Genetic Diversity Analysis of Meretrix meretrix Based on Reduced-Representation Genome Sequencing and Transcriptome Sequencing

The hard clam Meretrix meretrix is a commercially important bivalve species in China, yet its aquaculture industry is increasingly threatened by germplasm degradation and recurrent mass summer mortality events associated with elevated temperatures and Vibrio infections. To characterize candidate germplasm resources with potential value for heat-tolerance breeding and to elucidate the genetic basis of adaptive differentiation, we integrated genotyping-by-sequencing (GBS) and gill transcriptome sequencing across five wild populations spanning the entire latitudinal range of China: Dandong (LD), Weihai (SW), and Rudong (JR) in the north, and Beihai (GB) and Qinzhou (GQ) in the south. Phylogenetic and population structure analyses resolved the five populations into two distinct genetic lineages corresponding to northern and southern clusters, with the Beihai population exhibiting the highest genetic diversity and the Weihai population showing signs of inbreeding that were elevated relative to the other populations. Comparative transcriptomic analysis revealed that differentially expressed genes between northern and southern populations were significantly enriched in immune-related pathways (including NOD-like receptor and IL-17 signaling pathways) and lipid metabolic pathways (including cholesterol and steroid biosynthesis). Notably, populations with similar genomic backgrounds still displayed pronounced transcriptional divergence, indicating that transcriptional divergence can arise even in the absence of strong genomic differentiation; because this conclusion is based on observational data, it cannot fully separate long-term genetic adaptation from environmentally induced transcriptional plasticity. These findings provide fundamental data for germplasm conservation and for future selective breeding programs targeting stress resistance in M. meretrix.