Estimation of Genetic Parameters for Growth and WSSV Resistance Traits in Litopenaeus vannamei.

The current study aimed to provide a precise assessment of the genetic parameters associated with growth and white spot syndrome virus (WSSV) resistance traits in Pacific white shrimp (Litopenaeus vannamei). This was achieved through a controlled WSSV challenge assay and the analysis of phenotypic values of five traits: body weight (BW), overall length (OL), body length (BL), tail length (TL), and survival hour post-infection (HPI). The analysis included test data from a total of 1017 individuals belonging to 20 families, of which 293 individuals underwent whole-genome resequencing, resulting in 18,137,179 high-quality SNP loci being obtained. Three methods, including pedigree-based best linear unbiased prediction (pBLUP), genomic best linear unbiased prediction (GBLUP), and single-step genomic BLUP (ssGBLUP) were utilized. Compared to the pBLUP model, the heritability of growth-related traits obtained from GBLUP and ssGBLUP was lower, whereas the heritability of WSSV resistance was higher. Both the GBLUP and ssGBLUP models significantly enhanced prediction accuracy. Specifically, the GBLUP model improved the prediction accuracy of BW, OL, BL, TL, and HPI by 4.77%, 21.93%, 19.73%, 19.34%, and 63.44%, respectively. Similarly, the ssGBLUP model improved prediction accuracy by 10.07%, 25.44%, 25.72%, 19.34%, and 122.58%, respectively. The WSSV resistance trait demonstrated the most substantial enhancement using both genomic prediction models, followed by body size traits (e.g., OL, BL, and TL), with BW showing the least improvement. Furthermore, the choice of models minimally impacted the assessment of genetic and phenotypic correlations. Genetic correlations among growth traits ranged from 0.767 to 0.999 across models, indicating high levels of positive correlations. Genetic correlations between growth and WSSV resistance traits ranged from (-0.198) to (-0.019), indicating low levels of negative correlations. This study assured significant advantages of the GBLUP and ssGBLUP models over the pBLUP model in the genetic parameter estimation of growth and WSSV resistance in L. vannamei, providing a foundation for further breeding programs.

Comparative Transcriptomic Analysis of WSSV-Challenged Penaeus vannamei with Variable Resistance Levels.

The Pacific white shrimp, Penaeus vannamei, is highly susceptible to white spot syndrome virus (WSSV). Our study explored the transcriptomic responses of P. vannamei from resistant and susceptible families, uncovering distinct expression patterns after WSSV infection. The analysis revealed a higher number of differentially expressed genes (DEGs) in the susceptible family following WSSV infection compared to the resistant family, when both were evaluated against their respective control groups, indicating that the host resistance of the family line influences the transcriptome. The results also showed that subsequent to an identical duration following WSSV infection, there were more DEGs in P. vannamei with a high viral load than in those with a low viral load. To identify common transcriptomic responses, we profiled DEGs across families at 96 and 228 h post-infection (hpi). The analysis yielded 64 up-regulated and 37 down-regulated DEGs at 96 hpi, with 33 up-regulated and 34 down-regulated DEGs at 228 hpi, showcasing the dynamics of the transcriptomic response over time. Real-time RT-PCR assays confirmed significant DEG expression changes post-infection. Our results offer new insights into shrimp's molecular defense mechanisms against WSSV.

Molecular Characterization and Expression Analysis of the C-Type Lectin Domain Family 4 Member F in Litopenaeus vannamei against White Spot Syndrome Virus.

White spot disease (WSD) outbreaks pose a significant threat to the Pacific white shrimp (Litopenaeus vannamei) farming industry. The causative agent is the white spot syndrome virus (WSSV). There are no effective treatments for WSD so far. Therefore, understanding the resistance mechanisms of L. vannamei against the WSSV is crucial. C-type lectins (CTLs) are important pattern recognition receptors (PRRs) that promote agglutination, phagocytosis, encapsulation, bacteriostasis, and antiviral infections. This study cloned the C-type lectin domain family 4 member F (LvCLEC4F) from L. vannamei. LvCLEC4F contains a 492 bp open reading frame (ORF) encoding a protein of 163 amino acids, including a carbohydrate recognition domain (CRD). Following a challenge with the WSSV, the expression profile of LvCLEC4F was significantly altered. Using RNA interference (RNAi) technology, it was found that LvCLEC4F promotes WSSV replication and affects the expression levels of genes related to the regulation of apoptosis, signaling and cellular stress response, and immune defense. Meanwhile, the hemolymph agglutination phenomenon in vivo was weakened when LvCLEC4F was knocked down. These results indicated that LvCLEC4F may play an important role in the interaction between L. vannamei and WSSV.

Reproductive Ability Disparity in the Pacific Whiteleg Shrimp (Penaeus vannamei): Insights from Ovarian Cellular and Molecular Levels.

The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the inability to spawn, while others undergo multiple maturations and contribute to the majority of larval supply. Despite numerous studies that have been conducted on the regulatory mechanisms of ovarian development in shrimp, the factors contributing to the differences in reproductive capacity among females remain unclear. To elucidate the underlying mechanisms, this study examined the differences in the ovarian characteristics between high and low reproductive bulks at different maturity stages, focusing on the cellular and molecular levels. Transmission electron microscopy analysis revealed that the abundance of the endoplasmic reticulum, ribosomes, mitochondria, and mitochondrial cristae in oocytes of high reproductive bulk was significantly higher than that of the low reproductive bulk in the early stages of ovarian maturation (stages I and II). As the ovaries progressed to late-stage maturation (stages III and IV), differences in the internal structures of oocytes between females with different reproductive capacities gradually diminished. Transcriptome analysis identified differentially expressed genes (DEGs) related to the mitochondria between two groups, suggesting that energy production processes might play a crucial role in the observed variations in ovary development. The expression levels of the ETS homology factor (EHF) and PRDI-BF1 and RIZ homology domain containing 9 (PRDM9), which were significantly different between the two groups, were compared using qRT-PCR in individuals at different stages of ovarian maturation. The results showed a significantly higher expression of the EHF gene in the ovaries of high reproductive bulk at the II and IV maturity stages compared to the low reproductive bulk, while almost no expression was detected in the eyestalk tissue of the high reproductive bulk. The PRDM9 gene was exclusively expressed in ovarian tissue, with significantly higher expression in the ovaries of the high reproductive bulk at the four maturity stages compared to the low reproductive bulk. Fluorescence in situ hybridization further compared the expression patterns of EHF and PRDM9 in the ovaries of individuals with different fertility levels, with both genes showing stronger positive signals in the high reproductive bulk at the four ovarian stages. These findings not only contribute to our understanding of the regulatory mechanisms involved in shrimp ovarian development, but also provide valuable insights for the cultivation of new varieties aimed at improving shrimp fecundity.

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

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

Recent Advances in Nanowire-Based Wearable Physical Sensors.

Wearable electronics is a technology that closely integrates electronic devices with the human body or clothing, which can realize human-computer interaction, health monitoring, smart medical, and other functions. Wearable physical sensors are an important part of wearable electronics. They can sense various physical signals from the human body or the surrounding environment and convert them into electrical signals for processing and analysis. Nanowires (NW) have unique properties such as a high surface-to-volume ratio, high flexibility, high carrier mobility, a tunable bandgap, a large piezoresistive coefficient, and a strong light-matter interaction. They are one of the ideal candidates for the fabrication of wearable physical sensors with high sensitivity, fast response, and low power consumption. In this review, we summarize recent advances in various types of NW-based wearable physical sensors, specifically including mechanical, photoelectric, temperature, and multifunctional sensors. The discussion revolves around the structural design, sensing mechanisms, manufacture, and practical applications of these sensors, highlighting the positive role that NWs play in the sensing process. Finally, we present the conclusions with perspectives on current challenges and future opportunities in this field.

Mapping the immunological battlefield in gastric cancer: prognostic implications of an immune gene expression signature.

BACKGROUND: Gastric cancer (GC) is a heterogeneous malignancy with variable clinical outcomes. The immune system has been implicated in GC development and progression, highlighting the importance of immune-related gene expression patterns and their prognostic significance. OBJECTIVE: This study aimed to identify differentially expressed immune-related genes (DEIRGs) and establish a prognostic index for GC patients using comprehensive bioinformatic analyses. METHODS: We integrated RNA sequencing data from multiple databases and identified DEIRGs by overlapping differentially expressed genes with immune-related genes. Functional enrichment analysis was performed to uncover the biological processes and signaling pathways associated with DEIRGs. We conducted a Weighted Gene Co-expression Network Analysis (WGCNA) to identify key gene modules related to with GC. Cox regression analysis was conducted to determine independent prognostic DEIRGs for overall survival prediction. Based on these findings, we developed an immune-related gene prognostic index (IRGPI) based on these findings. The prognostic value of the IRGPI was validated using survival analysis and an independent validation cohort. Functional enrichment analysis, gene mutation analysis, and immune cell profiling were performed to gain insights into the biological functions and immune characteristics associated with the IRGPI-based subgroups. RESULTS: We identified 493 DEIRGs significantly enriched in immune-related biological processes and signaling pathways associated with GC. WGCNA analysis revealed a significant module (turquoise module) associated with GC, revealing potential therapeutic targets. Cox regression analysis identified RNASE2, CGB5, CTLA4, and DUSP1 as independent prognostic DEIRGs. The IRGPI, incorporating the expression levels of these genes, demonstrated significant prognostic value in predicting overall survival. The IRGPI-based subgroups exhibited distinct biological functions, genetic alterations, and immune cell compositions. CONCLUSION: Our study identified DEIRGs and established a prognostic index (IRGPI) for GC patients. The IRGPI exhibited promising prognostic potential and provided insights into GC tumor biology and immune characteristics. These findings have implications for guiding therapeutic strategies.

Effect of snow cover on water and heat transfer in alpine meadows in the source region of Yellow River.

Extreme snowfall events have been increasing in the Tibetan Plateau, causing greater variations in the snow cover conditions. However, the soil water-heat transfer under different snow conditions has rarely been characterized in detail. Here, by using the multi-source observation data of five years, we analyzed the influences of snow cover on water-heat transfer in alpine meadows of the source region of the Yellow River. The main findings are as follows: In the deep soil, the yearly warming rate from spring to summer was much faster than the cooling rate from autumn to winter, while in the shallow soil, conversely, the former was slower than the latter. Snow cover not only decreased the average soil temperature but also inhibited the occurrence of extremely low temperatures in the soil. The insulation effect of snow was mainly in the mid-frozen period. It was insufficient to balance out the heat lost by the high albedo during early and late frozen periods. In years with more snow, different depths of the soil featured similar thawing dates and plenty of soil voids due to small solid water content and high gravel content, together creating favorable conditions for the snowmelt infiltration, which passed through the frozen layer and infiltrated into the soil of 3.20 m or deeper. In years with less snow, the long-term freezing-thawing cycles aggravated the evaporation and loss of surface soil water in spring. Under different snow cover conditions, the difference in the sensible heat flux was much larger than the latent heat flux in winter and early spring. This study provides a refined physical image of soil water-heat transfer under extreme snow cover conditions in the Tibetan Plateau, which is expected to light the snow cover-frozen soil interaction in the mid-latitude and high-elevation areas.

Characteristics of volatile organic compounds and secondary organic aerosol pollution in different functional areas of petrochemical industrial cities in Northwest China.

The aim of this study was to better understand the characteristics of volatile organic compounds (VOCs) and secondary organic aerosol (SOA) pollution in different functional areas of petrochemical industrial cities. In Lanzhou, a typical petrochemical industrial city in Northwest China, with the use of an Integrated Atmospheric Mobile Monitoring Vehicle (IAMMV), various real-time online monitoring instruments, including a VOC monitoring instrument (TH-300B) and single-particle aerosol mass spectrometer (SPAMS), were used in combination. These instruments were employed to determine PM2.5, VOCs and other factors at monitoring sites in Xigu (XG) and Chengguan (CG) districts in September 2020 and 2021, respectively. The results revealed that during the monitoring period, the average VOC concentrations at the XG and CG monitoring sites were 102.3 and 35.8 ppb, respectively. Benzene (45.58 %) and toluene (24.47 %) significantly contributed to the SOA formation potential at the XG site. M/P-xylene (27.88 %) and toluene (23.64 %) more notably contributed to the SOA formation potential at the CG site. The PM2.5 mass concentration at the XG site (24.1 µg·m-3) was similar to that at the CG site (21.2 µg·m-3), but the proportion of particulate matter components greatly differed. The proportion of organic carbon (OC) at the XG site (19.00 %) was higher than that at the CG site (9.97 %). The number of particles containing C2H3O+ (m/z = 43) accounted for 36.96 % and 15.41 % of the total particles at the XG and CG sites, respectively. The mixing ratios of OC and hybrid carbon (OCEC) with C2H3O+ (m/z = 43) were 0.81 and 0.53, respectively, at the XG site and reached only 0.48 and 0.25, respectively, at the CG site. The secondary ageing degree of particles in XG district was high. These results could provide a reference for ambient air quality improvement and the formulation of governance measures in different functional areas of petrochemical industrial cities.

Recent Advances in Multifunctional Wearable Sensors and Systems: Design, Fabrication, and Applications.

Multifunctional wearable sensors and systems are of growing interest over the past decades because of real-time health monitoring and disease diagnosis capability. Owing to the tremendous efforts of scientists, wearable sensors and systems with attractive advantages such as flexibility, comfort, and long-term stability have been developed, which are widely used in temperature monitoring, pulse wave detection, gait pattern analysis, etc. Due to the complexity of human physiological signals, it is necessary to measure multiple physiological information simultaneously to evaluate human health comprehensively. This review summarizes the recent advances in multifunctional wearable sensors, including single sensors with various functions, planar integrated sensors, three-dimensional assembled sensors, and stacked integrated sensors. The design strategy, manufacturing method, and potential application of each type of sensor are discussed. Finally, we offer an outlook on future developments and provide perspectives on the remaining challenges and opportunities of wearable multifunctional sensing technology.

Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei.

Penaeus vannamei is the most important economic shrimp in the world. Many selective breeding programs are carried out to improve its production and performance traits. Although significant differences in the reproductive ability of female P. vannamei under artificial breeding conditions have been reported, the genome-wide adaption of the reproductive ability of domesticated female P. vannamei is less investigated. In this study, whole-genome analysis was performed along with pooled DNA sequencing on two fecundity separated bulks, high fecundity bulk (HB), and low fecundity bulk (LB). Each bulk contained 30 individuals from 3 commercial populations. A sequencing depth of >30× was achieved for each bulk, leading to the identification of 625,181 and 629,748 single nucleotide polymorphisms (SNPs) in HB and LB, respectively. Fixation index (Fst) combined with p ratio allowed for the identification of 145 selective sweep regions, with a sequence length of 14.5 Mb, accounting for 0.59% of the genome. Among the 145 selective sweep regions, a total of 64,046 SNPs were identified, and further verification was performed by genotyping 50 candidate SNPs on 60 samples from the offspring of the three populations. Furthermore, 121 genes were screened from the sweep regions. GO annotation and KEGG enrichment analyses showed that partial genes were essential for fecundity regulation. This study provides important information for in-depth investigation of genomic characteristics for long-term selective breeding on the fecundity of female P. vannamei and will also be important for genome-assisted breeding of P. vannamei in the future.

Identification of candidate biomarkers associated with gastric cancer prognosis based on an integrated bioinformatics analysis.

Background: This study sought to identify candidate biomarkers associated with gastric cancer (GC) prognosis based on an integrated bioinformatics analysis. Methods: First, the GSE54129 and GSE79973 data sets were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) identified between the 2 data sets were screened using the limma software package in R, and the intersection DEGs were obtained by a Venn analysis. Subsequently, gene clustering and a functional analysis were performed to explore the roles of the DEGs. The protein-protein interaction (PPI) network of the genes in clusters was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins. A survival analysis evaluated the associations between the candidate genes and the overall survival of GC patients. A drug-gene interaction analysis and an external data set analysis were conducted using The Cancer Genome Atlas-Stomach Adenocarcinoma (TCGA-STAD) data set to validate the prognostic genes. Results: We extracted 421 intersection DEGs from the 2 GEO data sets. There were 5 gene clusters, and the functional analysis revealed that they were mainly associated with the extracellular matrix-receptor interaction pathway. The PPI interaction analysis identified the top 36 hub genes. The survival analysis revealed that 7 upregulated genes [i.e., platelet-derived growth factor receptor beta (PDGFRB), angiopoietin 2 (ANGPT2), vascular endothelial growth factor C (VEGFC), collagen type IV alpha 2 chain (COL4A2), collagen type IV alpha 1 chain (COL4A1), thrombospondin 1 (THBS1), and fibronectin 1 (FN1)] were associated with the survival prognosis of GC patients. The 20 drug-gene interaction pairs among the 4 genes and 18 drugs were obtained. Finally, TCGA-STAD data set was used to validate the expression levels of COL4A1, PDGFRB, and FN1. Conclusions: We found that 7 upregulated genes (i.e., PDGFRB, ANGPT2, VEGFC, COL4A2, COL4A1, THBS1, and FN1) were promising markers of prognosis in GC patients.

Neutrophil Transcriptional Deregulation by the Periodontal Pathogen Fusobacterium nucleatum in Gastric Cancer: A Bioinformatic Study.

Background: Infection with the periodontal pathogen Fusobacterium nucleatum (F. nucleatum) has been associated with gastric cancer. The present study is aimed at uncovering the putative biological mechanisms underlying effects of F. nucleatum-mediated neutrophil transcriptional deregulation in gastric cancer. Materials and Methods: A gene expression dataset pertaining to F. nucleatum-infected human neutrophils was utilized to identify differentially expressed genes (DEGs) using the GEO2R tool. Candidate genes associated with gastric cancer were sourced from the "Candidate Cancer Gene Database" (CCGD). Overlapping genes among these were identified as link genes. Functional profiling of the link genes was performed using "g:Profiler" tool to identify enriched Gene Ontology (GO) terms, pathways, miRNAs, transcription factors, and human phenotype ontology terms. Protein-protein interaction (PPI) network was constructed for the link genes using the "STRING" tool, hub nodes were identified as key candidate genes, and functionally enriched terms were determined. Results: The gene expression dataset GEO20151 was downloaded, and 589 DEGs were identified through differential analysis. 886 candidate gastric cancer genes were identified in the CGGD database. Among these, 36 overlapping genes were identified as the link genes. Enriched GO terms included molecular function "enzyme building," biological process "protein folding,'" cellular components related to membrane-bound organelles, transcription factors ER71 and Sp1, miRNAs miR580 and miR155, and several human phenotype ontology terms including squamous epithelium of esophagus. The PPI network contained 36 nodes and 53 edges, where the top nodes included PH4 and CANX, and functional terms related to intracellular membrane trafficking were enriched. Conclusion: F nucleatum-induced neutrophil transcriptional activation may be implicated in gastric cancer via several candidate genes including DNAJB1, EHD1, IER2, CANX, and PH4B. Functional analysis revealed membrane-bound organelle dysfunction, intracellular trafficking, transcription factors ER71 and Sp1, and miRNAs miR580 and miR155 as other candidate mechanisms, which should be investigated in experimental studies.

Contamination characteristics, source identification, and source-specific health risks of heavy metal(loid)s in groundwater of an arid oasis region in Northwest China.

Heavy metal(loid)s accumulation in groundwater has posed serious ecological and health concerns worldwide. Source-specific risk apportionment is crucial to prevent and control potential heavy metal(loid)s pollution in groundwater. However, there is very limited comprehensive information on the health risk apportionment for groundwater heavy metal(loid)s in arid regions. Thus, the Zhangye Basin, a typical arid oasis region in Northwest China, was selected to investigate the contamination characteristics, possible pollution sources, and source-specific health risks of groundwater heavy metal(loid)s. The heavy metal pollution index (HPI), the Nemerow index (NI), and the contamination degree (CD) were adopted to assess the pollution level of heavy metal(loid)s; then source-specific health risk was apportioned integrating the absolute principal component scores-multiple linear regression (APCS-MLR) with health risk assessment. Noticeable accumulation of Mn, Fe, and As was observed in this region with especially Fe/As in 12.68%/2.11% of the samples revealing significant enrichment. Approximately 3.5% of the groundwater samples caused moderate or higher pollution level based on the HPI. The APCS-MLR model was more physically applicable for the current research than the positive matrix factorization (PMF) model. Industrial-agricultural activity factor (12.56%) was the major source of non-cancer (infants: 59.15%, children: 64.87%, teens: 64.06%, adults: 64.02%) and cancer risks (infants: 77.36%, children: 77.35%, teens: 77.40%, adults: 77.41%). Industrial-agricultural activities should be given priority to control health risks of heavy metal(loid)s in groundwater. These findings provide fundamental and significant information for mitigating health risks caused by heavy metal(loid)s in groundwater of typical arid oasis regions by controlling priority sources.

Changes in climate and snow cover and their synergistic influence on spring runoff in the source region of the Yellow River.

As an important runoff-producing area, the runoff variation in the source region of the Yellow River (SRYR) has critical importance for the whole basin in broad aspects. In recent decades, the climate in the SRYR has undergone drastic changes, which affected runoff across different time scales. Many studies have focused on runoff in the SRYR with a long-time series, and presented a discordant relationship between precipitation and runoff. However, differences in this relationship over different time scales are ignored. Here, by using multi-source observation data and correlation analysis, climate elasticity, and principal component analysis methods, we document the changes in climate and snow cover and their synergistic influence on spring runoff. When the 20-year period was innovatively adopted, the runoff and precipitation coincided well during last three periods (1960-2019). The yearly precipitation presented a bimodal pattern, with the most significant increase in late spring and early summer. A bimodal pattern also appeared in annual runoff, and the rate of increase was much greater than that of precipitation (2.51%/year vs 1.01%/year). The runoff during main increase period (particularly in April) showed a high correlation with the remote sensing snow depth from November to March, but a poor correlation with snow depth from meteorological stations. Climate warming in the SRYR was much more reflected in minimum surface temperature (0.235 °C/year) than in air temperature minimum (0.081 °C/year) in last 20 years. However, the principal component analysis shows that the effect of temperature on spring runoff was obviously less than that of snow cover. A 1% variation in snow depth in the SRYR from November to March caused a 0.43% variation in runoff in April, and a 1% variation in snow days caused a 0.82% variation in runoff. This study will bring to light for understanding the evolution mechanism of spring runoff in the SRYR.

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

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

Identification of two genes potentially related to myogenesis and muscle growth in Fenneropenaeus chinensis: Activin receptor II and Follistatin-like protein.

Activin receptor (ActR) and follistatin-like (FSTL) genes, which are involved in the Myostatin (Mstn) related TGF-ß/Smad signaling pathway, play important roles in regulating the muscle generation, development and growth of muscle in vertebrate. Our previous studies have confirmed that Mstn negatively regulates muscle development and growth in Fenneropenaeus chinensis as that in vertebrate. However, the roles of ActR and FSTL in muscle development and growth in invertebrate remains unclear. In the present study, type II ActR(FcActRII) and FSTL (FcFSTL) genes from F. chinensis were cloned and characterized, and their functions on muscle development and growth were investigated. The full-length cDNAs of FcActRII and FcFSTL were 2366 bp that encoded 572 amino acids and 2474 bp that encoded 717 amino acids, respectively. Sequence analysis revealed that the overall protein sequences of the two genes shared 97% and 96% identities with Penaeus vannamei and 50%-59% and 35%-36% identities with vertebrates, respectively. In the early development stages, muscles firstly appeared in nauplius stage and developed gradually until post larval, and the mRNA expressions of FcActRII increased from gastrula to zoea stage and then decreased from zoea stage to post larval stage while that of FcFSTL was lowest in gastrula stage and increased rapidly in nauplius stage and then expressed stably from nauplius stage to post-larval stage. In the adult shrimp, the two genes were widely distributed in the examined tissues. The FcActRII expression in muscle of L group was significantly lower than that of S group, but the FcFSTL expression showed an opposite result. After down-regulating the expression of FcMstn by RNAi, FcActRII expression was significantly down-regulated while that of FcFSTL was up-regulated. The present study suggested that FcActRII and FcFSTL, regulated by FcMstn, might be involved in myogenesis and muscle growth.

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

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

Feed competition reduces heritable variation for body weight in Litopenaeus vannamei.

BACKGROUND: Competition is a common social interaction among shrimp and depending on its intensity, it can affect heritable variation and response to selection. Little is known about the variance of indirect genetic effects (IGE) under competitive and non-competitive conditions in shrimp. In this study, we used extended mixed linear models to estimate genetic parameters for the direct genetic effect (DGE) and IGE on body weight in Litopenaeus vannamei raised under ad libitum (AF, non-competitive environment) and restricted (RF, competitive environment) feeding regimes. RESULTS: Estimates of heritabilities for body weight obtained with a traditional animal model (i.e. without accounting for IGE) were 0.11 ± 0.09 under AF and 0.25 ± 0.11 under RF. With extended animal models that accounted for IGE, the corresponding estimates for body weight were 0.07 ± 0.08 and 0.34 ± 0.11. Thus, heritabilities were higher under the RF regime than under the AF regime, regardless of whether IGE was accounted for or not. The log-likelihood ratio test revealed significant IGE under the RF regime. Although estimates of indirect genetic variance were low (0.0023 ± 0.0013 for AF and 0.0028 ± 0.0012 for RF), they contributed substantially to the total heritable variance: 66.8% for AF and 692.2% for RF. The total heritable variance was smaller under the RF regime (0.7 ± 1.3) than under the AF regime (5.8 ± 2.6) because of the high contribution of the negative covariance between DGE and IGE (- 7.03). Estimates of the correlation between DGE and IGE were 0.32 ± 0.47 under AF and - 0.93 ± 0.15 under RF, those of DGE and IGE for body weight between both regimes were 0.94 ± 0.07 and 0.67 ± 0.20, respectively, and those of IGE for body weight with DGE for survival were - 0.12 ± 0.22 under AF and - 0.58 ± 0.20 under RF. CONCLUSIONS: These results indicate that strong competitive interactions occurred under the RF regime in L. vannamei. Significant reranking and variation in IGE of individuals were observed between the two feeding regimes. Strong competitive interactions reduced the total heritable variation for body weight when food was restricted. These results indicate that the extent of competition among L. vannamei depends on the feeding regime applied and that this competition affects the genetic basis of body weight.

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

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