The toggle switch model for gene expression change during duck skeletal muscle development

Skeletal muscle development, a precisely orchestrated process, is vital for animal movement, energy metabolism, and meat production. Among Chinese poultry breeds, the Pekin duck and Liancheng duck are prominent, distinguished by their unique meat qualities and growth rates. In this study, we identified developmentally dynamic genes (DDG) by RNA sequencing of skeletal muscle tissues at different time points, from 1 to 42 days after birth, and found DDGs with opposite expression patterns in the early and late periods of skeletal muscle development. The high-to-low (earlyDDGs) and low-to-high (lateDDGs) expressed genes in two duck breeds, which show different functional enrichment features, were potentially regulated by different mutually inhibitory toggle-switch developmentally dynamic transcription factor (DDTF) pairs and alternative splicing. In Pekin ducks, interactions between earlyDDTFs (ZEB1, RORA, E2F6, PLAG1, MSANTD3) and lateDDTFs (ATF4, SIX2, ZBED4) predominantly affect earlyDDGs, prioritizing neuron establishment and optimization and lateDDGs enriched in VEGF-VEGFR2 signaling and cell division. In contrast, in Liancheng ducks, interactions between earlyDDTFs ATF2, FOXP2, NR2C1, GLIS2 and lateDDTFs ESRRB, MYCN are likely to affect earlyDDGs more involved in intracellular coordination and proliferation and lateDDGs involved in aerobic respiration and fatty acid beta-oxidation. Besides, differences in alternative splicing were observed for DDGs such as COL13A1 and RNF10, which may affect neurotransmission and vascular smooth muscle cell proliferation during skeletal muscle development between two duck breeds. These findings enhance our understanding of differences in regulatory mechanisms of skeletal muscle development between Pekin duck and Liancheng duck.