Assessment of how the hard clam, Mercenaria mercenaria (Linnaeus, 1758), responds to environmental changes, like salinity fluctuations, is an existing need. The hard clam is an important ecological and economic resource along the US Eastern Seaboard. In Virginia alone, the farm gate value of the hard clam in 2018 was $38.8 million, making it the largest aquaculture industry in Virginia . This growing industry is primarily limited to higher salinity habitats on the seaside of the Eastern Shore of Virginia or lower Chesapeake Bay . Even in areas of higher salinity, hard clams are vulnerable to extreme precipitation events, which can lead to hyposaline (low salinity) stress and threaten natural and aquacultured hard clam populations . Osmotic stress , like a drop in salinity, can lead to altered gene expression and cell cycle events . Transcriptomic analysis is a powerful tool for exploring the relationship between phenotype and genotype, enabling a better understanding of how hard clams respond to stress.
Genetically distinct hard clam populations originating from varying salinity habitats along the U.S. Eastern Seaboard have been identified and some of these populations were used to establish lines at the VIMS Eastern Shore Laboratory (ESL) : Wachapreague Channel, VA (WC) ; Pocomoke Sound, VA (PS) ; Mobjack Bay, VA (MB); Great Bay, NJ (NJ); Cape Cod, MA (CC) ; and Bogue Sound, NC (NC). As small juveniles, clams spawned from these lines were shown to have differences in respiration performance after low salinity exposures as part of the graduate work of VIMS student Anthony Himes. In 2019, F1 generations of WC, PS, MB, NJ, and CC clams were spawned, and i n 2021, F1 crosses were spawned and include WC x WC (control), WC x PS, and NC x CC . Three clams from each of the 2019 spawns were exposed to 35 ppt and 15 ppt salinities for 26 hours. After exposures, gill tissue was sampled and placed in RNA preservative. Four replicates of 10 clams spawned in 2021 were also exposed to 35 ppt and 15 ppt salinities for 26 hours. Tissue from two groups of four clams from each replicate was pooled and placed in RNA preservative.
Whole transcriptome shotgun sequencing (WTSS), also known as RNA-Seq, will be used to explore the mRNA expression patterns of the hard clam when faced with ideal (35 ppt) and low (15 ppt) salinity conditions . C omparing mRNA expression patterns among genetically distinct clam lines that are derived from populations that experience different salinity patterns will provide important information about genes involved in response to salinity stress . RNA-seq will also be used to identify genotypic differences in the form of single nucleotide polymorphisms (SNPs). SNPs associated with specific genes that are linked with traits of interest can be powerful molecular markers . A comparative transcriptomic study is the link between the genetic and physiological variation seen among hard clam populations and could lead to SNPs for improved selection of hard clams for better low salinity tolerance by the aquaculture industry.