Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

Abstract

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (Fst value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

Genetic Evaluation of Black Sea Bream (Acanthopagrus schlegelii) Stock Enhancement in the South China Sea Based on Microsatellite DNA Markers

“…Therefore, we suggested that broodstock should be selected according to the mating system and reproductive success of black sea bream in order to avoid biased reproductive contribution. Expanding the number of native breeders and collecting fertilized eggs at several times could also help in decreasing the genetic differences and conserving a larger genetic resource of natural populations [54,55]. Moreover, substantial loss of genetic variation can happen after just one generation [56].…”

High Spatiotemporal Genetic Connectivity in the Pacific Razor Clam (Siliqua patula) throughout Cook Inlet, Alaska

“…In contrast, population genetic work conducted on related pharids, including Chinese razor clams ( Sinonovacula constricta ) along the coasts of China and Japan (Guo et al 1999, Niu et al 2012, Orita 2021) and the pod razor shell ( Ensis siliqua ) in European coastal waters (Fernández-Tajes et al 2007, Varela et al 2012), do not describe consistent patterns of structuring, except perhaps on broader spatial scales (1,000 s of km). Instead, gene flow appears to be regionally specific and dependent on myriad factors like hydrographic processes, habitat availability, anthropogenic influences, or other unidentified mechanisms.…”

Genome-Wide Population Structure and Selection Signatures of Yunling Goat Based on RAD-seq

“…This method has great advantages in the number of SNPs acquired and the ability to identify novel SNPs compared with SNP chip technology. Restriction site-associated DNA sequencing (RAD-seq) is one of the RRS technologies, which can be used to survey a host of unlinked genetic markers adjacent to restriction sites [ 12 , 13 ] and applied to the research of the gene flow [ 14 , 15 , 16 ], phylogenetic research [ 17 ], and mapping genes of important traits [ 10 , 12 , 18 , 19 , 20 ]. In particular, RAD-seq technology is widely used in some domestic animals, including chickens [ 21 , 22 ] and pigs [ 23 ].…”