Genome-Wide Association Analysis Reveals the Genetic Architecture of Parasite (Cryptocaryon irritans) Resistance in Large Yellow Croaker (Larimichthys crocea)

Machine vision-assisted genomic prediction and genome-wide association of spleen-related traits in large yellow croaker infected with visceral white-nodules disease

High-resolution and high-throughput genotype-to-phenotype studies in fish are rapidly advancing, driven by innovative technologies that aim to address the challenges of modern breeding models. In recent years, machine vision and deep learning techniques, particularly convolutional neural networks (CNNs), have achieved significant success in image recognition and segmentation. Moreover, qualitative and quantitative analysis of disease resistance has always been a crucial field of research in genetics. This motivation has led us to investigate the potential of large yellow croaker visceral white-nodules disease (VWND) in encoding information on disease resistance for the task of accession classification. In this study, we proposed an image segmentation framework for the feature extraction of the spleen after VWND infection based on machine vision. We utilized deep CNNs and threshold segmentation for automatic feature learning and object segmentation. This approach eliminates subjectivity and enhances work efficiency compared to using hand-crafted features. Additionally, we employed spleen-related traits to conduct genome-wide association analysis (GWAS), which led to the identification of 24 significant SNPs and 10 major quantitative trait loci. The results of function enrichment analysis on candidate genes also indicated potential relationships with immune regulation mechanisms. Furthermore, we explored the use of genomic selection (GS) technology for phenotype prediction of extreme individuals, which further supports the predictability of spleen-related phenotypes for VWND resistance in large yellow croakers. Our findings demonstrate that artificial intelligence (AI)-based phenotyping approaches can deliver state-of-the-art performance for genetics research. We hope this work will provide a paradigm for applying deep learning and machine vision to phenotyping in aquaculture species.

First insight of the genome-wide association study and genomic prediction into enteritis disease (Vibrio harveyi) resistance trait in the lined seahorse (Hippocampus erectus)

Enteritis caused by Vibrio is a highly die-off disease that severely impeded substantial production in seahorse aquaculture. In the present study, challenged with LD50 of concentration of Vibrio harveyi, a total of 161 of susceptible and 166 of resistant individuals were allocated into binary survival phenotypes, thus, to firstly investigate the genetic architecture by genome-wide association study (GWAS) analysis, as well as to evaluate the feasibility of genomic selection (GS) in enteritis disease resistance trait of the lined seahorse Hippocampus erectus. Results indicated that the heritability for resistance to Vibrio harveyi was estimated to be 0.10. And a set of 10 significant/suggestive SNPs in a multiple chromosomes localization were identified, explaining 7.76% to 13.28% of genetic variance. Associated 82 of candidate genes were clustered into signal transduction, cell proliferation, response of external stress, bacteria defence, and anti-inflammatory processes. Moreover, the potential performance of genomic selection (GS) in application in selective breeding for enteritis disease resistance seahorses was assessed by genomic prediction (GP). In general, the predictive accuracy of the genomic estimated breeding value (GEBV) of BayesC exceeded the rrBLUP, BayesA, RKHS, and SVM models while with no significant difference. And the GWAS-informative SNPs was significantly superior in efficience than random selected markers by comparison of predictive performance on different selection strategies of SNPs. Overall, the genetic basis of enteritis disease resistance trait in the lined seahorse is a polygenic genetic architecture. SNPs associated with the important genes of cathepsin L1-like previously reported with respect to disease resistance are consider as potential molecular markers of genetic breeding. Furthermore, GS approach is an appropriate, effective, and less-cost application in breeding enteritis disease-resistant seahorses.

Decoding the fish genome opens a new era in important trait research and molecular breeding in China

Aquaculture represents the fastest-growing global food production sector, as it has become an essential component of the global food supply. China has the world's largest aquaculture industry in terms of production volume. However, the sustainable development of fish culture is hindered by several concerns, including germplasm degradation and disease outbreaks. The practice of genomic breeding, which relies heavily on genome information and genotypephenotype relationships, has significant potential for increasing the efficiency of aquaculture production. In 2014, the completion of the genome sequencing and annotation of the Chinese tongue sole signified the beginning of the fish genomics era in China. Since then, domestic researchers have made dramatic progress in functional genomic studies. To date, the genomes of more than 60 species of fish in China have been assembled and annotated. Based on these reference genomes, evolutionary, comparative, and functional genomic studies have revolutionized our understanding of a wide range of biologically and economically important traits of fishes, including growth and development, sex determination, disease resistance, metamorphosis, and pigmentation. Furthermore, genomic tools and breeding techniques such as SNP arrays, genomic selection, and genome editing have greatly accelerated genetic improvement through the incorporation of functional genomic information into breeding activities. This review aims to summarize the current status, advances, and perspectives of the genome resources, genomic study of important traits, and genomic breeding techniques of fish in China. The review will provide aquaculture researchers, fish breeders, and farmers with updated information concerning fish genomic research and breeding technology. The summary will help to promote the genetic improvement of production traits and thus will support the sustainable development of fish aquaculture.

Genome-Wide Association Study of Resistance to Largemouth Bass Ranavirus (LMBV) in Micropterus salmoides

The disease caused by Largemouth bass ranavirus (LMBV) is one of the most severe viral diseases in largemouth bass (Micropterus salmoides). It is crucial to evaluate the genetic resistance of largemouth bass to LMBV and develop markers for disease-resistance breeding. In this study, 100 individuals (45 resistant and 55 susceptible) were sequenced and evaluated for resistance to LMBV and a total of 2,579,770 variant sites (SNPs-single-nucleotide polymorphisms (SNPs) and insertions-deletions (InDels)) were identified. A total of 2348 SNPs-InDels and 1018 putative candidate genes associated with LMBV resistance were identified by genome-wide association analyses (GWAS). Furthermore, GO and KEGG analyses revealed that the 10 candidate genes (MHC II, p38 MAPK, AMPK, SGK1, FOXO3, FOXO6, S1PR1, IL7R, RBL2, and GADD45) were related to intestinal immune network for IgA production pathway and FoxO signaling pathway. The acquisition of candidate genes related to resistance will help to explore the molecular mechanism of resistance to LMBV in largemouth bass. The potential polymorphic markers identified in this study are important molecular markers for disease resistance breeding in largemouth bass.

Effects of Gene Alternative Splicing Events on Resistance to Cryptocaryonosis of Large Yellow Croaker (Larimichthys crocea)

Large yellow croaker (L. crocea) is a productive species in marine aquaculture with great economic value in China. However, the sustainable development of large yellow croaker is hampered by various diseases including cryptocaryonosis caused by Cryptocaryon irritans. The genetic regulation processes for cryptocaryonosis in large yellow croaker are still unclear. In this present study, we analyzed differential alternative splicing events between a C. irritans resistance strain (RS) and a commercial strain (CS). We identified 678 differential alternative splicing (DAS) events from 453 genes in RS and 719 DAS events from 500 genes in CS. A set of genes that are specifically alternatively spliced in RS was identified including mfap5, emp1, and trim33. Further pathway analysis revealed that the specifically alternative spliced genes in RS were involved in innate immune responses through the PRR pathway and the Toll and Imd pathway, suggesting their important roles in the genetic regulation processes for cryptocaryonosis in large yellow croaker. This study would be helpful for the studies of the pathogenesis of cryptocaryonosis and dissection of C. irritans resistance for L. crocea.

Genomic Selection of Large Yellow Croaker (Larimichthys crocea) with a High Plant Protein Diet Enhances the Growth Performance of Offspring

Fishmeal is over-represented in the diets of large yellow croaker (Larimichthys crocea), and this farming mode, which relies heavily on fishmeal, is highly susceptible to the price of fishmeal and is unsustainable. Therefore, more and more studies on the large yellow croaker tend to replace fishmeal with land-based animal or plant proteins, but few studies have considered it from the genomic selection. In this study, we evaluated the survival rate (SR), final body weight (FBW), body weight gain (BWG), weight gain rate (WGR), and specific growth rate (SGR) of the large yellow croaker GS7 strain, which was obtained through genomic selection for tolerance to plant proteins and analyzed the differences in plant protein utilization between the GS7 strain and unselected commercial large yellow croaker (control group). The results of separate feeding for 60 days showed that although there was no significant difference in SR between the control and GS7 strains (P > 0.05), the BWG, WGR, and SGR of the control were significantly lower (P < 0.05) than those of the GS7 group. Results of mixed feeding after PIT marking showed that compared to the control fish, the GS7 strain had significantly higher BWG, WGR, and SGR (P < 0.0001). To make the experimental results more precise, we compared fishes with equivalent initial body weight (IBW) in the GS7 strain and the control group. The final fish body weight (FBW) of Ctrl-2 (IBW 300-399 g) and Ctrl-4 (IBW 500-599 g) was significantly lower than those of the corresponding GS7-2 and GS7-4 (P < 0.05), while the FBW of Ctrl-1 (IBW 200-299 g) and Ctrl-3 (IBW 400-499 g) was much significantly lower than the corresponding GS7-1 and GS7-3 (P < 0.01). The BWG, WGR, and SGR of Ctrl-1 and Ctrl-4 were more significantly lower than those of the corresponding GS7-1 and GS7-4 (P < 0.01), while the BWG, WGR, and SGR of Ctrl-2 and Ctrl-3 were more significantly different from the corresponding GS7-2 and GS7-3 (P < 0.0001). Our results seem to point toward the same conclusion that the GS7 strain is better adapted to high plant protein diets than the unselected commercial large yellow croaker. These results will provide a reference for the low-fishmeal culture industry of large yellow croakers and the selection and breeding of strains tolerant to a high percentage of plant proteins in other marine fishes.

Detection and prediction of pathogenic microorganisms in aquaculture (Zhejiang Province, China)

The detection and prediction of pathogenic microorganisms play a crucial role in the sustainable development of the aquaculture industry. Currently, researchers mainly focus on the prediction of water quality parameters such as dissolved oxygen for early warning. To provide early warning directly from the pathogenic source, this study proposes an innovative approach for the detection and prediction of pathogenic microorganisms based on yellow croaker aquaculture. Specifically, a method based on quantitative polymerase chain reaction (qPCR) is designed to detect the Cryptocaryon irritans (Cri) pathogenic microorganisms. Furthermore, we design a predictive combination model for small samples and high noise data to achieve early warning. After performing wavelet analysis to denoise the data, two data augmentation strategies are used to expand the dataset and then combined with the BP neural network (BPNN) to build the fusion prediction model. To ensure the stability of the detection method, we conduct repeatability and sensitivity tests on the designed qPCR detection technique. To verify the validity of the model, we compare the combined BPNN to long short-term memory (LSTM). The experimental results show that the qPCR method provides accurate quantitative measurement of Cri pathogenic microorganisms, and the combined model achieves a good level. The prediction model demonstrates higher accuracy in predicting Cri pathogenic microorganisms compared to the LSTM method, with evaluation indicators including mean absolute error (MAE), recall rate, and accuracy rate. Especially, the accuracy of early warning is increased by 54.02%.

Genome-wide association study (GWAS) analysis of black color trait in the leopard coral grouper (Plectropomus leopardus) using whole genome resequencing

The leopard coral grouper (Plectropomus leopardus) is a coral reef fish species that exhibits rapid and diverse color variation. However, the presence of melanoma and the high proportion of individuals displaying black color in artificial breeding have led to reduced economic and ornamental value. To pinpoint single nucleotide polymorphisms (SNPs) and potential genes linked to the black pigmentation characteristic in this particular species, This study gathered a cohort of 360 specimens from diverse origins and conducted a comprehensive genome-wide association analysis (GWAS) employing whole-genome resequencing. As a result, 57 SNPs related to the black skin trait were identified, and a grand total of 158 genes were annotated within 50 kb of these SNPs. Subsequently, GWAS was applied to three populations (LED, QHH, and QHL), and the corresponding results were compared with the analysis results of the total population. The results of the four GWAS models showed significant enrichment in Rap1 signaling pathway, melanin biosynthesis, metabolic pathways, tyrosine metabolism, cAMP signaling pathway, AMPK signaling pathway, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, HIF-1 signaling pathway, Ras signaling pathway, MAPK signaling pathway, etc. (p < 0.05), which were mainly associated with eleven genes (POL4, MET, E2F2, COMT, ZBED1, TYRP2, FOXP2, THIKA, LORF2, MYH16 and SOX2). Significant differences (p < 0.05) were observed in the expression of all 11 genes in the dorsal skin tissue, in 10 genes except COMT in the ventral skin tissue, and in all 11 genes in the caudal fin tissue. These findings imply that the control of body color in the P. leopardus is the result of the joint action of multiple genes and signaling pathways. These findings will contribute to a more profound comprehension of the genetic attributes that underlie the development of black skin in the vibrant P. leopardus, thus furnishing a theoretical foundation for genetic enhancement.

First Genomic Prediction of Single-Step Models in Large Yellow Croaker

Genome selection is mainly used in disease-resistant traits of aquatic species; however, its implementation is hindered by a high cost of genotype and phenotype data collection. Single-step genomic best linear unbiased prediction (SSGBLUP) can integrate phenotypes, genetic markers, and pedigree records into simultaneous prediction without increasing genotyping costs. The objective of this study is to investigate the performance of SSGBLUP in large yellow croaker and to evaluate the effects of the number of phenotypic records and genotyping per family on the predictive ability of SSGBLUP. A large yellow croaker population consists of 6898 individuals from 14 families with survival time resistant against Cryptocaryon irritans (C. irritans), body weight (BW), and body length (BL) traits were collected, of which 669 individuals were genotyped. Results showed that the mean predictive ability of all traits in the individuals randomly sampling for SSGBLUP, GBLUP, and BLUP was 0.738, 0.738, and 0.736, respectively. Moreover, the predictive ability of SSGBLUP and BLUP models did not increase with the extra phenotypic records per family, in which the predictive ability of SSGBLUP and BLUP in survival time was 0.853 and 0.851 for only genotyped data (N = 0) used, and 0.852, 0.845 for all phenotypic records (N = 600) used, respectively. However, with the increase in the genotype number of training set, the prediction ability of SSGBLUP and GBLUP model was increased and the highest predictive ability was gained when the genotype number per family was 40 or 45. In addition, the prediction ability of SSGBLUP model was higher than that of GBLUP. Our study showed that the SSGBLUP model still has great potential and advantages in genomic breeding of large yellow croakers. It is recommended that each family provide 100 phenotypic individuals, of which 40 individuals with genotyping data for SSGBLUP model prediction and family resistance evaluation.

Integrated mRNA and miRNA expression analyses for Cryptocaryon irritans resistance in large yellow croaker (Larimichthys crocea)

Large yellow croaker (Larimichthys crocea) is one of the most important mariculture fish in China. However, cryptocaryonosis caused by Cryptocryon irritans infection has brought huge economic losses and threatened the healthy and sustainable development of L. crocea industry. Recently, a new C. irritans resistance strain of L. crocea (RS) has been bred using genomic selection technology in our laboratory work. However, the molecular mechanisms for C. irritans resistance of RS have not been fully understood. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that are post-transcriptional regulators, and they play vital roles in immune process of bony fish. Identification of anti-C.irritans relevant miRNA signatures could, therefore, be of tremendous translational value. In the present study, integrated mRNA and miRNA expression analysis was used to explore C. irritans resistance mechanisms of the L. crocea. RS as well as a control strain (CS) of L. crocea, were artificially infected with C. irritans for 100 h, and their gill was collected at 0 h (pre-infection), 24 h (initial infection), and 72 h (peak infection) time points. The total RNA from gill tissues was extracted and used for transcriptome sequencing and small RNA sequencing. After sequencing, 23,172 known mRNAs and 289 known miRNAs were identified. The differential expression was analyzed in these mRNAs and mRNAs and the interactions of miRNA-mRNA pairs were constructed. KEGG pathway enrichment analyses showed that these putative target mRNAs of differentially expressed miRNAs (DEMs) were enriched in different immune-related pathways after C. irritans infection in RS and CS. Among them, necroptosis was the immune-related pathway that was only significantly enriched at two infection stages of RS group (RS-24 h/RS-0h and RS-72 h/RS-0h). Further investigation indicates that necroptosis may be activated by DEMs such as miR-133a-3p, miR-142a-3p and miR-135c, this promotes inflammation responses and pathogen elimination. These DEMs were selected as miRNAs that could potentially regulate the C. irritans resistance of L. crocea. Though these inferences need to be further verified, these findings will be helpful for the research of the molecular mechanism of C. irritans resistance of L. crocea and miRNA-assisted molecular breeding of aquatic animals.

Integrative analysis of GWAS and transcriptome reveals p53 signaling pathway mediates resistance to visceral white-nodules disease in large yellow croaker

Visceral white-nodules disease (VWND), caused by Pseudomonas plecoglossicida, is one of the primary causes of morbidity and mortality in large yellow croaker aquaculture. Host disease resistance is a heritable trait that involves complex regulatory processes. However, the regulatory mechanism of bacterial resistance in large yellow croaker is still unclear. This study attempted to systematically evaluate the major genetic loci and transcriptional regulatory mechanisms associated with the resistance to VWND in large yellow croaker by crossover method studies. A large population of large yellow croaker was challenged with P. plecoglossicida, with survival time recorded and samples were taken for genotyping. Meanwhile, spleen samples that were used for RNA-seq to compare their transcriptomic profiles before and after infection were taken from resistant populations (RS) and susceptible control populations (CS) bred using the genomic selection (GS) technique. Genome-wide association analyses using 46 K imputed SNP genotypes highlighted that resistance is a polygenic trait. The integrative analysis results show the co-localization of the cd82a gene between disease resistance-related genetic loci and comparative transcriptional analysis. And functional enrichment analysis showed differential enrichment of the p53 signaling pathway in RS and CS groups, suggesting that there may be cd82a-mediated p53 signaling pathway activation for VWND resistance. This large-scale study provides further evidence for the heritability and transcriptional regulatory mechanisms of host inheritance of VWND resistance.

Genome-Wide Association and Expression Analysis Revealed the Candidate Variants and Molecular Underpinnings of Cold-Stress Response in Large Yellow Croaker

Large yellow croaker (Larimichthys crocea) is one of the most economically important fish in China. Recently, global climate change has caused more and more intense and extreme low temperature weathers, resulting in huge losses to the large yellow croaker industry. Therefore, it is essential to understand the mechanisms of low-temperature tolerance in large yellow croaker. Here, we conducted an integrative analysis of genome-wide association study (GWAS) and transcriptome analysis to identify candidate variants and reveal the molecular underpinning of cold-stress response in large yellow croaker. A total of 8 significant single nucleotide polymorphisms (SNPs) loci on 6 chromosomes were identified in the GWAS analysis, and 5764 (gill) and 3588 (liver) differentially expressed genes (DEGs) were detected in cold-stressed large yellow croaker, respectively. Further comparative and functional analysis of the candidate genes and DEGs highlighted the importance of pathways/genes related to immune response, cellular stress response, lipid transport, and metabolism in the cold-stress response of large yellow croaker. Our results provide insights into the cold tolerance of large yellow croaker and contribute to genomic-based selection for low-temperature-resistant large yellow croaker.

pH Regulates the Formation and Hatching of Cryptocaryon irritans Tomonts, Which Affects Cryptocaryoniasis Occurrence in Larimichthys crocea Aquaculture

Cryptocaryon irritans are the main pathogens of white spot disease in marine teleost. However, the occurrence of cryptocaryoniasis is influenced by several abiotic factors including the pH. To explore the effect of pH on the life cycle of C. irritans (encystment, cleavage, and hatchability), protomonts and tomonts of C. irritans were incubated in seawater of 10 different pH levels (2-11). pH 8 was used as the control. The change in morphology and infectivity of theronts that hatched from tomonts against Larimichthys crocea were then recorded. We found that pH 6-9 had no significant effect on the encystment, cleavage, and hatching of the parasites. However, pH beyond this limit decreased the cleavage and hatching of the tomonts. Furthermore, extreme pH decreased the number of theronts hatched by each tomont and the pathogenicity of the theronts, but increased the aspect ratio of the theronts. Infectivity experiments further revealed that extreme pH significantly decreased the infectivity of C. irritans against L. crocea. In conclusion, the C. irritans can survive in pH of 5 to 10, but pH 6-9 is the optimal range for the reproduction and infectivity of C. irritans. However, extreme pH negatively affects these aspects. IMPORTANCECryptocaryon irritans is a ciliate parasite that causes "white spot disease" in marine teleosts. The disease outbreak is influenced by hosts and a range of abiotic factors, such as temperature, salinity, and pH. Studies have shown that change in pH of seawater affects the structure (diversity and abundance of marine organisms) of marine ecosystem. However, how pH affects the life cycle and survival of C. irritans, and how future ocean acidification will affect the occurrence of cryptocaryoniasis, are not well understood. In this study, we explored the effect of pH on the formation and hatching of C. irritans tomonts. The findings of this study provide the foundation of the environmental adaptation of C. irritans, the occurrence of cryptocaryoniasis, and better management of marine fish culture.