Genome Scan for Genomic Regions and Genes Associated with Growth Trait in Pacific White Shrimp Litopeneaus vannamei

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.

Molecular mechanisms of Mmd2 gene in regulating growth of the Pacific white shrimp Litopenaeus vannamei

Growth of the Pacific white shrimp Litopenaeus vannamei, the most important farmed crustacean, has consistently been a focal point for breeders. Over the past decades, some candidate genes for shrimp growth have been identified. However, further research is needed to elucidate the molecular regulatory mechanism of these genes. LvMmd2 was previously identified as a candidate gene that may inhibit the growth of L. vannamei. In this study, we analyzed the genotype and expression of the LvMmd2 gene in a breeding family and indicated its role as a growth-inhibiting gene. We found that LvMmd2 co-localized with its homolog LvPAQR3 at the Golgi apparatus. Using co-immunoprecipitation (Co-IP) and DUAL membrane system yeast two-hybrid (MbY2H), we indicated the interactions between LvMmd2 and LvPAQR3, LvPAQR3 and LvRaf1, as well as LvMmd2 and LvRho. These results suggest that LvMmd2 directly and indirectly regulates the Ras signaling pathway. Furthermore, we show that the LvMmd2 gene may indirectly affect the PI3K/AKT, insulin, and Hippo signaling pathways to regulate cell proliferation and differentiation via LvPAQR3 and LvRaf1. Through transcriptome and MbY2H analyses, we have also revealed the interaction between LvMmd2 and proteins involved in growth, immunity, protein transport, synthesis, and modification. These findings demonstrate the various molecular pathways through which LvMmd2 regulates L. vannamei growth. This study provides insights into the mechanism of shrimp growth regulated by Mmd2, enhances our understanding of LvMmd2 function, and highlights its potential application in shrimp breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-024-00273-7.

Genome-wide association and transcriptomic analysis and the identification of growth-related genes in Macrobrachium nipponense

Macrobrachium nipponense is a commercially important freshwater species of prawn that is widely distributed across Asian countries. In order to investigate the molecular mechanisms of growth in M. nipponense, and to provide a foundation for molecular breeding, we used genome-wide association analysis (GWAS) and transcriptomic analysis to screen polymorphisms and genes related to growth traits. We recorded the growth traits of 100 adult M. nipponense at the same growth stage, and each individual genotype was evaluated by whole genome resequencing. GWAS of growth traits detected 12 growth-related single-nucleotide polymorphisms (SNPs) and eight growth-related genes from 49 chromosomes. Of the 100 individuals, we sampled muscle tissue from a total of 18 female and male M. nipponense exhibiting large differences in growth rate for RNA-seq. Transcriptome analysis revealed a total of 27,996 unigenes; of these, 33 and 60 differentially expressed genes were identified from males and females, respectively. Of these, 12 genes associated with energy metabolism and cytoskeletal pathways were identified as growth-related genes. Notably, genes from the actin family and the ubiquitin C-terminal hydrolase 2 (UCH2) gene were identified by both GWAS and transcriptomic analysis. Two growth-related SNPs, S40_12327385 and S40_12327391, were found to be mapped to the ACTB gene. The ACTA1 gene, also from the actin family, was up-regulated in fast-growing males and females, while the ACT57B was down-regulated. In addition, the growth associated SNP S7_35313774 was located in the UCH2 gene; transcriptomics analysis revealed that the UCH2 gene was up-regulated in female individuals exhibiting high growth rates. Overall, our results provided a set of markers and candidate genes related to the growth of M. nipponense. These findings could facilitate the breeding management of this species and help us to further understand the genetic mechanisms of growth in crustaceans.

Genomic analysis of hypoxia-tolerant population of the Chinese mitten crab (Eriocheir sinensis)

Hypoxic stress, triggered by a multitude of factors, has inflicted significant economic repercussions on the aquaculture of Eriocheir sinensis. In this research, we sequenced a collective of 60 samples from both hypoxia-sensitive and hypoxia-resistant groups utilizing streamlined genome sequencing techniques. Subsequently, we delved into population evolution, scrutinized the selective sweep within these populations, and performed a genome-wide association study (GWAS) focused on the hypoxia tolerance traits within the population, all through the lens of SNPs molecular markers. This comprehensive analysis aimed to uncover the SNPs and pinpoint the pertinent candidate genes that influence the hypoxia tolerance capabilities of E. sinensis. The selective sweep analysis revealed that genes harboring potential genetic variations within the two populations were predominantly enriched in areas such as signaling molecules and interactions, energy metabolism, glycolipid metabolism, and immune response. In the genome-wide association study focusing on hypoxia tolerance traits, we identified four SNPs significantly associated with hypoxia resistance. Furthermore, one potential candidate gene, Dscam2, which is believed to influence hypoxia tolerance, was discovered within a 50 kb vicinity of these SNPs. These identified SNPs can serve as molecular markers for screening hypoxia tolerance, offering valuable insights for the genetic improvement of E. sinensis.

Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome

In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.

Structure and function analyses of the SRC gene in Pacific white shrimp Litopenaeus vannamei

SRC gene encodes scavenger receptor class C, a member of the scavenger receptor family, and has only been identified and investigated in invertebrates. Our previous studies have revealed that SRC is a novel candidate gene associated with body weight in Pacific white shrimp (Litopenaeus vannamei). In order to comprehend the underlying mechanism by which LvSRC affects shrimp growth, we analyzed the structure, phylogeny, expression profiles and RNA interference (RNAi) of this gene in L. vannamei. We found that LvSRC contains two CCP domains and one MAM domain, with the highest expression level in the heart and relatively low expression level in other tissues. Notably, LvSRC exhibited significantly higher expression levels in the fast-growing group among groups with different growth rates, suggesting its potential involvement as a gene contributing to the growth of L. vannamei. RNAi of LvSRC inhibited body length and body weight gain compared to the control groups. Moreover, through RNA-seq analysis, we identified 598 differentially expressed genes (DEGs), including genes associated with growth, immunity, protein processing and modification, signal transduction, lipid synthesis and metabolism. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed significant changes in the signaling pathways related to growth, lipid metabolism and immune response, suggesting that LvSRC exhibits the potential to participate in diverse physiological processes and immune regulation. These findings deepen our understanding of the structure and function of the SRC in shrimp and lay the foundation for further research into the regulatory mechanism of LvSRC. Additionally, they provide potential applications in shrimp genetics and breeding.

Identification of Growth-Related Gene BAMBI and Analysis of Gene Structure and Function in the Pacific White Shrimp Litopenaeus vannamei

As one of the most important aquaculture species in the world, the improvement of growth traits of the Pacific white shrimp (Litopenaeus vannamei), has always been a primary focus. In this study, we conducted SNP-specific locus analysis and identified a growth-related gene, BAMBI, in L. vannamei. We analyzed the structure and function of LvBAMBI using genomic, transcriptomic, metabolomic, and RNA interference (RNAi) assays. The LvBAMBI possessed highly conserved structural domains and widely expressed in various tissues. Knockdown of LvBAMBI significantly inhibited the gain of body length and weight of the shrimp, underscoring its role as a growth-promoting factor. Specifically, knockdown of LvBAMBI resulted in a significant downregulation of genes involved in lipid metabolism, protein synthesis, catabolism and transport, and immunity. Conversely, genes related to glucose metabolism exhibited significant upregulations. Analysis of differential metabolites (DMs) in metabolomics further revealed that LvBAMBI knockdown may primarily affect shrimp growth by regulating biological processes related to lipid and glucose metabolism. These results suggested that LvBAMBI plays a crucial role in regulating lipid metabolism, glucose metabolism, and protein transport in shrimp. This study provides valuable insights for future research and utilization of BAMBI genes in shrimp and crustaceans.

Genome-Wide Association Analysis of Heat Tolerance in F2 Progeny from the Hybridization between Two Congeneric Oyster Species

As the world's largest farmed marine animal, oysters have enormous economic and ecological value. However, mass summer mortality caused by high temperature poses a significant threat to the oyster industry. To investigate the molecular mechanisms underlying heat adaptation and improve the heat tolerance ability in the oyster, we conducted genome-wide association analysis (GWAS) analysis on the F2 generation derived from the hybridization of relatively heat-tolerant Crassostrea angulata ♀ and heat-sensitive Crassostrea gigas ♂, which are the dominant cultured species in southern and northern China, respectively. Acute heat stress experiment (semi-lethal temperature 42 °C) demonstrated that the F2 population showed differentiation in heat tolerance, leading to extremely differentiated individuals (approximately 20% of individuals die within the first four days with 10% survival after 14 days). Genome resequencing and GWAS of the two divergent groups had identified 18 significant SNPs associated with heat tolerance, with 26 candidate genes located near these SNPs. Eleven candidate genes that may associate with the thermal resistance were identified, which were classified into five categories: temperature sensor (Trpm2), transcriptional factor (Gata3), protein ubiquitination (Ube2h, Usp50, Uchl3), heat shock subfamily (Dnajc17, Dnaja1), and transporters (Slc16a9, Slc16a14, Slc16a9, Slc16a2). The expressional differentiation of the above genes between C. gigas and C. angulata under sublethal temperature (37 °C) further supports their crucial role in coping with high temperature. Our results will contribute to understanding the molecular mechanisms underlying heat tolerance, and provide genetic markers for heat-resistance breeding in the oyster industry.

Structure and function analyses of the Mmd2 gene in pacific white shrimp Litopenaeus vannamei

Monocyte to macrophage differentiation factor 2 gene (Mmd2) encodes a member of the progestin and adipoQ receptor (PAQR) family, and plays a key role in growth and development. Our previous studies had found Mmd2 (Monocyte to macrophage differentiation factor 2) is a new candidate gene for growth traits in Pacific white shrimp (Litopenaeus vannamei). For the purpose of understanding the underlying mechanism of LvMmd2 affecting the growth of shrimp, we analyzed the gene structure, phylogeny, expression profiles and RNA interference of this gene in L. vannamei. We found the LvMmd2 gene sequence was highly conserved in transmembrane regions, it was widely expressed in different tissues, with the highest expression level in the eye stalk. Knockdown LvMmd2 could significantly promote body length and body weight gain, suggesting it is a growth suppressor. Through transcriptome analysis we identified 422 differentially expressed genes (DEGs) between the dsMmd2 group and control group, among which 337 genes were upregulated in the dsMmd2 group, including numerous muscle-related genes and protein synthesis genes. Further bioinformatics analysis showed that growth, metabolism, and immune-related signal pathway had changed significantly. The above results greatly increase our understanding on the conservative structure and function of LvMmd2 gene, and provide potential application prospects in genetics and breeding.

Assessment of Performance, Microbial Community, Bacterial Food Quality, and Gene Expression of Whiteleg Shrimp (Litopenaeus vannamei) Reared under Different Density Biofloc Systems

Biofloc shrimp culture, as a way of improving shrimp production, gains worldwide consideration. However, the effects of the biofloc system on shrimp culture at high densities could be a challenge. Here, this study is aimed at identifying a better stocking density of whiteleg shrimp (Litopenaeus vannamei) between two intensive biofloc systems of 100 and 300 org./m2. Achieving that was done by comparing growth performance, water quality, feed utilization, microbial loads from water and shrimps, and gene expression of growth, stress, and immune-related genes. Shrimp postlarvae with a mean weight of 35.4 ± 3.7 mg were reared in six indoor cement tanks (36 m3 total capacity each) at two stocking densities (3 replicates each) for a rearing period of 135 days. Better final weight, weight gain, average daily weight gain, specific growth rate, biomass increase percentage, and survival rate were associated with lower density (100/m2), whereas high-density showed significantly higher total biomass. Better feed utilization was found in the lower density treatment. Lower density treatment enhanced water quality parameters, including higher dissolved oxygen and lower nitrogenous wastes. Heterotrophic bacterial count in water samples was recorded as 5.28 ± 0.15 and 5.11 ± 0.28 log CFU/ml from the high- and low-density systems, respectively, with no significant difference. Beneficial bacteria such as Bacillus spp. were identified in water samples from both systems, still, the Vibrio-like count was developed in the higher density system. Regarding shrimp food bacterial quality, the total bacterial count in the shrimp was recorded as 5.09 ± 0.1 log CFU/g in the 300 org./m2 treatment compared to 4.75 ± 0.24 log CFU/g in the lower density. Escherichia coli was isolated from the shrimps in a lower density group while Aeromonas hydrophila and Citrobacter freundii were associated with shrimps from a higher density system. Immune-related genes including prophenoloxidase, superoxide dismutase (SOD), and lysozyme (LYZ) expressions were all significantly higher expressed in the shrimp from the lower density treatment. Toll receptor (LvToll), penaiedin4 (PEN4), and stress-related gene (HSP 70) showed a decreased gene expression in the shrimp raised in the lower density. Significant upregulation of growth-related gene (Ras-related protein-RAP) expression was associated with the lower stocking density system. In conclusion, the current study found that applying high stocking density (300 org./m2) contributes negatively to performance, water quality, microbial community, bacterial food quality, and gene expression of immune, stress, and growth-related genes when compared with the lower stocking density system (100 org./m2) under biofloc system.

Genome-wide association study identified genes associated with ammonia nitrogen tolerance in Litopenaeus vannamei

Ammonia nitrogen tolerance is an economically important trait of the farmed penaeid shrimp Litopenaeus vannamei. To identify the genes associated with ammonia nitrogen tolerance, we performed an extreme phenotype genome-wide association study method (XP-GWAS) on a population of 200 individuals. The single nucleotide polymorphism (SNP) genotyping array method was used to construct the libraries and 36,048 SNPs were genotyped. Using the MLM, FarmCPU and Blink models, six different SNPs, located on SEQ3, SEQ4, SEQ5, SEQ7 and SEQ8, were determined to be significantly associated with ammonia nitrogen tolerance. By integrating the results of the GWAS and the biological functions of the genes, seven candidate genes (PDI, OZF, UPF2, VPS16, TMEM19, MYCBP2, and HOX7) were found to be associated with ammonia nitrogen tolerance in L. vannamei. These genes are involved in cell transcription, cell division, metabolism, and immunity, providing the basis for further study of the genetic mechanisms of ammonia nitrogen tolerance in L. vannamei. Further candidate gene association analysis in the offspring population revealed that the SNPs in the genes zinc finger protein OZF-like (OZF) and homeobox protein Hox-B7-like (HOX7) were significantly associated with ammonia nitrogen tolerance trait of L. vannamei. Our results provide fundamental genetic information that will be useful for further investigation of the molecular mechanisms of ammonia nitrogen tolerance. These associated SNPs may also be promising candidates for improving ammonia nitrogen tolerance in L. vannamei.

Potential synbiotic effects of a Bacillus mixture and chitosan on growth, immune responses and VP(AHPND) resistance in Pacific white shrimp (Litopenaeus vannamei, Boone, 1931)

The potential synbiotic effects of a Bacillus mixture and chitosan on growth, immune responses and disease resistance against Vibrio parahaemolyticus, the causative agent of acute hepatopancreatic necrosis disease (AHPND) in Pacific white shrimp, were intensively investigated. Three effective strains of Bacillus amyloliquefaciens (A), Bacillus pumilus (P) and Bacillus subtilis (S) were mixed in pairs at a ratio of 5 × 10⁸:5 × 10⁸ CFU/kg diet and coated with the prebiotic chitosan (C) at a concentration of 20 mL/kg diet. Five different feed treatments were used to feed experimental shrimp for 5 weeks: control (control, no synbiotics), chitosan (coat, C) and the synbiotic treatments PAC, PSC and ASC. At week 5, the final length, final weight gain, weight gain, length, average daily gain, specific growth rate and feed conversion ratio, measured as growth parameters, were significantly upregulated in the PSC and ASC groups compared with the control and coat groups (P < 0.05). This result was consistent with the expression analysis of two growth-related genes (Rap-2a and GF-II) in the hepatopancreas and intestines of treated shrimp, as determined using qRT-PCR. The prebiotic chitosan and synbiotics PAC, PSC and ASC strongly induced significant differences in the expression of the Rap-2a and GF-II genes in the target organs compared with the expression in the control group at various time points (P < 0.05). Additionally, application of the synbiotic treatments also significantly enhanced the hepatopancreas characteristics and epithelial and intestinal wall thicknesses of the shrimp compared with the control. Interestingly, all the synbiotic treatments elevated phagocytic activity significantly at weeks 3 and 5 compared with that in the other groups. qRT-PCR analysis of immune-related genes also indicated that the prebiotic group and all synbiotic groups showed strong expression of anti-lipopolysaccharide (ALF) and prophenoloxidase (proPO) genes in the intestine. Finally, the synbiotic groups PAC, PSC and ASC exhibited stronger VP_AHPND resistance at 120 h after exposure than the chitosan coat and control groups, with survival rates of 41.7 ± 11.55, 41.7 ± 0.00, 52.8 ± 5.77, 30.6 ± 15.28 and 22.2 ± 5.77%, respectively (P < 0.05). Based on the obtained information, all synbiotics were recommended for improved growth and immune responses, while ASC was the best for disease resistance against VP_AHPND in Pacific white shrimp.

ATP synthase subunit e is a shrimp growth-associated breeding marker

Penaeus vannamei is one of the most popular aquaculture species in the world. This species is featured with its fast-growing and delicious taste, which drives people develop various strains. During this process identification of trait-associated markers could effectively increase breeding efficiency. Driven by this, we tried to screen fast-growing key regulators via a FACS-based high throughput method, in which 2-NBDG was applied as a fluorescent indicator for direct glucose uptake measurement. Totally six candidate genes were screened out followed by in vitro validation in 293T cells. After that, the correlation between these genes and shrimp growing was further verified in a hybrid lineage. The expression level of two genes including ATP synthase subunit e and inhibitor of apoptosis protein showed some correlation with shrimp growth speed. Furthermore, we tested these two candidate markers in various lineages and confirmed that ATP synthase subunit e could be a shrimp growth-associated breeding marker.

Combined stress of acute cold exposure and waterless duration at low temperature induces mortality of shrimp Litopenaeus vannamei through injuring antioxidative and immunological response in hepatopancreas tissue

High mortality is a frequent occurrence during live transport of shrimp species and the biochemical mechanism remains unknown. This study aimed to explore the influence of combined stress of acute cold exposure (AC) and waterless duration (WD) on survivability and biochemical response of shrimp L. vannamei during live transport. The shrimps in NC and AC groups remained the total survivability throughout the experiment while the shrimps exposed to AC + WD stress exhibited significantly higher mortality since 6h afterwards (P < 0.05) and the median survival time was calculated at 10.46 h. Moreover, the typical combined stress points at AC + WD3h, AC + WD6h and AC + WD9h were assigned for exploring the immunological and antioxidative responses. For immunity response, the total hemocyte counts (THC) decreased with the prolongation of duration time and the activities of non-specific immunity enzymes such as phenol oxidase (PO), acid phosphatase (ACP), alkaline phosphatase (AKP), aspartate aminotransferase (AST) and alanine transaminase (ALT) were significantly elevated in AC + WD9h groups (P < 0.05). Moreover, compared with that in NC group, the significant accumulation of reactive oxygen species (ROS) was observed in AC group and then reduced in combined stress groups (P < 0.05), with the highest level of malonaldehyde (MDA) in AC and AC + WD3h groups. Overall, the significant elevation of superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GSH-Px) and total antioxidant capacity (T-AOC) was detected in AC + WD9h group (P < 0.05). Furthermore, the accumulative pathological impairment on hepatopancreas tissue revealed the cytoskeleton degradation. In addition, correlation analyses visualized the correlation between oxidative stress and biochemical response. This study not only deepens our understanding on the biochemical mechanism of shrimp mortality induced by combined stress, but also provides a potential strategy for improving the management of L. vannamei during live transport.

Identification of Growth-Associated Genes by Genome-Wide Association Study and Their Potential Application in the Breeding of Pacific White Shrimp (Litopenaeus vannamei)

The Pacific white shrimp (Litopenaeus vannamei) is the most widely cultured shrimp in the world. A great attention has been paid to improve its body weight (BW) at harvest through genetic selection for decades. Genome-wide association study (GWAS) is a tool to dissect the genetic basis of the traits. In this study, a GWAS approach was conducted to find genes related to BW through genotyping 94,113 single nucleotide polymorphisms (SNPs) in 200 individuals from a breeding population. Four BW-related SNPs located in LG19 and LG39 were identified. Through further candidate gene association analysis, the SNPs in two candidate genes, deoxycytidylate deaminase and non-receptor protein tyrosine kinase, were found to be related with the body weight of the shrimp. Marker-assisted best linear unbiased prediction (MA-BLUP) based on the SNPs in these two genes was used to estimate the breeding values, and the result showed that the highest prediction accuracy of MA-BLUP was increased by 9.4% than traditional BLUP. These results will provide useful information for the marker-assisted breeding in L. vannamei.

Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei

Despite the considerable number of genetic markers published for Penaeus vannamei, the classification of these markers and their standardization in specific databases is still insufficient. As a consequence, access to these markers is difficult, hampering their application in genetic association studies. In this study, all previously described single nucleotide polymorphisms (SNPs) related to resistance for P. vannamei were revised, and 512 SNPs were identified and classified in detail. We observed that most of the SNPs occurred in the proteins including Toll like receptors 1 and 3, hemocyanin large and small subunits, and anti-lipopolysaccharide factors 1 and 2, allowing to propose to use them as targets in association studies involving resistance in P. vannamei. Additionally, the potential effects of the most frequent non-synonymous coding SNPs in the secondary structure of the main target proteins were evaluated using an in silico approach. These data can serve as the starting point for the development of new genetic and computational tools as well as for the design of new association studies that involve resistance in P. vannamei.

A SNP of the hemocyanin gene (LvHc) is a marker for high growth and ammonia-tolerance in Pacific white shrimp Litopenaeus vannamei

Expression levels of hemocyanin (LvHc), activating transcription factor 4 (LvAtf4), glutathione S-transferase (LvGst), caspase 2 (LvCasp2) and anti-lipopolysaccharide factor (LvAlf) were examined in the hepatopancreas of Pacific white shrimp Litopenaeus vannamei juveniles exposed to a lethal concentration of ammonia-N (32.15 mg/l). The expression levels of all transcripts except LvAlf were significantly greater (P < 0.05) in tolerant shrimp (Lv-AT; N = 30) that survived up to 72 h post treatment (hpt) than in susceptible shrimp (Lv-AS24 and Lv-AS72; N = 45 and 15), that died within 24 h or between 24 and 72 hpt, respectively. Subsequently, effects of non-lethal concentrations of ammonia-N (control, 10 and 20 mg/l) on the expression of LvHc in juvenile shrimp were examined. Compared to the control, expression levels of LvHc transcripts in hemocytes and the hepatopancreas of tested shrimp changed after exposure to ammonia-N. One SNP (C > T₅₄₅) was found in the LvHc₃₂₂ gene segment. Real-time PCR amplification of specific alleles (real-time PASA) was developed for detection of C > T₅₄₅ genotypes. Juveniles in the lethal exposure test that carried a C/T₅₄₅ genotype showed a greater average body weight and total length (8.46 ± 0.36 g and 10.05 ± 0.16 cm) than those with a C/C₅₄₅ genotype (7.48 ± 0.31 g and 9.60 ± 0.13 cm) (P < 0.05). Similar results were found in the second generation (G2) of a growth-improved stock (3 and 4 families of BIOTEC-G2-L1 and BIOTEC-G2-L2) and in commercially farmed shrimp (2 groups). Accordingly, expression levels and SNP of LvHc can serve as markers for selection high growth performance in ammonia-tolerant L. vannamei.

Identification of a Growth-Associated Single Nucleotide Polymorphism (SNP) in Cyclin C of the Giant Tiger Shrimp Penaeus monodon

The full-length cDNA of cyclin C of the giant tiger shrimp Penaeus monodon (PmCyC) was isolated by RACE-PCR. It was 1443 bp in length containing an open reading frame (ORF) of 804 bp and 267 deduced amino acids. Tissue distribution analysis indicated that PmCyC was more abundantly expressed in ovaries and testes than other tissues of female and male juveniles (P < 0.05). A pair of primers was designed, and an amplification product of 403 bp containing an intron of 123 bp was obtained. Polymorphism of amplified PmCyC gene segments of the 5th (3-month-old G5, N = 30) and 7th (5-month-old G7, N = 18) generations of domesticated juveniles was analyzed. Four conserved SNPs (T>C₁₃₄, T>C₁₈₈, G>A₃₇₉, and T>C₃₈₂) were found within the examined sequences. A TaqMan genotyping assay was developed for detection of a T>C₁₃₄ SNP. Association analysis indicated that this SNP displayed significant association with body weight (P < 4.2e-10) and total length (P < 2e-09) of the examined G7 P. monodon (N = 419) with an allele substitution effect of 5.02 ± 0.78 g and 1.41 ± 0.19 cm, respectively. Juveniles with C/C₁₃₄ (22.80 ± 2.51 g and 12.97 ± 0.53 cm, N = 19) and T/C₁₃₄ (20.41 ± 0.93 g and 12.77 ± 0.21 cm, N = 129) genotypes exhibited a significantly greater average body weight and total length than those with a T/T₁₃₄ genotype (14.72 ± 0.53 g and 11.37 ± 0.13 cm, N = 271) (P < 0.05).

The Polymorphism of LvMMD2 and Its Association with Growth Traits in Litopenaeus vannamei

The Pacific white shrimp Litopenaeus vannamei is one of the major economic aquaculture species. The growth trait is considered as the most important trait in L. vannamei aquaculture. Identification of the genetic components underlying growth-related traits in L. vannamei could be useful for the selective breeding of growth trait. Our previous work identified several growth-related SNPs by genome-wide association study (GWAS). Based on the assembled genome, we identified a new candidate gene (LvMMD2) beside the associated marker. This gene encodes the progestin and AdipoQ receptor 10 (PAQR10) protein. We further investigate the polymorphisms of LvMMD2 and their association with body weight of L. vannamei. By resequencing the coding region of LvMMD2, a total of 8 SNPs were identified, including 6 synonymous mutations and 2 nonsynonymous mutations. Association analyses based on a population of 322 individuals revealed that several SNPs located in the coding region of LvMMD2 were significantly associated with the body weight, especially the nonsynonymous mutation named as MMD_5 contributed the most association to the trait and it could explain 10.5% of phenotypic variance. In addition, several genes involved in growth and development have been identified as LvMMD2-interacting genes. These findings strongly suggested that LvMMD2 might be an important gene regulating the shrimp growth. More importantly, the MMD_5 could be a promising candidate locus for marker-assisted selection (MAS) of the body weight in L. vannamei.

Integrative phenotypic and gene expression data identify myostatin as a muscle growth inhibitor in Chinese shrimp Fenneropenaeus chinensis

Growth traits, largely determined by muscle growth, are the most critical economic traits in shrimp breeding. Myostatin (Mstn) is a conserved inhibitor of muscle growth in vertebrates, but until now solid evidence supporting a similar function of Mstn in invertebrates has been lacking. In the present study, we examined the Mstn expression along with growth trait data in a Fenneropenaeus chinensis population, to establish a potential correlation between Mstn and growth. The heritabilities of FcMstn expression, body weight at 190 days of culture, body weight and length at 230 days of culture, and average daily gain were estimated using 773 individuals and a thirteen-generation pedigree. The results showed FcMstn expression was negatively correlated with the growth traits, and the mean FcMstn expression in females was significantly lower than that of males, indicating Mstn negatively regulates muscle growth in shrimp, and its lower expression may underscore the faster growth of females. Low heritabilities were detected for FcMstn expression, suggesting that the expression of Mstn might be heritable in shrimp. These results provide strong support for a growth inhibitory function of Mstn in F. chinensis, and suggest a potential method for selective breeding of this species without substantial experimental resources and labor force.

Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei)

High-pH tolerance and growth are important traits for the shrimp culture industry in areas with saline-alkali water. In the present study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was generated with a new "semidirectional cross" method, and double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology was applied to genotype the 2 parents and 148 progenies. A total of 3567 high-quality markers were constructed for the genetic linkage map, and the total map length was 4161.555 centimorgans (cM), showing 48 linkage groups (LGs) with an average interlocus length of 1.167 cM. With a constrained logarithm of odds (LOD) score ≥ 2.50, 12 high-pH tolerance and 2 growth (body weight) QTLs were located. L. vannamei genomic scaffolds were used to assist with the detection of 21 stress- and 5 growth-related scaffold genes. According to the high-pH transcriptome data of our previous study, 6 candidate high-pH response genes were discovered, and 5 of these 6 genes were consistently expressed with the high-pH transcriptome data, validating the locations of the high-pH tolerance trait-related QTLs in this study. This paper is the first report of fine-mapping high-pH tolerance and growth (body weight) trait QTLs in one L. vannamei genetic map. Our results will further benefit marker-assisted selection work and might be useful for promoting genomic research on the shrimp L. vannamei.

Molecular characterization of a RNA polymerase (RNAP) II (DNA directed) polypeptide H (POLR2H) in Pacific white shrimp (Litopenaeus vannamei) and its role in response to high-pH stress

RNA polymerase (RNAP) II (DNA-directed) (POLR2) genes are essential for cell viability under environmental stress and for the transfer of biological information from DNA to RNA. However, the function and characteristics of POLR2 genes in crustaceans are still unknown. In the present study, a POLR2H cDNA was isolated from Pacific white shrimp (Litopenaeus vannamei) and designated as Lv-POLR2H. The full-length Lv-POLR2H cDNA is 772 bp in length and contains a 32-bp 5'- untranslated region (UTR), a 284-bp 3'- UTR with a poly (A) sequence, and an open reading frame (ORF) of 456 bp encoding an Lv-POLR2H protein of 151 amino acids with a deduced molecular weight of 17.21 kDa. The Lv-POLR2H protein only contains one functional domain, harbors no transmembrane domains and mainly locates in the nucleus. The expression of the Lv-POLR2H mRNA was ubiquitously detected in all selected tissues, with the highest level in the gills. In situ hybridization (ISH) analysis showed that Lv-POLR2H was mainly located in the secondary gill filaments, the transcript levels of Lv-POLR2H in the gills were found to be significantly affected after challenge by pH, low salinity and high concentrations of NO₂^- and NH₄⁺, indicating that Lv-POLR2H in gill tissues might play roles under various physical stresses. Specifically, under high-pH stress, knockdown of Lv-POLR2H via siRNA significantly decreased the survival rate of the shrimp, indicating its key roles in the response to high-pH stress. Our study may provide the first evidence of the role of POLR2H in shrimp responding to high-pH stress and provides new insight into molecular regulation in response to high pH in crustaceans.

Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora)

Yellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)-informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.