Integrative morphological and transcriptomic analysis reveals pectoral girdle adaptation in domesticated paddy field carp.

The paddy-field carp, domesticated in paddy ecosystems and cocultured with rice in Qingtian for over a millennium, exhibits physiology, behavior and morphology shift from its local wild progenitor. To investigate genetic and morphological adaptations of pectoral girdle, a key locomotor structure for extremely shallow water, we integrated skeletal anatomy, SMRT full-length transcriptome sequencing, and Illumina RNA-seq across developmental stages. Anatomical comparisons revealed significant morphological shifts in pectoral girdle (including clavicle and scapula) relative to wild populations. SMRT sequencing identified 2215 novel genes, 25,226 annotated transcripts, 6290 long non-coding RNAs (lncRNAs), 42,594 alternative splicing (AS) events, and 10 transposon families. Notably, genes involved in skeletal development exhibited significant AS (P < 0.05). Using 12 cDNA libraries from one- and four-month-old fish, we identified differently expression genes (DEGs). Weighted gene co-expression network analysis of these DEGs revealed that genes related to pectoral girdle development were predominantly associated with the turquoise module, and KEGG enrichment analysis highlighted the Wnt signaling pathway. Further evidence suggests that lncRNAs are candidate modulators of Wnt inhibitors (sost and dkk1b), thereby repressing Wnt signaling and influencing pectoral girdle development. Protein-protein interaction networks identified key hub genes, and active transposons appear to contribute to developmental regulation. These findings suggest that transcriptional regulation is closely associated with the adaptive changes in paddy-field carp, providing a potential molecular basis for its morphological shift and offering insights into adaptive evolution in domesticated species.