Linkage mapping aided by de novo genome and transcriptome assembly in Portunus trituberculatus: applications in growth-related QTL and gene identification

Association analysis reveals SNP markers associated with growth traits in swimming crabs (Portunus trituberculatus)

The swimming crab (Portunus trituberculatus) is an economically important species in mariculture, widely distributed along the coastal areas of China. Due to its rapid growth and high nutritional value, it is a key target for selective breeding to enhance production efficiency and reduce costs. In this study, we conducted an association analysis between 233 high-quality SNPs and seven growth traits of 244 P. trituberculatus individuals: full carapace width (FCW), carapace width (CW), carapace length (CL), fixed length of the claw (FLC), meropodit length of the claw (MLC), body height (BH), and body weight (BW). The analysis identified 11 SNPs significantly associated with growth, which are distributed across multiple chromosomes, underscoring the polygenic nature of these traits. Multiple comparisons of diplotypes revealed that the diplotype D1 (AA-AT) exhibited a significant advantage for all seven growth-related traits. Additionally, we annotated 33 candidate genes located near these significant SNPs, including cytochrome c oxidase subunit (COX), NADH dehydrogenase subunit (ND), cytochrome b (CYTB), and 15-hydroxyprostaglandin dehydrogenase (15-PGDH). These genes play key roles in oxidative phosphorylation, ATP synthesis, and energy metabolism-key processes for cellular function and growth. These findings enhance our understanding of the genetic architecture underlying growth-related traits in P. trituberculatus and provide valuable SNP markers for marker-assisted selection to improve breeding efficiency in this economically important species.

Characterization of Myf6 and association with growth traits in swimming crab (Portunus trituberculatus)

BACKGROUND

Myogenic factor 6 (Myf6) plays an important role in muscle growth and differentiation. In aquatic animals and livestock, Myf6 contributes to improving meat quality and strengthening the accumulation of muscle flavor substances. However, studies on Myf6 gene polymorphisms in crustaceans have not been reported.

RESULTS

In the current study, we characterized the Myf6 gene for Portunus trituberculatus to better understand its biological function. The full-length cDNA of Myf6 was 4,101 bp, with a 915 bp open reading frame encoding 304 amino acids. In addition, Myf6 included a conservative bHLH domain. Homology analysis showed that Myf6 shared the highest identity with Penaeus vannamei. Expression pattern analysis of Myf6 in fast- and slow-growing groups revealed that the expression level of the latter was significantly higher than that of the former (P < 0.05). qPCR studies revealed that Myf6 was expressed in various tissues with the highest level in muscle. Nineteen single nucleotide polymorphisms (SNPs) of Myf6 were identified and five of them were significantly associated with growth-related traits of P. trituberculatus (P < 0.05), including full carapace width, carapace length, body height, and body weight. The AG and GG genotypes of g.1,187,834 A > G exhibited superior growth-related traits than the AA genotype. In the combined genotypes of g.1,187,324 C > T and g.1,187,834 A > G, the average body weight of diplotype D5 (CT-GG) was higher than that of diplotype D1 (CC-AA), D2 (CC-AG), and D3 (CC-GG) in a cultivated population. A haploblock was generated by three significant SNPs (g.1187834 A > G, g.1188616 A > G, and g.1189024 C > A), containing four haplotypes (AAA, AAC, AGC, and GGC), among which GGC haplotype exhibited superior growth traits (full carapace width and body weight) than the AAA haplotype.

CONCLUSIONS

To our knowledge, this is the first report on Myf6 in crustaceans. The results of this study would contribute to elucidating multiple functions of the Myf6 gene in crustaceans and exploring the potential as a candidate gene in selective breeding programs of P. trituberculatus.

Characterization of a pseudohemocyanin gene (PtPhc1) and its immunity function in response to Vibrio parahaemolyticus infection in the swimming crab Portunus trituberculatus

Pseudohemocyanin is a member of the hemocyanin superfamily, but little research is available on its function in immunology. In this study, a Portunus trituberculatus pseudohemocyanin gene, named PtPhc1, was obtained by gene cloning. The PtPhc1 cDNA was 2312 bp in length, encoding 684 amino acids while exhibiting a characteristic hemocyanin structural domain. Tissue expression analysis revealed ubiquitous expression of PtPhc1 across all tissues, with the highest level of expression observed in the hepatopancreas. The expression pattern of PtPhc1 in response to Vibrio parahaemolyticus infection was clarified using RT-qPCR in swimming crabs. Notably, the expression peaked at 24 h, and increased 1435-fold compared to the control group in the hepatopancreas. While the expression level reached the maximum value at 72 h, which was 3.24 times higher than that of the control group in hemocytes. Remarkably, the reduction in PtPhc1 expression led to a noteworthy 30% increase in the mortality rate of P. trituberculatus when exposed to V. parahaemolyticus. In addition, in vitro bacterial inhibition assays exhibited a dose-dependent suppression of bacterial proliferation by recombinant PtPhc1 protein, with a notable inhibition rate of 48.33% against V. parahaemolyticus at a concentration of 0.03 mg/mL. To the best of our knowledge, the results establish the function of pseudohaemocyanin in immunity for the first time, contributing to a deeper comprehension of innate immune regulatory mechanisms in aquatic organisms and advancing strategies for disease-resistant breeding.

Identification and functional characterization of C-type lectins and crustins provide new insights into the immune response of Portunus trituberculatus

A meticulous understanding of the immune characteristics of aquaculture animals is the basis for developing precise disease prevention and control strategies. In this study, four novel C-type lectins (PtCTL-5, PtCTL-6, PtCTL-7 and PtCTL-8) including a single carbohydrate-recognition domain (CRD), and four novel crustins (Ptcrustin-1, Ptcrustin-2, Ptcrustin-3 and Ptcrustin-4) with a single whey acidic protein (WAP) domain were identified from the swimming crab Portunus trituberculatus. Tissue distribution analysis indicated that most of the target genes were predominantly expressed in the hepatopancreas in all examined tissues, except for Ptcrustin-1 which were mainly expressed in the gills. Our results showed that the eight genes displayed various transcriptional profiles across different tissues. In hemocytes, the PtCTL-7 responded quickly to Vibrio alginolyticus and exhibited much more strongly up-regulation than other three PtCTLs. The Ptcrustin-1 rapidly responded to V. alginolyticus within 3 h in all the three tested tissues. Furthermore, recombinant proteins of PtCTL-5 and PtCTL-8 were successfully obtained, and both of them displayed bacterial binding activities toward V. alginolyticus, V. harveyi and Staphylococcus aureus, and only showed antibacterial activity against V. harveyi. These findings provided new insights into the diverse immune response of P. trituberculatus and laid theoretical foundations for the development of precise disease prevention and control strategies in P. trituberculatus farming. Moreover, the specific anti-V. harveyi activities exhibited by rPtCTL-5 and rPtCTL-8 suggested their promising application prospects for controlling diseases caused by V. harveyi.

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise F_ST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.

Screening and Verification of Molecular Markers and Genes Related to Salt-Alkali Tolerance in Portunus trituberculatus

Salt-alkali tolerance is one of the important breeding traits of Portunus trituberculatus. Identification of molecular markers linked to salt-alkali tolerance is prerequisite to develop such molecular marker-assisted breeding. In this study, Bulked Segregant Analysis (BSA) was used to screen molecular markers associated with salt-alkali tolerance trait in P. trituberculatus. Two DNA mixing pools with significant difference in salt-alkali tolerance were prepared and 94.83G of high-quality sequencing data was obtained. 855 SNPs and 1051 Indels were firstly selected as candidate markers by BSA analysis, out of which, 20 markers were further selected via △index value (close to 0 or 1) and eight of those were successfully verified. In addition, based on the located information of the markers in genome, eight candidate genes related to salt-alkali tolerance were anchored including ubiquitin-conjugating enzyme, aspartate-tRNA ligase, vesicle-trafficking protein, and so on. qPCR results showed that the expression patterns of all these genes changed significantly after salt-alkali stress, suggesting that they play certain roles in salt-alkali adaptation. Our results will provide applicable markers for molecular marker-assisted breeding and help to clarify the mechanisms of salt-alkali adaptation of P. trituberculatus.

QTL mapping and marker identification for sex determination in the ridgetail white prawn, Exopalaemon carinicauda

Sex determination is an important and intriguing research topic in the field of evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex is helpful in clarifying the sex determination system of species. In this study, a second high-resolution genetic linkage map was constructed for the ridgetail white prawn, Exopalaemon carinicauda, which included 9280 markers, covering 99.98% of the complete genome. Based on the linkage map, a highly significant sex-related QTL was first mapped to a single linkage group (LG3, LOD > 55.6). Fifty-two markers in the QTL region were significantly associated with sex (p ≤ 10^-40), of which heterogametic genotypes in females supported the ZW sex determination mechanism. Six markers were verified to be significantly associated with sex in the wild population. Some sex-related genes were identified, including phospholipase D, protein kinase shaggy, and longitudinals lacking protein. These results inform our understanding of the mechanisms of sex determination in E. carinicauda.

Phosphatidylserine from Portunus trituberculatus Eggs Alleviates Insulin Resistance and Alters the Gut Microbiota in High-Fat-Diet-Fed Mice

Portunus trituberculatus eggs contain phospholipids, whose components and bioactivity are unclear. Here, we investigated the fatty acid composition of phosphatidylserine from P. trituberculatus eggs (Pt-PS). Moreover, its effects on insulin resistance and gut microbiota were also evaluated in high-fat-diet-fed mice. Our results showed that Pt-PS accounted for 26.51% of phospholipids and contained abundant polyunsaturated fatty acids (more than 50% of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)). Animal experiments indicated that Pt-PS significantly decreased body weight and adipose weight gain, improved hyperglycemia and hyperinsulinemia, mitigated insulin resistance, and regulated circulatory cytokines. Pt-PS activated insulin receptor substrate 1 (IRS1) and increased the levels of IRS1-associated phosphatidylinositol 3-hydroxy kinase (PI3K), phosphorylated protein kinase B (Akt) protein, and plasma membrane glucose transporter 4 protein. Furthermore, Pt-PS modified the gut microbiota, inducing, especially, a dramatic decrease in the ratio of Firmicutes to Bacteroidetes at the phylum level, as well as a remarkable improvement in their subordinate categories. Pt-PS also reduced fecal lipopolysaccharide concentration and enhanced fecal acetate, propionate, and butyrate concentrations. Additionally, the effects of Pt-PS on alleviation of insulin resistance and regulation of intestinal bacteria were better than those of phosphatidylserine from soybean. These results suggest that Pt-PS mitigates insulin resistance by altering the gut microbiota. Therefore, Pt-PS may be developed as an effective food supplement for the inhibition of insulin resistance and the regulation of human gut health.

Validation of growth-related quantitative trait loci markers in different Exopalaemon carinicauda families for marker-assisted selection

We detected growth-related QTL and associated markers from the backcross population of Exopalaemon carinicauda in the previous study. Based on our previous study, the 47 SNP markers associated with candidate growth trait QTL were selected to analyze the association between these markers and body weight (BW), body length and abdominal segment length traits in four different populations including wild population, a full-sib family, a half-sib family and a backcross population for evaluating their potential application of marker-assisted selection in E. carinicauda. The general linear model (GLM) and mixed linear model were applied and the associations between SNP loci and three growth-related traits verified. The results showed that the Marker79268 and Marker100644 were significantly associated with the BW trait in more than three populations by the GLM method. The Marker100644 was significantly associated with BW in the full-sib family, half-sib family and backcross populations by the GLM and mixed linear model methods. Our findings will provide useful SNP markers to go forward to improve growth performance through more refined marker-assisted selection in E. carinicauda.

Chromosome-level genome assembly reveals the unique genome evolution of the swimming crab (Portunus trituberculatus)

BACKGROUND

The swimming crab, Portunus trituberculatus, is an important commercial species in China and is widely distributed in the coastal waters of Asia-Pacific countries. Despite increasing interest in swimming crab research, a high-quality chromosome-level genome is still lacking.

FINDINGS

Here, we assembled the first chromosome-level reference genome of P. trituberculatus by combining the short reads, Nanopore long reads, and Hi-C data. The genome assembly size was 1.00 Gb with a contig N50 length of 4.12 Mb. In addition, BUSCO assessment indicated that 94.7% of core eukaryotic genes were present in the genome assembly. Approximately 54.52% of the genome was identified as repetitive sequences, with a total of 16,796 annotated protein-coding genes. In addition, we anchored contigs into chromosomes and identified 50 chromosomes with an N50 length of 21.80 Mb by Hi-C technology.

CONCLUSIONS

We anticipate that this chromosome-level assembly of the P. trituberculatus genome will not only promote study of basic development and evolution but also provide important resources for swimming crab reproduction.

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.

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.

Egg oil from Portunus trituberculatus alleviates insulin resistance through activation of insulin signaling in mice

Marine bioactive lipids have been utilized to overcome insulin resistance. However, oil from swimming crab has never been studied. Here, we analyzed the constituents of egg oil from Portunus trituberculatus (Pt-egg oil) and investigated its protective effects against insulin resistance in mice on a high-fat diet. The results showed that Pt-egg oil contained 52.05% phospholipids, 8.61% free fatty acids (especially eicosapentaenoic acid and docosahexaenoic acid), 32.38% triglyceride, 4.79% total cholesterol, and ditissimus astaxanthin. Animal experiments showed that Pt-egg oil significantly mitigated insulin resistance and was associated with reductions in blood glucose, insulin, glucose tolerance, insulin tolerance, serum lipids, and hepatic glycogen. Pt-egg oil activated the phosphatidylinositol 3-hydroxy kinase (PI3K)/protein kinase B (Akt)/glucose transporter 4 pathway in skeletal muscle both at the transcriptional level and at the translational level. Pt-egg oil also promoted hepatic glycogen synthesis through activation of the PI3K/Akt/glycogen synthase kinase-3 beta pathway. These indicate that Pt-egg oil can be used as an alternative to marine bioactive lipids to improve insulin resistance.

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.

High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab (Scylla paramamosain)

Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.

Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain

Scylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.

QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab (Portunus trituberculatus)

Sex determination is an important area of research, which has always had an intriguing aspect in evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex will be helpful in clarifying the sex determination system. In this study, the sex QTL mapping of the swimming crab (Portunus trituberculatus) was performed based on a high-density linkage map, and a highly significant QTL specifically mapped on a single linkage group (LG) was firstly identified (LG24, LOD > 14). Twenty markers in the QTL region showed significant associations with sex by association analysis, of which heterogametic genotypes in males supported the XY sex determination mechanism. Two sex-specific markers at the family level were identified via segregation distortion analysis, which were known to be the most closely linked to the sex of P. trituberculatus. Based on sex marker sequences (Marker3840, Marker20320, and Marker10494), three potential sex-related genes were identified, and the quantitative real-time PCR results suggested that these genes were important in spermatogenesis or sex characteristics in males. Our results will contribute to the fine-mapping of sex-determining genes and clarify the sex determination mechanism of P. trituberculatus.