Traits For Aquaculture Research Articles

Improved liver lipid catabolism and utilization in growth hormone transgenic common carp (Cyprinus carpio L.) through enhanced lipolytic and fatty acid β-oxidation pathways.

Growth hormone (GH) transgenic common carp (Cyprinus carpio L.) show desirable aquaculture traits. Their specific growth rate (SGR) and feed efficiency (FE) are approximately 12% and 17% higher than the wild-type (WT) common carp, respectively. However, the mechanisms of lipid catabolism (lipolysis and fatty acid β-oxidation) and utilization in GH transgenic common carp are still unclear. In this study, we firstly compared the lipid metabolism of GH transgenic (initial weight 3.72 ± 0.32 g) and WT (initial weight 3.30 ± 0.28 g) common carp fed with a normal fat level diet (6% lipid, 33% protein) for two months, then compared the growth performance of GH transgenic (initial weight 3.65 ± 0.33 g) and WT (initial weight 3.27 ± 0.26 g) common carp fed with different fat levels diets (6% lipid and 12% lipid, 33% protein) for two months. We found that the lipid content in serum, liver and whole body was significantly reduced in GH transgenic common carp, the hepatic activities of the lipolytic enzymes hormone-sensitive lipase and adipose triglyceride lipase were enhanced, and the hepatic expression level of hormone-sensitive lipase was upregulated. In addition, the mitochondrion numbers were increased, and the expression level of carnitine palmitoyltransferase-1a and carnitine palmitoyltransferase-1b was upregulated in the liver of GH transgenic common carp. GH transgenic common carp showed higher weight gain and SGR than that in WT carp when fed with a normal-fat diet as they did when fed with a high-fat diet, and GH transgenic common carp showed higher FE than that in WT carp when fed with a high-fat diet. These results suggested that the lipid catabolism and utilization was improved in the GH transgenic common carp liver through enhanced lipolytic and fatty acid β-oxidation pathways. Our study provides new insights into improving lipid utilization in some aquaculture fish species.

Molecular cloning and expression profiling of insulin-like growth factor 2 and IGF-binding protein 6 in Clarias magur (Hamilton 1822)

Growth is an important trait in aquaculture and the major genes that regulate it are Insulin-like growth factors (IGFs) and IGF binding proteins (IGFBPs). In this study, the full-length coding sequences of IGF2 and IGFBP6 genes in the Indian catfish Clarias magur were cloned and characterized. The full-length cDNA sequences of IGF2 and IGFBP6 were 885 bp (ORF 642 bp) and 928 bp (ORF 600 bp), encoding 213 and 199 amino acids, respectively. Bioinformatics analyses revealed that the magur IGF2 and IGFBP6 proteins are hydrophilic and secretory in nature. Sequence alignment with other teleosts and mammalian orthologues shows conservation of the functional domains. Gene expression analysis in 6 individuals each of high (298 ± 5.0 g) and low (210 ± 6.0 g) growth performing families showed significantly (p < 0.05) higher expression (2.5–3 fold) of IGF2, and lower expression (∼2.5 fold) of IGFBP6 in liver and muscle of fast-growing fish. This study suggests that IGF2 could be playing a major role in the growth regulation of magur. These genes and their expression patterns could be developed into growth-associated markers for magur and other catfishes.

Electroporation-Based CRISPR/Cas9 Mosaic Mutagenesis of β-Tubulin in the Cultured Oyster

Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 is enabling genetics improvement of productive traits in aquaculture. Previous studies have proven CRISPR/Cas9 to be feasible in oyster, one of the most cultured shellfish species. Here, we applied electroporation-based CRISPR/Cas9 knockout of β-tubulin and built a highly efficient genome editing system in Crassostrea gigas angulate. We identified the β-tubulin gene in the oyster genome and showed its spatiotemporal expression patterns by analyzing RNA-seq data and larval in situ hybridization. We further designed multiple highly specific guide RNAs (sgRNAs) for its coding sequences. Long fragment deletions were detected in the mutants by agarose gel electrophoresis screening and further verified by Sanger sequencing. In addition, the expression patterns of Cgβ-tubulin in the trochophore peritroch and intestinal cilia cells were altered in the mutants. Scanning electron microscopy represented shortened and almost complete depleted cilia at the positions of peritroch and the posterior cilium ring in Cgβ-tubulin mosaic knockout trochophores. Moreover, the larval swimming behavior in the mutants was detected to be significantly decreased by motility assay. These results demonstrate that β-tubulin is sufficient to mediate cilia development and swimming behavior in oyster larvae. By applying Cgβ-tubulin as a marker gene, our study established CRISPR/Cas9-mediated mosaic mutagenesis technology based on electroporation, providing an efficient tool for gene function validation in the oyster. Moreover, our research also set up an example that can be used in genetic engineering breeding and productive traits improvement in oysters and other aquaculture species.

First genetic evaluation of growth traits in Larimichthys polyactis to guide the formulation of selective breeding programs

Growth is an economically important trait in aquaculture. For the genetic improvement of growth traits in Larimichthys polyactis, a relatively new aquaculture species with great potential in large-scale farming, a genetic evaluation of these traits is necessary. In the present study, 34 families of L. polyactis were used to estimate genetic parameters for body weight, total length, and body length at the age of 11 months. Heritability estimates for the three growth traits including body weight, total length, and body length were 0.17 ± 0.06 to 0.23 ± 0.07 and were significantly different from zero (P < 0.05). The genetic correlation coefficients among the three traits were highly positive (i.e., 0.88–0.96). A selection ratio of 30% can result in an expected genetic gain (ΔG) of 3.41% and relative genetic gain (ΔG′) of 5.31% per generation for body weight in L. polyactis. There were significant differences in the response to selection when using parents selected by estimated breeding values (EBVs) and by phenotypic values (PVs). The concordance rate of individuals selected by the two methods was only 42.72%–46.02%. The average breeding value of the individuals selected based on EBVs (6.87 for body weight) was much higher than that for individuals selected based on PVs (3.48 for body weight). Environmental factors had a substantial impact on the growth phenotype of L. polyactis; accordingly, the EBV selection method is more efficient than the PVs method for breeding. The results of this study confirm that L. polyactis shows genetic variation for growth traits and highlight the enormous potential for improvements in growth by selective breeding based on EBVs.

Improving genomic prediction accuracy for harvest traits in Asian seabass (Lates calcarifer, Bloch 1790) via marker selection

Genomic selection provides an efficient strategy to improve growth performance and processing traits in aquaculture. However, the high cost of genotyping animals using high-density SNP arrays may prevent its application in small-sized breeding programs. The aim of this study was to evaluate the utility of low-density SNPs for genomic prediction of harvest traits in Asian seabass. A total of 1047 fish were genotyped for 29,521 single nucleotide polymorphisms. Genome-wide association studies (GWAS) using the weighted genomic best linear unbiased prediction (wGBLUP) procedure revealed polygenic nature of harvest traits. GBLUP and BayesB were implemented using five sets of informative SNPs specific to each trait (ranging from 500 to 12,000) and five sets of evenly-spaced markers at the same density. Prediction accuracies were evaluated using five-fold cross-validation with five replications. Using trait-specific panels with the largest effects of 500 to 2000 SNPs under GBLUP, prediction accuracies increased substantially for all traits relative to those from full SNPs, i.e., by ~70% for body weight (BW), by ~100% for standard length (SL), by ~97% for fillet weight (FW) and by ~660% for fillet yield (FY). A similar trend in prediction accuracy was observed from BayesB. Improvement in accuracy was marginal for evenly-spaced markers compared to full SNPs, i.e., by ~25% for BW, SL, FW and by ~30% for FY. Close relationship between training and validation fish appeared to be a major contributing factor to the favorable performance of prediction models for the within-family selection scheme of Asian seabass.

Transcriptomic analysis of pituitary in female and male spotted scat (Scatophagus argus) after 17β-estradiol injection

Spotted scat (Scatophagus argus) is a popular species of marine fish cultured in China. It shows normal sexual growth dimorphism. Female spotted scat grows quicker and bigger than males. Growth and reproduction are the most important traits in aquaculture. In vertebrates, the pituitary gland occupies an important position in the growth and reproduction axis. Estrogen is involved in regulating growth and reproduction in the pituitary gland in an endocrine fashion. Transcriptome sequencing of the pituitary was performed in female and male fish at 6 h after 17β-estradiol injection (4.0 μg E2/g body weight, BW). Compared with the pituitary of female and male groups, 144 and 64 genes [|log2(fold change)| ≥ 1.0 and false discovery rate (FDR) < 0.05] were significantly differentially expressed in E2-injected females and males, respectively (p < 0.05). Of these, 59 and 48 were up-regulated, and 85 and 16 were down-regulated. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway analyses, DEGs were involved in signal pathways, such as growth, reproduction, oocyte meiosis and steroid biosynthesis. Of these, estrogen affected the expression of some sex steroid synthesis and receptor genes in the pituitary gland through feedback, such as hsd17b7, pgr and cyp19a1b, regulating the reproductive activities. Besides, some growth-related genes, such as gap43, junbb, mstn2 and insm1a responded to estrogen. E2 might affect the expression level of gh mRNA by regulating the expression levels of growth-related genes. Our results provide a theoretical basis for studying the molecular mechanism of growth and reproduction regulation at the pituitary level of spotted scat responded to E2.

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

BackgroundConsidering 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.ResultsWe 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.ConclusionFor 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.

Evaluation of advantages in the growth, survival and reproductive aspects of triploid hybrids derived from Crassostrea gigas tetraploids and C. ariakensis diploids in northern China

Crossbreeding and polyploid breeding are two important tools for the genetic improvement of oysters, and their cross-application is expected to provide new benefits to oyster breeding. To evaluate the aquaculture traits of allotriploids between Crassostrea gigas and Crassostrea ariakensis, two triploid hybrids (TAG (diploid C. ariakensis ♀ × tetraploid C. gigas ♂) and TGA (tetraploid C. gigas ♀ × diploid C. ariakensis ♂)) were established. Phenotypic traits including growth, survival and reproduction were analyzed in two diploid hybrids (AG (diploid C. ariakensis ♀ × diploid C. gigas ♂) and GA (diploid C. gigas ♂ × diploid C. ariakensis ♀)) as controls. The results showed that TAG presented triploid advantage in fertilization rates and hatching rates, up to 11.34% and 26.50% respectively, while TGA did not. The survival rate of TAG and the shell height of TGA exhibited triploid advantage throughout the larval stage and were significantly higher (P < 0.05) than those of AG and GA at day 25. During the grow-out stage, triploid advantages appeared in the shell height of TAG and TGA, but only TAG showed triploid advantages in the survival rate. The triploid rates of TAG and TGA began to decrease during the grow-out stage, and reached 96.11% ± 4.41% and 90.56% ± 3.47%, respectively, at day 350. It was also found that the reproduction of TAG and TGA on day 350 was poor, manifesting as a high proportion of individuals with no gametes or a low number of gametes. Overall, TAG always presents triploid advantages in terms of growth and survival throughout the grow-out stage and shows potential value as a new resource of oyster farming or genetic improvement.

Transcriptome analysis and candidate gene identification reveals insights into the molecular mechanisms of hypermelanosis in Chinese tongue sole (Cynoglossus semilaevis)

Blind-side hypermelanosis has emerged as a major concern in flatfish aquaculture worldwide, including tongue sole (Cynoglossus semilaevis) in China. The causative gene and the molecular basis are still unclear. In this study, comparative transcriptome analyses were performed using different skin tissues of tongue sole: ocular-side normal (pigmented) skin, blind-side normal (non-pigmented) skin and blind-side hypermelanotic (pigmented) skin. Finally, 60 key hypermelanosis-related genes were mined, providing potential candidate gene resources involved in blind-side hypermelanosis. These genes were selected based on the log2(FoldChange) and false discovery rate (FDR) values (with corresponding P-Values < 0.05), and they were verified in other species to assess if they were directly or indirectly related to melanogenesis. The protein-protein interaction network of these 60 genes and the relationship between tyr and other key hypermelanosis-related genes were illustrated. The qRT-PCR validation of 16 differentially expressed genes (DEGs) showed that the data of qRT-PCR were consistent with those of RNA-seq. Further analyses revealed that the selected DEGs were significantly overrepresented in several pigment metabolic processes and in the melanogenesis pathway. Our results may imply that blind-side hypermelanosis is a pattern of environmental regulation of gene expression and adaptation in flatfish. Membrane transport proteins (such as OCA2 and SLC45A2) may serve as a “switch” for melanogenesis in tongue sole. Overall, this study provided novel insights into the molecular mechanism of hypermelanosis in flatfish species and will facilitate future selective breeding of tongue sole for this market-favoured trait in aquaculture.

Genome-wide identification and comparison of differentially expressed profiles of miRNAs and lncRNAs with associated ceRNA networks in the gonads of Chinese soft-shelled turtle, Pelodiscus sinensis

BackgroundThe gonad is the major factor affecting animal reproduction. The regulatory mechanism of the expression of protein-coding genes involved in reproduction still remains to be elucidated. Increasing evidence has shown that ncRNAs play key regulatory roles in gene expression in many life processes. The roles of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in reproduction have been investigated in some species. However, the regulatory patterns of miRNA and lncRNA in the sex biased expression of protein coding genes remains to be elucidated. In this study, we performed an integrated analysis of miRNA, messenger RNA (mRNA), and lncRNA expression profiles to explore their regulatory patterns in the female ovary and male testis of Pelodiscus sinensis.ResultsWe identified 10,446 mature miRNAs, 20,414 mRNAs and 28,500 lncRNAs in the ovaries and testes, and 633 miRNAs, 11,319 mRNAs, and 10,495 lncRNAs showed differential expression. A total of 2814 target genes were identified for miRNAs. The predicted target genes of these differentially expressed (DE) miRNAs and lncRNAs included abundant genes related to reproductive regulation. Furthermore, we found that 189 DEmiRNAs and 5408 DElncRNAs showed sex-specific expression. Of these, 3 DEmiRNAs and 917 DElncRNAs were testis-specific, and 186 DEmiRNAs and 4491 DElncRNAs were ovary-specific. We further constructed complete endogenous lncRNA-miRNA-mRNA networks using bioinformatics, including 103 DEmiRNAs, 636 DEmRNAs, and 1622 DElncRNAs. The target genes for the differentially expressed miRNAs and lncRNAs included abundant genes involved in gonadal development, including Wt1, Creb3l2, Gata4, Wnt2, Nr5a1, Hsd17, Igf2r, H2afz, Lin52, Trim71, Zar1, and Jazf1.ConclusionsIn animals, miRNA and lncRNA as master regulators regulate reproductive processes by controlling the expression of mRNAs. Considering their importance, the identified miRNAs, lncRNAs, and their targets in P. sinensis might be useful for studying the molecular processes involved in sexual reproduction and genome editing to produce higher quality aquaculture animals. A thorough understanding of ncRNA-based cellular regulatory networks will aid in the improvement of P. sinensis reproductive traits for aquaculture.

Crossbreeding of three different shell color lines in the Pacific oyster reveals high heterosis for survival but low heterosis for growth

Heterosis is important for improving productive traits in aquaculture, but the heterosis between selected lines remains unclear in bivalve molluscs. Here, a diallel crosses among black shell (B, 7th generation), white shell (W, 7th generation) and orange shell (O, 6th generation) lines of the Pacific oyster were performed to examine the potential for exploiting heterosis of productive traits by crossbreeding of selected lines. Heterosis and combining abilities for growth and survival of 27 full-sib families were analyzed at both larval and juvenile stages, of which the juvenile stage was examined at two environments (Rongcheng and Rushan) for 10 months. The variance of specific combining ability accounts for the majority of the total variance for larval and juvenile survival and juvenile growth, which revealed the importance of non-additive genetic effects (heterosis) among these lines. Moreover, all reciprocal hybrids showed low or no heterosis for growth at both larval and juvenile stages, but a high heterosis for larval survival. This finding suggested that inter-line crossbreeding can be applied to improve the larval survival in hatcheries. Furthermore, four of six hybrid crosses showed positive HPH in Rushan but negative HPH in Rongcheng. The higher HPH at Rushan suggested that inter-line crossbreeding in C. gigas has more application value in Rushan. In addition, the survival of both black shell and white shell lines have been improved by crossing with the orange shell line. Especially, the hybrid cross WO (W♀ × O♂) can improve the survival rate of purebred WW by nearly 130% at larval stage and nearly 40% at juvenile stage. Overall, this study reveals the high heterosis for survival among selected lines in the Pacific oyster, and will be helpful for the utilization of non-additive genetic effects among existing selected lines in bivalves.

Genome-wide identification of loci associated with growth in rainbow trout

BackgroundGrowth is a major economic production trait in aquaculture. Improvements in growth performance will reduce time and cost for fish to reach market size. However, genes underlying growth have not been fully explored in rainbow trout.ResultsA previously developed 50 K gene-transcribed SNP chip, containing ~ 21 K SNPs showing allelic imbalances potentially associated with important aquaculture production traits including body weight, muscle yield, was used for genotyping a total of 789 fish with available phenotypic data for bodyweight gain. Genotyped fish were obtained from two consecutive generations produced in the NCCCWA growth-selection breeding program. Weighted single-step GBLUP (WssGBLUP) was used to perform a genome-wide association (GWA) analysis to identify quantitative trait loci (QTL) associated with bodyweight gain. Using genomic sliding windows of 50 adjacent SNPs, 247 SNPs associated with bodyweight gain were identified. SNP-harboring genes were involved in cell growth, cell proliferation, cell cycle, lipid metabolism, proteolytic activities, chromatin modification, and developmental processes. Chromosome 14 harbored the highest number of SNPs (n = 50). An SNP window explaining the highest additive genetic variance for bodyweight gain (~ 6.4%) included a nonsynonymous SNP in a gene encoding inositol polyphosphate 5-phosphatase OCRL-1. Additionally, based on a single-marker GWA analysis, 33 SNPs were identified in association with bodyweight gain. The highest SNP explaining variation in bodyweight gain was identified in a gene coding for thrombospondin-1 (THBS1) (R2 = 0.09).ConclusionThe majority of SNP-harboring genes, including OCRL-1 and THBS1, were involved in developmental processes. Our results suggest that development-related genes are important determinants for growth and could be prioritized and used for genomic selection in breeding programs.

Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon

BackgroundUnderstanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest.ResultsHere, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes (P-values: 8.7 × 10−133–9.8 × 10−8), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans.DiscussionThese results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations.

Heritability of resistance-related gene expression traits and their correlation with body size of clam Meretrix petechialis

Gene expression variation can be considered as a phenotype, and it plays an important role in both acclimation and adaption. However, genetic variation of gene expression received much less attention than traditional commercial traits in aquaculture. To estimate the genetic variation and heritability of gene transcription in clam Meretrix petechialis, five Vibrio resistance-related genes were selected for gene expression analysis in the digestive gland, and an animal linear model was used to analyze data from quantitative real-time PCR (qRT-PCR). Among the five genes, BIRC7 showed significant additive genetic variations, the heritability of this gene of 12-month- and 15-month-old clams were 0.84±0.32 and 0.91±0.34, respectively. The heritability of other four genes (Bax, NFIL3, Big-Def, and CTL9) expression were low-to-moderate but not significantly expressed. Additionally, no significant phenotypic and genetic correlations between the BIRC7 transcription trait and body size were detected. This study highlights that certain gene expression variation is heritable and provides a reference for indirect selection of M. petechialis with high Vibrio resistance.

SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes

BackgroundRecently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important traits in aquaculture and the evolutionary consequences of whole genome duplications. Although genome assemblies now exist for a number of salmonid species, the lack of regulatory annotations are holding back our mechanistic understanding of how genetic variation in non-coding regulatory regions affect gene expression and the downstream phenotypic effects.ResultsWe present SalMotifDB, a database and associated web and R interface for the analysis of transcription factors (TFs) and their cis-regulatory binding sites in five salmonid genomes. SalMotifDB integrates TF-binding site information for 3072 non-redundant DNA patterns (motifs) assembled from a large number of metazoan motif databases. Through motif matching and TF prediction, we have used these multi-species databases to construct putative regulatory networks in salmonid species. The utility of SalMotifDB is demonstrated by showing that key lipid metabolism regulators are predicted to regulate a set of genes affected by different lipid and fatty acid content in the feed, and by showing that our motif database explains a significant proportion of gene expression divergence in gene duplicates originating from the salmonid specific whole genome duplication.ConclusionsSalMotifDB is an effective tool for analyzing transcription factors, their binding sites and the resulting gene regulatory networks in salmonid species, and will be an important tool for gaining a better mechanistic understanding of gene regulation and the associated phenotypes in salmonids. SalMotifDB is available at https://salmobase.org/apps/SalMotifDB.

Selection of group and individual traits of Pacific oysters (Crassostrea gigas) on the West Coast, US

Several Pacific oysters breeding programs selecting for improved aquaculture traits have been described in the literature; however, there are differences in the approaches and traits under selection. Here we discuss the approach and results of the Molluscan Broodstock Program (MBP) to improve traits of interest for US West Coast oyster farmers. In particular, we compare selection methods based on individual versus group traits measured per grow-out container. A total of 442 group records (per container) and 2197 individual records for field traits of up to 55 families were used for statistical analyses. Heritability estimates for group traits at harvest for survival, yield and individual average harvest weight were moderate-to-high and the latter estimate was not statistically significantly different from harvest weight based on individual measurements. Family-by-site (G × E) correlations were moderately negative between shell length and shell shape and strongly positive between yield and individual average weight. Genetic correlations were all positive among group traits, ranging from moderately positive between individual average weight and survival to highly positive between individual average weight and yield. Genetic correlations between individual average weight (a group trait) and individual weight (an individual trait) ranged from 0.95 to 0.99. In contrast, genetic correlations between shell shape and group traits (yield, individual average weight and survival) ranged from −0.63 to −0.22. The potential genetic gains were higher for group traits (12.1%, 8.4% and 6.9% for yield, individual average weight and survival, respectively) than for individual weight (5.6%). The BLUP accuracies were similar between group traits and individual weight. High genetic correlations between individual average weight and individual weight at harvest suggest that gains in individual weight can be achieved by selection for either individual average weight or individual weight; however, our results indicated that selecting families for shell shape will cause an unfavorable decrease of other commercially important traits. Statement of relevanceThe Pacific oyster, Crassostrea gigas, is a globally cultivated species that is grown under a wide range of environmental and husbandry conditions. In this study, we describe genetic parameters for desirable traits of selected Pacific oysters planted at commercial farms on the West Coast, US, as well as a comparison of selection methods based on individual versus group traits measured per grow-out container. Our results indicate that group traits and individual traits are genetically associated and have moderate-to-high heritabilities. Furthermore, we found a very high genetic correlation between individual average weight per container (a group trait) and weights of individual oysters sampled per container (an individual trait) at harvest, suggesting that individual average weight is a valid and less costly alternative to measurements of sampled individual oysters in breeding programs designed to improve oyster harvest weight. The results will be of interest to other breeding programs for Pacific oysters.

Transcriptome Analysis Identified Genes for Growth and Omega-3/-6 Ratio in Saline Tilapia.

Growth and omega-3/-6 ratio are important traits in aquaculture. The mechanisms underlying quick growth and high omega-3/-6 ratio in fish are not fully understood. The consumption of the meat of tilapia suffers a bad reputation due to its low omega-3/-6 ratio. To facilitate the improvement of these traits and to understand more about the mechanisms underlying quick growth and high omega-3/-6 ratio, we conducted transcriptome analysis in the muscle and liver of fast- and slow-growing hybrid saline tilapia generated by crossing Mozambique tilapia and red tilapia. A transcriptome with an average length of 963 bp was generated by using 486.65 million clean 100 bp paired-end reads. A total of 42,699 annotated unique sequences with an average length of 3.4 kb were obtained. Differentially expressed genes (DEGs) in the muscle and liver were identified between fast- and slow-growing tilapia. Pathway analysis classified these genes into many pathways. Ten genes, including foxK1, sparc, smad3, usp38, crot, fadps, sqlea, cyp7b1, impa1, and gss, from the DEGs were located within QTL for growth and omega-3, which were previously detected content in tilapia, suggesting that these ten genes could be important candidate genes for growth and omega-3 fatty acid content. Analysis of SNPs in introns 1 and 2 of foxK1 revealed that the SNPs were significantly associated with growth and omega-3/-6 ratio. This study lays the groundwork for further investigation of the molecular mechanisms underlying the phenotypic variation of these two traits and provides SNPs for selecting these traits at fingerling stage.

Comparative transcriptome analysis reveals expression signatures of albino Russian sturgeon, Acipenseriformes gueldenstaedtii

Albinism is a genetically inherited condition that is caused by a series of genetic abnormalities leading to a reduction in melanin production. Russian sturgeon is one of the most valuable freshwater fish species worldwide, and albino individuals have been found in fish farms. Due to its complicated genome and scarce genome-wide genetic resources, the underlying molecular basis of albinism in Russian sturgeon is unknown. In the present study, we first generated transcriptome profile of Acipenser gueldenstaedtii using pooled tissues, which provided reliable reference sequences for future molecular genetic studies. A total of 369,441 contigs were assembled, corresponding to 32,965 unique genes. A comparative analysis of the transcripts from the skin of albino and wildtype individuals was conducted afterwards. A total of 785 unique genes were differentially expressed, including the upregulation of 385 genes and the downregulation of 400 genes in albino individuals. The expression pattern of 16 selected differentially expressed genes was validated using qRT-PCR. Additional annotation, GO enrichment analysis and gene pathway analysis indicated that the melanogenesis pathway may be interrupted in albinism. Eight potential causative genes that were highly likely to be responsible for sturgeon albinism were identified, including Dct, Tyrp1b, Slc45a2, Ctns, Pmela, Pmelb, Cd63, and Bloc1s3, which were found to be significantly down-regulated in albino Russian sturgeon. Moreover, a sliding window analysis of the ratio of nonsynonymous to synonymous nucleotide substitution rates (Ka/Ks) ratios indicated that seven out of the eight genes underwent positive selection during evolution. Our results provide a valuable basis for understanding the molecular mechanism of albinism in fish species and will facilitate future genetic selection and breeding of sturgeon with market-favored traits in aquaculture.

Targeted Gene Disruption in Pacific Oyster Based on CRISPR/Cas9 Ribonucleoprotein Complexes.

The Pacific oyster (Crassostrea gigas) is a representative bivalve mollusc that is widely cultured in the world. In recent years, it has become an important model species for ecological, evolutionary, and developmental studies because of its ability to survive in extreme environmental conditions as a sessile filter feeder and its classical mosaic pattern of development. Although the complete genome sequence of C. gigas is available and omics data have been rapidly generated for the past few years, the genetic tools for gene functional studies have thus far been limited to RNA interference technology. In this study, we developed a gene editing system for C. gigas based on CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 ribonucleoprotein complexes. Two candidate genes, myostatin (MSTN) and Twist, were selected as targets. After microinjecting CRISPR/Cas9 ribonucleoprotein complexes into fertilized eggs, CRISPR-induced indel mutations were detected in the target genes. The CRISPR/Cas9-induced mutations were predominantly small indel mutations ranging in size from 1 to 24bp in these two target genes. These results demonstrate that CRISPR/Cas9 can be successfully used as an effective targeted gene editing system in C. gigas. The method reported here provides a powerful tool for gene functional studies in oysters and other marine bivalves, and potentially as a new technology for genetic engineering to improve oyster traits for aquaculture.

Hybrid Origin of the Thai-Chitralada Tilapia Strain Using DNA Barcoding and Microsatellite Analysis

The Thai-Chitralada strain originates from Egypt and was transferred to Japan. From there a stock of 50 fish were introduced to the Royal Chitralada Palace in Thailand. The commercially cultured strain of Nile tilapia O. niloticus in Thailand, Thai-Chitralada, possesses desirable traits for aquaculture, such as high growth rate integrated with reasonable fecundity and excellent performance in Asian countries. In 2010 a few dozen Thai-Chitralada fish were introduced to Israel from Thailand. The objective of this study is to trace the origin of Thai-Chitralada using DNA barcoding and microsatellite genetic markers. Cytochrome Oxidase I and D-loop sequences of 19 Thai-Chitralada fish clustered into three groups comprising 6, 7, and 6 individuals were homologous to the consensus sequences of O. aureus, O. niloticus, and O. mossambicus, respectively. The allele ranges for microsatellites UNH168 and G7A exclude O. niloticus (Ghana) as potential contributor to the ThaiChitralada strain. Genotyping for three microsatellites indicate overlap of alleles between Thai-Chitralada and O. niloticus (Egypt) and O. aureus, while O. mossambicus was not tested. Thus, our data based on mitochondrial and genomic analyses demonstrate that O. aureus, O. niloticus (Egypt), and O. mossambicus contributed to the formation of Thai-Chitralada. Thai-Chitralada can be used as a genetic resource for selection and adaptation to different geographical regions because of its diverse genetic background and desirable traits.