Population Structure and Genetic Diversity of Nile Tilapia (Oreochromis niloticus) Strains Cultured in Tanzania

Genome-Assisted Gene-Flow Rescued Genetic Diversity Without Hindering Growth Performance in an Inbred Coho Salmon (Oncorhynchus kisutch) Population Selected for High Growth Phenotype

Selective breeding is a powerful tool for improving aquaculture production. A well-managed breeding program is essential, as populations can otherwise lose genetic diversity, leading to reduced selection response and inbreeding excesses. In such cases, genetic diversity in broodstock must be restored by introducing individuals from external populations. However, this can reduce the accumulated genetic gains from selective breeding. However, the selective introduction of individuals with superior phenotypes will allow the restoration of genetic diversity without sacrificing these gains. In this study, we demonstrated this possibility using a selectively bred (SB) and a randomly bred (RB) population of coho salmon (Oncorhynchus kisutch). Forty males with superior growth were selected from the RB population using genomic selection and crossed with 127 randomly collected females from the SB population, producing a newly bred (NB) population. Genetic diversity, assessed from population statistics such as effective number of alleles, allele richness, and observed heterozygosity of 11 microsatellite markers, was higher in NB than in SB and RB. Additionally, fork length and body weight were compared among the three populations after 12 months of growth post-fertilization in common tanks. The least-squares means of fork length and body weight were similar between NB (164.9 mm and 57.9 g) and SB (161.1 mm and 53.7 g), while both were significantly greater than RB (150.4 mm and 43.0 g). Our results highlight the effectiveness of genome-assisted gene flow in restoring the genetic diversity of a population without compromising accumulated genetic gain in growth.

SNP Fingerprinting for Germplasm Identification of the Fast-Growing Pacific oyster (Crassostrea gigas) "Haida No. 1" Variety

The Pacific oyster (Crassostrea gigas) is a global aquaculture species of economic significance. Selective breeding programs have been conducted to produce multiple strains with fast growth as well as other desirable traits. However, due to the phenotypic plasticity of oysters, challenges existed for precise germplasm identification among selectively bred strains. In this work, we identified selection signatures of three fast-growing Pacific oyster strains originated from wild populations collected from China, Japan, and Korea, respectively, which were used for development of SNP-based molecular fingerprinting for precise identification of germplasm. We performed whole-genome resequencing of 59 oysters from three selectively bred strains and a wild population for genome-wide SNP analyses. Population structure analysis with these SNPs revealed significant genetic differentiation among the selectively bred strains. Based on the FST index, we identified 41, 49, and 36 strain-specific SNPs from the three selectively bred strains. Taking into account the "hitch-hiking effect" that occurs in the genome during positive selection, we identified two, three, and two molecular fingerprints for the three strains, respectively. We validated the molecular fingerprints of the China selectively bred strain (i.e., "Haida No. 1" variety) with a separate population of 42 oysters with diverse genetic background, demonstrating the accuracy of germplasm identification of over 96%. This work provides a reliable tool for precise germplasm identification of the "Haida No. 1" variety as well as other two selectively bred strains, which is valuable in germplasm conservation and breeding design in the C. gigas.

Identification of the effects of hypoxia on the liver tissues of Nile tilapia Oreochromis Niloticus

BACKGROUND

Hypoxia stress resulted in mortality during the fish aquaculture program, affecting the sustainable development of the aquaculture industry. The Egyptian strain of O. niloticus showed a strong ability to hypoxia. In this study, a Nile tilapia strain that was kept and selected for 45 years by the author's team was used to elucidate the mechanism of the hypoxia response in the liver, including the identification of metabolic pathways and genes, involved in the hypoxia response of this strain.

RESULTS

The effects of hypoxia stress were detected at 0-hour, 6-hour, and 72-hour time points (0 h, 6 h, 72 h) on tilapia liver at 1 mg/L dissolved oxygen conditions. The blood triglyceride, blood glucose and cholesterol values exhibited significantly different change trends, but the hemoglobin content showed no significant differences between 0 h, 6 h and 72 h (P > 0.05). The activities of catalase (CAT), glutathione peroxidase (GSH-PX), total antioxidant capacity (T-AOC), lactate dehydrogenase (LDH), and acid phosphatase (ACP) in the liver tissue gradually increased at 0 h, 6 h and 72 h (P < 0.05). Histological analyses revealed structural changes in intracellular lipid droplets, nuclear migration and dissolution, and cell vacuolization in liver tissues. Six pathways were identified as the main enriched metabolic pathways according to the transcriptome profiling analysis, which were protein processing in endoplasmic reticulum, steroid biosynthesis, peroxisome, PPAR signaling pathway, glycolysis/gluconeogenesis and Insulin signaling pathway. The expressions of the important differentially expressed genes were verified by qPCR analysis, including erola, LOC100692144, sqle, cratb, pipox, cpt1a2b, hik and acss2l, ehhadh, prkcz, fasn and plaa, which showed the same expressions trends as those of RNA-Seq.

CONCLUSIONS

The Nile tilapia strain improves the abilities of hypoxia response through energy metabolism. Antioxidant enzyme measurements in the liver indicate that these five antioxidant enzymes play important roles in protecting the body from hypoxic damage. The histological changes in liver cells indicate that the damage caused by hypoxia stress. The immune-related metabolic pathways and energy metabolism-related pathways were obtained by transcriptome profiling, and these metabolic pathways and the differentially expressed genes selected from these metabolic pathways may be involved in the mechanism of hypoxia tolerance in this strain. These findings provide a better understanding of the hypoxia response mechanism of fish, and represent a useful resource for the genetic breeding of O. niloticus.

Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes

Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)-HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (Pcrit) of the corresponding species. Our results demonstrate that Pcrit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A, two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in Pcrit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates.

Morphometric and genetic characterization of cultured and wild populations of tilapia, Oreochromis niloticus in India

To study genetic variation in Indian populations of tilapia, Oreochromis niloticus, both truss morphometrics and genetic characterization have been performed. In the present study, 88 individuals from two farm populations (GIFT and West Bengal) and one reservoir population (Gujarat) were selected to analyse variations at ten morphometric landmarks and eight microsatellite loci. Truss morphometric analysis showed PCI, PCII, and PCIII expressing 29.1%, 21.36%, and 15.48% of the variance, respectively. Results showed no clear shift in shape between the studied populations of O. niloticus, indicating low morphological variability among them. The number of microsatellite alleles ranged from 3 to 9, while expected heterozygosity (HE) and observed heterozygosity (HO) values ranged from 0.56 (WB) to 0.68 (Guj) and 0.59 (GIFT) to 0.72 (Guj), respectively. The Gujarat and West Bengal populations had the smallest pairwise distance (0.0123) between them, indicating that they were genetically closer. Individuals from GIFT, however, showed the largest distance from the other populations. DNA marker variations revealed the highest genetic variability in the Gujarat population and the lowest variability in the GIFT population. The results of this study will help establish a base population for genetic improvement program and conservation of wild populations.

Novel Microsatellite Loci, Cross-Species Validation of Multiplex Assays, and By-Catch Mitochondrial Genomes on Ochthebius Beetles from Supratidal Rockpools

Here we focus on designing, for the first time, microsatellite markers for evolutionary and ecological research on aquatic beetles from the genus Ochthebius (Coleoptera, Hydraenidae). Some of these non-model species, with high cryptic diversity, exclusively inhabit supratidal rockpools, extreme and highly dynamic habitats with important anthropogenic threats. We analysed 15 individuals of four species (O. lejolisii, O. subinteger, O. celatus, and O. quadricollis) across 10 localities from the Mediterranean coasts of Spain and Malta. Using next-generation sequencing technology, two libraries were constructed to interpret the species of the two subgenera present consistently (Ochthebius s. str., O. quadricollis; and Cobalius, the rest of the species). Finally, 20 markers (10 for each subgenus) were obtained and successfully tested by cross-validation in the four species under study. As a by-catch, we could retrieve the complete mitochondrial genomes of O. lejolisii, O. quadricollis, and O. subinteger. Interestingly, the mitochondrial genome of O. quadricollis exhibited high genetic variability compared to already published data. The novel SSR panels and mitochondrial genomes for Ochthebius will be valuable in future research on species identification, diversity, genetic structure, and population connectivity in highly dynamic and threatened habitats such as supratidal coastal rockpools.

Population structure and genetic diversity of Nile tilapia (Oreochromis niloticus) using microsatellite markers from selected water bodies in southwest Ethiopia

BACKGROUND

The Ethiopian southwest drainage has been designated a huge potential for fishery and aquaculture development. However, the genetic diversity of Nile tilapia along the main water bodies has yet to be uncovered. Therefore, this study used microsatellite markers to assess the genetic structure and diversity of Nile cichlid (Oreochromis niloticus) populations.

METHODS

One hundred and sixty-seven fish were collected from Alwero Dam, Baro River, Gilgel Gibe I Dam and Gojeb River southwest of Ethiopia. Genomic DNA was extracted from 40 tissue samples using a Qiagen DNA tissue extraction kit and genetic polymorphism was estimated using GenAlEx6.502 software.

RESULTS

The result showed that four loci were polymorphic and produced 3-6 alleles per locus, while the number of effective alleles (Ne) and the number of distinct alleles (Na) were 1.370 and 2.063, respectively. Observed heterozygosity (Ho) and expected heterozygosity (He) were expanded between 0.100.50 and 0.115-0.265, respectively. Baro River population revealed the highest mean expected heterozygosity of 0.265, whereas the lowest expected mean heterozygosity of 0.115 was from the Alwero Dam. The genetic differentiation between populations (FST) resulted in a moderate to a very high degree of divergence between the populations. The Alwero Dam and Gojeb River populations were the most divergent populations (FST = 0.524), unlike those from the Alwero Dam and Baro River. The genetic variation among individuals within populations was 69%, whereas 31% appeared among populations and no variation within individuals to the overall variance.

CONCLUSION

This study confirmed the presence of significant genetic variations and differentiation among populations except between Gilgel Gibe I Dam and Gojeb River. This study highlights the genetic structure and differentiation amongst wild Nile tilapia (O. niloticus) populations in south-western Ethiopia and paves the way for selective aquaculture breeding programs in the study area.

Genetic Structure and Genetic Diversity of the Endemic Korean Aucha Perch, Coreoperca herzi (Centropomidae), in Korea

The Korean endemic aucha perch, Coreoperca herzi, belongs to the family Centropomidae. Thus far, studies on C. herzi have focused on mitochondrial genomes, egg development, and early life history, while studies on their genetic diversity or genetic structure are lacking. We investigated these aspects in this study using mitochondrial DNA data. Haplotypes were divided into the Hangang River, Nakdonggang River, Geumgang River, and southwest region water system populations. A translocated population, the Yangyang Namdaechun Stream, was confirmed to have originated from the Hangang River water system population based on haplotype distribution and genetic structure results. The FST of the mitochondrial DNA indicated distinct genetic differentiation in the Hangang, Nakdonggang, Geumgang, and southwest regions. According to COI and analyses, the analysis of molecular variance revealed a higher variance in the four water system groups (98.41%) than in the southwest region water system versus the Hangang River water system (80.27%) groups. This study presents basic data for conservation by providing extensive information on the genetic diversity, genetic structure, and translocation population of C. herzi.

Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting

BACKGROUND

Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau.

RESULTS

Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system.

CONCLUSIONS

Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.

Mosaic or melting pot: The use of monogeneans as a biological tag and magnifying glass to discriminate introduced populations of Nile tilapia in sub-Saharan Africa

The origin of introduced Nile tilapia stocks in sub-Saharan Africa is largely unknown. In this study, the potential of monogeneans as a biological tag and magnifying glass is tested to reveal their hosts' stocking history. The monogenean gill community of different Nile tilapia populations in sub-Saharan Africa was explored, and a phylogeographic analysis was performed based on the mitogenomes of four dactylogyrid species (Cichlidogyrus halli, C. sclerosus, C. thurstonae, and Scutogyrus longicornis). Our results encourage the use of dactylogyrids as biological tags. The magnifying glass hypothesis is only confirmed for C. thurstonae, highlighting the importance of the absence of other potential hosts as prerequisites for a parasite to act as a magnifying glass. With the data generated here, we are the first to extract mitogenomes from individual monogeneans and to perform an upscaled survey of the comparative phylogeography of several monogenean species with unprecedented diagnostic resolution.

Genome-wide SNPs reveal the fine-scale population structure of Laodelphax striatellus in China using double-digest restriction site-associated DNA sequencing

The small brown planthopper (SBPH), Laodelphax striatellus (Fallén) is one of the most destructive rice pests and has caused serious economic losses in China. To clarify the genetic differentiation and population genetic structure of this insect pest, we investigated the genomic polymorphisms, genetic differentiation, and phylogeography of 31 SBPH populations from 28 sampling sites from three climatic zones of China using double-digest restriction site-associated DNA sequencing (ddRADseq). In total, 2,813,221,369 high-quality paired-end reads from 306 individuals and 1925 single nucleotide polymorphisms (SNPs) were obtained. Low levels of genetic diversity and significant genetic differentiation were observed among the SBPH populations, and three genetic clusters were detected in China. Neutrality tests and bottleneck analysis provided strong evidence for recent rapid expansion with a severe bottleneck in most populations. Our work provides new insights into the genetics of the SBPH and will contribute to the development of effective management strategies for this pest.

Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources

During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.

Population genetics unveils large-scale migration dynamics and population turnover of Spodoptera exigua

BACKGROUND

Migration is a widespread phenomenon among many insect species, including herbivorous crop pests. At present, scant information exists on the long-range migration of the polyphagous armyworm, Spodoptera exigua and its underlying climatic determinants (i.e. East Asian or South Asian monsoon circulation). In this study, we employed a population genetics approach to delineate S. exigua migration patterns across multiple Asian countries.

RESULTS

Using mitochondrial cytochrome I (COI) and microsatellite markers, low-to-moderate levels of genetic diversity were detected among 101 S. exigua populations collected across China, Pakistan and Vietnam. Haplotype diversity and nucleotide diversity did not differ between years. Two spatially explicit genetic clusters were detected, an eastern and a western clade, with the former comprising populations in the East Asia monsoon area. No genetic differentiation was recorded among armyworm populations in the year-round breeding area, nor among those of the overwintering and nonoverwintering areas. Five of the most widespread mitochondrial haplotypes reflected the extensive gene flow across at a large spatial scale.

CONCLUSION

Low-to-moderate levels of genetic diversity were observed, and evidence was found for genetic clustering in certain geographical areas. Accordingly, our unique insights into S. exigua population genetics and spatiotemporal migration dynamics help to guide applied ecological studies, ecological intensification schemes or (area-wide) pest management campaigns in China and abroad. © 2021 Society of Chemical Industry.

Genome Editing Using the CRISPR-Cas9 System to Generate a Solid-Red Germline of Nile Tilapia (Oreochromis niloticus)

In recent years, there has been increasing demand for red tilapia, which are commercial strains of hybrids of different tilapiine species or red variants of highly inbred Nile tilapia. However, red tilapia phenotypes are genetically unstable and affected by environmental factors, resulting in nonuniform coloration with black or dark-red color blotches that reduce their market value. Solute carrier family 45 member 2 (SLC45A2) is a membrane transporter that mediates melanin biosynthesis and is evolutionarily conserved from fish to humans. In the present study, we describe the generation of a stable and heritable red tilapia phenotype by inducing loss-of-function mutations in the slc45a2 gene. For this purpose, we identified the slc45a2 gene in Nile tilapia and designed highly specific guide RNAs (gRNA) for its genomic sequence. Multiplex microinjection of slc45a2-specific ribonucleoproteins to Nile tilapia zygotes induced up to 97-99% albinism, including loss of melanin in the eye. Next-generation sequencing of the injected zygotes demonstrated that all injected fish carried mutant alleles with variable mutagenesis efficiencies. Sanger sequencing of the genomic target region in the slc45a2 gene from fin clips, sperm, and F1 offspring of a highly mutant male identified various genomic indels and germline transmission of the sperm-identified indels. Overall, this work demonstrates the generation of somatic and germline slc45a2 mutant alleles, which leads to complete albinism in Nile tilapia.

The first mitochondrial 5-methylcytosine map in a non-model teleost (Oreochromis niloticus) reveals extensive strand-specific and non-CpG methylation

DNA methylation is one of the main epigenetic mechanisms that regulate gene expression in a manner that depends on the genomic context and varies considerably across taxa. This DNA modification was first found in nuclear genomes of eukaryote several decades ago and it has also been described in mitochondrial DNA. It has recently been shown that mitochondrial DNA is extensively methylated in mammals and other vertebrates. Our current knowledge of mitochondrial DNA methylation in fish is very limited, especially in non-model teleosts. In this study, using whole-genome bisulfite sequencing, we determined methylation patterns within non-CpG (CH) and CpG (CG) contexts in the mitochondrial genome of Nile tilapia, a non-model teleost of high economic importance. Our results demonstrate the presence of mitochondrial DNA methylation in this species predominantly within a non-CpG context, similarly to mammals. We found a strand-specific distribution of methylation, in which highly methylated cytosines were located on the minus strand. The D-loop region had the highest mean methylation level among all mitochondrial loci. Our data provide new insights into the potential role of epigenetic mechanisms in regulating metabolic flexibility of mitochondria in fish, with implications in various biological processes, such as growth and development.

Growth performance of five different strains of Nile tilapia (Oreochromis niloticus) introduced to Tanzania reared in fresh and brackish waters

Five introduced strains of Nile tilapia (Oreochromis niloticus) were tested for growth performance both in fresh- and brackish-water (2 salinity units) environments for 56 days. The BIG NIN, GIFT, Chitralada, "Ruvu Farm" and Silver YY strains with initial mean average weight (± standard error) of 96.4 ± 6.90 g, 104.1 ± 7.19 g, 137.2 ± 7.21 g, 53.2 ± 6.98 g and 95.3 ± 7.11 g, respectively were used. Individuals were tagged and pooled in hapas (12 m × 8.5 m × 2 m each), aligned into different ponds (20 m × 20 m each). Stocking density of 5 fish/m² and 350 g/kg crude protein diet were used. Overall, the average weight gain for GIFT strain was 7.5%, 32%, 45% and 86.5% higher than BIG NIN, Chitralada, "Ruvu Farm" and Silver YY strains, respectively, across both environments. All strains performed significantly better (p < 0.05) when reared in brackish-water than their respective counterparts in freshwater, except for the BIG NIN strain. The morphometric correlations for all strains in both environments ranged from moderate (0.50) to strong positive (0.92). The GIFT strain demonstrated superior growth and genotype by environment interaction was weak and not important to be prioritized in breeding programs.

Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus)

Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.

Assessing the genetic diversity of farmed and wild Rufiji tilapia (Oreochromis urolepis urolepis) populations using ddRAD sequencing

Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.

Application of Low Coverage Genotyping by Sequencing in Selectively Bred Arctic Charr (Salvelinus alpinus)

Arctic charr (Salvelinus alpinus) is a species of high economic value for the aquaculture industry, and of high ecological value due to its Holarctic distribution in both marine and freshwater environments. Novel genome sequencing approaches enable the study of population and quantitative genetic parameters even on species with limited or no prior genomic resources. Low coverage genotyping by sequencing (GBS) was applied in a selected strain of Arctic charr in Sweden originating from a landlocked freshwater population. For the needs of the current study, animals from year classes 2013 (171 animals, parental population) and 2017 (759 animals; 13 full sib families) were used as a template for identifying genome wide single nucleotide polymorphisms (SNPs). GBS libraries were constructed using the PstI and MspI restriction enzymes. Approximately 14.5K SNPs passed quality control and were used for estimating a genomic relationship matrix. Thereafter a wide range of analyses were conducted in order to gain insights regarding genetic diversity and investigate the efficiency of the genomic information for parentage assignment and breeding value estimation. Heterozygosity estimates for both year classes suggested a slight excess of heterozygotes. Furthermore, FST estimates among the families of year class 2017 ranged between 0.009 - 0.066. Principal components analysis (PCA) and discriminant analysis of principal components (DAPC) were applied aiming to identify the existence of genetic clusters among the studied population. Results obtained were in accordance with pedigree records allowing the identification of individual families. Additionally, DNA parentage verification was performed, with results in accordance with the pedigree records with the exception of a putative dam where full sib genotypes suggested a potential recording error. Breeding value estimation for juvenile growth through the usage of the estimated genomic relationship matrix clearly outperformed the pedigree equivalent in terms of prediction accuracy (0.51 opposed to 0.31). Overall, low coverage GBS has proven to be a cost-effective genotyping platform that is expected to boost the selection efficiency of the Arctic charr breeding program.