Abstract

Simple SummaryPearl culture is a significant global industry, with China being a leading producer in utilizing the freshwater musselSinohyriopsis cumingii. The color of the pearl is closely linked to the shell color of the mussel, yet the molecular genetic basis driving this variation remains unclear. This study investigated the mechanisms underlying shell and pearl coloration by analyzing the transcriptomes of juvenileS. cumingiiwith four distinct inner-shell colors. The results revealed significant differential expression of key genes regulating pigment metabolism, and genes involved in mineral metabolism and absorption. These findings indicate that shell color phenotypes are under stable genetic control, with the identified genes directly influencing color formation through pigment deposition and mineral integration. This study shows that specific genetic pathways govern color variation inS. cumingii, providing a molecular foundation for selective breeding. This knowledge holds considerable social and economic value, as it enables the targeted cultivation of mussels to produce pearls with desirable and consistent colors, thereby enhancing product quality, market value, and sustainability for the global pearl industry.Pearl culture has long been a major global industry. As a significant global producer, China mainly produces pearls from the freshwater mussel (Sinohyriopsis cumingii).S. cumingiiwith various shell colors can produce pearls of different colors; for example, mussels with a blue-white shell can produce white pearls, while those with a purple shell can produce light-purple pearls. Therefore, investigating the molecular genetics of shell color variation inS. cumingiican advance our understanding of the mechanisms underlying differences in shell and pearl coloration in these mussels. In this study, we selected juvenileS. cumingiiwith four differently colore