Carp Genome Research Articles

Characterization of 36 insert/deletion mutations by STR genotyping method in grass carp, Ctenopharyngodon idella

Grass carp is one of the most important freshwater aquaculture fish in China. Though a few molecular markers had been reported, it was not enough for grass carp germplasm improvement and protection. In order to verify the effectiveness and practicability of insert/deletion mutations reported in grass carp genome, 85 insert/deletion mutations were randomly selected and analyzed. After simple sequence analysis and attempting primer design, 49 markers were removed due to being simple sequence repeats or unable to design primer for them. Finally, 36 insert/deletion mutations were successfully characterized by STR genotyping method in 32 wild grass carp (collected from Pearl River). The mean effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) were 1.4976, 0.3190, 0.2970 and 0.2349, respectively. Among all the 36 insert/deletion mutations, three deviated significantly from Hardy–Weinberg equilibrium (P < 0.05). In addition, three pairs of loci (ID-13F with ID-24H, ID-20F with ID-21H and ID-39F with ID-64H) had significant linkage disequilibrium (P < 0.05). Those insert/deletion mutations may lay the foundation for germplasm improvement and protection in grass carp.

The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp.

With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS)of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.112.216.104.

Genome wide identification of taste receptor genes in common carp (Cyprinus carpio) and phylogenetic analysis in teleost

Taste receptors (TRs) are seven trans-membrane G protein-coupled receptors as well as the interface between internal and external milieus, which playing pivotal roles in nutrient identification and acquisition. To better understand the scope and function of tr gene family in common carp, one of the most economic and important breeding fish species, which has undergone an additional round of whole genome duplication (WGD), we characterized 13 tr gene homologues including eight type I and five type II taste receptor genes from common carp genome, which were more than any other teleosts. Phylogenetic and syntenic analysis revealed the evolution dynamics of tr gene family, which was highly conserved, though gene duplication and gene loss do exist recently. Furthermore, the motif and dN/dS analyses indicated that these receptors were under different negative selection pressure. Additionally, the gene expression divergences were observed in 12 health tissues of common carp, with a relatively high level in barbel and head kidney, demonstrating tissue-specific expression of tr genes in the tetraploidized genome. The overarching goals of this study were to identify the abundance of tr genes in common carp, compare the gene divergence among species with varied feeding habits and provide genomic resources for future studies on teleost taste sensation.

The complete mitochondrial genome of Jinbian carp Cyprinus carpio (Cypriniformes: Cyprinidae)

Jinbian carp (Cyprinus carpio) is an endemic species in China. The complete mitochondrial genome of Jinbian carp is determined to be 16,581 bp in length and includes 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Its structural organization and gene order are equivalent to other common carp strains. The phylogenetic analyses will contribute to further insights of the taxonomy and phylogeny in Cyprinidae family.

Quantitative trait loci mapping for feed conversion efficiency in crucian carp (Carassius auratus)

QTL is a chromosomal region including single gene or gene clusters that determine a quantitative trait. While feed efficiency is highly important in aquaculture fish, little genetic and genomic progresses have been made for this trait. In this study, we constructed a high-resolution genetic linkage map in a full-sib F1 family of crucian carp (Carassius auratus) consisting of 113 progenies with 8,460 SNP markers assigning onto 50 linkage groups (LGs). This genetic map spanned 4,047.824 cM (0.478 cM/marker) and covered 98.76% of the crucian carp genome. 35 chromosome-wide QTL affecting feed conversion efficiency (FCE, 8 QTL), relative growth rate (RGR, 9 QTL), average daily gain (ADG, 13 QTL) and average daily feed intake (ADFI, 5 QTL) were detected on 14 LGs, explaining 14.0–20.9% of the phenotypic variations. In LGs of LG16, LG25, LG36 and LG49, several QTL affecting different traits clustered together at the identical or close regions of the same linkage group. Seven candidate genes, whose biological functions may involve in the energy metabolism, digestion, biosynthesis and signal transduction, were identified from these QTL intervals by comparative genomics analysis. These results provide a basis for elucidating genetic mechanism of feed efficiency and potential marker-assisted selection in crucian carp.

Comparative expression analyses of bone morphogenetic protein 4 (BMP4) expressions in muscles of tilapia and common carp indicate that BMP4 plays a role in the intermuscular bone distribution in a dose-dependent manner

Intermuscular bones in fish negatively influence both meet processing and attractiveness to consumers. Tilapia (Oreochromis niloticus) and common carp (Cyprinus carpio) are both major farmed fish species globally, but whereas the former does not possess intermuscular bones, the latter does. Therefore, these two species might present a good model to study the genetic control of distribution of intermuscular bones in fish. Bone morphogenetic protein 4 (BMP4) gene is associated with tissue ossification and bone regeneration in mammals, but in fish its role in ossification remains understudied. To study the relationship between BMP4 and bone distribution in fish, we determined the expression of BMP4 in muscle tissues of common carp and tilapia on transcriptional and translational levels. As the gene has been merely predicted in silico from the genome of common carp, we have cloned and characterized it. The gene (GenBank: HQ446455) contains one intron and two exons, which encode a 400-amino acid protein with high homology to other known BMP4 protein sequences. Phylogenetic analysis showed that common carp clustered within the Cypriniformes clade (zebrafish was the closest ortholog) and tilapia within the Percomorpha clade. Using microCT scanning, we confirmed that intermuscular bones could be observed only in common carp (none in tilapia), but only in dorsal and caudal muscles (none in the ventral muscle). Expression levels of BMP4 in the muscles of common carp were in agreement with this observation both on transcriptional (qPCR) and translational (immunohistochemistry) level: higher in dorsal and caudal muscles, and lower in the ventral muscle. In tilapia, expression of BMP4 gene was also detectable in all three muscles, but expression levels in all three muscles were comparable to the one observed in the ventral muscle of carp, i.e., very low. Therefore, among the six studied muscles, the expression of BMP4 was high only in the two that possess intermuscular bones: dorsal and caudal muscles of common carp. The results of this study suggest that BMP4 is likely to play a key role in the determination of intermuscular bone distribution in fish in a dose-dependent manner.

Identification, expression analysis, and antibacterial activity of NK-lysin from common carp Cyprinus carpio

Natural killer lysin (NK-lysin), produced by cytotoxic T lymphocytes and natural killer cells, is a cationic antimicrobial peptide that has a broad antimicrobial spectrum, including bacteria, viruses, and parasites. Nevertheless, the implication of NK-lysin in the protection against bacterial infection is not aware in common carp. In this study, six different NK-lysin genes (nkl1, nkl2, nkl3, nkl4, nkl5 and nkl6) were identified in the common carp genome. Each of the mature peptides of common carp NK-lysin has six well-conserved cysteine residues, and shares a Saposin B domain, characteristic of saposin-like protein (SALIP) family. The gene nkl1 contains 5 extrons and 4 introns, and nkl2, nkl3, nkl4 or nkl5 contains 4 extrons and 3 introns, however, the nkl6 has 3 extrons and 2 introns. By quantitative real-time PCR, nkl2 transcripts were predominantly expressed in spleen of healthy common carp, while elevated mainly in gill and spleen upon Aeromonas hydrophila infection. The recombinant NK-lysin-2 purified from Pichia pastoris shows antibacterial activity against Staphylococcus aureus (Gram-positive), and Escherichia coli M15, Aeromonas hydrophila, as well as Edwardsiella tarda (Gram-negative), the latter two are important pathogens of aquaculture. Our results indicate that NK-lysin in common carp might play an important role in fish immune response by enhancing antibacterial defense against bacterial pathogens.

Fine mapping of growth-related quantitative trait loci in Yellow River carp (Cyprinus carpio haematoperus)

Genetic linkage map and quantitative trait loci (QTL) mapping are powerful tools for genetic analysis of a series of economic traits in aquatic animals. Yellow River carp (Cyprinus carpio haematoperus), one of the famous common carp strains, is widely cultured in northern China, however, genetic and genomic bases of growth-related traits have been rarely studied in this carp strain. In present study, an F2 family of Yellow River carp (8months old) was used for constructing genetic linkage map and detecting potential QTL for growth traits, including total length (TL), body length (BL), body height (BH), head length (HL) and body weight (BW). A high-density genetic linkage map was constructed mainly based on 2b-RAD technology, with 6230 SNPs and 65 SSRs assigned onto 50 linkage groups, covering 98.2% of the Yellow River carp genome (average 0.59cM/marker). Comparative mapping showed high levels of syntenic relationship between our map and the genomes of two cyprinid fish (Denio rerio and Ctenopharyngodon idellus), while a lower synteny was detected between our map and C. c. carpio genome. Twelve chromosome-wide and two genome-wide growth-associated QTL were detected in our study, with the phenotypic variance explained ranging from 11.9% to 16.2%. These QTL were scatteredly distributed on 8 LGs of our sex-averaged linkage map. Fifteen candidate genes (e.g. INSIG1, 3β-HSD, HGF) were identified by BLAST searching the sequences of QTL-linked markers in Yellow River carp against Denio rerio genome, and their functions involve in the regulation of development, cell-proliferation, energy metabolism, and so on. The identification of significant QTL and potential growth-related genes in this study provides valuable genomic resources for the study of genetic mechanism underlying growth and development, and would contribute to accelerate the progress of marker-assisted selection in Yellow River carp.

Viral infections in common carp lead to a disturbance of mucin expression in mucosal tissues

In response to the constant challenge by potential pathogens, external surfaces of fish, their skin, gills and intestinal tract, are coated with mucus, a gel like substance which largely prevents the entry of pathogens. This mucus gel consists mainly of water and mucins, large O-glycosylated proteins, which are responsible for forming a gel like mixture. A modulation of the mRNA expression of mucins, was described in viral diseases in mammals however there is a knowledge gap about the regulation of mucins during viral infection in fish. Therefore, novel sequences for common carp mucins were located in an early version of the common carp genome and their mRNA expression measured in carp under infection with three different viral pathogens: (i) the alloherpesvirus cyprinid herpesvirus 3, (ii) the rhabdovirus spring viremia of carp virus and (iii) the poxvirus carp edema virus. The results showed a downregulation of mucin mRNA expression in gills and gut of common carp under infection with these pathogenic viruses. This could be a sign of a severe distress to the mucosal tissues in carp which occurs under viral infection. The reduced expression of mucins could help explaining the increased susceptibility of virus-infected carp to secondary bacterial infection.

Fertility of triploid hybrids of Prussian carp (Carassius gibelio) with common carp (Cyprinus carpio L.)

Fertility of backcross triploid hybrids containing one genome of Prussian carp and two genomes of common carp is investigated. The females of hybrids of Prussian carp and common carp (Prussian × common carp) are prolific and produce diploid gametes. Since males of such hybrids are sterile, their reproduction is realized by means of induced gynogenesis. Triploid progeny is obtained by backcrossing female Prussian × common carp with carp males. Among triploids obtained from hybrids F1 and among hybrids of the first gynogenetic generation, there were no prolific specimens. However, in reproduction of diploid hybrids by means of gynogenesis during six generations, the female fertility in the backcross progeny is restored. From backcross triploid females (daughters of Prussian × common carp of the sixth gynogenetic generation), a viable triploid gynogenetic progeny and a tetraploid backcross (by carp) progeny are obtained. The obtained data may be considered as the experimental proof of the hypothesis of reticular speciation.

Succession and Fermentation Products of Grass Carp (Ctenopharyngodon idellus) Hindgut Microbiota in Response to an Extreme Dietary Shift.

Dietary intake affects the structure and function of microbes in host intestine. However, the succession of gut microbiota in response to changes in macronutrient levels during a long period of time remains insufficiently studied. Here, we determined the succession and metabolic products of intestinal microbiota in grass carp (Ctenopharyngodon idellus) undergoing an abrupt and extreme diet change, from fish meal to Sudan grass (Sorghum sudanense). Grass carp hindgut microbiota responded rapidly to the diet shift, reaching a new equilibrium approximately within 11 days. In comparison to animal-diet samples, Bacteroides, Lachnospiraceae and Erysipelotrichaceae increased significantly while Cetobacterium decreased significantly in plant-diet samples. Cetobacterium was negatively correlated with Bacteroides, Lachnospiraceae and Erysipelotrichaceae, while Bacteroides was positively correlated with Lachnospiraceae. Predicted glycoside hydrolase and polysaccharide lyase genes in Bacteroides and Lachnospiraceae from the Carbohydrate-Active enZymes (CAZy) database might be involved in degradation of the plant cell wall polysaccharides. However, none of these enzymes was detected in the grass carp genome searched against dbCAN database. Additionally, a significant decrease of short chain fatty acids levels in plant-based samples was observed. Generally, our results suggest a rapid adaption of grass carp intestinal microbiota to dietary shift, and that microbiota are likely to play an indispensable role in nutrient turnover and fermentation.

Computational identification of Y-linked markers and genes in the grass carp genome by using a pool-and-sequence method

The molecular analysis of sex in vertebrates is important, as it has the potential to provide vital information for theoretical and applied research alike. Teleost fish are the ancient vertebrates that present a broad sex chromosome system but lack differentiated sex chromosomes in most species. Hence understanding the sex in fish would not only illuminate the sex determination evolution in vertebrates but also shed light on fish farming. In the present study, we used grass carp as a teleost fish model, studied the Y chromosome by using a pool-and-sequence strategy in combination with fragment-ratio method. In total, we identified five Y-linked scaffolds (totaling 347 Kb) and six Y-specific sequences that could be used as sex-specific markers, demonstrating the suitability of NGS-based re-sequencing of pooled DNAs for the identification of sex markers in fish. Moreover, 14 putative Y-linked genes were described for the first time. All the genes, except for un-y1, un-y2, and ubq-y, showed high similarity to their female homologs. RT-PCR revealed that ubq-y was only expressed in the male hypothalamus and pituitary. These findings provided an abundant resource for the Y chromosome of grass carp, and may help elucidate sex chromosome evolution in cyprinid fish.

Genome wide identification, phylogeny, and expression of bone morphogenetic protein genes in tetraploidized common carp (Cyprinus carpio)

Bone morphogenetic proteins (Bmps) are a group of signaling molecules known to play important roles during formation and maintenance of various organs, not only bone, but also muscle, blood and so on. Common carp (Cyprinus carpio) is one of the most intensively studied fish due to its economic and environmental importance. Besides, common carp has encountered an additional round of whole genome duplication (WGD) compared with many closely related diploid teleost, which make it one of the most important models for genome evolutionary studies in teleost. Comprehensive genome resources of common carp have been developed recently, which facilitate the thorough characterization of bmp gene family in the tetraploidized common carp genome. We identified a total of 44 bmps from the common carp genome, which are twice as many as that of zebrafish. Phylogenetic analysis revealed that most of bmps are highly conserved. Comparative analysis was performed across six typical vertebrate genomes. It appeared that all the bmp genes in common carp were duplicated. Obviously, the expansion of the bmp gene family in common carp was due to the latest additional round of whole genome duplication and made it more abundant than other diploid teleosts. Expression signatures were assessed in major tissues, including gill, intestine, liver, spleen, skin, heart, gonad, muscle, kidney, head kidney, brain and blood, which demonstrated the comprehensive expression profiles of bmp genes in the tetraploidized genome. Significant gene expression divergences were observed which revealed substantial functional divergences of those duplicated bmp genes post the latest WGD event. The conserved synteny blocks of bmp5s revealed the genome rearrangement of common carp post the 4R WGD. The whole set of bmp gene family in common carp provides insight into gene fate of tetraploidized common carp genome post recent WGD.

Genome-wide identification and characterization of microRNAs and target prediction by computational approaches in common carp

MicroRNAs (miRNAs) are a type of small non-coding RNAs, approximately 22nt in length, are considered as key indispensable players in the regulation of a broad range of biological processes. In this study, we used a homology search based computational approach for identifying miRNAs in common carp genome. A total of 271 miRNAs were predicted and were found to belong to 95 families. Among them, 169 were novel miRNAs and 102 were previously known miRNAs. These identified common carp miRNAs possess a difference of 0–2 nucleotides from their homologous counterparts. Furthermore, nine identified miRNAs were randomly selected for expression confirmation by qRT-PCR and the results showed that the differential expression of miRNAs in four common carp tissues. By target prediction, these miRNAs potentially target 7684 mRNAs. To understand the miRNA mediated gene regulatory control, functional enrichment analysis (GO and KEGG) were carried out. Results indicated that the targets of common carp miRNA were involved in wide range of regulatory functions. Overall, findings from this study will accelerate the way for further research of miRNAs, their functions in common carp and laid the foundation for the prediction and analysis of miRNAs to those species whose genomes are available.

Transcriptomic analysis of common carp anterior kidney during Cyprinid herpesvirus 3 infection: Immunoglobulin repertoire and homologue functional divergence

Cyprinid herpesvirus 3 (CyHV-3) infects koi and common carp and causes widespread mortalities. While the virus is a significant concern for aquaculture operations in many countries, in Australia the virus may be a useful biocontrol agent for pest carp. However, carp immune responses to CyHV-3, and the molecular mechanisms underpinning resistance, are not well understood. Here we used RNA-Seq on carp during different phases of CyHV-3 infection to detect the gene expression dynamics of both host and virus simultaneously. During acute CyHV-3 infection, the carp host modified the expression of genes involved in various immune systems and detoxification pathways. Moreover, the activated pathways were skewed toward humoral immune responses, which may have been influenced by the virus itself. Many immune-related genes were duplicated in the carp genome, and often these were expressed differently across the infection phases. Of particular interest were two interleukin-10 homologues that were not expressed synchronously, suggesting neo- or sub-functionalization. The carp immunoglobulin repertoire significantly diversified during active CyHV-3 infection, which was followed by the selection of high-affinity B-cells. This is indicative of a developing adaptive immune response, and is the first attempt to use RNA-Seq to understand this process in fish during a viral infection.

The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations.

As one of the four major Chinese carps of important economic value, the grass carp (Ctenopharyngodon idellus) has attracted increasing attention from the scientific community. Recently, the draft genome has been released as a milestone in research of grass carp. In order to facilitate the utilization of these genome data, we developed the grass carp genome database (GCGD). GCGD provides visual presentation of the grass carp genome along with annotations and amino acid sequences of predicted protein-coding genes. Other related genetic and genomic data available in this database include the genetic linkage maps, microsatellite genetic markers (i.e. Short Sequence Repeats, SSRs), and some selected transcriptomic datasets. A series of tools have been integrated into GCGD for visualization, analysis and retrieval of data, e.g. JBrowse for navigation of genome annotations, BLAST for sequence alignment, EC2KEGG for comparison of metabolic pathways, IDConvert for conversion of terms across databases and ReadContigs for extraction of sequences from the grass carp genome. Database URL: http://bioinfo.ihb.ac.cn/gcgd

Genome Wide Identification, Phylogeny, and Expression of Aquaporin Genes in Common Carp (Cyprinus carpio).

BackgroundAquaporins (Aqps) are integral membrane proteins that facilitate the transport of water and small solutes across cell membranes. Among vertebrate species, Aqps are highly conserved in both gene structure and amino acid sequence. These proteins are vital for maintaining water homeostasis in living organisms, especially for aquatic animals such as teleost fish. Studies on teleost Aqps are mainly limited to several model species with diploid genomes. Common carp, which has a tetraploidized genome, is one of the most common aquaculture species being adapted to a wide range of aquatic environments. The complete common carp genome has recently been released, providing us the possibility for gene evolution of aqp gene family after whole genome duplication.ResultsIn this study, we identified a total of 37 aqp genes from common carp genome. Phylogenetic analysis revealed that most of aqps are highly conserved. Comparative analysis was performed across five typical vertebrate genomes. We found that almost all of the aqp genes in common carp were duplicated in the evolution of the gene family. We postulated that the expansion of the aqp gene family in common carp was the result of an additional whole genome duplication event and that the aqp gene family in other teleosts has been lost in their evolution history with the reason that the functions of genes are redundant and conservation. Expression patterns were assessed in various tissues, including brain, heart, spleen, liver, intestine, gill, muscle, and skin, which demonstrated the comprehensive expression profiles of aqp genes in the tetraploidized genome. Significant gene expression divergences have been observed, revealing substantial expression divergences or functional divergences in those duplicated aqp genes post the latest WGD event.ConclusionsTo some extent, the gene families are also considered as a unique source for evolutionary studies. Moreover, the whole set of common carp aqp gene family provides an essential genomic resource for future biochemical, toxicological, physiological, and evolutionary studies in common carp.

Complexity of gap junctions between horizontal cells of the carp retina

In the vertebrate retina, horizontal cells (HCs) reveal homologous coupling by gap junctions (gj), which are thought to consist of different connexins (Cx). However, recent studies in mouse, rabbit and zebrafish retina indicate that individual HCs express more than one connexin. To provide further insights into the composition of gj connecting HCs and to determine whether HCs express multiple connexins, we examined the molecular identity and distribution of gj between HCs of the carp retina.We have cloned four carp connexins designated Cx49.5, Cx55.5, Cx52.6 and Cx53.8 with a close relationship to connexins previously reported in HCs of mouse, rabbit and zebrafish, respectively. Using in situ hybridization, Cx49.5 expression was detected in different subpopulations of retinal neurons including HCs, whereas the Cx52.6 transcript was localized exclusively in HCs. Using specific antibodies, Cx55.5 and Cx53.8 were detected on dendrites of all four HC subtypes and axon terminals. Immunoelectron microscopy confirmed the presence of Cx55.5 and Cx53.8 in gap junctions between these processes and Cx55.5 was additionally observed in HC dendrites invaginating cone pedicles, suggesting its participation in the modulation of photoreceptor output in the carp retina. Furthermore, using single-cell RT–PCR, all four connexins were detected in different subtypes of HCs, suggesting overlapping expression patterns. Thus, the composition of gj mediating homologous coupling between subtypes of carp HCs appears to be more complex than expected. Moreover, BLAST searches of the preliminary carp genome, using novel sequences as query, suggest that most of the analyzed connexin genes are duplicated in carp.

A full-body transcriptome and proteome resource for the European common carp.

BackgroundThe common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies.ResultsHere we have used 19 different tissues from an F1 hybrid strain of the common carp to perform transcriptome analyses using RNA-Seq. For a subset of the tissues we also have performed deep proteomic studies. As a reference, we updated the European common carp genome assembly using low coverage Pacific Biosciences sequencing to permit high-quality gene annotation. These annotated gene lists were linked to zebrafish homologs, enabling direct comparisons with published datasets. Using clustering, we have identified sets of genes that are potential selective markers for various types of tissues. In addition, we provide a script for a schematic anatomical viewer for visualizing organ-specific expression data.ConclusionsThe identified transcriptome and proteome data for carp tissues represent a useful resource for further translational studies of tissue-specific markers for this economically important fish species that can lead to new markers for organ development. The similarity to zebrafish expression patterns confirms the value of common carp as a resource for studying tissue-specific expression in cyprinid fish. The availability of the annotated gene set of common carp will enable further research with both applied and fundamental purposes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3038-y) contains supplementary material, which is available to authorized users.

QTL fine mapping and identification of candidate genes for growth-related traits in bighead carp (Hypophthalmichehys nobilis)

Bighead carp (Hypophthalmichthys nobilis) is a popular Asian aquaculture species, but its genetic improvement is still in infancy. Marker-assisted selection (MAS) can improve the selection efficiency of breeding programs in fish. In this study, we constructed a genetic linkage map in a F1 family of bighead carp using microsatellite markers. A total of 905 microsatellites were assigned onto 24 linkage groups (LGs) of a consensus map, which spanned 1631.7cM of bighead carp genome with an average interval of 1.8cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish. QTL mapping for growth traits was performed based on this linkage map, and three significant and 8 suggestive QTL associated with four growth traits (body length, body height, head length, body weight) were detected on LG9 and LG17, with 18.6–25.5% of phenotypic variance explained. Three candidate genes for growth were identified in or near the QTL intervals, and a SNP in one of the three genes, TP53BP2, was significantly associated with growth traits in different populations of bighead carp. These results of the high-density SSR genetic map and genome scan for QTL provide a basis for MAS and breeding programs for growth in bighead carp.