In a previous study, we reported on a quantitative transcriptomic method which confirmed the temporal transcription of developmental fast skeletal muscle myosin heavy chain (fsMyHC) embryonic isoforms in the embryonic Pectoralis major (PM) of the Single Comb White Leghorn (SCWL). The objective of the current study was to further investigate the transcriptional events underlying embryonic PM growth in the SCWL and a genotype exhibiting partial muscular dystrophy, the Low Score Normal (LSN). We hypothesized that within the SCWL and LSN embryos, there would be differences in the temporal transcription of the fsMyHC isoforms and other myogenic regulatory genes. Samples of PM tissues were collected daily from embryonic day (ED) 6 through ED19. Total RNA was isolated from each PM tissue sample and mRNA transcripts from 28 target genes were simultaneously quantified using a probe hybridization method. Raw data counts were normalized against the geometric mean of 5 housekeeping genes and analyzed using Local Regression (LOESS) smoothing methods. Predicted estimates based on LOESS smoothing were plotted with 95% upper and lower confidence intervals, allowing for line comparisons between the SCWL and LSN. Differences (P < 0.05) were determined by non-overlapping confidence intervals between the SCWL and LSN. Among genes exhibiting line differences (P < 0.05), were the developmental fsMyHC isoforms, transcription factors, growth factors, and proteoglycans. The current study is the first to report transcription of the chicken fast skeletal adult myosin isoform (Cad) during PM myogenesis. Samples were submitted for capillary-liquid chromatography-tandem mass spectrometry analysis which confirmed the translation of all the developmental fsMyHC isoforms including Cad in both lines. The LSN exhibited altered transcription patterns of early myogenic markers (MYOD, MRF4, Cemb1, six4, and pax3) during late embryogenesis, continued transcription of Cvent, and delayed transcription of Cneo.