Defining criteria for the reintroduction of locally extinct populations based on contemporary and ancient genetic diversity: The case of the Adriatic Beluga sturgeon ( Huso huso )

Nuclear Multi-Microsatellite Marker Profiling Provides Clues to Molecular Genetic Diversity in Culture-Based Caspian Beluga Sturgeon (Huso huso) Brood Stocks: Ecological Mirror for Restoration

The decreasing natural genetic diversity within intense beluga sturgeon aquaculture presents a complex challenge for culture-based sturgeon stocks. The present report aims to assess the situation by utilizing advanced capillary electrophoresis (CE) and multi-microsatellite nuclear marker tools. We conducted a study involving 436 individuals of both sexes, collected from eight breeder private farms with diverse breeding histories and generational backgrounds. Through the application of eight microsatellites, we amplified a non-coding core genomic region in the species, followed by CE to provide double confirmation of observed genotype and actual allelic size SSR profiling. Utilizing molecular descriptive statistics in the POPGENE software, we calculated allele frequencies, expected and observed heterozygosity within populations, the number of observed and effective alleles (na and ne) and the Shannon's Information Index. Furthermore, we performed molecular analysis of variance (AMOVA), model-based clustering, principal coordinate analysis (PCoA) and STRUCTURE analysis to genetically characterize the populations. It was revealed that LS19 (na = 16) and Afu54 (na  = 3) exhibited the highest and lowest levels of polymorphisms, respectively, within the studied families. Moreover, the Iranian Fisheries Research Organization (IFRO) farm population was found to have the highest genetic diversity (Ave_Het = 0.67), whereas the Rajaeei Sturgeon Private Farm (RJI) displayed the lowest diversity score (Ave_Het = 0.55) among the examined populations. INS and Jahanpouri Sturgeon Private Farm (JPR) showed the highest similarity (0.91), whereas the Saeei Sturgeon Private Farm had the lowest genetic distance, with a similarity score of 0.74 among the populations studied. Furthermore, the evidence from the STRUCTURE analysis highlighted notable levels of allelic sharing and admixture among the eight studied populations, indirectly indicating the presence of genetic diversity within each population and the relatively low genetic distance between the populations. The results demonstrate a significant level of genetic variability, providing evidence that supports the low value of inbreeding in brood management.

Using Weighted Goal Programming Model to Achieve Genetic Gain in a Beluga Sturgeon Breeding Program

We estimated the desired genetic gains for important traits in Beluga sturgeon (Huso huso) using an analytic hierarchy process (AHP) and weighted goal programming (WGP). Two questionnaires were distributed to 122 private Beluga sturgeon farmers in Iran in two stages. The initial stage involved the first questionnaire, which aimed to gather information on the environmental and management aspects of the farms. Additionally, farmers were requested to rate 4 important traits from a list of 12 traits for genetic improvement in the Beluga breeding program. Based on the results, four traits, that is, ovarian fat lobe weight (OFW), total caviar weight (CW), body weight of broodstock (BW) and larval body area at hatching (LBA) were rated highest. In the second stage, the second questionnaire asked farmers to make six pairwise comparisons between the above traits to determine preferences of these traits. The analytical hierarchy process was used to estimate individual preference (Ind-P) values using Super Decisions software. The medians of the Ind-P values were OFW and CW (0.30), BW (0.27) and LBA (0.10). Social group preference (Soc-P) values were estimated for five categories, with 13 social groups using the WGP model in LINGO software. Most disagreements in Soc-P values were found between the commercial products and water temperature categories. Consensus preference values (Con-P) for the above two categories were obtained by the extended WGP model with the range of λ between 0 and 1 in LINGO software. The average best Con-P values were OFW = BW (0.29), LBA (0.21) and CW (0.19). Desired genetic gains (%) were calculated using the percentage genetic improvement (G%) multiplied by the mean of Con-P, yielding values of 2.09, 1.88, 1.44 and 0.62 for BW, CW, LBA and OFW, respectively. The most important achievements of this research are the determination of the economic traits importance and multi-traits selection in the Beluga breeding program.

Metabolomics in sturgeon research: a mini-review

Sturgeons are ancient fish, with 27 species distributed in the Northern Hemisphere. This review first touches upon the significance of sturgeons in the context of their biological, ecological, and economic importance, highlighting their status as "living fossils" and the challenges they face in genomic research due to their diverse chromosome numbers. This review then discusses how omics technologies (genomics, transcriptomics, proteomics, and metabolomics) have been used in sturgeon research, which so far has only been done on Acipenser species. It focuses on metabolomics as a way to better understand how sturgeons work and how they react to their environment. Specific studies in sturgeon metabolomics are cited, showing how metabolomics has been used to investigate various aspects of sturgeon biology, such as growth, reproduction, stress responses, and nutrition. These studies demonstrate the potential of metabolomics in improving sturgeon aquaculture practices and conservation efforts. Overall, the review suggests that metabolomics, as a relatively new scientific tool, has the potential to enhance our understanding of sturgeon biology and aid in their conservation and sustainable aquaculture, contributing to global food security efforts.

Microsatellite Characterization and Panel Selection for Brown Bear (Ursus arctos) Population Assessment

An assessment of the genetic diversity and structure of a population is essential for designing recovery plans for threatened species. Italy hosts two brown bear populations, Ursus arctos marsicanus (Uam), endemic to the Apennines of central Italy, and Ursus arctos arctos (Uaa), in the Italian Alps. Both populations are endangered and occasionally involved in human-wildlife conflict; thus, detailed management plans have been in place for several decades, including genetic monitoring. Here, we propose a simple cost-effective microsatellite-based protocol for the management of populations with low genetic variation. We sampled 22 Uam and 22 Uaa individuals and analyzed a total of 32 microsatellite loci in order to evaluate their applicability in individual identification. Based on genetic variability estimates, we compared data from four different STR marker sets, to evaluate the optimal settings in long-term monitoring projects. Allelic richness and gene diversity were the highest for the Uaa population, whereas depleted genetic variability was noted for the Uam population, which should be regarded as a conservation priority. Our results identified the most effective STR sets for the estimation of genetic diversity and individual discrimination in Uam (9 loci, PIC 0.45; PID 2.0 × 10-5), and Uaa (12 loci, PIC 0.64; PID 6.9 × 10-11) populations, which can easily be utilized by smaller laboratories to support local governments in regular population monitoring. The method we proposed to select the most variable markers could be adopted for the genetic characterization of other small and isolated populations.

New developments in the field of genomic technologies and their relevance to conservation management

Recent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.

Genetic Investigation of Four Beluga Sturgeon (Huso huso, L.) Broodstocks for its Reintroduction in the Po River Basin

The reintroduction of the extinct beluga sturgeon (Huso huso L.), an anadromous species with economic and traditional relevance, is a priority in next conservation strategies in Northern Italy. The EU-LIFE NATURA project aims to reintroduce the beluga sturgeon in the Po River basin through a captive breeding program. Critical requirements for the success of the program are river connectivity and knowledge of genetic diversity of the selected broodstocks to ensure self-sustainability of reintroduced populations. Here, the four broodstocks used for the reintroduction of beluga sturgeon have been genetically screened, genotyping 13 loci and sequencing mitochondrial DNA cytochrome b (Cyt b) gene and the entire mitochondrial DNA control region (D-Loop). The four broodstocks showed a medium-high level of nuclear genetic variability and the presence of two sub-populations, evidencing a total level of inbreeding coefficients able to sustain the good potential as future breeders. Mitochondrial analyses showed a genetic variability comparable to wild populations, further strengthening the positive potential of the investigated broodstock. Therefore, this study, showed how the degree of genetic diversity found within the four broodstocks used for H. huso reintroduction in the Po River basin could be suitable to ensure the success of the program, avoiding the inbreeding depression associated with founder effect and captive breeding.