulated post-transcriptional programs, making the identification of maternal-effect genes particularly challenging. High-throughput sequencing technologies have fundamentally reshaped gene discovery during these stages, especially in genetically tractable vertebrate models such as zebrafish, where sequencing-based approaches enable rapid and largely unbiased identification of causal loci underlying maternal-effect phenotypes. Classical fine mapping, grounded in recombination and linkage analysis, has historically provided robust causal inference but is often labor-intensive and time-consuming. The advent of mapping-by-sequencing, which combines bulk segregant analysis with whole-genome sequencing, has transformed gene discovery by enabling efficient localization of causal variants associated with defects in oogenesis, egg activation, cleavage, and early patterning. Complementarily, RNA sequencing (RNA-seq) provides functional insight into disrupted maternal transcript programs, aberrant splicing, nonsense-mediated decay, and early zygotic responses. In some contexts, RNA-seq can also serve as a mapping substrate, although such approaches remain constrained by developmental stage and expression bias. In this review, we discuss how fine mapping, genome sequencing, and transcriptomic approaches can be strategically integrated to identify maternal-effect genes during the OET. Using zebrafish as a central model, we highlight key discoveries, methodological considerations, and emerging directions that extend phenotype-to-gene discovery toward mechanistic understanding of early development.