Transcriptome analysis provides new insights into heterosis in hybrid progeny of two geographical populations of the Manila clam (Ruditapes philippinarum)

The rapid development of global aquaculture has led to the significant degradation of germplasm resources, particularly in economically important species such as the Manila clam ( Ruditapes philippinarum) . This study performed crossbreeding experiments involving Manila clam populations from northern and southern China with distinct genetic backgrounds to elucidate the molecular mechanisms underlying growth regulation via transcriptome analysis. The hybrid offspring (ZL) from Zhangpu females and Laizhou males exhibited remarkable heterosis in shell length and height across the juvenile and adult stages. The greatest heterosis was observed at the age of 270 days, with shell length showing 35.52 % midparent heterosis (MPH) and 15.48 % best parent heterosis (BPH), and shell height 37.54 % MPH and 26.41 % BPH. At 270 days, transcriptome analysis (RNA-seq) identified and validated 12 key growth-related genes linked to the growth advantages of the intraspecific hybrid offspring. These genes were significantly enriched in pathways such as Hippo signaling, focal adhesion, and carbon metabolism, which are critical for regulating organ development. In conclusion, hybrid breeding improved the growth performance of Manila clams by activating key genes and signaling pathways. These findings provide new insights into the molecular basis underlying heterosis between different populations of R. philippinarum and offer valuable guidance for enhancing growth performance in clam aquaculture. • Hybrid offspring (ZL) produced by crossbreeding Laizhou males and Zhangpu females exhibited remarkable heterosis. • The DEGs were significantly enriched in pathways such as Hippo signaling, focal adhesion, and carbon metabolism. • Hybrid breeding improved the growth performance of Manila clams by activating key genes and signaling pathways.