Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus)

Whole-genome resequencing and RNA-seq analysis implicates GPR75 as a potential genetic basis related to retarded growth in South China carp (Cyprinus carpio rubrofuscus)

The south China carp (Cyprinus carpio rubrofuscus) is an indigenous and important fish species, widely cultured in south China. However, part of individuals experienced retarded growth, the genetic basis of which has yet to be elucidated. In this study, whole-genome resequencing of 35 fast-growing and 35 retarded-growing south China carp were conducted to identify promising genes associated with retarded growth. Twelve candidate SNPs were detected and annotated to the Gpr75 gene, which has been reported to be related with body weight through regulating insulin homeostasis. RNA-seq analysis of muscle suggested that differentially expressed genes were significantly enriched in the insulin signaling pathway. Additionally, the fasting serum insulin level was significantly lower while the blood glucose level was significantly higher in the retarded-growing group. Our preliminary study provides insights into the genetic basis underlying the retarded growth and may facilitate further genetic improvement of south China carp.

Identification of candidate SNPs and genes associated with resistance to nervous necrosis virus in leopard coral grouper (Plectropomus leopardus) using GWAS

The leopard coral grouper (Plectropomus leopardus), which has become increasingly popular in consumption due to its bright body color and great nutritional, holds a high economic and breeding potential. However, in recent years, the P.leopardus aquaculture industry has been impeded by the nervous necrosis virus (NNV) outbreak, leading to widespread mortality among fry and juvenile grouper. However, the genetic basis of resistance to NNV in P. leopardus remains to be investigated. In the present study, we conducted a genome-wide association analysis (GWAS) on 100 resistant and 100 susceptible samples to discover variants and potential genes linked with NNV resistance. For this study, 157,926 high-quality single nucleotide polymorphisms (SNPs) based on whole genome resequencing were discovered, and eighteen SNPs loci linked to disease resistance were discovered. We annotated six relevant candidate genes, including sik2, herc2, pip5k1c, npr1, mybpc3, and arhgap9, which showed important roles in lipid metabolism, oxidative stress, and neuronal survival. In the brain tissues of resistant and susceptible groups, candidate genes against NNV infection showed significant differential expression. The results indicate that regulating neuronal survival or pathways involved in lipid metabolism may result in increased resistance to NNV. Understanding the molecular mechanisms that lead to NNV resistance will be beneficial for the growth of the P. leopardus breeding sector. Additionally, the identified SNPs could be employed as biomarkers of disease resistance in P. leopardus, which will facilitate the selective breeding of grouper.

Assembly of Genome and Resequencing Provide Insights into Genetic Differentiation between Parents of Hulong Hybrid Grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂)

The Hulong hybrid grouper was bred from the brown-marbled grouper (Epinephelus fuscoguttatus) ♀ and the giant grouper (E. lanceolatus) ♂, combining the advantageous traits of both parents. Possessing an excellent performance, this hybrid's cultivation promotes the development of the grouper industry. Its male parent, the giant grouper, possesses the fastest growth and the largest body size among all coral-reef-dwelling fish. This species is not only an economically important species in marine aquaculture, but it is also an ideal male parent in the interspecific crossing of grouper species. In the present study, a high-quality chromosome-level genome of the giant grouper was constructed with a total length of 1.06 Gb, consisting of 24 chromosomes and 69 scaffolds. To analyze the genetic differences between the parents of the Hulong hybrid grouper, the structural variations (SVs) between both parental genomes were detected, and a total of 46,643 SVs were obtained. High-quality SNPs were identified from resequencing data. There were significant differences between the two genomes, and the average FST reached 0.685. A total of 234 highly differentiated regions were detected with an FST > 0.9. The protein-coding genes involved in SVs and highly differentiated regions were significantly enriched in metabolic pathways, including fatty metabolism, carbohydrate metabolism, amino acid metabolism and the TCA cycle. These genes may be related to the differences in feeding preferences and the ability to digest carbohydrates between the two grouper species under natural conditions. In addition, protein-coding genes related to the cell cycle and p53-signaling pathway were also detected. These genes may play important roles in the regulation of body size and growth performance. This research provides genomic resources for further breeding works and evolutionary analyses.

Identification of crucial factors involved in Cynoglossus semilaevis sexual size dimorphism by GWAS and demonstration of zbed1 regulatory network by DAP-seq

Sexual size dimorphism (SSD), whereby females and males exhibit different body sizes, are widely documented in animals. To explore crucial regulators implicated in female-biased SSD of Chinese tongue sole (Cynoglossus semilaevis), GWAS was conducted on 350 females and 59 males. Twenty SNPs and 25 genes including zbed1, nsd3, cdc45, klhl29, and smad4 with -log(p) > 7 were screened, mainly mapping to sex chromosome. The chromosome W-linked gene zbed1 attracted particular attention because it is a master key for cell proliferation. Thus, the regulatory network of zbed1 in C. semilaevis was explored by DAP-seq and 1352 peaks were discovered in the female brain. Moreover, zbed1 potentially regulated hippo signaling pathway, cell cycle, translation, and PI3k-Akt signaling pathway in C. semilaevis. These findings identify crucial SNPs and genes associated with female-biased SSD in C. semilaevis, also provide the first genome-wide survey for the zbed1 regulatory network in fish species.

Unraveling the complex genetic basis of growth in New Zealand silver trevally (Pseudocaranx georgianus)

Growth directly influences production rate and therefore is one of the most important and well-studied traits in animal breeding. However, understanding the genetic basis of growth has been hindered by its typically complex polygenic architecture. Here, we performed quantitative trait locus mapping and genome-wide association studies for 10 growth traits that were observed over 2 years in 1,100 F1 captive-bred trevally (Pseudocaranx georgianus). We constructed the first high-density linkage map for trevally, which included 19,861 single nucleotide polymorphism markers, and discovered 8 quantitative trait loci for height, length, and weight on linkage groups 3, 14, and 18. Using genome-wide association studies, we further identified 113 single nucleotide polymorphism-trait associations, uncovering 10 genetic hot spots involved in growth. Two of the markers found in the genome-wide association studies colocated with the quantitative trait loci previously mentioned, demonstrating that combining quantitative trait locus mapping and genome-wide association studies represents a powerful approach for the identification and validation of loci controlling complex traits. This is the first study of its kind for trevally. Our findings provide important insights into the genetic architecture of growth in this species and supply a basis for fine mapping quantitative trait loci, genomic selection, and further detailed functional analysis of the genes underlying growth in trevally.

A new insight into the SNP genotyping using high-resolution melting method after the correlation analysis of the SNPs with WSSV-resistant traits

Procambarus clarkii is an important freshwater cultured crayfish in China. With the gradual development of its aquaculture industry, research on white spot disease, which is harmful to healthy culture of P. clarkii, increases gradually. The prophenoloxidase (proPO) system is an important part of crayfish's innate immunity and plays a role in virus resistance. In this study, based on the early discovery of three SNP sites in the intron of proPO gene, the linkage disequilibrium and haplotype were analyzed for the SNPs, and it was found that there was a strong linkage disequilibrium relationship among them. Through the analysis on association between the haplotypes and genotype of each SNP site with the WSSV-resistant traits, the detection of the SNP_7081 genotype was considered as the most convenient and efficient way for WSSV-resistant group selection. Furtherly, the high-resolution melting curve (HRM), which is a rapid and economic genotyping method, was chosen to establish for SNP_7081 site genotyping. The 68 bp target fragment with 27.94% GC content was amplified and melting curve analysis were performed. However, the appearance of false negatives which led to unable automatically grouped although the melting curves of genotypes CC, C>T and T>C were obviously different, and could be treated as standard to manually genotype the samples with an accuracy rate of 97.61%. The low GC content which correlated with the Tm value, was confirmed as the reason for the false negatives by the assay about the recombinant plasmid PMD18-T-SNP_7081 constructed with 45.24% GC content. Eventually, the adaptor primers were used to increase the GC content of the target fragment, and a modified HRM method for genotyping SNP_7081 site that could group automatically was established, which could provide a new insight for the HRM method to genotype SNPs.

Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum

R. esculentum is a popular seafood in Asian countries and an economic marine fishery resource in China. However, the genetic linkage map and growth-related molecular markers are still lacking, hindering marker assisted selection (MAS) for genetic improvement of R. esculentum. Therefore, we firstly used 2b-restriction site-associated DNA (2b-RAD) method to sequence 152 R. esculentum specimens and obtained 9100 single nucleotide polymorphism (SNP) markers. A 1456.34 cM linkage map was constructed using 2508 SNP markers with an average interval of 0.58 cM. Then, six quantitative trait loci (QTLs) for umbrella diameter and body weight were detected by QTL analysis based on the new linkage map. The six QTLs are located on four linkage groups (LGs), LG4, LG13, LG14 and LG15, explaining 9.4% to 13.4% of the phenotypic variation. Finally, 27 candidate genes in QTLs regions of LG 14 and 15 were found associated with growth and one gene named RE13670 (sushi, von Willebrand factor type A, EGF and pentraxin domain-containing protein 1-like) may play an important role in controlling the growth of R. esculentum. This study provides valuable information for investigating the growth mechanism and MAS breeding in R. esculentum.

Whole-genome sequencing of brown-marbled grouper (Epinephelus fuscoguttatus) provides insights into adaptive evolution and growth differences

The brown-marbled grouper (Epinephelus fuscoguttatus) is an important species of fish in the coral reef ecosystem and marine aquaculture industry. In this study, a high-quality chromosome-level genome of brown-marbled grouper was assembled using Oxford Nanopore technology and Hi-C technology. The GC content and heterozygosity were approximately 42% and 0.35%, respectively. A total of 230 contigs with a total length of 1047 Mb and contig N50 of 13.8 Mb were assembled, and 228 contigs (99.13%) were anchored into 24 chromosomes. A total of 24,005 protein-coding genes were predicted, among which 23,862 (99.4%) predicted genes were annotated. Phylogenetic analysis showed that brown-marbled grouper and humpback grouper were clustered into one clade that separated approximately 11-23 million years ago. Collinearity analyses showed that there was no obvious duplication of large fragments between chromosomes in the brown-marbled grouper. Genomes of the humpback grouper and giant grouper showed a high collinearity with that of the brown-marbled grouper. A total of 305 expanded gene families were detected in the brown-marbled grouper genome, which is mainly involved in disease resistance. In addition, a genetic linkage map with 3061.88 cM was constructed. Based on the physical and genetic map, one growth-related quantitative trait loci was detected in 32,332,447 bp of chromosome 20, and meox1 and etv4 were considered candidate growth-related genes. This study provides pivotal genetic resources for further evolutionary analyses and artificial breeding of groupers.

Bioinformatics Approach to Mitigate Mislabeling in EU Seafood Market and Protect Consumer Health

Fisheries products are some of the most traded commodities world-wide and the potential for fraud is a serious concern. Fish fraud represents a threat to human health and poses serious concerns due to the consumption of toxins, highly allergenic species, contaminates or zoonotic parasites, which may be present in substituted fish. The substitution of more expensive fish by cheaper species, with similar morphological characteristics but different origins, reflects the need for greater transparency and traceability upon which which the security of the entire seafood value-chain depends. Even though EU regulations have made significant progress in consumer information by stringent labelling requirements, fraud is still widespread. Many molecular techniques such as DNA barcoding provide valuable support to enhance the Common Fisheries Policy (CFP) in the protection of consumer interests by unequivocally detecting any kind of fraud. This paper aims to highlight both the engagement of EU fishery policy and the opportunity offered by new biotechnology instruments to mitigate the growing fraud in the globalized fish market and to enforce the food security system to protect consumers' health. In this paper, after a presentation of EU rules on fish labeling and a general overview on the current state of the global fish market, we discuss the public health implications and the opportunities offered by several techniques based on genetics, reporting a case study to show the efficacy of the DNA barcoding methodology in assessing fish traceability and identification, comparing different species of the Epinephelus genus, Mottled Grouper (Mycteroperca rubra) and Wreckfish (Polyprion americanus), often improperly sold with the commercial name of "grouper".

Prognostic Value of Circadian Rhythm of Brain Temperature in Traumatic Brain Injury

Hypothermia has been used in postoperative management of traumatic brain injury (TBI); however, the rhythmic variation and prognostic value of brain temperature after TBI have never been studied. This study describes diurnal brain temperature patterns in comatose patients with TBI. Mesors of brain temperature, amplitude, and acrophase were estimated from recorded temperature measurements using cosinor analysis. The association of these patterns with clinical parameters, mortality, and functional outcomes in a 12-month follow-up was examined. According to the cosinor analysis, 59.3% of patients presented with circadian rhythms of brain temperature in the first 72 h postoperatively. The rhythm-adjusted mesor of brain temperature was 37.39 ± 1.21 °C, with a diminished mean amplitude of 0.28 (±0.25) °C; a shift of temperature acrophase was also observed. Multivariate logistic regression analysis revealed that initial Glasgow coma scale score, age, elevated blood glucose level, and circadian rhythm of brain temperature seemed to be predictive and prognostic factors of patients' functional outcomes. For the prediction of survival status, younger patients or those patients with mesor within the middle 50% of brain temperature were more likely to survive. The analysis of brain temperature rhythms in patients with moderate and severe TBI provided additional predictive information related to mortality and functional outcomes.

Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara

The red-spotted grouper, Epinephelus akaara, has been cultured widely in China, and in several countries of Southeast Asia, due to its important economic value. However, in recent years the outbreak of disease caused by red-spotted grouper nervous necrosis virus (RGNNV) has caused mass mortality in the stage of the grouper lifecycle from fry to juvenile, resulting in considerable economic loss in commercial aquaculture. However, the molecular mechanism underlying anti-RGNNV infection in red-spotted grouper has never been fully understood. To identify the anti-RGNNV related markers and candidate genes, we performed a genome-wide association study (GWAS) on a natural population of 100 individuals for a full-genome screen of the red-spotted grouper. In this research, 36,311 single, high quality nucleotide polymorphisms (SNPs) were developed. Two significantly associated SNPs and three suggestively associated SNPs were identified at the genome level. From these identified SNPs, five candidate genes were annotated: EPHA7, Osbpl2, GPC5, CDH4 and Pou3f1. These genes are involved in nervous system development, retinal formation, and lipid metabolism regulation. In combination with studies on the characteristics of NNV infection, it was speculated that in the fry stage of the grouper lifecycle, the immune system is not fully developed. Therefore, improved resistance to RGNNV may come through regulating nervous system development or lipid metabolism related pathways. In addition, the genotypes of SNPs associated with disease-resistant traits were analyzed. The markers and genes obtained in this study may facilitate a marker-assisted selection for red-spotted grouper aiming at disease resistance to RGNNV.

Combining Random Forests and a Signal Detection Method Leads to the Robust Detection of Genotype-Phenotype Associations

Genome wide association studies (GWAS) are a well established methodology to identify genomic variants and genes that are responsible for traits of interest in all branches of the life sciences. Despite the long time this methodology has had to mature the reliable detection of genotype-phenotype associations is still a challenge for many quantitative traits mainly because of the large number of genomic loci with weak individual effects on the trait under investigation. Thus, it can be hypothesized that many genomic variants that have a small, however real, effect remain unnoticed in many GWAS approaches. Here, we propose a two-step procedure to address this problem. In a first step, cubic splines are fitted to the test statistic values and genomic regions with spline-peaks that are higher than expected by chance are considered as quantitative trait loci (QTL). Then the SNPs in these QTLs are prioritized with respect to the strength of their association with the phenotype using a Random Forests approach. As a case study, we apply our procedure to real data sets and find trustworthy numbers of, partially novel, genomic variants and genes involved in various egg quality traits.

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.

Whole-genome sequencing of leopard coral grouper ( Plectropomus leopardus) and exploration of regulation mechanism of skin color and adaptive evolution

Leopard coral groupers belong to the Plectropomus genus of the Epinephelidae family and are important fish for coral reef ecosystems and the marine aquaculture industry. To promote future research of this species, a high-quality chromosome-level genome was assembled using PacBio sequencing and Hi-C technology. A 787.06 Mb genome was assembled, with 99.7% (784.57 Mb) of bases anchored to 24 chromosomes. The leopard coral grouper genome size was smaller than that of other groupers, which may be related to its ancient status among grouper species. A total of 22 317 protein-coding genes were predicted. This high-quality genome of the leopard coral grouper is the first genomic resource for Plectropomus and should provide a pivotal genetic foundation for further research. Phylogenetic analysis of the leopard coral grouper and 12 other fish species showed that this fish is closely related to the brown-marbled grouper. Expanded genes in the leopard coral grouper genome were mainly associated with immune response and movement ability, which may be related to the adaptive evolution of this species to its habitat. In addition, we also identified differentially expressed genes (DEGs) associated with carotenoid metabolism between red and brown-colored leopard coral groupers. These genes may play roles in skin color decision by regulating carotenoid content in these groupers.