Analysis of Autozygosity Using Whole-Genome Sequence Data of Full-Sib Families in Pikeperch (Sander lucioperca)

Pikeperch (Sander lucioperca) has emerged as a high value species to the aquaculture industry. However, its farming techniques are at an early stage and its production is often performed without a selective breeding program, potentially leading to high levels of inbreeding. In this study, we identified and characterized autozygosity based on genome-wide runs of homozygosity (ROH) on a sample of parental and offspring individuals, determined effective population size (Ne), and assessed relatedness among parental individuals. A mean of 2,235 ± 526 and 1,841 ± 363 ROH segments per individual, resulting in a mean inbreeding coefficient of 0.33 ± 0.06 and 0.25 ± 0.06 were estimated for the progeny and parents, respectively. Ne was about 12 until four generations ago and at most 106 for 63 generations in the past, with varying genetic relatedness amongst the parents. This study shows the importance of genomic information when family relationships are unknown and the need of selective breeding programs for reproductive management decisions in the aquaculture industry.

Development of Disease-Resistance-Associated Microsatellite DNA Markers for Selective Breeding of Tilapia (Oreochromis spp.) Farmed in Taiwan

There are numerous means to improve the tilapia aquaculture industry, and one is to develop disease resistance through selective breeding using molecular markers. In this study, 11 disease-resistance-associated microsatellite markers including 3 markers linked to hamp2, 4 linked to hamp1, 1 linked to pgrn2, 2 linked to pgrn1, and 1 linked to piscidin 4 (TP4) genes were established for tilapia strains farmed in Taiwan after challenge with Streptococcus inae. The correlation analysis of genotypes and survival revealed a total of 55 genotypes related to survival by the chi-square and Z-test. Although fewer markers were found in B and N2 strains compared with A strain, they performed well in terms of disease resistance. It suggested that this may be due to the low potency of some genotypes and the combinatorial arrangement between them. Therefore, a predictive model was built by the genotypes of the parental generation and the mortality rate of different combinations was calculated. The results show the same trend of predicted mortality in the offspring of three new disease-resistant strains as in the challenge experiment. The present findings is a nonkilling method without requiring the selection by challenge with bacteria or viruses and might increase the possibility of utilization of selective breeding using SSR markers in farms.

Effective and Low-Maintenance IMTA System as Effluent Treatment Unit for Promoting Sustainability in Coastal Aquaculture

Integrated multitrophic aquaculture (IMTA) is a versatile technology emerging as an ecological and sustainable solution for traditional monoculture aquacultures in terms of effluent treatment. Nevertheless, IMTA is still poorly applied in aquaculture industry due to, among other reasons, the lack of effective, low-investment and low-maintenance solutions. In this study, one has developed a practical and low maintenance IMTA-pilot system, settled in a semi-intensive coastal aquaculture. The optimisation and performance of the system was validated using Ulva spp., a macroalgae that naturally grows in the fishponds of the local aquaculture. Several cultivation experiments were performed at lab-scale and in the IMTA-pilot system, in static mode. The specific growth rate (SGR), yield, nutrient removal, N and C enrichment, protein and pigment content were monitored. Ulva spp. successfully thrived in effluent from the fish species sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax) production tanks and significantly reduced inorganic nutrient load in the effluent, particularly, NH4+, PO43− and NO3−. The enrichment of nitrogen in Ulva spp.’s tissues indicated nitrogen assimilation by the algae, though, the cultivated Ulva spp. showed lower amounts of protein and pigments in comparison to the wild type. This study indicates that the designed IMTA-pilot system is an efficient solution for fish effluent treatment and Ulva spp., a suitable effluent remediator.

Aquaculture State, Challenges and Technologies in the Middle East

The aquaculture industry in the Middle East (ME) is still relatively new compared to other parts of the world, making this region highly dependent on other countries for the production of food and feed needs. Aquaculture activities in the world at current is mainly focused in China; this may be propelled by its own internal demand for seafood as determined by the United Nations Food and Agriculture Organization (FAO). Challenges faced in the ME has not been elucidated so far and the issues arising might be unique only to this region due to aquaculture being in the initial stages coupled with water access and limitations, climate and geography, in addition to pollution. This review paper will present and discuss global needs for seafood focusing later on the needs in the ME, followed by a discourse into the importance, types and challenges of aquaculture in the ME. Baseline knowledge and infrastructure to enhance knowledge is a pressing need at this stage of infancy. It is hope this sector will continue to develop, and with the support of stakeholders, aquaculture in the ME will achieve a state of independence.

A Risk-Based Approach for Managing Aquaculture Used Oxytetracycline-Induced TetR in Surface Water Across Taiwan Regions

Oxytetracycline (OTC), one of the most important antibiotics in aquaculture industry, has been linked to emergence of antibiotic resistant genes in the aquatic environment. Given rapid growth of the aquaculture industry and unregulated use of antibiotics, it is necessary to implement measures to mitigate the impact of antibiotic resistance risk on environmental and human health. However, there is a lack of quantitative models to properly assess risk of antibiotic resistance associated with environmentally relevant antibiotic residues. To address this issue, here we developed a computational framework to assess antibiotic resistance risk posed by low-concentration OTC in aquaculture ponds and rivers across Taiwan regions. To this end, estimated amount of aquaculture used OTC as a crucial input parameter was incorporated into a multimedia fugacity model to predict environmental concentrations of OTC in surface water/sediment. A pharmacodynamic-based dose–response model was used to characterize the OTC concentration–antibiotic resistance relationships. The risk of antibiotic resistance selection in an aquatic environment could be assessed based on a probabilistic risk model. We also established a control measure model to manage the risks of substantial OTC-induced antibiotic resistance impacts. We found that OTC residues were likely to pose a high risk of tetracycline resistance (tetR) genes selection in aquaculture ponds among all the study basins, whereas risk of tetR genes selection in rivers experienced a variably changing fashion. We also showed that it was extremely difficult to moderate the tetR genes selection rates to less than 10% increase in aquaculture ponds situated at northeastern river basins in that the minimum reductions on OTC emission rates during spring, summer, and autumn were greater than 90%. On the other hand, water concentrations of OTC during spring and summer in southwestern rivers should be prioritized to be severely limited by reducing 67 and 25% of OTC emission rate, respectively. Overall, incorporating a computational fugacity model into a risk assessment framework can identify relative higher risk regions to provide the risk-based control strategies for public health decision-making and development of robust quantitative methods to zero-in on environment with high risk of tetR genes selection in relation to aquaculture-used pharmaceutical residues.

Loop-mediated isothermal amplification for diagnosing marine pathogens in tissues of Crassostrea spp. and white shrimp, Litopenaeus vannamei, farmed in Mexico

Loop-mediated isothermal amplification (LAMP) is an accurate, sensitive, rapid, and easy-to-perform method for gene amplification under isothermal conditions, and it has served as a powerful diagnostic tool. In this study, we used LAMP to develop a diagnostic protocol for detecting Vibrio parahaemolyticus and white spot syndrome virus in whiteleg shrimp, and Perkinsus spp. in Crassostrea spp. in Mexico. These pathogens are associated with different diseases and are considered a threat in the aquaculture industry. Infected and uninfected oysters and shrimp were obtained from farms in the northwest coast of Mexico to standardize the LAMP assay. We determined the candidate target genes in the first-round analysis of many sets of primers, and then we chose a set of primers that successfully amplified with Mexican samples. We optimized the LAMP reactions for each pathogen with the chosen primer sets using temperature gradients from 61 to 65 ºC, DNA concentrations from 2.5 pg to 250.0 ng, and reaction times from 10 to 60 min. This study established a diagnostic procedure for detecting pathogens in oysters and shrimp from Mexico. Early diagnosis and treatment of pathogens can immensely reduce disease transmission in aquaculture farms.

Activation of the TCA Cycle to Provide Immune Protection in Zebrafish Immunized by High Magnesium-Prepared Vibrio alginolyticus Vaccine

Vaccines are safe and efficient in controlling bacterial diseases in the aquaculture industry and are in line with green farming. The present study develops a previously unreported approach to prepare a live-attenuated V. alginolyticus vaccine by culturing bacteria in a high concentration of magnesium to attenuate bacterial virulence. Furthermore, metabolomes of zebrafish immunized with the live-attenuated vaccines were compared with those of survival and dying zebrafish infected by V. alginolyticus. The enhanced TCA cycle and increased fumarate were identified as the most key metabolic pathways and the crucial biomarker of vaccine-mediated and survival fish, respectively. Exogenous fumarate promoted expression of il1β, il8, il21, nf-κb, and lysozyme in a dose-dependent manner. Among the five innate immune genes, the elevated il1β, il8, and lysozyme are overlapped in the vaccine-immunized zebrafish and the survival from the infection. These findings highlight a way in development of vaccines and exploration of the underlying mechanisms.

Efektivitas Kerjasama Pihak Ketiga Dalam Proses Pembinaan Warga Binaan Berbasis Masyarakat (Community Based Corrections) Lapas Terbuka Nusakambangan

Collaborate with third parties between the Nusakambangan Open Prison and PT Noerman in the form of implementing the Community Based Correction concept in order to prepare social reintegration as mandated by PERMENKUMHAM No. 3 of 2018 concerning Conditions and Procedures for Granting Remission, Assimilation, Leave to Visit Family, Conditional Release, Leave Prior to Release, and Conditional Leave with reference to the 5 (five) principles put forward by P. Corney, namely the availability of employment opportunities, the existence of selection, not being exploited, minimum security, and responsibility for the transfer of Prisoner. This research was conducted to see the extent of the cooperation of third parties in implementing the concept of Community Based Correction in order to prepare towards social reintegration. The results of this study a comprehensive coaching and mentoring process because of the Terms of Reference (KAK) agreed upon by the Open Prison with PT Noerman which is stated in Number: PAS-19. HH 05.05 of 2019, Number: 01/PTNJA/PKS/IV/2019 of 2019 the Independence Development Program for correctional Prisoner in the field of Aquaculture Industry. This research was conducted using juridical-empirical research methods. This method is a research method that examines the applicable legal provisions and what happens in actual reality to find facts that are used as research data, which are then analyzed to identify problems and ultimately to solve problems. The approach used is a mixed approach between the rule of law and case studies.