Applications of genotyping by sequencing in aquaculture breeding and genetics

FishSNP: a high quality cross-species SNP database of fishes

The progress of aquaculture heavily depends on the efficient utilization of diverse genetic resources to enhance production efficiency and maximize profitability. Single nucleotide polymorphisms (SNPs) have been widely used in the study of aquaculture genomics, genetics, and breeding research since they are the most prevalent molecular markers on the genome. Currently, a large number of SNP markers from cultured fish species are scattered in individual studies, making querying complicated and data reuse problematic. We compiled relevant SNP data from literature and public databases to create a fish SNP database, FishSNP ( http://bioinfo.ihb.ac.cn/fishsnp ), and also used a unified analysis pipeline to process raw data that the author of the literature did not perform SNP calling on to obtain SNPs with high reliability. This database presently contains 45,690,243 (45 million) nonredundant SNP data for 13 fish species, with 30,288,958 (30 million) of those being high-quality SNPs. The main function of FishSNP is to search, browse, annotate and download SNPs, which provide researchers various and comprehensive associated information.

Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis

Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from -0.9643 to 1.0000. The global Fst value was 0.1248 (p < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy-Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.

Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data

Rainbow trout is one of the most popular aquaculture species worldwide, with a long history of domestication. However, limited information exists about the genetic diversity of farmed rainbow trout populations globally, with most available reports relying on low-throughput genotyping technologies. Notably, no information exists about the genetic diversity status of farmed rainbow trout in Sweden. Double-digest restriction-site-associated DNA sequencing was performed on more than 500 broodfish from two leading producers in Sweden and from the country's national breeding program. Following the detection of single nucleotide polymorphisms (SNPs), genetic diversity was studied by using either individual SNPs (n = 8680; one SNP retained per 300 bp sequence reads) or through SNP haplotypes (n = 20 558; all SNPs retained in 300 bp sequence reads). Similar amounts of genetic diversity were found amongst the three populations when individual SNPs were used. Furthermore, principal component analysis and discriminant analysis of principal components suggested two genetic clusters with the two industry populations grouped together. Genetic differentiation based on the FST fixation index was ~0.01 between the industry populations and ~0.05 when those were compared with the breeding program. Preliminary estimates of effective population size (Ne ) and inbreeding (based on runs of homozygosity; FROH ) were similar amongst the three populations (Ne  ≈ 50-80; median FROH  ≈ 0.11). Finally, the haplotype-based analysis suggested that animals from the breeding program had higher shared coancestry levels than those from the other two populations. Overall, our study provides novel insights into the genetic diversity and structure of Sweden's three main farmed rainbow trout populations, which could guide their future management.

Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China

BACKGROUND

Corybas taliensis is an endemic species of sky islands in China. Its habitat is fragile and unstable, and it is likely that the species is threatened. However, it is difficult to determine the conservation priority or unit without knowing the genetic background and the overall distribution of this species. In this study, we used double digest restriction-site associated DNA-sequencing (ddRAD-seq) to investigate the conservation genomics of C. taliensis. At the same time, we modeled the extent of suitable habitat for C. taliensis in present and future (2030 and 2090) habitat using the maximum-entropy (MaxEnt) model.

RESULTS

The results suggested that the related C. fanjingshanensis belongs to C. taliensis and should not be considered a separate species. All the sampling locations were divided into three genetic groups: the Sichuan & Guizhou population (SG population), the Hengduan Mountains population (HD population) and Himalayan population (HM population), and we found that there was complex gene flow between the sampling locations of HD population. MT was distinct genetically from the other sampling locations due to the unique environment in Motuo. The genetic diversity (π, He) of C. taliensis was relatively high, but its contemporary effective population size (Ne) was small. C. taliensis might be currently affected by inbreeding depression, although its large population density may be able to reduce the effect of this. The predicted areas of suitable habitat currently found in higher mountains will not change significantly in the future, and these suitable habitats are predicted to spread to other higher mountains under future climate change. However, suitable habitat in relatively low altitude areas may disappear in the future. This suggests that C. taliensis will be caught in a 'summit trap' in low altitude areas, however, in contrast, the high altitude of the Himalaya and the Hengduan Mountains are predicted to act as 'biological refuges' for C. taliensis in the future.

CONCLUSIONS

These results not only provide a new understanding of the genetic background and potential resource distribution of C. taliensis, but also lay the foundation for its conservation and management.

Genome-wide SNP analysis provides insights into the XX/XY sex-determination system in silver barb (Barbonymus gonionotus)

Silver barb (Barbonymus gonionotus) is among the most economically important freshwater fish species in Thailand. It ranks fourth in economic value and third in production weight for fisheries and culture in Thailand. An XX/XY sex-determination system based on gynogenesis was previously reported for this fish. In this study, the molecular basis underlying the sex-determination system was further investigated. Genome-wide single-nucleotide polymorphism data were generated for 32 captive-bred silver barb individuals, previously scored by phenotypic sex, to identify sex-linked regions associated with sex determination. Sixty-three male-linked loci, indicating putative XY chromosomes, were identified. Male-specific loci were not observed, which indicates that the putative Y chromosome is young and the sex determination region is cryptic. A homology search revealed that most male-linked loci were homologous to the Mariner/Tc1 and Gypsy transposable elements and are probably the remnants of an initial accumulation of repeats on the Y chromosome from the early stages of sex chromosome differentiation. This research provides convincing insights into the mechanism of sex determination and reveals the potential sex determination regions in silver barb. The study provides the basic data necessary for increasing the commercial value of silver barbs through genetic improvements.

Development of genomic markers associated to growth-related traits and sex determination in lumpfish (Cyclopterus lumpus)

Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 high Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal's phenotype by machine learning. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programmes in lumpfish.

High genome heterozygosity revealed vegetative propagation over the sea in Moso bamboo

BACKGROUND

Moso bamboo (Phyllostachys edulis) is a typical East Asian bamboo that does not flower for > 60 years and propagates without seed reproduction. Thus, Moso bamboo can be propagated vegetatively, possibly resulting in highly heterozygous genetic inheritance. Recently, a draft genome of Moso bamboo was reported, followed by whole genome single nucleotide polymorphisms (SNP) analysis, which showed that the genome of Moso bamboo in China has regional characteristics. Moso bamboo in Japan is thought to have been introduced from China over the sea in 1736. However, it is unclear where and how Moso bamboo was introduced in Japan from China. Here, based on detailed analysis of heterozygosity in genome diversity, we estimate the spread of genome diversity and its pedigree of Moso bamboo.

RESULTS

We sequenced the whole genome of Moso bamboo in Japan and compared them with data reported previously from 15 regions of China. Only 4.1 million loci (0.37% of the analyzed genomic region) were identified as polymorphic loci. We next narrowed down the number of polymorphic loci using several filters and extracted more reliable SNPs. Among the 414,952 high-quality SNPs, 319,431 (77%) loci were identified as heterozygous common to all tested samples. The result suggested that all tested samples were clones via vegetative reproduction. Somatic mutations may accumulate in a heterozygous manner within a single clone. We examined common heterozygous loci between samples from Japan and elsewhere, from which we inferred that an individual closely related to the sample from Fujian, China, was introduced to Japan across the sea without seed reproduction. In addition, we collected 16 samples from four nearby bamboo forests in Japan and performed SNP and insertion/deletion analyses using a genotyping by sequencing (GBS) method. The results suggested that a small number of somatic mutations would spread within and between bamboo groves.

CONCLUSIONS

High heterozygosity in the genome-wide diversity of Moso bamboo implies the vegetative propagation of Moso bamboo from China to Japan, the pedigree of Moso bamboo in Japan, and becomes a useful marker to approach the spread of genome diversity in clonal plants.

Genomics-driven prophylactic measures to increase streptococcosis resistance in tilapia

Streptococcosis caused by Streptococcus agalactiae and S. iniae is a significant problem that affects the success of tilapia aquaculture industries worldwide. In this critical review, we summarize the applicable practical strategies which may effectively enhance the world tilapia aquaculture development. Recently, the effect of vaccination and selective breeding programmes has been recognized as valuable tools to control the target disease and other consequent negative impacts caused by chemical and drug application. Advances in sequencing and molecular technologies are vital helpful factors with which to develop robust vaccines and increase the selective breeding programme's precision against streptococcosis. The genomic selection for streptococcosis-resistant tilapia strains and crucial genomic application for genomics' contribution to the development of novel Streptococcus vaccine, comparative genomics approach identifying vaccine candidates by reverse vaccinology, and next-generation vaccine design were described. Information from our review is encouraging for practical implementation of the development of vaccination and genomic selection in tilapia for streptococcosis resistance, which may be vital factors to sustain the world tilapia aquaculture industry effectively.

SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array

Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.

Applying genetic technologies to combat infectious diseases in aquaculture

Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.

Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr ( Salvelinus alpinus ) populations of anadromous and landlocked origin from Scandinavia

Arctic charr (Salvelinus alpinus) is a niche-market high-value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole-genome re-sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.

Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

Exploiting animal personality to reduce chronic stress in captive fish populations

Chronic stress is a major source of welfare problems in many captive populations, including fishes. While we have long known that chronic stress effects arise from maladaptive expression of acute stress response pathways, predicting where and when problems will arise is difficult. Here we highlight how insights from animal personality research could be useful in this regard. Since behavior is the first line of organismal defense when challenged by a stressor, assays of shy-bold type personality variation can provide information about individual stress response that is expected to predict susceptibility to chronic stress. Moreover, recent demonstrations that among-individual differences in stress-related physiology and behaviors are underpinned by genetic factors means that selection on behavioral biomarkers could offer a route to genetic improvement of welfare outcomes in captive fish stocks. Here we review the evidence in support of this proposition, identify remaining empirical gaps in our understanding, and set out appropriate criteria to guide development of biomarkers. The article is largely prospective: fundamental research into fish personality shows how behavioral biomarkers could be used to achieve welfare gains in captive fish populations. However, translating potential to actual gains will require an interdisciplinary approach that integrates the expertise and viewpoints of researchers working across animal behavior, genetics, and welfare science.

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.

Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture

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The extent of application of genetic technologies to aquaculture production varies widely by species and geography.

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Achieving a more universal application of seed derived from scientifically based breeding programmes is an important goal in order to meet increasing global demands for seafood production.

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This article reviews the status of genetic technologies across the world’s top 10 highly produced species.

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Opportunities and barriers to achieving broad-scale uptake of genetic technologies in global aquaculture are discussed.

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A future outlook for potential disruptive genetic technologies and how they might affect global aquaculture production is given.

Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.

Comparing mixed models and Random Forest association tests using naturalGWAS and a Striped Bass SNP dataset

In this study, we used the phenotype simulation package naturalGWAS to test the performance of Zhao's Random Forest method in comparison to an uncorrected Random Forest test, latent factor mixed models (LFMM), genome-wide efficient mixed models (GEMMA), and confounder adjusted linear regression (CATE). We created 400 sets of phenotypes, corresponding to five effect sizes and 2, 5, 15, or 30 causal loci, simulated from two empirical datasets containing SNPs from Striped Bass representing three and 13 populations. All association methods were evaluated for their ability to detect genotype-phenotype associations based on power, false discovery rates, and number of false positives. Genomic inflation was highest for uncorrected Random Forest and LFMM tests and lowest for Gemma and Zhao's Random Forest. All association tests had similar power to detect causal loci, and Zhao's Random Forest had the lowest false discovery rate in all scenarios. To measure the performance of association tests in small datasets with few loci surrounding a causal gene we also ran analyses again after removing causal loci from each dataset. All association tests were only able to find true positives, defined as loci located within 30k bp of a causal locus, in 3%-18% of simulations. In contrast, at least one false positive was found in 17%-44% of simulations. Zhao's Random Forest again identified the fewest false positives of all association tests studied. The ability to test the power of association tests for individual empirical datasets can be an extremely useful first step when designing a GWAS study.

Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin

Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.

Linkage mapping, comparative genome analysis, and QTL detection for growth in a non-model teleost, the meagre Argyrosomus regius, using ddRAD sequencing

Meagre (Argyrosomus regius), is a benthopelagic species rapidly emerging in aquaculture, due to its low food to biomass conversion rate, good fillet yield and ease of production. Tracing a species genomic background along with describing the genetic basis of important traits can greatly influence both conservation strategies and production perspectives. In this study, we employed ddRAD sequencing of 266 fish from six F1 meagre families, to construct a high-density genetic map comprising 4529 polymorphic SNP markers. The QTL mapping analysis provided a genomic appreciation for the weight trait identifying a statistically significant QTL on linkage group 15 (LG15). The comparative genomics analysis with six teleost species revealed an evolutionarily conserved karyotype structure. The synteny observed, verified the already well-known fusion events of the three-spine stickleback genome, reinforced the evidence of reduced evolutionary distance of Sciaenids with the Sparidae family, reflected the evolutionary proximity with Dicentrarchus labrax, traced several putative chromosomal rearrangements and a prominent putative fusion event in meagre’s LG17. This study presents novel elements concerning the genome evolutionary history of a non-model teleost species recently adopted in aquaculture, starts to unravel the genetic basis of the species growth-related traits, and provides a high-density genetic map as a tool that can help to further establish meagre as a valuable resource for research and production.

Genetic and Phenotypic Characteristics of the Salmo trutta Complex in Italy

Salmonid fish have become ecological and research models of study in the field of conservation genetics and genomics. Over the last decade, brown trout have received a high level of interest in research and publications. The term Salmo trutta complex is used to indicate the large number of geographic forms present in the species Salmo trutta. In Europe, the S. trutta complex consists (based on mitochondrial DNA control region analysis) of seven major evolutionary lineages: Atlantic (AT), Mediterranean (ME), Adriatic (AD), Danubian (DA), Marmoratus (MA), Duero (DU) and Tigris (TI). In several nations, the difficulty of identifying some lineages derives from their wide phenotypic and geographic plasticity and the presence of mixed lineages (due to introgressive hybridization with domestic AT populations). In Italy, the S. trutta complex populations living in the Tyrrhenian area and on the main islands (Sicily, Sardinia and Corsica) showed high genetic diversity. Currently, on the Italian Red List, the protected (near threatened) populations are the AD and ME lineages. Recent studies based on traditional (mitochondrial and nuclear markers) and NGS (next-generation sequencing) analyses have clarified some genetic differences between the populations of the Tyrrhenian region, Sicily, Sardinia and Corsica. Native populations in Sardinia belong to the AD lineage, while those living in Corsica are mainly characterized by the AD, MA and ME haplotypes. In Sicily, in the area of the Iblei mountains, an AT lineage (North African) exists. According to some authors, the term Salmo macrostigma should only be used for populations in North Africa. The use of genotyping methods based on mtDNA and nuclear markers and the latest generation sequencing techniques can improve the study of populations and evolutionary lineages in areas where there are overlaps and hybridization phenomena.

Comparison of lipid metabolism between broodstock and hybrid offspring in the hepatopancreas of juvenile shrimp (Macrobrachium nipponense): Response to chronic ammonia stress

Ammonia nitrogen is a major pollutant that causes great physiological harm to crustaceans in culture. In this study, we conducted a 28 day chronic ammonia nitrogen stress experiment with broodstock populations (Dianshan, DS) and hybrid offspring populations (DS ♀ × CD (Changjiang ♂ × Dongting ♀), SCD) exposed to 0, 1 and 10 mg/L of ammonia concentrations. A 28 day feeding trial and chronic ammonia nitrogen stress were used to investigate the effects on the growth performance, histological structure and lipid metabolism of juvenile shrimp, Macrobrachium nipponense. Our results indicated that survival rates in the SCD groups were significantly higher than those in the DS groups, whereas weight and length gain rates were not significantly different between the groups (p > 0.05). Histological structure results showed that the number of vacuoles in the DS group was significantly higher than that in the SCD group and hepatopancreas cell structures were disrupted in the ammonia treatment groups. The results of oil red staining showed that the number of lipid droplets increased significantly with the increase in ammonia concentration. As the ammonia concentration increased, fatty acid contents, lipid enzyme activities and lipid metabolism-related gene expression all tended to rise. In conclusion, ammonia nitrogen exposure caused damage to the hepatopancreas structure of juvenile shrimp and disturbed the lipid metabolism of the hepatopancreas. In addition, the SCD population had stronger stress resistance than the DS population when subjected to the same concentration of ammonia nitrogen stress.

A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia

The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F₁ population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F₁ individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.

Genomic Predictions of Phenotypes and Pseudo-Phenotypes for Viral Nervous Necrosis Resistance, Cortisol Concentration, Antibody Titer and Body Weight in European Sea Bass

Simple Summary

Selective breeding programs based on genomic data are still not a common practice in aquaculture, although genomic selection has been widely demonstrated to be advantageous when trait phenotyping is a difficult task. In this study, we investigated the accuracy of predicting the phenotype and the estimated breeding value (EBV) of three Bayesian models and a Random Forest algorithm exploiting the information of a genome-wide SNP panel for European sea bass. The genomic predictions were developed for mortality caused by viral nervous necrosis, post-stress cortisol concentration, antibody titer against nervous necrosis virus and body weight. Selective breeding based on genomic data is a possible option for improving these traits while overcoming difficulties related to individual phenotyping of the investigated traits. Our results evidenced that the EBV used as a pseudo-phenotype enhances the predictive performances of genomic models, and that EBV can be predicted with satisfactory accuracy. The genomic prediction of the EBV for mortality might also be used to classify the phenotype for the same trait.

Abstract

In European sea bass (Dicentrarchus labrax L.), the viral nervous necrosis mortality (MORT), post-stress cortisol concentration (HC), antibody titer (AT) against nervous necrosis virus and body weight (BW) show significant heritability, which makes selective breeding a possible option for their improvement. An experimental population (N = 650) generated by a commercial broodstock was phenotyped for the aforementioned traits and genotyped with a genome-wide SNP panel (16,075 markers). We compared the predictive accuracies of three Bayesian models (Bayes B, Bayes C and Bayesian Ridge Regression) and a machine-learning method (Random Forest). The prediction accuracy of the EBV for MORT was approximately 0.90, whereas the prediction accuracies of the EBV and the phenotype were 0.86 and 0.21 for HC, 0.79 and 0.26 for AT and 0.71 and 0.38 for BW. The genomic prediction of the EBV for MORT used to classify the phenotype for the same trait showed moderate classification performance. Genome-wide association studies confirmed the polygenic nature of MORT and demonstrated a complex genetic structure for HC and AT. Genomic predictions of the EBV for MORT could potentially be used to classify the phenotype of the same trait, though further investigations on a larger experimental population are needed.

Genomic selection signatures in farmed Colossoma macropomum from tropical and subtropical regions in South America

Tambaqui or cachama (Colossoma macropomum) is one of the most important neotropical freshwater fish used for aquaculture in South America, and its production is concentrated at low latitudes (close to the Equator, 0°), where the water temperature is warm. Therefore, understanding how selection shapes genetic variations and structure in farmed populations is of paramount importance in evolutionary biology. High‐throughput sequencing to generate genome‐wide data for fish species allows for elucidating the genomic basis of adaptation to local or farmed conditions and uncovering genes that control the phenotypes of interest. The present study aimed to detect genomic selection signatures and analyze the genetic variability in farmed populations of tambaqui in South America using single‐nucleotide polymorphism (SNP) markers obtained with double‐digest restriction site‐associated DNA sequencing. Initially, 199 samples of tambaqui farmed populations from different locations (located in Brazil, Colombia, and Peru), a wild population (Amazon River, Brazil), and the base population of a breeding program (Aquaculture Center, CAUNESP, Jaboticabal, SP, Brazil) were genotyped. Observed and expected heterozygosity was 0.231–0.350 and 0.288–0.360, respectively. Significant genetic differentiation was observed using global FST analyses of SNP loci (FST = 0.064, p < 0.050). Farmed populations from Colombia and Peru that differentiated from the Brazilian populations formed distinct groups. Several regions, particularly those harboring the genes of significance to aquaculture, were identified to be under positive selection, suggesting local adaptation to stress under different farming conditions and management practices. Studies aimed at improving the knowledge of genomics of tambaqui farmed populations are essential for aquaculture to gain deeper insights into the evolutionary history of these fish and provide resources for the establishment of breeding programs.

Genomic Selection and Genome-Wide Association Analysis for Stress Response, Disease Resistance and Body Weight in European Seabass

Simple Summary

In the present study, the genetic architecture of the stress response, body weight, and disease resistance in European seabass were studied, providing fruitful results for further research. Initially, the above traits were recorded and genotyping on a large scale was performed in those fish. The recorded data and genotypes were combined and analyzed to find genomic areas affecting them as well as to estimate the heritability of those traits. Stress response traits and body weight were medium heritable, while genomic regions affecting them were detected. However, no genomic areas related to disease resistance were revealed. These findings improve our knowledge of the genetic structure of those traits and can be utilized in a breeding program for the genetic improvement of aquaculture broodstocks.

Abstract

The majority of the genetic studies in aquaculture breeding programs focus on commercial traits such as body weight, morphology, and resistance against diseases. However, studying stress response in European seabass may contribute to the understanding of the genetic component of stress and its future use to select broodstock whose offspring may potentially be less affected by handling. A total of 865 European seabass offspring were used to measure body weight and stress response. Moreover, a disease challenge experiment with Vibrio anguillarum was conducted in a subset (332) of the above fish to study disease resistance. Fish were genotyped with a 57k SNP array, and a Genome-Wide Association study (GWAS) was performed. Five SNPs were found to be statistically significant, three of which affect stress indicators and body weight (in a subgroup of the population), and a putative SNP affects growth performance, while no SNP associated with resistance to Vibrio was found. A moderate to high genomic heritability regarding stress indicators and body weight was estimated using the Restricted Maximum Likelihood (REML) process. Finally, the accuracy, along with the correlation between Estimated Breeding Values (EBVs) and Genomic Estimated Breeding Values (GEBVs), were calculated for all the traits.

Construction of Genetic Linkage Maps From a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F₁ family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.

Genomic Selection in Aquaculture Species

To date, genomic prediction has been conducted in about 20 aquaculture species, with a preference for intra-family genomic selection (GS). For every trait under GS, the increase in accuracy obtained by genomic estimated breeding values instead of classical pedigree-based estimation of breeding values is very important in aquaculture species ranging from 15% to 89% for growth traits, and from 0% to 567% for disease resistance. Although the implementation of GS in aquaculture is of little additional investment in breeding programs already implementing sib testing on pedigree, the deployment of GS remains sparse, but could be boosted by adaptation of cost-effective imputation from low-density panels. Moreover, GS could help to anticipate the effect of climate change by improving sustainability-related traits such as production yield (e.g., carcass or fillet yields), feed efficiency or disease resistance, and by improving resistance to environmental variation (tolerance to temperature or salinity variation). This chapter synthesized the literature in applications of GS in finfish, crustaceans and molluscs aquaculture in the present and future breeding programs.

Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks

High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline (“HBimpute”) that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced at 0.5X read-depth. The overall imputing error rates are cut in half compared to state-of-the-art software like BEAGLE and STITCH, while the average read-depth is increased to 83X, thus enabling the calling of copy number variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance of sequence data in common breeding applications to that of genomic data generated with a genotyping array. For both genome-wide association studies and genomic prediction, results are on par or even slightly better than results obtained with high-density array data (600k). In particular for genomic prediction, we observe slightly higher data quality for the sequence data compared to the 600k array in the form of higher prediction accuracies. This occurred specifically when reducing the data panel to the set of overlapping markers between sequence and array, indicating that sequencing data can benefit from the same marker ascertainment as used in the array process to increase the quality and usability of genomic data.

High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics and breeding. Cost, precision, and throughput must be balanced to achieve optimal efficiency given available technologies and finite resources. Although genotyping arrays are still considered the gold standard in high-throughput quantitative genetics, recent advances in sequencing provide new opportunities. Both the quality and cost of genomic data generated based on sequencing are highly dependent on the used read-depth. In this work, we propose a new imputation pipeline (“HBimpute”) that uses haplotype blocks to detect individuals of the same genetic origin and subsequently uses all reads of those individuals in the variant calling. Thus, the obtained virtual read-depth is artificially increased, leading to higher calling accuracy, coverage, and the ability to call copy number variation based on low read-depth sequencing data. To conclude, our approach makes sequencing a cost-competitive alternative to genotyping arrays with the added benefit of allowing the calling of structural variation.

Linking Pedigree Information to the Gene Expression Phenotype to Understand Differential Family Survival Mechanisms in Highly Fecund Fish: A Case Study in the Larviculture of Pacific Bluefin Tuna

Mass spawning in fish culture often brings about a marked variance in family size, which can cause a reduction in effective population sizes in seed production for stock enhancement. This study reports an example of combined pedigree information and gene expression phenotypes to understand differential family survival mechanisms in early stages of Pacific bluefin tuna, Thunnus orientalis, in a mass culture tank. Initially, parentage was determined using the partial mitochondrial DNA control region sequence and 11 microsatellite loci at 1, 10, 15, and 40 days post-hatch (DPH). A dramatic proportional change in the families was observed at around 15 DPH; therefore, transcriptome analysis was conducted for the 15 DPH larvae using a previously developed oligonucleotide microarray. This analysis successfully addressed the family-specific gene expression phenotypes with 5739 differentially expressed genes and highlighted the importance of expression levels of gastric-function-related genes at the developmental stage for subsequent survival. This strategy demonstrated herein can be broadly applicable to species of interest in aquaculture to comprehend the molecular mechanism of parental effects on offspring survival, which will contribute to the optimization of breeding technologies.

Split it up and see: using proxies to highlight divergent inter-populational performances in aquaculture standardised conditions

Background

Considering wild inter-populational phenotypic differentiation can facilitate domestication and subsequent production of new species. However, comparing all populations across a species range to identify those exhibiting suitable key traits for aquaculture (KTA; i.e. important for domestication and subsequent production) expressions is not feasible. Therefore, proxies highlighting inter-populational divergences in KTA are needed. The use of such proxies would allow to identify, prior to bioassays, the wild population pairs which are likely to present differentiations in KTA expressions in aquaculture conditions. Here, we assessed the relevance of three alternative proxies: (i) genetic distance, (ii) habitat divergence, and (iii) geographic/hydrologic distances. We performed this evaluation on seven allopatric populations of Perca fluviatilis for which divergences in KTA had already been shown.

Results

We showed differences in the correlation degree between the alternative proxy-based and KTA-based distance matrices, with the genetic proxy being correlated to the highest number of KTA. However, no proxy was correlated to all inter-populational divergences in KTA.

Conclusion

For future domestication trials, we suggest using a multi-proxy assessment along with a prioritisation strategy to identify population pairs which are of interest for further evaluation in bioassays.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01937-z.

Comparison of Sample Preparation Methods for Shotgun Proteomic Studies in Aquaculture Species

Proteomics has been recently introduced in aquaculture research, and more methodological studies are needed to improve the quality of proteomics studies. Therefore, this work aims to compare three sample preparation methods for shotgun LC–MS/MS proteomics using tissues of two aquaculture species: liver of turbot Scophthalmus maximus and hepatopancreas of Mediterranean mussel Mytilus galloprovincialis. We compared the three most common sample preparation workflows for shotgun analysis: filter-aided sample preparation (FASP), suspension-trapping (S-Trap), and solid-phase-enhanced sample preparations (SP3). FASP showed the highest number of protein identifications for turbot samples, and S-Trap outperformed other methods for mussel samples. Subsequent functional analysis revealed a large number of Gene Ontology (GO) terms in turbot liver proteins (nearly 300 GO terms), while fewer GOs were found in mussel proteins (nearly 150 GO terms for FASP and S-Trap and 107 for SP3). This result may reflect the poor annotation of the genomic information in this specific group of animals. FASP was confirmed as the most consistent method for shotgun proteomic studies; however, the use of the other two methods might be important in specific experimental conditions (e.g., when samples have a very low amount of protein).

Accuracies of genomic predictions for disease resistance of striped catfish to Edwardsiella ictaluri using artificial intelligence algorithms

Assessments of genomic prediction accuracies using artificial intelligent (AI) algorithms (i.e., machine and deep learning methods) are currently not available or very limited in aquaculture species. The principal aim of this study was to examine the predictive performance of these new methods for disease resistance to Edwardsiella ictaluri in a population of striped catfish Pangasianodon hypophthalmus and to make comparisons with four common methods, i.e., pedigree-based best linear unbiased prediction (PBLUP), genomic-based best linear unbiased prediction (GBLUP), single-step GBLUP (ssGBLUP) and a nonlinear Bayesian approach (notably BayesR). Our analyses using machine learning (i.e., ML-KAML) and deep learning (i.e., DL-MLP and DL-CNN) together with the four common methods (PBLUP, GBLUP, ssGBLUP, and BayesR) were conducted for two main disease resistance traits (i.e., survival status coded as 0 and 1 and survival time, i.e., days that the animals were still alive after the challenge test) in a pedigree consisting of 560 individual animals (490 offspring and 70 parents) genotyped for 14,154 single nucleotide polymorphism (SNPs). The results using 6,470 SNPs after quality control showed that machine learning methods outperformed PBLUP, GBLUP, and ssGBLUP, with the increases in the prediction accuracies for both traits by 9.1–15.4%. However, the prediction accuracies obtained from machine learning methods were comparable to those estimated using BayesR. Imputation of missing genotypes using AlphaFamImpute increased the prediction accuracies by 5.3–19.2% in all the methods and data used. On the other hand, there were insignificant decreases (0.3–5.6%) in the prediction accuracies for both survival status and survival time when multivariate models were used in comparison to univariate analyses. Interestingly, the genomic prediction accuracies based on only highly significant SNPs (P < 0.00001, 318–400 SNPs for survival status and 1,362–1,589 SNPs for survival time) were somewhat lower (0.3–15.6%) than those obtained from the whole set of 6,470 SNPs. In most of our analyses, the accuracies of genomic prediction were somewhat higher for survival time than survival status (0/1 data). It is concluded that although there are prospects for the application of genomic selection to increase disease resistance to E. ictaluri in striped catfish breeding programs, further evaluation of these methods should be made in independent families/populations when more data are accumulated in future generations to avoid possible biases in the genetic parameters estimates and prediction accuracies for the disease-resistant traits studied in this population of striped catfish P. hypophthalmus.

Genomic prediction for testes weight of the tiger pufferfish, Takifugu rubripes, using medium to low density SNPs

Aquaculture production is expected to increase with the help of genomic selection (GS). The possibility of performing GS using only a small number of SNPs has been examined in order to reduce genotyping costs; however, the practicality of this approach is still unclear. Here, we tested whether the effects of reducing the number of SNPs impaired the prediction accuracy of GS for standard length, body weight, and testes weight in the tiger pufferfish (Takifugu rubripes). High values for predictive ability (0.563-0.606) were obtained with 4000 SNPs for all traits under a genomic best linear unbiased predictor (GBLUP) model. These values were still within an acceptable range with 1200 SNPs (0.554-0.588). However, predictive abilities and prediction accuracies deteriorated using less than 1200 SNPs largely due to the reduced power in accurately estimating the genetic relationship among individuals; family structure could still be resolved with as few as 400 SNPs. This suggests that the SNPs informative for estimation of genetic relatedness among individuals differ from those for inference of family structure, and that non-random SNP selection based on the effects on family structure (e.g., site-F_ST, principal components, or random forest) is unlikely to increase the prediction accuracy for these traits.

A high-density linkage map and sex-linked markers for the Amazon Tambaqui Colossoma macropomum

Background

Tambaqui (Colossoma macropomum, Cuvier, 1818) is the most economically important native freshwater fish species in Brazil. It can reach a total length of over 1 m and a weight of over 40 kg. The species displays a clear sex dimorphism in growth performance, with females reaching larger sizes at harvest. In aquaculture, the production of monosex populations in selective breeding programmes has been therefore identified as a key priority.

Results

In the present study, a genetic linkage map was generated by double digest restriction-site associated DNA (ddRAD) sequencing from 248 individuals sampled from two F1 families. The map was constructed using 14,805 informative SNPs and spanned 27 linkage groups. From this, the tambaqui draft genome was improved, by ordering the scaffolds into chromosomes, and sex-linked markers were identified. A total of 235 markers on linkage group 26 showed a significant association with the phenotypic sex, supporting an XX/XY sex determination system in the species. The four most informative sex-linked markers were validated on another 206 sexed individuals, demonstrating an accuracy in predicting sex ranging from 90.0 to 96.7%.

Conclusions

The genetic mapping and novel sex-linked DNA markers identified and validated offer new tools for rapid progeny sexing, thus supporting the development of monosex female production in the industry while also supporting breeding programmes of the species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08037-8.

Cross-species Exon Capture and Whole Exome Sequencing: Application, Utility and Challenges for Genomic Resource Development in Non-model Species

Comprehending the genetic architecture of complex traits has many applications in evolution, ecology, conservation biology and plant and animal production systems. Underlying research questions in these fields are diverse species that often have limited genetic information available. In aquaculture, for example, genetic progress has been slow in many species due to a lack in such genetic information. In this study, zebrafish (as a well-studied model species) was used in cross-species transfer to develop genomic resources and identify candidate genes underling growth differentials in dusky kob. Dusky kob is a Sciaenid finfish and an emerging aquaculture species. The zebrafish All Exon Predesigned Probe-set capture protocol was used to enrich fractionated DNA samples from kob, classified as either large or small, before massive parallel sequencing on the Ion Torrent platform. Although vast quantities of sequence data were generated, only about 30% of contigs could be identified as zebrafish homologues. There were numerous species-specific sequences and inconsistent coverage of sequencing products across samples, likely due to non-specific binding of the probe-set as a result of the evolutionary divergence between zebrafish and kob. Nonetheless, more than 55,000 SNPs could be reliably identified and genotyped to the individual level. Using SNP genotypic divergence estimates, between large and small cohorts, a number of candidate genes associated with growth was also identified for future investigation. These findings contribute to the growing body of evidence demonstrating the utility of a cross-species capture approach in the development of important genomic resources for understanding traits of interest in species without reference genomes.

Characterization of Penaeus vannamei mitogenome focusing on genetic diversity

The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P. vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.

Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

This study aimed to identify quantitative trait loci (QTLs) for growth-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers in Japanese quail. A QTL mapping population of 277 F₂ birds was obtained from an intercross between a male of a large-sized strain and three females of a normal-sized strain. Body weight (BW) was measured weekly from hatching to 16 weeks of age. Non-linear regression growth models of Weibull, Logistic, Gompertz, Richards, and Brody were analyzed, and growth curve parameters of Richards was selected as the best model to describe the quail growth curve of the F₂ birds. Restriction-site associated DNA sequencing developed 125 SNP markers that were informative between their parental strains. The SNP markers were distributed on 16 linkage groups that spanned 795.9 centiMorgan (cM) with an average marker interval of 7.3 cM. QTL analysis of phenotypic traits revealed four main-effect QTLs. Detected QTLs were located on chromosomes 1 and 3 and were associated with BW from 4 to 16 weeks of age and asymptotic weight of Richards model at genome-wide significant at 1% or 5% level. No QTL was detected for BW from 0 to 3 weeks of age. This is the first report identified QTLs for asymptotic weight of the Richards parameter in Japanese quail. These results highlight that the combination of QTL studies and the RAD-seq method will aid future breeding programs identify genes underlying the QTL and the application of marker-assisted selection in the poultry industry, particularly the Japanese quail.

Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.

Genomic Prediction for Whole Weight, Body Shape, Meat Yield, and Color Traits in the Portuguese Oyster Crassostrea angulata

Genetic improvement for quality traits, especially color and meat yield, has been limited in aquaculture because the assessment of these traits requires that the animals be slaughtered first. Genotyping technologies do, however, provide an opportunity to improve the selection efficiency for these traits. The main purpose of this study is to assess the potential for using genomic information to improve meat yield (soft tissue weight and condition index), body shape (cup and fan ratios), color (shell and mantle), and whole weight traits at harvest in the Portuguese oyster, Crassostrea angulata. The study consisted of 647 oysters: 188 oysters from 57 full-sib families from the first generation and 459 oysters from 33 full-sib families from the second generation. The number per family ranged from two to eight oysters for the first and 12–15 oysters for the second generation. After quality control, a set of 13,048 markers were analyzed to estimate the genetic parameters (heritability and genetic correlation) and predictive accuracy of the genomic selection for these traits. The multi-locus mixed model analysis indicated high estimates of heritability for meat yield traits: 0.43 for soft tissue weight and 0.77 for condition index. The estimated genomic heritabilities were 0.45 for whole weight, 0.24 for cup ratio, and 0.33 for fan ratio and ranged from 0.14 to 0.54 for color traits. The genetic correlations among whole weight, meat yield, and body shape traits were favorably positive, suggesting that the selection for whole weight would have beneficial effects on meat yield and body shape traits. Of paramount importance is the fact that the genomic prediction showed moderate to high accuracy for the traits studied (0.38–0.92). Therefore, there are good prospects to improve whole weight, meat yield, body shape, and color traits using genomic information. A multi-trait selection program using the genomic information can boost the genetic gain and minimize inbreeding in the long-term for this population.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean H_o = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr ( Salvelinus alpinus )

Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise F_st values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner.

Comparison of morphology and genetic diversity between broodstock and hybrid offspring of oriental river prawn, Macrobrachium nipponense based on morphological analysis and SNP markers

Hybridization is an effective method for the genetic improvement of farmed species. In this study, three broodstock populations (Changjiang, CJ, Dongting, DT, and Dianshan, DS) of oriental river prawn, Macrobrachium nipponense were used, and DS was used as the female broodstock. Through three-line hybridization, two hybrid populations were finally obtained. The F3 generation of the broodstock population and the F1 generation of the hybrid population were cultured indoors for 3 months. Through morphological analysis (cluster analysis, discriminant analysis and path analysis) it was found that the hybrid population and the broodstock had some differences, but not enough to reach the subspecies level, and the dominant traits exhibited differentiation and reorganization. This study identified SNP genetic markers, carried out systematic evolution analysis and genetic diversity analysis and found that the nucleotide diversity π and heterozygosity Het of the hybrid population were higher than those of the broodstock. Among broodstocks, the differentiation index (F_st ) of SCD and SDC was smallest (0.055). This research provides some valuable reference for genetic breeding.

Potential of genomic technologies to improve disease resistance in molluscan aquaculture

Molluscan aquaculture is a major contributor to global seafood production, but is hampered by infectious disease outbreaks that can cause serious economic losses. Selective breeding has been widely used to improve disease resistance in major agricultural and aquaculture species, and has clear potential in molluscs, albeit its commercial application remains at a formative stage. Advances in genomic technologies, especially the development of cost-efficient genomic selection, have the potential to accelerate genetic improvement. However, tailored approaches are required owing to the distinctive reproductive and life cycle characteristics of molluscan species. Transgenesis and genome editing, in particular CRISPR/Cas systems, have been successfully trialled in molluscs and may further understanding and improvement of genetic resistance to disease through targeted changes to the host genome. Whole-organism genome editing is achievable on a much greater scale compared to other farmed species, making genome-wide CRISPR screening approaches plausible. This review discusses the current state and future potential of selective breeding, genomic tools and genome editing approaches to understand and improve host resistance to infectious disease in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F₂ females were produced by full-sib mating of F₁ birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata)

SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole-genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass; 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection.

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Α 60 K SNP array (MedFish) was designed for European seabass and gilthead seabream from wild and domesticated populations.

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The array exhibited a high conversion rate (92% in seabass; 89% in seabream) and repeatability (99.4 and 99.7%).

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The MedFish array is expected to facilitate stock management and acceleration of selective breeding via genomic selection.

Genetic diversity and population structure of razor clam Sinonovacula constricta in Ariake Bay, Japan, revealed using RAD-Seq SNP markers

The razor clam Sinonovacula constricta is a commercially important bivalve in Japan. The current distribution of this species in Japan is limited to Ariake Bay, where the fishery stock is declining. It is necessary to understand the genetic population structure of this species in order to restore the fishery stock while preserving the genetic diversity of the clam. Here, we report for the first time the genetic population structure of S. constricta in Ariake Bay, Japan. Paired-end restriction site-associated DNA sequencing (RAD-Seq) analyzed samples of S. constricta collected from seven mudflats located along Ariake Bay. Two different genetic populations exist in Ariake Bay, one inhabiting wild habitats and the other inhabiting the transplanted area of artificial seedlings. Our results suggest that genetic differentiation occurred between these two populations (F_st value = 0.052), and a high level of genetic differentiation is maintained between the two groups. In the future, monitoring the interbreeding status of the two genetically distinct populations and the genetic differentiation within each population is important for conserving the genetic diversity of S. constricta in Japan.

Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di)

The novel non-targeted PCR-based genotyping system, namely Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di), is characterized by the simplicity in library construction and robustness against DNA degradation and is expected to facilitate advancements in genetics, in both basic and applied sciences. In this study, we tested the utility of GRAS-Di for genetic analysis in a cultured population of the tiger pufferfish Takifugu rubripes. The genetic analyses included family structure analysis, genetic map construction, and quantitative trait locus (QTL) analysis for the male precocious phenotype using a population consisting of four full-sib families derived from a genetically precocious line. An average of 4.7 million raw reads were obtained from 198 fish. Trimmed reads were mapped onto a Fugu reference genome for genotyping, and 21,938 putative single-nucleotide polymorphisms (SNPs) were obtained. These 22 K SNPs accurately resolved the sibship and parent-offspring pairs. A fine-scale linkage map (total size: 1,949 cM; average interval: 1.75 cM) was constructed from 1,423 effective SNPs, for which the allele inheritance patterns were known. QTL analysis detected a significant locus for testes weight on Chr_14 and three suggestive loci on Chr_1, Chr_8, and Chr_19. The significant QTL was shared by body length and body weight. The effect of each QTL was small (phenotypic variation explained, PVE: 3.1-5.9%), suggesting that the precociousness seen in the cultured pufferfish is polygenic. Taken together, these results indicate that GRAS-Di is a practical genotyping tool for aquaculture species and applicable for molecular breeding programs, such as marker-assisted selection and genomic selection.

Resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax L.): heritability and relationships with body weight, cortisol concentration, and antibody titer

Background

Susceptibility of European sea bass (Dicentrarchus labrax L.) to viral nervous necrosis (VNN) is well-known. Interest towards selective breeding as a tool to enhance genetic resistance in this species has increased sharply due to the major threat represented by VNN for farmed sea bass and limitations concerning specific therapeutical measures. A sea bass experimental population (N = 650) was challenged with nervous necrosis virus (NNV) to investigate genetic variation in VNN mortality. In addition, relationships of this trait with serum cortisol concentration after stress exposure, antibody titer against NNV antigens, and body weight at a fixed age were studied to identify potential indicator traits of VNN resistance.

Results

The estimate of heritability for VNN mortality was moderate and ranged from 0.15 (HPD95%, 95% highest posterior density interval: 0.02, 0.31) to 0.23 (HPD95%: 0.06, 0.47). Heritability estimates for cortisol concentration, antibody titer, and body weight were 0.19 (HPD95%: 0.07, 0.34), 0.36 (HPD95%: 0.16, 0.59) and 0.57 (HPD95%: 0.33, 0.84), respectively. Phenotypic relationships between traits were trivial and not statistically significant, except for the estimated correlation between antibody titer and body weight (0.24). Genetic correlations of mortality with body weight or antibody titer (− 0.39) exhibited a 0.89 probability of being negative. A negligible genetic correlation between mortality and cortisol concentration was detected. Antibody titer was estimated to be positively correlated with body weight (0.49).

Conclusions

Antibody titer against NNV offers the opportunity to use indirect selection to enhance resistance, while the use of cortisol concentration as an indicator trait in breeding programs for VNN resistance is questionable. The estimate of heritability for VNN mortality indicates the feasibility of selective breeding to enhance resistance to NNV and raises attention to the development of genomic prediction tools to simplify testing procedures for selection candidates.

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.

Community Parameters and Genome-Wide RAD-Seq Loci of Ceratothoa oestroides Imply Its Transfer between Farmed European Sea Bass and Wild Farm-Aggregating Fish

Wild fish assemblages that aggregate within commercial marine aquaculture sites for feeding and shelter have been considered as a primary source of pathogenic parasites vectored to farmed fish maintained in net pens at an elevated density. In order to evaluate whether Ceratothoa oestroides (Isopoda, Cymothoidae), a generalist and pestilent isopod that is frequently found in Adriatic and Greek stocks of farmed European sea bass (Dicentrarchus labrax), transfers between wild and farmed fish, a RAD-Seq (restriction-site-associated DNA sequencing)-mediated genetic screening approach was employed. The double-digest RAD-Seq of 310 C. oestroides specimens collected from farmed European sea bass (138) and different wild farm-aggregating fish (172) identified 313 robust SNPs that evidenced a close genetic relatedness between the “wild” and “farmed” genotypes. ddRAD-Seq proved to be an effective method for detecting the discrete genetic structuring of C. oestroides and genotype intermixing between two populations. The parasite prevalence in the farmed sea bass was 1.02%, with a mean intensity of 2.0 and mean abundance of 0.02, while in the wild fish, the prevalence was 8.1%; the mean intensity, 1.81; and the mean abundance, 0.15. Such differences are likely a consequence of human interventions during the farmed fish’s rearing cycle that, nevertheless, did not affect the transfer of C. oestroides.