Genome-Scale Association Study of Abnormal Scale Pattern in Yellow River Carp Identified Previously Known Causative Gene in European Mirror Carp

Genomic signatures associated with recurrent scale loss in cyprinid fish

Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.

Asymmetric and parallel subgenome selection co-shape common carp domestication

BACKGROUND

The common carp (Cyprinus carpio) might best represent the domesticated allopolyploid animals. Although subgenome divergence which is well-known to be a key to allopolyploid domestication has been comprehensively characterized in common carps, the link between genetic architecture underlying agronomic traits and subgenome divergence is unknown in the selective breeding of common carps globally.

RESULTS

We utilized a comprehensive SNP dataset in 13 representative common carp strains worldwide to detect genome-wide genetic variations associated with scale reduction, vibrant skin color, and high growth rate in common carp domestication. We identified numerous novel candidate genes underlie the three agronomically most desirable traits in domesticated common carps, providing potential molecular targets for future genetic improvement in the selective breeding of common carps. We found that independently selective breeding of the same agronomic trait (e.g., fast growing) in common carp domestication could result from completely different genetic variations, indicating the potential advantage of allopolyploid in domestication. We observed that candidate genes associated with scale reduction, vibrant skin color, and/or high growth rate are repeatedly enriched in the immune system, suggesting that domestication of common carps was often accompanied by the disease resistance improvement.

CONCLUSIONS

In common carp domestication, asymmetric subgenome selection is prevalent, while parallel subgenome selection occurs in selective breeding of common carps. This observation is not due to asymmetric gene retention/loss between subgenomes but might be better explained by reduced pleiotropy through transposable element-mediated expression divergence between ohnologs. Our results demonstrate that domestication benefits from polyploidy not only in plants but also in animals.

Interspecific differences and ecological correlations between scale number and skin structure in freshwater fishes

Fish skin is mainly composed of the epidermis, dermis, and its derivative scales. There is a wide diversity in scale number in fishes, but the diversity of skin structure lacks systematic histological comparison. This research aimed to improve our understanding of the functional relationship between the scale number and the skin structure in freshwater fishes and to determine which ecological factors affect the scale number and skin structure. First, we presented a method to quantify skin structure in fish and histologically quantified the skin structure of 54 freshwater fishes. Second, we collected the scale number and habitat information of 509 Cyprinidae fishes in China and explored which ecological factors were related to their scale number. Third, common carp and scaleless carp were used as models to study the effects of scale loss on swimming. We found a strong negative correlation between scale thickness and scale number. The main factor affecting the skin structure of fishes was the species' water column position, and the skin of benthic fishes was the most well-developed (thicker skin layers (dermis, epidermis) or more/larger goblet cells and club cells). The scale number was related to two factors, namely, temperature and water column position, and cold, benthic and pelagic adaptation may have contributed to increased scale numbers. Only in benthic fishes, the more well-developed their skin, the more scales. In common carp, scale loss did not affect its swimming performance. In summary, we suggest that there is a rich diversity of skin structure in freshwater fishes, and the scales of fish with well-developed skin tend to degenerate (greater number/smaller size/thinner, or even disappear), but the skin of fish with degenerated scales is not necessarily well developed.

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.

Genome-Wide Association Study of Body Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea)

Large yellow croaker (Larimichthys crocea) is one of the most important cultured marine fish on the southeast coast of China. Its body shape is important for the aquaculture industry since it affects the behavior such as swimming, ingesting, and evading, as well as customer preference. Due to the greater consumer demand of small head, slender body large yellow croaker, selecting and breeding of slender individuals with the assistance of genetic markers will benefit the industry quickly. In this study, several traits were employed to represent body shape, including body depth/body length (BD/BL), body thickness/body length (BT/BL), caudal peduncle depth/caudal peduncle length (CPDLR), tail length/body length (TL/BL), and body area/head area (BA/HA). Genome-wide association study was conducted with a panmictic population of 280 individuals to identify SNP and genes potentially associated with body shape. A set of 20 SNPs on 12 chromosomes were identified to be significantly associated with body shape-related traits. Besides, 5 SNPs were identified to be suggestive associated with CPDLR and BT/BL. Surrounding these SNPs, we found some body shape-related candidate genes, including fabp1, acrv1, bcor, mstn, bambi, and neo1, which involved in lipid metabolism, TGF-β signaling, and BMP pathway and other important regulatory pathways. These results will be useful for the understanding of the genetic basis of body shape formation and helpful for body shape controlling of large yellow croaker by using marker-assisted selection.

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.

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

Brown-marbled grouper, Epinephelus fuscoguttatus, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which, bmp2k, wasf1, and acyp2 involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of bmp2k was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.

Genome-Wide Association Study of Growth and Body-Shape-Related Traits in Large Yellow Croaker (Larimichthys crocea) Using ddRAD Sequencing

Large yellow croaker (Larimichthys crocea) is an economically important marine fish species of China. Due to overfishing and marine pollution, the wild stocks of this croaker have collapsed in the past decades. Meanwhile, the cultured croaker is facing the difficulties of reduced genetic diversity and low growth rate. To explore the molecular markers related to the growth traits of croaker and providing the related SNPs for the marker-assisted selection, we used double-digest restriction-site associated DNA (ddRAD) sequencing to dissect the genetic bases of growth traits in a cultured population and identify the SNPs that associated with important growth traits by GWAS. A total of 220 individuals were genotyped by ddRAD sequencing. After quality control, 27,227 SNPs were identified in 220 samples and used for GWAS analysis. We identified 13 genome-wide significant associated SNPs of growth traits on 8 chromosomes, and the beta P of these SNPs ranged from 0.01 to 0.86. Through the definition of candidate regions and gene annotation, candidate genes related to growth were identified, including important regulators such as fgf18, fgf1, nr3c1, cyp8b1, fabp2, cyp2r1, ppara, and ccm2l. We also identified SNPs and candidate genes that significantly associated with body shape, including bmp7, col1a1, col11a2, and col18a1, which are also economically important traits for large yellow croaker aquaculture. The results provided insights into the genetic basis of growth and body shape in large yellow croaker population and would provide reliable genetic markers for molecular marker-assisted selection in the future. Meanwhile, the result established a basis for our subsequent fine mapping and related gene study.

First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus)

The giant grouper, Epinephelus lanceolatus, is the largest coral reef-dwelling bony fish species. However, despite extremely fast growth performance and the considerable economic importance in this species, its genetic regulation of growth remains unknown. Here, we performed the first genome-wide association study (GWAS) for five growth traits in 289 giant groupers using 42,323 single nucleotide polymorphisms (SNPs) obtained by genotyping-by-sequencing (GBS). We identified a total of 36 growth-related SNPs, of which 11 SNPs reached a genome-wide significance level. The phenotypic variance explained by these SNPs varied from 7.09% for body height to 18.42% for body length. Moreover, 22 quantitative trait loci (QTLs) for growth traits, including nine significant QTLs and 13 suggestive QTLs, were found on multiple chromosomes. Interestingly, the QTL (LG17: 6934451) was shared between body weight and body height, while two significant QTLs (LG7: 22596399 and LG15: 11877836) for body length were consistent with the associated regions of total length at the genome-wide suggestive level. Eight potential candidate genes close to the associated SNPs were selected for expression analysis, of which four genes (phosphatidylinositol transfer protein cytoplasmic 1, protein tyrosine phosphatase receptor type E, alpha/beta hydrolase domain-containing protein 17C, and vascular endothelial growth factor A-A) were differentially expressed and involved in metabolism, development, response stress, etc. This study improves our understanding of the complex genetic architecture of growth in the giant grouper. The results contribute to the selective breeding of grouper species and the conservation of coral reef fishes.

Constructing a High-Density Genetic Linkage Map for Large Yellow Croaker (Larimichthys crocea) and Mapping Resistance Trait Against Ciliate Parasite Cryptocaryon irritans

The large yellow croaker (Larimichthys crocea) is the most economically important marine cage-farming fish in China in the past decade. However, the sustainable development of large yellow croaker aquaculture has been severely hampered by several diseases, of which, the white spot disease caused by ciliate protozoan parasite Cryptocaryon irritans ranks the most damaging disease in large yellow croaker cage farms. To better understand the genetic basis of parasite infection and disease resistance to C. irritans, it is vital to map the traits and localize the underlying candidate genes in L. crocea genome. Here, we constructed a high-density genetic linkage map using double-digest restriction-site associated DNA (ddRAD)-based high-throughput SNP genotyping data of a F1 mapping family, which had been challenged with C. irritans for resistant trait measure. A total of 5261 SNPs was grouped and oriented into 24 linkage groups (LGs), representing 24 chromosomes of L. crocea. The total genetic map length was 1885.67 cM with an average inter-locus distance of 0.36 cM. Quantitative trait loci (QTL) mapping identified seven significant QTLs in four LGs linked to C. irritans disease resistance. Candidate genes underlying disease resistance were identified from the reference genome, including ifnar1, ifngr2, ikbke, and CD112. Comparative genomic analysis between large yellow croaker and the four closely related species revealed high evolutionary conservation of chromosomes, though inter-chromosomal rearrangements do exist. Especially, the croaker genome structure was closer to the medaka genome than stickleback, indicating that the croaker genome might retain the teleost ancestral genome structure. The high-density genetic linkage map provides an important tool and resource for fine mapping, comparative genome analysis, and molecular selective breeding of large yellow croaker.

Association and Functional Analyses Revealed That PPP1R3B Plays an Important Role in the Regulation of Glycogen Content in the Pacific Oyster Crassostrea gigas

The Pacific oyster (Crassostrea gigas) is one of the most important aquaculture species worldwide. Glycogen contributes greatly to the special taste and creamy white color of oysters. Previous genome-wide association studies (GWAS) identified several single nucleotide polymorphism (SNP) sites that were strongly related to glycogen content. Genes within 100 kb upstream and downstream of the associated SNPs were screened. One gene annotated as protein phosphatase 1 regulatory subunit 3B (PPP1R3B), which can promote glycogen synthesis together with protein phosphatase 1 catalytic subunit (PPP1C) in mammals, was selected as a candidate gene in this study. First, full-length CgPPP1R3B was cloned and its function was characterized. The gene expression profiles of CgPPP1R3B in different tissues and seasons showed a close relationship to glycogen content. RNA interference (RNAi) experiments of this gene in vivo showed that decreased CgPPP1R3B levels resulted in lower glycogen contents in the experimental group than in the control group. Co-immunoprecipitation (Co-IP) and yeast two-hybrid (Y2H) assays indicated that CgPPP1R3B can interact with CgPPP1C, glycogen synthase (CgGS) and glycogen phosphorylase (CgGP), thus participating in glycogen metabolism. Co-sedimentation analysis in vitro demonstrated that the CgPPP1R3B protein can bind to glycogen molecules directly, and these results indicated the conserved function of the CgPPP1R3B protein compared to that of mammals. In addition, thirteen SNPs were precisely mapped in this gene. Ten of the thirteen SNPs were confirmed to be significantly (p < 0.05) related to glycogen content in an independent wild population (n = 288). The CgPPP1R3B levels in oysters with high glycogen content were significantly higher than those of oysters with low glycogen content, and gene expression levels were significantly associated with various genotypes of four associated SNPs (p < 0.05). The data indicated that the associated SNPs may control glycogen content by regulating CgPPP1R3B expression. These results suggest that CgPPP1R3B is an important gene for glycogen metabolic regulation and that the associated SNPs of this gene are potential markers for oyster molecular breeding for increased glycogen content.