Integrative genomic and functional analyses identify NFKBIA as a key regulator of salinity tolerance in Corbicula mortoni

Salinity tolerance is critical for the aquaculture of bivalves, especially for species inhabiting both freshwater and estuarine environments. Enhanced understanding of genetic mechanisms underlying salinity tolerance will support precision breeding and targeted genetic improvement in aquaculture species. In this study, we conducted a comprehensive comparative genomic analysis of Corbicula mortoni, a euryhaline representative of the Corbicula species complex. Our results revealed that immune- and stress-related pathways, particularly the NF-κB signaling pathway, have undergone gene family expansion. Population genomic analysis based on whole-genome resequencing showed that freshwater and estuarine populations formed two distinct clusters, with highly differentiated genomic regions harboring the NFKBIA gene, which is potentially involved in salinity tolerance. Functional validation using RNA interference (RNAi) targeting NFKBIA in the estuarine population under different salinity conditions (5 and 25 psu) showed that knockdown of NFKBIA significantly affected the expression of salinity-related genes and induced marked histological changes in gill tissues. These findings highlight the pivotal role of the NF-κB pathway in the salinity stress of C. mortoni and provide valuable molecular targets for the genetic improvement of salinity tolerance in bivalve aquaculture.