Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.

Sperm Repository for a Breeding Program of the Eastern Oyster Crassostrea virginica: Sample Collection, Processing, Cryopreservation, and Data Management Plan.

The Eastern oyster Crassostrea virginica (Family Ostreidae) is one of the most important fishery and aquaculture species in the U.S. and is a keystone species for coastal reefs. A breeding program was initiated in 2019 to support the fast-growing aquaculture industry culturing this species in the Gulf of Mexico. Oysters from 17 wild populations in embayment along the U.S. Gulf of Mexico coast from southwest Florida to the Matagorda Bay, Texas were used as broodstock for the program to maximize genetic diversity in the base population. A sperm repository of the broodstock was established to support the breeding project. The goal of this study was to demonstrate the sperm sample collection, processing, cryopreservation, and the data management plan involved in the establishment of a sperm germplasm repository of base populations. The supporting objectives were to: (1) develop a data management plan for the sperm repository; (2) streamline the procedure for sample collection, processing, and cryopreservation; (3) incorporate sperm quality analysis into the procedure, and (4) archive the cryopreserved samples as a repository for future use in the breeding program. This sperm repository included a total of 102 male oysters from the 17 collection sites (six oysters per site). A data management plan was developed with six categories, including sample collection, phenotype, fresh sperm, genotype, cryopreservation, and post-thaw sperm, as guide for data collection. Sperm collection was accomplished by strip spawn, and fresh sperm production, motility, and fertility were recorded for quality analysis. Cryopreserved sperm samples were sorted, labelled, archived, and stored in liquid nitrogen for future use. Post-thaw motility (1-30%) and plasm membrane integrity (15.34-70.36%) were recorded as post-thaw quality parameters. Overall, this study demonstrated a streamlined procedure of oyster sperm collection, processing, and cryopreservation for establishing a sperm repository that can serve as a template for construction of oyster germplasm repositories for breeding programs.

Regulation of sperm motility in Eastern oyster (Crassostrea virginica) spawning naturally in seawater with low salinity.

Oyster aquaculture is expanding worldwide, where many farms rely on seed produced by artificial spawning. As sperm motility and velocity are key determinants for fertilization success, understanding the regulation of sperm motility and identifying optimal environmental conditions can increase fertility and seed production. In the present study, we investigated the physiological mechanisms regulating sperm motility in Eastern oyster, Crassostrea virginica. Sperm motility was activated in ambient seawater with salinity 4-32 PSU with highest motility and velocity observed at 12-24 PSU. In artificial seawater (ASW) with salinity of 20 PSU, sperm motility was activated at pH 6.5-10.5 with the highest motility and velocity recorded at pH 7.5-10.0. Sperm motility was inhibited or totally suppressed in Na+, K+, Ca2+, and Mg2+-free ASW at 20 PSU. Applications of K+ (500 µM glybenclamide and 10-50 mM 4-aminopyridine), Ca2+ (1-50 µM mibefradil and 10-200 µM verapamil), or Na+ (0.2-2.0 mM amiloride) channel blockers into ASW at 20 PSU inhibited or suppressed sperm motility and velocity. Chelating extracellular Ca2+ ions by 3.0 and 3.5 mM EGTA resulted in a significant reduction and full suppression of sperm motility by 4 to 6 min post-activation. These results suggest that extracellular K+, Ca2+, and Na+ ions are involved in regulation of ionic-dependent sperm motility in Eastern oyster. A comparison with other bivalve species typically spawning at higher salinities or in full-strength seawater shows that ionic regulation of sperm motility is physiologically conserved in bivalves. Elucidating sperm regulation in C. virginica has implications to develop artificial reproduction, sperm short-term storage, or cryopreservation protocols, and to better predict how changes in the ocean will impact oyster spawning dynamics.

Characterization of the Microbiota of Oyster Larvae (Crassostrea virginica) and Tank Water from an Aquaculture System with High and Low Larval Survival Rates.

Aquaculture plays an increasingly important role in the growing demand for seafood. Hatchery production of oyster larvae is an integral component of oyster farming, providing single seed for off-bottom farming or larvae for setting on larger substrates for on-bottom farming. Larvae from certain tanks in an established aquaculture enterprise were dying from an unknown etiologic agent. A metagenomic approach was used to examine oyster larvae and water from larval tanks with high and low survival rates to evaluate the epidemiological efficacy of this approach.

Impact of dispersant on early life stages of the water flea Daphnia magna and the eastern oyster Crassostrea virginica.

In response to the 2010 Deepwater Horizon oil spill, over 1 million gallons of dispersant were applied in Gulf of Mexico offshore waters; Corexit 9500 was the most applied dispersant. The impact on organisms in nearshore and freshwaters has received little scrutiny. Acute 48 h toxicity of Corexit 9500 and a new hyperbranched polyethylenimine (HPEI) dispersant-like compound were evaluated for the freshwater indicator organism, Daphnia magna and for larval and early spat stages of the Eastern oyster, Crassostrea virginica. For D. magna, Corexit 9500 demonstrated toxicity (EC50 of 0.14 [0.13, 0.15] ppm) similar to the 10-kDa HPEI (EC50 of 0.16 [0.12, 0.19] ppm). HPEI toxicity increased as a function of molecular weight (1.2 to 750 kDa). The 10 kDa size HPEI was further investigated because it dispersed crude oil with equal effectiveness as Corexit. For Corexit, 100% oyster mortality was detected for the ≤0.2-mm size classes and mortality >50% for the 0.3- and 0.7-mm size classes at the two greatest concentrations (25 and 50 ppm). HPEI (10 kDa) exhibited low mortality rates (<30%) for all concentrations for all oyster size classes except the 0.1-mm class. Although mortality rates for this size class were up to 60%, mortality was still less than the mortality caused by Corexit 9500. The low toxicity of HPEI polymers for C. virginica in comparison with Corexit 9500 suggests that HPEI polymers warrant further study.