High-resolution linkage and quantitative trait locus mapping aided by genome survey sequencing: building up an integrative genomic framework for a bivalve mollusc

Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae)

Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.

Analysis of Elimination Effects of Inbreeding on Genotype Frequency in Larval Stages of Chinese Shrimp

Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

BACKGROUND

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species.

RESULTS

The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low.

CONCLUSIONS

Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

(Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions

Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.

Fine mapping of the Cepaea nemoralis shell colour and mid-banded loci using a high-density linkage map

Molluscs are a highly speciose phylum that exhibits an astonishing array of colours and patterns, yet relatively little progress has been made in identifying the underlying genes that determine phenotypic variation. One prominent example is the land snail Cepaea nemoralis for which classical genetic studies have shown that around nine loci, several physically linked and inherited together as a 'supergene', control the shell colour and banding polymorphism. As a first step towards identifying the genes involved, we used whole-genome resequencing of individuals from a laboratory cross to construct a high-density linkage map, and then trait mapping to identify 95% confidence intervals for the chromosomal region that contains the supergene, specifically the colour locus (C), and the unlinked mid-banded locus (U). The linkage map is made up of 215,593 markers, ordered into 22 linkage groups, with one large group making up ~27% of the genome. The C locus was mapped to a ~1.3 cM region on linkage group 11, and the U locus was mapped to a ~0.7 cM region on linkage group 15. The linkage map will serve as an important resource for further evolutionary and population genomic studies of C. nemoralis and related species, as well as the identification of candidate genes within the supergene and for the mid-banding phenotype.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.

Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation

Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid chromosome-scale degeneration. Molluscs constitute the second largest, Precambrian-originated animal phylum and have ancient, uncharacterized homomorphic sex chromosomes. Here, we profile eight genomes of the bivalve mollusc family of Pectinidae in a phylogenetic context and show 350 million years sex-chromosome homomorphy, which is the oldest known sex-chromosome homomorphy in the animal kingdom, far exceeding the ages of well-known heteromorphic sex chromosomes such as 130-200 million years in mammals, birds and flies. The long-term undifferentiation of molluscan sex chromosomes is potentially sustained by the unexpected intertwined regulation of reversible sex-biased genes, together with the lack of sexual dimorphism and occasional sex chromosome turnover. The pleiotropic constraint of regulation of reversible sex-biased genes is widely present in ancient homomorphic sex chromosomes and might be resolved in heteromorphic sex chromosomes through gene duplication followed by subfunctionalization. The evolutionary dynamics of sex chromosomes suggest a mechanism for 'inheritance' turnover of sex-determining genes that is mediated by translocation of a sex-determining enhancer. On the basis of these findings, we propose an evolutionary model for the long-term preservation of homomorphic sex chromosomes.

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.

Comparative genomics analysis and genome assembly integration with the recombination landscape contribute to Takifugu bimaculatus assembly refinement

Takifugu genus has been brought to the fore in scientific and practical research due to its compact genome, explosive speciation progress and economic value. Here we updated the chromosome-level genome of Takifugu bimaculatus by an ultra-high-density linkage map, a classic and accurate way of chromosome assembly. The map constituted a robust assembly frame, with 92.2% (372.77 Mb) of the draft genome cumulatively placed. With intraspecies and interspecies comparative genomic analysis, we developed a criterion to quantify the differences between assemblies and established a novel way to integrate information from multiple assemblies. The integrated assembly rectified potential mis-assemblies, greatly improving the genome contiguity and correctness. Our results rendered profound information on the genetic recombination of T. bimaculatus and provided new insights into effective genome assembly. The consolidated assembly will be a contributory tool of T. bimaculatus and broadly across the Takifugu by providing a convincing reference for genomic research.

Mantle Transcriptome Provides Insights into Biomineralization and Growth Regulation in the Eastern Oyster (Crassostrea virginica)

Growth of the eastern oyster Crassostrea virginica, a major aquaculture species in the USA, is highly variable and not well understood at molecular levels. As growth of mollusks is confined in shells constructed by the mantle, mantle transcriptomes of large (fast-growing) and small (slow-growing) eastern oysters were sequenced and compared in this study. Transcription was observed for 31,186 genes, among which 104 genes were differentially expressed between the large and small oysters, including 48 upregulated and 56 downregulated in large oysters. Differentially expressed genes (DEGs) included genes from diverse pathways highlighting the complexity of shell formation and growth regulations. Seventeen of the 48 upregulated DEGs were related to shell matrix formation, most of which were upregulated in large oysters, indicating that large oysters are more active in biomineralization and shell formation. Genomic and transcriptomic analyses identified 22 genes encoding novel polyalanine containing proteins (Pacps) with characteristic motifs for matrix function that are tandemly duplicated on one chromosome, all specifically expressed in mantle and at higher levels in large oysters, suggesting that these expanded Pacps play important roles in shell formation and growth. Analysis of sequence variation identified 244,964 SNPs with 328 associated with growth. This study provides novel candidate genes and markers for shell formation and growth, and suggests that genes related to shell formation are important for the complex regulation of growth in the eastern oyster and possibly other bivalve mollusks. Results of this study show that both transcriptional modulation and functional polymorphism are important in determining growth.

Identification of quantitative trait loci associated with upper temperature tolerance in turbot, Scophthalmus maximus

Temperature tolerance is an important trait from both an economic and evolutionary perspective in fish. Because of difficulties with measurements, genome-wide selection using quantitative trait loci (QTLs) affecting Upper temperature tolerance may be an alternative for genetic improvement. Turbot Scophthalmus maximus (L.) is a cold-water marine fish with high economic value in Europe and Asia. The genetic bases of upper temperature tolerance (UTTs) traits have been rarely studied. In this study, we constructed a genetic linkage map of turbot using simple sequence repeats (SSRs) and single nucleotide polymorphism (SNP) markers. A total of 190 SSR and 8,123 SNP were assigned to 22 linkage groups (LGs) of a consensus map, which spanned 3,648.29 cM of the turbot genome, with an average interval of 0.44 cM. Moreover, we re-anchored genome sequences, allowing 93.8% physical sequences to be clustered into 22 turbot pseudo-chromosomes. A high synteny was observed between two assemblies from the literature. QTL mapping and validation analysis identified thirteen QLTs which are major effect QTLs, of these, 206 linked SNP loci, and two linked SSR loci were considered to have significant QTL effects. Association analysis for UTTs with 129 QTL markers was performed for different families, results showed that eight SNP loci were significantly correlated with UTT, which markers could be helpful in selecting thermal tolerant breeds of turbot. 1,363 gene sequences were genomically annotated, and 26 QTL markers were annotated. We believe these genes could be valuable candidates affecting high temperatures, providing valuable genomic resources for the study of genetic mechanisms regulating thermal stress. Similarly, they may be used in marker-assisted selection (MAS) programs to improve turbot performance.

Genetic Linkage and Physical Mapping for an Oyster Mushroom (Pleurotus cornucopiae) and Quantitative Trait Locus Analysis for Cap Color

Oyster mushrooms are grown commercially worldwide, especially in many developing countries, for their easy cultivation and high biological efficiency. Pleurotus cornucopiae is one of the main oyster mushroom species because of its gastronomic value and nutraceutical properties. Cap color is an important trait, since consumers prefer dark mushrooms, which are now represented by only a small portion of the commercial varieties. Breeding efforts are required to improve quality-related traits to satisfy various demands of consumers. Here, we present a saturated genetic linkage map of P. cornucopiae constructed by using a segregating population of 122 monokaryons and 3,449 single nucleotide polymorphism (SNP) markers generated by the 2b-RAD approach. The map contains 11 linkage groups covering 961.6 centimorgans (cM), with an average marker spacing of 0.27 cM. The genome of P. cornucopiae was de novo sequenced, resulting in 425 scaffolds (>1,000 bp) with a total genome size of 35.1 Mb. The scaffolds were assembled to the pseudochromosome level with the assistance of the genetic linkage map. A total of 97% SNP markers (3,357) were physically localized on 140 scaffolds that were assigned to 11 pseudochromosomes, with a total of 32.5 Mb, representing 92.5% of the whole genome. Six quantitative trait loci (QTL) controlling cap color of P. cornucopiae were detected, accounting for a total phenotypic variation of 65.6%, with the highest value for the QTL on pseudochromosome 5 (18%). The results of our study provide a solid base for marker-assisted breeding for agronomic traits and especially for studies on biological mechanisms controlling cap color in oyster mushrooms. IMPORTANCE Oyster mushrooms are produced and consumed all over the world. Pleurotus cornucopiae is one of the main oyster mushroom species. Dark-cap oyster mushrooms are becoming more and more popular with consumers, but dark varieties are rare on the market. Prerequisites for efficient breeding programs are the availability of high-quality whole genomes and genetic linkage maps. Genetic studies to fulfill some of these prerequisites have hardly been done for P. cornucopiae. In this study, we de novo sequenced the genome and constructed a saturated genetic linkage map for P. cornucopiae. The genetic linkage map was effectively used to assist the genome assembly and identify QTL that genetically control the trait cap color. As well, the genome characteristics of P. cornucopiae were compared to the closely related species Pleurotus ostreatus. The results provided a basis for understanding the genetic background and marker-assisted breeding of this economically important mushroom species.

Bacterial diversity in ballast water and sediments revealed by 2b-RAD sequencing

Despite that the ballast water management (BWM) convention has come into force to prevent the spread of harmful aquatic organisms, to date, very few bacteria can be identified through microbial culture method. In this study, we explored a reduced-representation sequencing of 2b-RAD approach to investigate the bacterial diversity in ballast water and sediments (BWS). Our results indicated a large amount of bacteria species (1496) detected in BWS up to now, including 13 pathogens that are seriously concerning in marine environment and aquaculture like the most harmful Vibrio harveyi and Aurantimonas coralicida. We showed that the ballast water had relative lower species, which was dominated by Proteobacteria. In contrast, the sediments had richer species, which was dominated by Bacteroidetes. Although BWS differed significantly in species composition, sediments shared most of the concerned pathogens with ballast water, highlighting the importance of sediment management. In conclusion, 2b-RAD sequencing shows promise in future BWM.

Genome-Wide Association Study Reveals PC4 as the Candidate Gene for Thermal Tolerance in Bay Scallop (Argopecten irradians irradians)

The increasing sea temperature caused by global warming has resulted in severe mortalities in maricultural scallops. Therefore, improving thermal tolerance has become an active research area in the scallop farming industry. Bay scallop (Argopecten irradians irradians) was introduced into China in 1982 and has developed into a vast aquaculture industry in northern China. To date, genetic studies on thermal tolerance in bay scallops are limited, and no systematic screening of thermal tolerance-related loci or genes has been conducted in this species. In the present study, we conducted a genome-wide association study (GWAS) for thermal tolerance using the Arrhenius break temperature (ABT) indicators of 435 bay scallops and 38,011 single nucleotide polymorphism (SNP) markers. The GWAS identified 1,906 significant thermal tolerance-associated SNPs located in 16 chromosomes of bay scallop. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that 638 genes were enriched in 42 GO terms, while 549 annotated genes were enriched in aggregation pathways. Additionally, the SNP (15-5091-20379557-1) with the lowest P value was located in the transcriptional coactivator p15 (PC4) gene, which is involved in regulating DNA damage repair and stabilizing genome functions. Further analysis in another population identified two new thermal tolerance-associated SNPs in the first coding sequence of PC4 in bay scallops (AiPC4). Moreover, AiPC4 expression levels were significantly correlated (r = 0.675–0.962; P < 0.05) with the ABT values of the examined bay scallops. Our data suggest that AiPC4 might be a positive regulator of thermal tolerance and a potential candidate gene for molecular breeding in bay scallop aiming at thermal tolerance improvement.

Genome survey and high-resolution genetic map provide valuable genetic resources for Fenneropenaeus chinensis

Fenneropenaeus chinensis is one of the most important aquaculture species in China. Research on its genomic and genetic structure not only helps us comprehend the genetic basis of complex economic traits, but also offers theoretical guidance in selective breeding. In the present study, a genome survey sequencing was performed to generate a rough reference genome utilized for groping preliminary genome characteristics and facilitate linkage and quantitative trait locus (QTL) mapping. Linkage mapping was conducted using a reduced-representation sequencing method 2b-RAD. In total, 36,762 SNPs were genotyped from 273 progenies in a mapping family, and a high-resolution linkage map was constructed. The consensus map contained 12,884 markers and spanned 5257.81 cM with an average marker interval of 0.41 cM, which was the first high-resolution genetic map in F. chinensis to our knowledge. QTL mapping and association analysis were carried out in 29 characters including body size, sex and disease resistance. 87 significant QTLs were detected in several traits and they were also evaluated by association analysis. Results of this study provide us valuable suggestions in genetic improvement and breeding of new varieties and also lay a basic foundation for further application of cloning of economic genes in selective breeding program and marker-assisted selection.

Sexual Development of the Hermaphroditic Scallop Argopecten irradians Revealed by Morphological, Endocrine and Molecular Analysis

Simultaneous or functional hermaphrodites possessing both ovary and testis at the same time are good materials for studying sexual development. However, previous research on sex determination and differentiation was mainly conducted in gonochoristic species and studies on simultaneous hermaphrodites are still limited. In this study, we conducted a combined morphological, endocrine and molecular study on the gonadal development of a hermaphroditic scallop Argopecten irradians aged 2–10 month old. Morphological analysis showed that sex differentiation occurred at 6 months of age. By examining the dynamic changes of progesterone, testosterone and estradiol, we found testosterone and estradiol were significantly different between the ovaries and testes almost throughout the whole process, suggesting the two hormones may be involved in scallop sex differentiation. In addition, we identified two critical sex-related genes FoxL2 and Dmrt1L, and investigated their spatiotemporal expression patterns. Results showed that FoxL2 and Dmrt1L were female- and male-biased, respectively, and mainly localized in the germ cells and follicular cells, indicating their feasibility as molecular markers for early identification of sex. Further analysis on the changes of FoxL2 and Dmrt1L expression in juveniles showed that significant sexual dimorphic expression of FoxL2 occurred at 2 months of age, earlier than that of Dmrt1L. Moreover, FoxL2 expression was significantly correlated with estradiol/testosterone ratio (E₂/T). All these results indicated that molecular sex differentiation occurs earlier than morphological sex differentiation, and FoxL2 may be a key driver that functions through regulating sex steroid hormones in the scallop. This study will deepen our understanding of the molecular mechanism underlying sex differentiation and development in spiralians.

Segregation distortion: high genetic load suggested by a Chinese shrimp family under high-intensity selection

Segregation distortion is a common phenomenon found in most genetic mapping studies and is an important resource to dissect the mechanism of action in gene loci that cause deviation. Marine animals possess high genetic diversity and genomic heterozygosity, they therefore are ideal model organisms to study segregation distortion induced by selection. In the present study, we constructed a full-sib family of Fenneropenaeus chinensis and exerted high-intensity selection on 10,000 incipient progenies. 2b-RAD method was employed in remaining 273 individuals to develop genome-wide SNPs for segregating analysis and 41,612 SNPs were developed. 50.77% of 32,229 high-quality representative markers deviated from the expected Mendelian ratio. Results showed that most of these distorted markers (91.57%) were influenced at zygotic level. Heterozygote excess (53.07%) and homozygous deletions (41.96%) may both play an important role, sum of which explained 95.03% of distortion after fertilization. However, further results identified highly probable linkage among deleterious alleles, which may account for a considerable portion of heterozygote excess rather than single locus with heterozygote advantage. Results of this study support a major role of deleterious alleles in genetic load, thus in favor of partial dominance hypothesis. It would also offer necessary recommendations for the formulation of breeding strategy in shrimps.

Molecular Cloning and Polymorphism Analysis of PmFGF18 from Pinctada fucata martensii

Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 amino acids. The domain analysis of PmFGF18 showed a distinctive FGF domain, with a high similarity to FGF18 protein sequences from Crassostrea gigas (43.35%) and C. virginica (37.43%). PmFGF18 expression was revealed in all analyzed tissues with a significantly higher expression level in the fast-growing group than the slow-growing group. The analysis of PmFGF18 polymorphism demonstrated 33 SNPs (single nucleotide polymorphisms) in the CDS and promoter region of PmFGF18 sequence. Association analysis revealed 19 SNPs (2 SNPs from CDS and 17 SNPs from the promoter region) associating significantly with growth traits. Among the associated SNPs, one SNP g.50918198 A > C was verified in the other breeding line. Therefore, PmFGF18 can be utilized as a candidate gene for growth, and its related SNPs could be used in selective breeding of P. f. martensii for the improvement of growth traits.

Adaptive venom evolution and toxicity in octopods is driven by extensive novel gene formation, expansion, and loss

BACKGROUND

Cephalopods represent a rich system for investigating the genetic basis underlying organismal novelties. This diverse group of specialized predators has evolved many adaptations including proteinaceous venom. Of particular interest is the blue-ringed octopus genus (Hapalochlaena), which are the only octopods known to store large quantities of the potent neurotoxin, tetrodotoxin, within their tissues and venom gland.

FINDINGS

To reveal genomic correlates of organismal novelties, we conducted a comparative study of 3 octopod genomes, including the Southern blue-ringed octopus (Hapalochlaena maculosa). We present the genome of this species and reveal highly dynamic evolutionary patterns at both non-coding and coding organizational levels. Gene family expansions previously reported in Octopus bimaculoides (e.g., zinc finger and cadherins, both associated with neural functions), as well as formation of novel gene families, dominate the genomic landscape in all octopods. Examination of tissue-specific genes in the posterior salivary gland revealed that expression was dominated by serine proteases in non-tetrodotoxin-bearing octopods, while this family was a minor component in H. maculosa. Moreover, voltage-gated sodium channels in H. maculosa contain a resistance mutation found in pufferfish and garter snakes, which is exclusive to the genus. Analysis of the posterior salivary gland microbiome revealed a diverse array of bacterial species, including genera that can produce tetrodotoxin, suggestive of a possible production source.

CONCLUSIONS

We present the first tetrodotoxin-bearing octopod genome H. maculosa, which displays lineage-specific adaptations to tetrodotoxin acquisition. This genome, along with other recently published cephalopod genomes, represents a valuable resource from which future work could advance our understanding of the evolution of genomic novelty in this family.

High accuracy of pooled DNA genotyping by 2b-RAD sequencing in the Pacific white shrimp, Litopenaeus vannamei

Using pooled DNA genotyping to estimate the proportional contributions from multiple families in a pooled sample is of particular interest for selective breeding in aquaculture. We compared different pooled libraries with separate 2b-RAD sequencing of Litopenaeus vannamei individuals to assess the effect of different population structures (different numbers of individuals and families) on pooled DNA sequencing, the accuracy of parent sequencing of the DNA pools and the effect of SNP numbers on pooled DNA sequencing. We demonstrated that small pooled DNA genotyping of up to 53 individuals by 2b-RAD sequencing could provide a highly accurate assessment of population allele frequencies. The accuracy increased as the number of individuals and families increased. The allele frequencies of the parents from each pool were highly correlated with those of the pools or the corresponding individuals in the pool. We chose 500-28,000 SNPs to test the effect of SNP number on the accuracy of pooled sequencing, and no linear relationship was found between them. When the SNP number was fixed, increasing the number of individuals in the mixed pool resulted in higher accuracy of each pooled genotyping. Our data confirmed that pooled DNA genotyping by 2b-RAD sequencing could achieve higher accuracy than that of individual-based genotyping. The results will provide important information for shrimp breeding programs.

A first genetic linage map construction and QTL mapping for growth traits in Larimichthys polyactis

Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. In particular, genetic linkage maps are critical tools for genetic breeding. In this study, we generated a high resolution linkage map from a family of 110 individuals and their parents by resequencing the individuals. 3,802 effective SNPs were mapped to 24 linkage groups (LGs). The map spanned 2,567.39 cm, with an average marker interval of 0.66 cm. We used the map to conduct QTL analysis for growth traits, and found 31 markers were significantly associated with growth-related traits. Specifically, three SNPs were identified for total length, nineteen SNPs for body length, and nine SNPs for body weight. The identified SNPs could explain 15.2-22.6% of the phenotypic variation. SNPs associated with growth traits were distributed on LG6 and LG11, and candidate genes included, kif26b, bat1, gna1, gbgt1, and amfr, which may regulate growth. The linkage map and mapped QTLs would be useful for improving the quality of L. polyactis via marker-assisted selection.

PacBio single molecule long-read sequencing provides insight into the complexity and diversity of the Pinctada fucata martensii transcriptome

BACKGROUND

The pearl oyster Pinctada fucata martensii is an economically valuable shellfish for seawater pearl production, and production of pearls depends on its growth. To date, the molecular mechanisms of the growth of this species remain poorly understood. The transcriptome sequencing has been considered to understanding of the complexity of mechanisms of the growth of P. f. martensii. The recently released genome sequences of P. f. martensii, as well as emerging Pacific Bioscience (PacBio) single-molecular sequencing technologies, provide an opportunity to thoroughly investigate these molecular mechanisms.

RESULTS

Herein, the full-length transcriptome was analysed by combining PacBio single-molecule long-read sequencing (PacBio sequencing) and Illumina sequencing. A total of 20.65 Gb of clean data were generated, including 574,561 circular consensus reads, among which 443,944 full-length non-chimeric (FLNC) sequences were identified. Through transcript clustering analysis of FLNC reads, 32,755 consensus isoforms were identified, including 32,095 high-quality consensus sequences. After removing redundant reads, 16,388 transcripts were obtained, and 641 fusion transcripts were derived by performing fusion transcript prediction of consensus sequences. Alternative splicing analysis of the 16,388 transcripts was performed after accounting for redundancy, and 9097 gene loci were detected, including 1607 new gene loci and 14,946 newly discovered transcripts. The original boundary of 11,235 genes on the chromosomes was corrected, 12,025 complete open reading frame sequences and 635 long non-coding RNAs (LncRNAs) were predicted, and functional annotation of 13,482 new transcripts was achieved. Two thousand three hundred eighteen alternative splicing events were detected. A total of 228 differentially expressed transcripts (DETs) were identified between the largest (L) and smallest (S) pearl oysters. Compared with the S, the L showed 99 and 129 significantly up-and down-regulated DETs, respectively. Six of these DETs were further confirmed by quantitative real-time RT-PCR (RT-qPCR) in independent experiment.

CONCLUSIONS

Our results significantly improve existing gene models and genome annotations, optimise the genome structure, and in-depth understanding of the complexity and diversity of the differential growth patterns of P. f. martensii.

Genome Wide Analysis for Growth at Two Growth Stages in A New Fast-Growing Common Carp Strain (Cyprinus carpio L.)

In order to identify candidate genes or loci associated with growth performance of the newly established common carp strain, Xinlong, we conducted a genome-wide association analysis using 2b-RAD technology on 123 individuals. We constructed two sets of libraries associated with growth-related parameters (weight, length, width and depth) measured at two different grow-out stages. Among the 413,059 SNPs identified using SOAP SNP calling, 147,131 were tested for GWAS after quality filtering. Finally, 39 overlapping SNPs, assigned to four genomic locations, were associated with growth traits in two stages. These loci were assigned to functional classes related to immune response, response to stress, neurogenesis, cholesterol metabolism and development, and proliferation and differentiation of cells. By overlapping results of Plink and EMMAX analyses, we identified three genes: TOX, PLK2 and CD163 (both methods P < 0.05). Our study results could be used for marker-assisted selection to further improve the growth of the Xinlong strain, and illustrate that largely different sets of genes drive the growth of carp in the early and late grow-out stages.

Identification of SNPs involved in Zn and Cu accumulation in the Pacific oyster (Crassostrea gigas) by genome-wide association analysis

Oysters accumulate high concentrations of zinc (Zn) and copper (Cu), which can be transferred to human due to sea food consumption. Breeding new oyster varieties with low Zn and Cu accumulations is one important way to improve food safety. However, the genetic basis for metal accumulation in mollusks is not well understood. To address this issue, oysters collected in the field were used for genome-wide association study (GWAS) and then the identified genes were used for mRNA expressions analysis in laboratory. First, GWAS were conducted for Zn and Cu accumulation in 288 wild Pacific oysters (Crassostrea gigas) farmed in the same ocean environment. The oysters did not show obvious population structure or kinship but exhibited 8.43- and 10.0- fold changes of Zn and Cu contents respectively. GWAS have identified 11 and 12 single nucleotide polymorphisms (SNPs) associated with Zn and Cu, respectively, as well as 16 genes, which were Zn-containing proteins or participated in caveolae-dependent endocytosis. Second, the mRNA expressions of these 16 genes were observed under Zn and Cu exposure. After 9 days of Zn exposure, Zn contents increased 3.1-fold, while the mRNA expression of cell number regulator 3 increased 1.65-fold. Under 9 days of Cu exposure, Cu contents increased 1.97-fold, while the mRNA expression of caveolin-1 decreased 0.61-fold. These provide the evidence for their roles in regulating physiological levels of these two metals. The findings advance our understanding of the genetic basis of Zn and Cu accumulation in mollusks, which can be useful for breeding new, less toxic varieties of oysters.

Chromosome-level genome assembly of the razor clam Sinonovacula constricta (Lamarck, 1818)

Bivalves, a highly diverse and the most evolutionarily successful class of invertebrates native to aquatic habitats, provide valuable molecular resources for understanding the evolutionary adaptation and aquatic ecology. Here, we reported a high-quality chromosome-level genome assembly of the razor clam Sinonovacula constricta using Pacific Bioscience single-molecule real-time sequencing, Illumina paired-end sequencing, 10X Genomics linked-reads and Hi-C reads. The genome size was 1,220.85 Mb, containing scaffold N50 of 65.93 Mb and contig N50 of 976.94 Kb. A total of 899 complete (91.92%) and seven partial (0.72%) matches of the 978 metazoa Benchmarking Universal Single-Copy Orthologs were determined in this genome assembly. And Hi-C scaffolding of the genome resulted in 19 pseudochromosomes. A total of 28,594 protein-coding genes were predicted in the S. constricta genome, of which 25,413 genes (88.88%) were functionally annotated. In addition, 39.79% of the assembled genome was composed of repetitive sequences, and 4,372 noncoding RNAs were identified. The enrichment analyses of the significantly expanded and contracted genes suggested an evolutionary adaptation of S. constricta to highly stressful living environments. In summary, the genomic resources generated in this work not only provide a valuable reference genome for investigating the molecular mechanisms of S. constricta biological functions and evolutionary adaptation, but also facilitate its genetic improvement and disease treatment. Meanwhile, the obtained genome greatly improves our understanding of the genetics of molluscs and their comparative evolution.

Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab (Portunus trituberculatus)

Low salinity is one of the most important abiotic factors that directly affect the abundance of the swimming crab, Portunus trituberculatus. Quantitative trait loci (QTL) mapping could be helpful in identifying the markers and genes involved in low salinity tolerance. In this study, two QTLs of low salt tolerance were mapped on linkage group 17 (LG17, 2.6-5.2 cM) based on a high-density linkage map. Ninety-five markers related to low salinity tolerance were identified via association analysis, and seventy-nine low salt-related candidate genes (including ammonium transport, aldehyde dehydrogenase, and glucosyltransferase) were screened from draft genome of the species via these markers. This represents the first report of QTL mapping for low salinity tolerance in the swimming crab, which may be useful to elucidate salinity adaptation mechanisms.

Construction of a high-density genetic linkage map and mapping of quantitative trait loci for growth-related traits in silver carp (Hypophthalmichthys molitrix)

High-density genetic map and quantitative trait loci (QTL) mapping are powerful tools for identifying genomic regions that may be responsible for such polygenic trait as growth. A high-density genetic linkage map was constructed by sequencing 198 individuals in a F₁ family of silver carp (Hypophthalmichthys molitrix) in this study. This genetic map spans a length of 2,721.07 cM with 3,134 SNPs distributed on 24 linkage groups (LGs). Comparative genomic mapping presented a high level of syntenic relationship between silver carp and zebrafish. We detected one major and nineteen suggestive QTL for 4 growth-related traits (body length, body height, head length and body weight) at 6, 12 and 18 months post hatch (mph), explaining 10.2~19.5% of phenotypic variation. All six QTL for growth traits of 12 mph generally overlapped with QTL for 6 mph, while the majority of QTL for 18 mph were identified on two additional LGs, which may reveal a different genetic modulation during early and late muscle growth stages. Four potential candidate genes were identified from the QTL regions by homology searching of marker sequences against zebrafish genome. Hepcidin, a potential candidate gene identified from a QTL interval on LG16, was significantly associated with growth traits in the analyses of both phenotype-SNP association and mRNA expression between small-size and large-size groups of silver carp. These results provide a basis for elucidating the genetic mechanisms for growth and body formation in silver carp, a world aquaculture fish.

Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)

Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g. bivalve mollusks). Here, we demonstrate a novel, non-invasive technique for sampling DNA based on the collection of environmental DNA using European Flat Oysters (Ostrea edulis) as an example. The live animals are placed in individual containers until sufficient genetic material is released into the seawater which is then recovered by filtration. We compared the results of tissue and eDNA derived SNP genotype calls using a PCR based genotyping platform. We found that 100% accurate genotype calls from eDNA are possible, but depend on appropriate filtration and the dilution of the sample throughout the workflow. We also developed an additional low-cost DNA extraction technique which provided >99% correct SNP genotype calls in comparison to tissue. It was concluded that eDNA sampling can be used in hatchery and selective breeding programs applicable to any aquatic organism for which direct tissue sampling may result in animal welfare concerns or mortality.

A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.

A chromosomal-level genome assembly for the giant African snail Achatina fulica

BACKGROUND

Achatina fulica, the giant African snail, is the largest terrestrial mollusk species. Owing to its voracious appetite, wide environmental adaptability, high growth rate, and reproductive capacity, it has become an invasive species across the world, mainly in Southeast Asia, Japan, the western Pacific islands, and China. This pest can damage agricultural crops and is an intermediate host of many parasites that can threaten human health. However, genomic information of A. fulica remains limited, hindering genetic and genomic studies for invasion control and management of the species.

FINDINGS

Using a k-mer-based method, we estimated the A. fulica genome size to be 2.12 Gb, with a high repeat content up to 71%. Roughly 101.6 Gb genomic long-read data of A. fulica were generated from the Pacific Biosciences sequencing platform and assembled to produce a first A. fulica genome of 1.85 Gb with a contig N50 length of 726 kb. Using contact information from the Hi-C sequencing data, we successfully anchored 99.32% contig sequences into 31 chromosomes, leading to the final contig and scaffold N50 length of 721 kb and 59.6 Mb, respectively. The continuity, completeness, and accuracy were evaluated by genome comparison with other mollusk genomes, BUSCO assessment, and genomic read mapping. A total of 23,726 protein-coding genes were predicted from the assembled genome, among which 96.34% of the genes were functionally annotated. The phylogenetic analysis using whole-genome protein-coding genes revealed that A. fulica separated from a common ancestor with Biomphalaria glabrata ∼182 million years ago.

CONCLUSION

To our knowledge, the A. fulica genome is the first terrestrial mollusk genome published to date. The chromosome sequence of A. fulica will provide the research community with a valuable resource for population genetics and environmental adaptation studies for the species, as well as investigations of the chromosome-level of evolution within mollusks.

Three Novel Players: PTK2B, SYK, and TNFRSF21 Were Identified to Be Involved in the Regulation of Bovine Mastitis Susceptibility via GWAS and Post-transcriptional Analysis

Bovine mastitis is a common inflammatory disease caused by multiple factors in early lactation or dry period. Genome wide association studies (GWAS) can provide a convenient and effective strategy for understanding the biological basis of mastitis and better prevention. 2b-RADseq is a high-throughput sequencing technique that offers a powerful method for genome-wide genetic marker development and genotyping. In this study, single nucleotide polymorphisms (SNPs) of the immune-regulated gene correlative with mastitis were screened and identified by two stage association analysis via GWAS-2b-RADseq in Chinese Holstein cows. We have screened 10,058 high quality SNPs from 7,957,920 tags and calculated their allele frequencies. Twenty-seven significant SNPs were co-labeled in two GWAS analysis models [Bayesian (P < 0.001) and Logistic regression (P < 0.01)], and only three SNPs (rs75762330, C > T, PIC = 0.2999; rs88640083, A > G, PIC = 0.1676; rs20438858, G > A, PIC = 0.3366) were annotated to immune-regulated genes (PTK2B, SYK, and TNFRSF21). Identified three SNPs are located in non-coding regions with low or moderate genetic polymorphisms. However, independent sample population validation (Case-control study) data showed that three important SNPs (rs75762330, P < 0.025, OR > 1; rs88640083, P < 0.005, OR > 1; rs20438858, P < 0.001, OR < 1) were significantly associated with clinical mastitis trait. Importantly, PTK2B and SYK expression was down-regulated in both peripheral blood leukocytes (PBLs) of clinical mastitis cows and in vitro LPS (E. coli)-stimulated bovine mammary epithelial cells, while TNFRSF21 was up-regulated. Under the same conditions, expression of Toll-like receptor 4 (TLR4), AKT1, and pro-inflammatory factors (IL-1β and IL-8) were also up-regulated. Interestingly, network analysis indicated that PTK2B and SYK are co-expressed in innate immune signaling pathway of Chinese Holstein. Taken together, these results provided strong evidence for the study of SNPs in bovine mastitis, and revealed the role of SYK, PTK2B, and TNFRSF21 in bovine mastitis susceptibility/tolerance.

Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network

Background

Oyster is rich in glycogen and free amino acids and is called “the milk of sea”. To understand the main genetic effects of these traits and the genetic networks underlying their correlation, we have conducted the whole genome resequencing with 427 oysters collected from the world-wide scale.

Results

After association analysis, 168 clustered significant single nucleotide polymorphism (SNP) loci were identified for glycogen content and 17 SNPs were verified with 288 oyster individuals in another wide populations. These were the most important candidate loci for oyster breeding. Among 24 genes in the 100-kb regions of the leading SNP loci, cytochrome P450 17A1 (CYP17A1) contained a non-synonymous SNP and displayed higher expressions in high glycogen content individuals. This might enhance the gluconeogenesis process by the transcriptionally regulating the expression of phosphoenolpyruvate carboxykinase (PEPCK) and glucose 6-phosphatase (G6Pase). Also, for amino acids content, 417 clustered significant SNPs were identified. After genetic network analysis, three node SNP regions were identified to be associated with glycogen, protein, and Asp content, which might explain their significant correlation.

Conclusion

Overall, this study provides insights into the genetic correlation among complex traits, which will facilitate future oyster functional studies and breeding through molecular design.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5971-z) contains supplementary material, which is available to authorized users.

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

BACKGROUND

High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.

RESULTS

In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation.

CONCLUSIONS

The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)

A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F₁ family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.

A carotenoid oxygenase is responsible for muscle coloration in scallop

As lipid microconstituents mainly of plant origin, carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Currently, the mechanism of carotenoid bioavailability in animals is largely unknown mainly due to the limited approaches applied, the shortage of suitable model systems and the restricted taxonomic focus. The mollusk Yesso scallop (Patinopecten yessoensis) possessing orange adductor muscle with carotenoid deposition, provides a unique opportunity to research the mechanism underlying carotenoid utilization in animals. Herein, through family construction and analysis, we found that carotenoid coloration in scallop muscle is inherited as a recessive Mendelian trait. Using a combination of genomic approaches, we mapped this trait onto chromosome 8, where PyBCO-like 1 encoding carotenoid oxygenase was the only differentially expressed gene between the white and orange muscles (FDR = 2.75E-21), with 11.28-fold downregulation in the orange muscle. Further functional assays showed that PyBCO-like 1 is capable of degrading β-carotene, and inhibiting PyBCO-like 1 expression in the white muscle resulted in muscle coloration and carotenoid deposition. In the hepatopancreas, which is the organ for digestion and absorption, neither the scallop carotenoid concentration nor PyBCO-like 1 expression were significantly different between the two scallops. These results indicate that carotenoids could be taken up in both white- and orange-muscle scallops and then degraded by PyBCO-like 1 in the white muscle. Our data suggest that PyBCO-like 1 is the essential gene for carotenoid metabolism in scallop muscle, and its downregulation leads to carotenoid deposition and muscle coloration.

A draft genome assembly of the solar-powered sea slug Elysia chlorotica

Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is well-known for its ability to sequester chloroplasts from its algal prey and survive by photosynthesis for up to 12 months in the absence of food supply. Here we present a draft genome assembly of E. chlorotica that was generated using a hybrid assembly strategy with Illumina short reads and PacBio long reads. The genome assembly comprised 9,989 scaffolds, with a total length of 557 Mb and a scaffold N50 of 442 kb. BUSCO assessment indicated that 93.3% of the expected metazoan genes were completely present in the genome assembly. Annotation of the E. chlorotica genome assembly identified 176 Mb (32.6%) of repetitive sequences and a total of 24,980 protein-coding genes. We anticipate that the annotated draft genome assembly of the E. chlorotica sea slug will promote the investigation of sacoglossan genetics, evolution, and particularly, the genetic signatures accounting for the long-term functioning of algal chloroplasts in an animal.

An Annotated Genome for Haliotis rufescens (Red Abalone) and Resequenced Green, Pink, Pinto, Black, and White Abalone Species

Abalone are one of the few marine taxa where aquaculture production dominates the global market as a result of increasing demand and declining natural stocks from overexploitation and disease. To better understand abalone biology, aid in conservation efforts for endangered abalone species, and gain insight into sustainable aquaculture, we created a draft genome of the red abalone (Haliotis rufescens). The approach to this genome draft included initial assembly using raw Illumina and PacBio sequencing data with MaSuRCA, before scaffolding using sequencing data generated from Chicago library preparations with HiRise2. This assembly approach resulted in 8,371 scaffolds and total length of 1.498 Gb; the N50 was 1.895 Mb, and the longest scaffold was 13.2 Mb. Gene models were predicted, using MAKER2, from RNA-Seq data and all related expressed sequence tags and proteins from NCBI; this resulted in 57,785 genes with an average length of 8,255 bp. In addition, single nucleotide polymorphisms were called on Illumina short-sequencing reads from five other eastern Pacific abalone species: the green (H. fulgens), pink (H. corrugata), pinto (H. kamtschatkana), black (H. cracherodii), and white (H. sorenseni) abalone. Phylogenetic relationships largely follow patterns detected by previous studies based on 1,784,991 high-quality single nucleotide polymorphisms. Among the six abalone species examined, the endangered white abalone appears to harbor the lowest levels of heterozygosity. This draft genome assembly and the sequencing data provide a foundation for genome-enabled aquaculture improvement for red abalone, and for genome-guided conservation efforts for the other five species and, in particular, for the endangered white and black abalone.

High-density SNP linkage map construction and QTL mapping for flavonoid-related traits in a tea plant (Camellia sinensis) using 2b-RAD sequencing

BACKGROUND

Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content is time consuming and labour intensive. High-density genetic map construction associated with quantitative trait locus (QTL) mapping provides an effective way to facilitate trait improvement in plant breeding. In this study, an F1 population (LJ43×BHZ) was genotyped using 2b-restriction site-associated DNA (2b-RAD) sequencing to obtain massive single nucleotide polymorphism (SNP) markers to construct a high-density genetic map for a tea plant. Furthermore, QTLs related to flavonoids were identified using our new genetic map.

RESULTS

A total of 13,446 polymorphic SNP markers were developed using 2b-RAD sequencing, and 4,463 of these markers were available for constructing the genetic linkage map. A 1,678.52-cM high-density map at an average interval of 0.40 cM with 4,217 markers, including 427 frameset simple sequence repeats (SSRs) and 3,800 novel SNPs, mapped into 15 linkage groups was successfully constructed. After QTL analysis, a total of 27 QTLs related to flavonoids or caffeine content (CAF) were mapped to 8 different linkage groups, LG01, LG03, LG06, LG08, LG10, LG11, LG12, and LG13, with an LOD from 3.14 to 39.54, constituting 7.5% to 42.8% of the phenotypic variation.

CONCLUSIONS

To our knowledge, the highest density genetic map ever reported was constructed since the largest mapping population of tea plants was adopted in present study. Moreover, novel QTLs related to flavonoids and CAF were identified based on the new high-density genetic map. In addition, two markers were located in candidate genes that may be involved in flavonoid metabolism. The present study provides valuable information for gene discovery, marker-assisted selection breeding and map-based cloning for functional genes that are related to flavonoid content in tea plants.

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

Predicting Growth Traits with Genomic Selection Methods in Zhikong Scallop (Chlamys farreri)

Selective breeding is a common and effective approach for genetic improvement of aquaculture stocks with parental selection as the key factor. Genomic selection (GS) has been proposed as a promising tool to facilitate selective breeding. Here, we evaluated the predictability of four GS methods in Zhikong scallop (Chlamys farreri) through real dataset analyses of four economical traits (e.g., shell length, shell height, shell width, and whole weight). Our analysis revealed that different GS models exhibited variable performance in prediction accuracy depending on genetic and statistical factors, but non-parametric method, including reproducing kernel Hilbert spaces regression (RKHS) and sparse neural networks (SNN), generally outperformed parametric linear method, such as genomic best linear unbiased prediction (GBLUP) and BayesB. Furthermore, we demonstrated that the predictability relied mainly on the heritability regardless of GS methods. The size of training population and marker density also had considerable effects on the predictive performance. In practice, increasing the training population size could better improve the genomic prediction than raising the marker density. This study is the first to apply non-linear model and neural networks for GS in scallop and should be valuable to help develop strategies for aquaculture breeding programs.

Population genetic structure of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) in the Northwest Pacific

Studying population genetics of deep-sea animals helps us understand their history of habitat colonization and population divergence. Here, we report a population genetic study of the deep-sea mussel Bathymodiolus platifrons (Bivalvia: Mytilidae) widely distributed in chemosynthesis-based ecosystems in the Northwest Pacific. Three mitochondrial genes (i.e., atp6, cox1, and nad4) and 6,398 genomewide single nucleotide polymorphisms (SNPs) were obtained from 110 individuals from four hydrothermal vents and two methane seeps. When using the three mitochondrial genes, nearly no genetic differentiation was detected for B. platifrons in the Northwest Pacific. Nevertheless, when using SNP datasets, all individuals in the South China Sea (SCS) and three individuals in Sagami Bay (SB) together formed one genetic cluster that was distinct from the remaining individuals. Such genetic divergence indicated a genetic barrier to gene flow between the SCS and the open Northwest Pacific, resulting in the co-occurrence of two cryptic semi-isolated lineages. When using 125 outlier SNPs identified focusing on individuals in the Okinawa Trough (OT) and SB, a minor genetic subdivision was detected between individuals in the southern OT (S-OT) and those in the middle OT (M-OT) and SB. This result indicated that, although under the influence of the Kuroshio Current and the North Pacific Intermediate Water, subtle geographic barriers may exist between the S-OT and the M-OT. Introgression analyses based on these outlier SNPs revealed that Hatoma Knoll in the S-OT represents a possible contact zone for individuals in the OT-SB region. Furthermore, migration dynamic analyses uncovered stronger gene flow from Dai-yon Yonaguni Knoll in the S-OT to the other local populations, compared to the reverse directions. Taken together, the present study offered novel perspectives on the genetic connectivity of B. platifrons mussels, revealing the potential interaction of ocean currents and geographic barriers with adaption and reproductive isolation in shaping their migration patterns and genetic differentiation in the Northwest Pacific.

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora)

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

Mapping and QTL Analysis of Early-Maturity Traits in Tetraploid Potato (Solanum tuberosum L.)

Early maturity is one of the most important agronomical traits in potato breeding. To identify the DNA segment that codes for early maturity, a tetraploid potato segregation population of “Zhongshu 19” × “Zhongshu 3” was genetically analyzed, using a combination of high throughput simplified genome sequencing (2b-RAD) and bulked segregant analysis (BSA). The DNA segment related to the early-maturity trait was identified at the 3.7~4.2 Mb locus on the short arm of chromosome 5. Eight molecular markers were developed, of which five were closely linked to the early-maturity trait loci. Additionally, 42 simple sequence repeats (SSR) markers were constructed based on the reference sequence of Solanum tuberosum group Phureja DM1-3 516 R44 (DM). Using the TetraploidMap software, the linkage map of chromosome 5 was constructed with 50 markers. The total map length was 172 centiMorgan (cM), with an average genetic distance of 3.44 cM. Correlating molecular and phenotypic data of the segregating population, the mapped Quantitative Trait Loci (QTL) on the short arm of chromosome 5 contributed to 33.55% of the early-maturity phenotype. The early-maturity QTL was located at 84 cM, flanked by the SSR5-85-1 and SCAR5-8 markers. The QTL was fine-mapped to 471 kb. Using DNA sequence annotation, 34 genes were identified in this region, 12 of them with unknown function. Among the other 22 annotated genes, E3 ubiquitin ligase gene PUB14 could be related to maturity and regulation of tuber formation. The constructed QTL map is a useful basic tool for the cloning of early-maturity related genes in tetraploid potatoes.

Mapping Genetic Loci for Quantitative Traits of Golden Shell Color, Mineral Element Contents, and Growth-Related Traits in Pacific Oyster (Crassostrea gigas)

Golden shell color and mineral content are important economic traits of Pacific oyster (Crassostrea gigas). In this study, we mapped a series of quantitative trait loci (QTLs) that control zinc (Zn) and magnesium (Mg) content, shell color and growth performance to two sex-averaged linkage maps from the FAM-A and FAM-B families. In total, ten QTLs were identified in seven linkage groups (LGs) in the FAM-B family, and seven QTLs were identified in four linkage groups in the FAM-A family. Two QTLs affecting the trait of golden shell color were identified in LG8 of the FAM-A and LG10 of the FAM-B families, which could explain 20.2 and 10.5% of the phenotypic variations, respectively. Two QTLs for Zn content were identified that could contribute to 17.9 and 34.44% of the phenotypic variations in FAM-A. Six QTLs for Zn and Mg contents were identified in four LGs (LG1, LG2, LG5, and LG9) in FAM-B, which explained 13.5-26.7% of the phenotypic variations. In addition, seven QTLs related to oyster growth were recognized in both FAM-A and FAM-B families accounting for 14.6-36.7% of the phenotypic variations. All of the DNA markers in QTL regions were blasted and 14 genes associated with above traits were identified. The mRNA expression of these genes was determined by quantitative RT-PCR. These QTLs and candidate genes could be used as potential targets for marker-assisted selection in C. gigas breeding.

Applications of genotyping by sequencing in aquaculture breeding and genetics

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high-density single-nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction-site associated DNA sequencing (RAD-Seq) and subsequent variations have been extensively applied to generate population-level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD-Seq techniques have included generation of genetic linkage maps, performing genome-wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

Genomic Tools and Selective Breeding in Molluscs

The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

Background

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain.

Results

A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin.

Conclusions

We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4613-1) contains supplementary material, which is available to authorized users.

Genome-wide single nucleotide polymorphisms (SNPs) for a model invasive ascidian Botryllus schlosseri

Invasive species cause huge damages to ecology, environment and economy globally. The comprehensive understanding of invasion mechanisms, particularly genetic bases of micro-evolutionary processes responsible for invasion success, is essential for reducing potential damages caused by invasive species. The golden star tunicate, Botryllus schlosseri, has become a model species in invasion biology, mainly owing to its high invasiveness nature and small well-sequenced genome. However, the genome-wide genetic markers have not been well developed in this highly invasive species, thus limiting the comprehensive understanding of genetic mechanisms of invasion success. Using restriction site-associated DNA (RAD) tag sequencing, here we developed a high-quality resource of 14,119 out of 158,821 SNPs for B. schlosseri. These SNPs were relatively evenly distributed at each chromosome. SNP annotations showed that the majority of SNPs (63.20%) were located at intergenic regions, and 21.51% and 14.58% were located at introns and exons, respectively. In addition, the potential use of the developed SNPs for population genomics studies was primarily assessed, such as the estimate of observed heterozygosity (H _O ), expected heterozygosity (H _E ), nucleotide diversity (π), Wright's inbreeding coefficient (F _IS ) and effective population size (Ne). Our developed SNP resource would provide future studies the genome-wide genetic markers for genetic and genomic investigations, such as genetic bases of micro-evolutionary processes responsible for invasion success.