Genetic structure and identification of divergent genomic regions of Solen grandis from three geographic populations based on whole genome resequencing

The grand jackknife clam, Solen grandis, is a crucial mariculture bivalve with high economic value. To investigate the genetic variation of S. grandis in China, the whole-genome resequencing was carried out on 81 individuals from three S. grandis geographical populations (Huludao [HLD], Rizhao [RZ], and Dongtai [DT]) to develop the genome-wide SNPs. Generally, all three populations indicated low genetic diversity. For each population, the observed heterozygosity (HO) ranged from 0.097 to 0.101, the expected heterozygosity (HE) from 0.105 to 0.109, the number of effective alleles (Ne) from 1.329 to 1.343, nucleotide diversity (π) between 0.0107 and 0.0111, the polymorphism information content (PIC) from 0.156 to 0.160, and the inbreeding coefficient (FIS) values of 0.042 to 0.053. Meanwhile, the fixation index pairwise (FST) values among the three S. grandis populations ranged from 0.008 to 0.023, which were low differentiation. Additionally, population structure analysis revealed that the RZ and DT populations first clustered together and were further grouped with the HLD population. Moreover, the genome-wide outlier analysis identified 32 candidate selected regions with a total size of 5.50Mb, as well as 10 candidate genes including ACE (Angiotensin-converting enzyme), KIAA1161 (Myogenesis regulating glycosidase), CES1 (Carboxylesterase 1), RPS13 (Ribosomal protein S13), APOD (Apolipoprotein D), PPP1R13B (Protein phosphatase 1 regulatory subunit 13B), and CHDH (Choline dehydrogenase), etc. Overall, this study enriches the genetic resources of S. grandis and improves our understanding of its population genetic structure and selection signatures, providing a useful reference for future genetic resource conservation and management.