Piecing together the data of the U.S. marine aquaculture puzzle

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BACKGROUND

The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

MAIN TEXT

Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

CONCLUSION

This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Downscaled climate change threats to United States freshwater finfish aquaculture

Climate change threatens food production, yet gaps remain in our understanding of these threats to aquaculture, the fastest growing food production subsector. To build climate-resilient practices and policies we need to quantify and map current and future climate threats to aquaculture. Here, we explore how downscaled climate change [SSP 2 (eq. RCP 4.5) and SSP 5 (eq. RCP8.5), CMIP6] threats - including water scarcity, flooding, and increasing temperature - may directly affect United States (US) freshwater farmed fish (N = 7) based on their biological thermal tolerances and indirectly challenge the operations required for production, including to the human workforce. Aquaculture in the US is dominated by catfish, trout, and tilapia production and is widespread, with some form of finfish aquaculture present in every state and nearly half of all counties across the country. Given the current location of catfish, tilapia, bass, and carp in the US and their tolerance to warmer conditions, we find increasing temperatures are less likely to biologically impact these species negatively. In contrast, current trout, sturgeon, and perch production will be biologically threatened by rising temperatures. With respect to operational needs for facilities, increases in 'wet bulb' temperatures in the Southeast will regularly challenge human physiological limits and constrain worker capacity. Drought in the Southwest will also limit an intrinsically water dependent system, affecting nearly all taxa. While current areas of aquaculture will tend to become increasingly challenging for farmed fishes, new potential habitats will open up for nearly all species. Overall, in the absence of immediate greenhouse gas mitigation, there are several non-mutually exclusive climate adaptations, yet these adaptations can be extremely costly. Ultimately, freshwater aquaculture in the US is going to be under intense climate pressure, which may drive out small operations and cause the country to further increase dependence on international aquatic food imports.

The Occurrence of Karenia species in mid-Atlantic coastal waters: Data from the Delmarva Peninsula, USA

A bloom of Karenia papilionacea that occurred along the Delaware coast in late summer of 2007 was the first Karenia bloom reported on the Delmarva Peninsula (Delaware, Maryland, and Virginia, USA). Limited spatial and temporal monitoring conducted by state agencies and citizen science groups since 2007 have documented that several Karenia species are an annual component of the coastal phytoplankton community along the Delmarva Peninsula, often present at background to low concentrations (100 to 10,000 cells L-1). Blooms of Karenia (> 105 cells L-1) occurred in 2010, 2016, 2018, and 2019 in different areas along the Delmarva Peninsula coast. In late summer and early autumn of 2017, the lower Chesapeake Bay experienced a K. papilionacea bloom, the first recorded in Bay waters. Blooms typically occurred summer into autumn but were not monospecific; rather, they were dominated by either K. mikimotoi or K. papilionacea, with K. selliformis, K. brevis-like cells, and an undescribed Karenia species also present. Cell concentrations during these mid-Atlantic Karenia spp. blooms equalled concentrations reported for other Karenia blooms. However, the negative impacts to environmental and human health often associated with Karenia red tides were not observed. The data compiled here report on the presence of multiple Karenia species in coastal waters of the Delmarva Peninsula detected through routine monitoring and opportunistic sampling conducted between 2007 and 2022, as well as findings from research cruises undertaken in 2018 and 2019. These data should be used as a baseline for future phytoplankton community analyses supporting coastal HAB monitoring programs.

Improving survival, growth, feed utilization, antioxidant status, and fatty acids profile of European seabass, Dicentrarchus labrax, larvae fed silymarin, Silybum marianum, supplemented weaning diet

To sustain normal development, high survival, and rapid growth, marine fish larvae require a diet rich in polyunsaturated fatty acids, which could decrease the risk of reactive oxygen species accumulations. Consequently, a 60-day feeding experiment was conducted to determine the effect of silymarin (SM) supplementation in weaning diets on the growth performance, survival, antioxidant enzyme activities, and fatty acids profile of European seabass (Dicentrarchus labrax) larvae. Four isonitrogenous and isolipidic diets were investigated using SM at levels of 0, 200, 400, and 600 mg kg−1 (SM0.00, SM200, SM400, and SM600, respectively). The findings showed that, in a dose-dependent manner, increasing dietary levels of SM enhanced survival, growth, and feed utilization. In the SM600 group, the weight gain, survival, and feed conversion ratio (FCR) improved by 123.21, 11.66, and 38.72%, respectively, compared to the control group. The dose-response analysis demonstrated a strong positive correlation (R2=0.96) between SM levels and weight increase, and a strong negative correlation (R2=0.88) between SM levels and FCR. The antioxidant enzyme activities of larvae given SM-enriched diets were significantly greater than those of the control group. Compared to the control group, the CAT and SOD improved by 81.77 and 5.08 % in the SM600 group. In addition, the saturated fatty acid content reduced while the unsaturated fatty acid content increased, particularly in the SM600 group. The results indicate that supplementing the micro diet of European seabass larvae during weaning with SM at a dose of 600 mg kg-1 increases growth, survival, antioxidant status, and fatty acid profiles.