Population genomics and GWAS reveal genetic basis of shell traits in Manila clam (Ruditapes philippinarum)

The Manila clam (Ruditapes philippinarum) is a key aquaculture species in China's intertidal zones, where body size and growth rates strongly influence market preference and commercial value. Nevertheless, the genetic basis of shell traits and population structure of coastal stocks remain poorly understood. Here, we performed RAD-seq sequencing of 301 individuals from 10 populations along the Chinese coast to analyze population genetics and conduct a genome-wide association study (GWAS). Population genetic analyses revealed nucleotide diversity (π) ranging from 0.259 to 0.273, with the Haiyang population showing the highest diversity. The Hongdao population exhibited the highest inbreeding coefficient (F_IS = 0.469) and lowest observed heterozygosity (H_o = 0.144), whereas the Sanya population had the lowest inbreeding (F_IS = 0.235) and highest heterozygosity (H_o = 0.199). Genetic differentiation (F_ST) was greatest between the Rizhao and Donggang populations (F_ST = 0.0484). In contrast, unexpectedly low differentiation between the geographically distant Donggang and Beihai populations (F_ST = 0.0122) suggests the possible anthropogenic translocation and gene flow. Using a mixed linear model (MLM) for GWAS, we identified 142 significant SNPs associated with shell traits after Bonferroni correction. Notably, 139 SNPs distributed across chromosomes from 1 to 19 were linked to shell thickness, while only three SNPs on chromosome 13 were associated with shell width. Within 50 kb flanking regions of these loci, 453 candidate genes were annotated. Functional enrichment analyses (GO and KEGG) highlighted seven candidate genes (e.g., Calml3, MC1R, and TBXT) that may be associated with biomineralization, calcium signaling, and shell-related trait variation. Additionally, a selective sweep analysis comparing Beihai and Hongdao populations identified 118 candidate genes located in putative outlier regions (top 1% of F_ST and π ratio). Enrichment of these regions revealed three candidate genes (Acp5, SLC6A1, and FNTA) related to metabolism and cellular transport, potentially reflecting local adaptation or artificial selection. Together, these findings provide important insights into the germplasm resources of R. philippinarum and offer valuable genomic targets for marker-assisted selection to improve shell traits in aquaculture breeding programs.