An ultra-high density linkage map and QTL mapping for sex and growth-related traits of common carp (Cyprinus carpio)

Renal autocrine neuropeptide FF (NPFF) signaling regulates blood pressure

The kidney and brain play critical roles in the regulation of blood pressure. Neuropeptide FF (NPFF), originally isolated from the bovine brain, has been suggested to contribute to the pathogenesis of hypertension. However, the roles of NPFF and its receptors, NPFF-R1 and NPFF-R2, in the regulation of blood pressure, via the kidney, are not known. In this study, we found that the transcripts and proteins of NPFF and its receptors, NPFF-R1 and NPFF-R2, were expressed in mouse and human renal proximal tubules (RPTs). In mouse RPT cells (RPTCs), NPFF, but not RF-amide-related peptide-2 (RFRP-2), decreased the forskolin-stimulated cAMP production in a concentration- and time-dependent manner. Furthermore, dopamine D1-like receptors colocalized and co-immunoprecipitated with NPFF-R1 and NPFF-R2 in human RPTCs. The increase in cAMP production in human RPTCs caused by fenoldopam, a D1-like receptor agonist, was attenuated by NPFF, indicating an antagonistic interaction between NPFF and D1-like receptors. The renal subcapsular infusion of NPFF in C57BL/6 mice decreased renal sodium excretion and increased blood pressure. The NPFF-mediated increase in blood pressure was prevented by RF-9, an antagonist of NPFF receptors. Taken together, our findings suggest that autocrine NPFF and its receptors in the kidney regulate blood pressure, but the mechanisms remain to be determined.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

BACKGROUND

The Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program.

RESULTS

In this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers).

CONCLUSIONS

The first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

Fine Mapping of QTLs for Alkaline Tolerance in Crucian Carp (Carassius auratus) Using Genome-Wide SNP Markers

Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for exploring alkali-tolerant molecular markers in an extremely alkaline environment. In this study, we constructed a high-density and high-resolution linkage map with 16,224 SNP markers based on genotyping-by-sequencing (GBS) consisting of 152 progenies and conducted QTL studies for alkali-tolerant traits. The total length of the linkage map was 3918.893 cM, with an average distance of 0.241 cM. Two QTLs for the ammonia-N-tolerant trait were detected on LG27 and LG45. A QTL for the urea-N-tolerant trait was detected on LG27. Interestingly, mapping the two QTLs on LG27 revealed that the mapped genes were both located in the intron of CDC42. GO functional annotation and KEGG enrichment analysis results indicated that the biological functions might be involved in the cell cycle, cellular senescence, MAPK, and Ras signaling pathways. These findings suggest that CDC42 may play an important role in the process of dealing with extremely alkaline environments.

Reproduction-associated pathways in females of gibel carp (Carassius gibelio) shed light on the molecular mechanisms of the coexistence of asexual and sexual reproduction

Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries) and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling, and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allows the populations of C. gibelio to combine the evolutionary and ecological advantages of the two reproductive strategies. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.

Expression of bone morphogenetic protein 10 and its role in biomineralization in Hyriopsis cumingii

Shells and pearls are the products of biomineralization of shellfish after ingesting external mineral ions. Bone morphogenetic proteins (BMPs) play a role in a variety of biological function, and the genes that encode them, are considered important shell-forming genes in mollusks and are associated with shell and pearl formation, embryonic development, and other functions, but bone morphogenetic protein 10 (BMP10) is poorly understood in Hyriopsis cumingii. In this study, we cloned Hc-BMP10 and obtained a 2477 bp full-length sequence encoding 460 amino acids with a conserved TGF-β structural domain. During the embryonic developmental stages, the cleavage stage had the highest expression of Hc-BMP10, followed by juvenile clams; the expression in the mantle gradually decreased with increasing mussel age. A strong signal was detected on epidermal cells on the mantle edge by in situ hybridization. In both the shell notching and inserting operations of the pearl fragment assay, we found that the expression of Hc-BMP10 increased after the above treatments. RNA interference assays showed that the silencing of Hc-BMP10 resulted in a change in the morphology of the prismatic layer and nacreous layer, with the prismatic layer less closely aligned and the disordered aragonite flakes in the nacreous layer. These findings indicate that Hc-BMP10 is involved in the growth and development of H. cumingii, as well as the formation of shells and pearls. Therefore, this study provides some reference for selecting superior species for growth and pearl breeding of H. cumingii at a molecular level and further investigation of the molecular mechanism for biomineralization of Hc-BMP10.

Construction of a high-density genetic linkage map and QTL mapping of growth and cold tolerance traits in Takifugu fasciatus

Takifugu fasciatus is an aquaculture species with high economic value. In recent years, problems such as environmental pollution and inbreeding have caused a serious decline in T. fasciatus germplasm resources. In this study, a high-density genetic linkage map was constructed by whole-genome resequencing. The map consists of 4891 bin markers distributed across 22 linkage groups (LGs), with a total genetic coverage of 2381.353 cM and a mean density of 0.535 cM. Quantitative trait locus (QTL) localization analysis showed that a total of 19 QTLs associated with growth traits of T. fasciatus in the genome-wide significance threshold range, distributed on 11 LGs. In addition, 11 QTLs associated with cold tolerance traits were identified, each scattered on a different LG. Furthermore, we used QTL localization analysis to screen out three candidate genes (IGF1, IGF2, ADGRB) related to growth in T. fasciatus. Meanwhile, we screened three candidate genes (HSP90, HSP70, and HMGB1) related to T. fasciatus cold tolerance. Our study can provide a theoretical basis for the selection and breeding of cold-tolerant or fast-growing T. fasciatus.

Construction of a high density genetic linkage map to define the locus conferring seedlessness from Mukaku Kishu mandarin

Mukaku Kishu ('MK'), a small sized mandarin, is an important source of seedlessness in citrus breeding. Identification and mapping the gene(s) governing 'MK' seedlessness will expedite seedless cultivar development. In this study, two 'MK'-derived mapping populations- LB8-9 Sugar Belle^® ('SB') × 'MK' (N=97) and Daisy ('D') × 'MK' (N=68) were genotyped using an Axiom_Citrus56 Array encompassing 58,433 SNP probe sets, and population specific male and female parent linkage maps were constructed. The parental maps of each population were integrated to produce sub-composite maps, which were further merged to develop a consensus linkage map. All the parental maps (except 'MK_D') had nine major linkage groups, and contained 930 ('SB'), 810 ('MK_SB'), 776 ('D') and 707 ('MK_D') SNPs. The linkage maps displayed 96.9 ('MK_D') to 98.5% ('SB') chromosomal synteny with the reference Clementine genome. The consensus map was comprised of 2588 markers including a phenotypic seedless (Fs)-locus and spanned a genetic distance of 1406.84 cM, with an average marker distance of 0.54 cM, which is substantially lower than the reference Clementine map. For the phenotypic Fs-locus, the distribution of seedy and seedless progenies in both 'SB' × 'MK' (55:42, χ² = 1.74) and 'D' × 'MK' populations (33:35, χ² = 0.06) followed a test cross pattern. The Fs-locus mapped on chromosome 5 with SNP marker 'AX-160417325' at 7.4 cM in 'MK_SB' map and between two SNP markers 'AX-160536283' and 'AX-160906995' at a distance of 2.4 and 4.9 cM, respectively in 'MK_D' map. The SNPs 'AX-160417325' and 'AX-160536283' correctly predicted seedlessness of 25-91.9% progenies in this study. Based on the alignment of flanking SNP markers to the Clementine reference genome, the candidate gene for seedlessness hovered in a ~ 6.0 Mb region between 3.97 Mb (AX-160906995) to 10.00 Mb (AX-160536283). This region has 131 genes of which 13 genes (belonging to seven gene families) reportedly express in seed coat or developing embryo. The findings of the study will prove helpful in directing future research for fine mapping this region and eventually underpinning the exact causative gene governing seedlessness in 'MK'.

The first high-density genetic map of common cockle (Cerastoderma edule) reveals a major QTL controlling shell color variation

Shell color shows broad variation within mollusc species and despite information on the genetic pathways involved in shell construction and color has recently increased, more studies are needed to understand its genetic architecture. The common cockle (Cerastoderma edule) is a valuable species from ecological and commercial perspectives which shows important variation in shell color across Northeast Atlantic. In this study, we constructed a high-density genetic map, as a tool for screening common cockle genome, which was applied to ascertain the genetic basis of color variation in the species. The consensus genetic map comprised 19 linkage groups (LGs) in accordance with the cockle karyotype (2n = 38) and spanned 1073 cM, including 730 markers per LG and an inter-marker distance of 0.13 cM. Five full-sib families showing segregation for several color-associated traits were used for a genome-wide association study and a major QTL on chromosome 13 associated to different color-traits was detected. Mining on this genomic region revealed several candidate genes related to shell construction and color. A genomic region previously reported associated with divergent selection in cockle distribution overlapped with this QTL suggesting its putative role on adaptation.

A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

Red swamp crayfish (Procambarus clarkii) is a commercially important species in global aquaculture and most successfully invasive freshwater shrimp in China. In order to determine the genetic basis of growth- and sex-related traits, a high-density genetic linkage map was constructed using 2b-RAD sequencing technology in a full-sib family. The consensus map contains 4,878 SNP markers assigned to 94 linkage groups (LGs) and spanned 6,157.737 cM with an average marker interval of 1.26 cM and 96.93% genome coverage. The quantitative trait locus (QTL) mapping for growth and sex traits was performed for the first time. QTL mapping uncovers 28 QTLs for growth-related traits in nine LGs, explaining 7.9-14.4% of the phenotypic variation, and identifies some potential candidate growth-related genes such as mih, lamr, golgb1, nurf301, and tbcd1 within the QTL intervals. A single major locus for sex determination was revealed in LG20 that explains 59.3-63.7% of the phenotypic variations. Some candidate sex-related genes, such as vps4bl, ssrf, and acot1, were identified in the QTL intervals and found to be differentially expressed in the muscle tissues between the females and the males. Furthermore, the identified SNPs were revealed to be female heterozygotes, suggesting that red swamp crayfish might have the female heterogametic ZZ/ZW sex determination system. The present study provides a valuable resource for marker-assisted selection and genetic improvement and for further genetic and genomic research in red swamp crayfish.

Construction of a High-Density Genetic Linkage Map for the Mapping of QTL Associated with Growth-Related Traits in Sea Cucumber (Apostichopus japonicus)

Simple Summary

Slow growth and germplasm degradation have restricted the sustainable commercial development of the sea cucumber industry. To analyze the genetic mechanism of growth traits of sea cucumbers, we constructed a high-density genetic linkage map based on single nucleotide polymorphism (SNP) molecular markers and performed a quantitative trait loci (QTL) mapping analysis. We annotated a critical candidate gene related to growth traits and explored mRNA expression levels. The results showed that the gene was significantly highly expressed during the larval developmental stages. These results can be used to genetically improve the growth traits of sea cucumbers.

Abstract

Genetic linkage maps have become an indispensable tool for genetics and genomics research. Sea cucumber (Apostichopus japonicus), which is an economically important mariculture species in Asia, is an edible echinoderm with medicinal properties. In this study, the first SNP-based high-density genetic linkage map was constructed by sequencing 132 A. japonicus individuals (2 parents and 130 offspring) according to a genotyping-by-sequencing (GBS) method. The consensus map was 3181.54 cM long, with an average genetic distance of 0.52 cM. A total of 6144 SNPs were assigned to 22 linkage groups (LGs). A Pearson analysis and QTL mapping revealed the correlations among body weight, body length, and papillae number. An important growth-related candidate gene, protein still life, isoforms C/SIF type 2 (sif), was identified in LG18. The gene was significantly highly expressed during the larval developmental stages. Its encoded protein reportedly functions as a guanine nucleotide exchange factor. These results would facilitate the genetic analysis of growth traits and provide valuable genomic resources for the selection and breeding of new varieties of sea cucumbers with excellent production traits.

Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp (Cyprinus carpio haematopterus)

To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio)

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9-15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

Parallel subgenome structure and divergent expression evolution of allo-tetraploid common carp and goldfish

How two subgenomes in allo-tetraploids adapt to coexistence and coordinate through structure and expression evolution requires extensive studies. In the present study, we report an improved genome assembly of allo-tetraploid common carp, an updated genome annotation of allo-tetraploid goldfish and the chromosome-scale assemblies of a progenitor-like diploid Puntius tetrazona and an outgroup diploid Paracanthobrama guichenoti. Parallel subgenome structure evolution in the allo-tetraploids was featured with equivalent chromosome components, higher protein identities, similar transposon divergence and contents, homoeologous exchanges, better synteny level, strong sequence compensation and symmetric purifying selection. Furthermore, we observed subgenome expression divergence processes in the allo-tetraploids, including inter-/intrasubgenome trans-splicing events, expression dominance, decreased expression levels, dosage compensation, stronger expression correlation, dynamic functionalization and balancing of differential expression. The potential disorders introduced by different progenitors in the allo-tetraploids were hypothesized to be alleviated by increasing structural homogeneity and performing versatile expression processes. Resequencing three common carp strains revealed two major ecotypes and uncovered candidate genes relevant to growth and survival rate.

A high-density genetic map construction and sex-related loci identification in Chinese Giant salamander

BACKGROUND

The Chinese giant salamander Andrias davidianus is an important amphibian species in China because of its increasing economic value, protection status and special evolutionary position from aquatic to terrestrial animal. Its large genome presents challenges to genetic research. Genetic linkage mapping is an important tool for genome assembly and determination of phenotype-related loci.

RESULTS

In this study, we constructed a high-density genetic linkage map using ddRAD sequencing technology to obtain SNP genotyping data of members from an full-sib family which sex had been determined. A total of 10,896 markers were grouped and oriented into 30 linkage groups, representing 30 chromosomes of A. davidianus. The genetic length of LGs ranged from 17.61 cM (LG30) to 280.81 cM (LG1), with a mean inter-locus distance ranging from 0.11(LG3) to 0.48 cM (LG26). The total genetic map length was 2643.10 cM with an average inter-locus distance of 0.24 cM. Three sex-related loci and four sex-related markers were found on LG6 and LG23, respectively.

CONCLUSION

We constructed the first High-density genetic linkage map and identified three sex-related loci in the Chinese giant salamander. Current results are expected to be a useful tool for future genomic studies aiming at the marker-assisted breeding of the species.

Genome-Wide Association Study Identifies Genomic Loci of Sex Determination and Gonadosomatic Index Traits in Large Yellow Croaker (Larimichthys crocea)

Larimichthys crocea is one of the traditional marine culture fishes in China, widely distributed in South China Sea, East Sea, and southern Yellow Sea. Sex dimorphism is evident in this species that females present a substantial growth strength than males, suggesting breeding females could obtain more economic benefits in L. crocea aquaculture industry. With the continuous expansion of aquaculture industry, both identifying sex-associated genome region and understanding the genetic basis underlying gonad differentiation and development matter to not only sex control aquaculture but also breeding industry. Thus, genome-wide association analysis (GWAS) of sex determination was conducted with a random breeding population of 905 individuals (including 463 females and 442 males) by ddRAD sequencing. For sex determination, 21 significant single nucleotide polymorphisms (SNPs) in chromosome (Chr) 22 were identified. Surrounding these SNPs, we founded 14 candidate genes, including dmrt1, dmrt3, and piwil2, fam102a, and odf2. The sex-associated region was narrowed down further to 2.4 Mb on Chr22 through F_st scanning and insertion-deletion (InDel) analysis. Besides, 3 SNPs in the supposed sex-determining region on Chr22 were identified as highly associated with gonad differentiation through GWAS on gonadosomatic index (GSI) in 350 males and 231 females. Because of the significant difference of GSI between females and males of L. crocea, GWAS on GSI of different genders was also conducted independently. Finally, we identified a SNP in Chr18 showing genome-wide significant association with male GSI (MGSI) and three genes axl, cyp2a10, and cyp2g1 involved in the gonadal development regulation process of aromatase. Overall, this study explored the genetic basis of sex determination mechanism and provided novel insights into gonad differentiation and development, offering solid genetic support for sex control breeding, marker-assisted selection, and marine resources conservation.

An ultra-high density SNP-based linkage map for enhancing the pikeperch (Sander lucioperca) genome assembly to chromosome-scale

Pikeperch (Sander lucioperca) is a fish species with growing economic significance in the aquaculture industry. However, successful positioning of pikeperch in large-scale aquaculture requires advances in our understanding of its genome organization. In this study, an ultra-high density linkage map for pikeperch comprising 24 linkage groups and 1,023,625 single nucleotide polymorphisms markers was constructed after genotyping whole-genome sequencing data from 11 broodstock and 363 progeny, belonging to 6 full-sib families. The sex-specific linkage maps spanned a total of 2985.16 cM in females and 2540.47 cM in males with an average inter-marker distance of 0.0030 and 0.0026 cM, respectively. The sex-averaged map spanned a total of 2725.53 cM with an average inter-marker distance of 0.0028 cM. Furthermore, the sex-averaged map was used for improving the contiguity and accuracy of the current pikeperch genome assembly. Based on 723,360 markers, 706 contigs were anchored and oriented into 24 pseudomolecules, covering a total of 896.48 Mb and accounting for 99.47% of the assembled genome size. The overall contiguity of the assembly improved with a scaffold N50 length of 41.06 Mb. Finally, an updated annotation of protein-coding genes and repetitive elements of the enhanced genome assembly is provided at NCBI.

First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus)

Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96 cM with an average marker interval of 0.33 cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.

A first genetic linage map construction and QTL mapping for growth traits in Larimichthys polyactis

Larimichthys polyactis is a commercially important marine fish species in Eastern Asia, yet very few genetic resources exist. In particular, genetic linkage maps are critical tools for genetic breeding. In this study, we generated a high resolution linkage map from a family of 110 individuals and their parents by resequencing the individuals. 3,802 effective SNPs were mapped to 24 linkage groups (LGs). The map spanned 2,567.39 cm, with an average marker interval of 0.66 cm. We used the map to conduct QTL analysis for growth traits, and found 31 markers were significantly associated with growth-related traits. Specifically, three SNPs were identified for total length, nineteen SNPs for body length, and nine SNPs for body weight. The identified SNPs could explain 15.2-22.6% of the phenotypic variation. SNPs associated with growth traits were distributed on LG6 and LG11, and candidate genes included, kif26b, bat1, gna1, gbgt1, and amfr, which may regulate growth. The linkage map and mapped QTLs would be useful for improving the quality of L. polyactis via marker-assisted selection.

Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus)

BACKGROUND

Grass carp (Ctenopharyngodon idellus) are important species in Asian aquaculture. A draft genome for grass carp has already been published in 2015. However, there is still a requirement for a suitable genetic linkage map to arrange scaffolds on chromosomal frameworks. QTL analysis is a powerful tool to detect key locations for quantitative traits, especially in aquaculture. There no growth related QTLs of grass carp have been published yet. Even the growth trait is one of the focuses in grass carp culture.

RESULTS

In this study, a pair of distantly related parent grass carps and their 100 six-month-old full-sib offspring were used to construct a high-density genetic map with 6429 single nucleotide polymorphisms (SNPs) by 2b-RAD technology. The total length of the consensus map is 5553.43 cM with the average marker interval of 1.92 cM. The map has a good collinearity with both the grass carp draft genome and the zebrafish genome, and it assembled 89.91% of the draft genome to a chromosomal level. Additionally, according to the growth-related traits of progenies, 30 quantitative trait loci (QTLs), including 7 for body weight, 9 for body length, 5 for body height and 9 for total length, were identified in 16 locations on 5 linkage groups. The phenotypic variance explained for these QTLs varies from 13.4 to 21.6%. Finally, 17 genes located in these regions were considered to be growth-related because they either had functional mutations predicted from the resequencing data of the parents.

CONCLUSION

A high density genetic linkage map of grass carp was built and it assembled the draft genome to a chromosomal level. Thirty growth related QTLs were detected. After the cross analysis of Parents resequencing data, 17 candidate genes were obtained for further researches.

The Piranha Genome Provides Molecular Insight Associated to Its Unique Feeding Behavior

The piranha enjoys notoriety due to its infamous predatory behavior but much is still not understood about its evolutionary origins and the underlying molecular mechanisms for its unusual feeding biology. We sequenced and assembled the red-bellied piranha (Pygocentrus nattereri) genome to aid future phenotypic and genetic investigations. The assembled draft genome is similar to other related fishes in repeat composition and gene count. Our evaluation of genes under positive selection suggests candidates for adaptations of piranhas’ feeding behavior in neural functions, behavior, and regulation of energy metabolism. In the fasted brain, we find genes differentially expressed that are involved in lipid metabolism and appetite regulation as well as genes that may control the aggression/boldness behavior of hungry piranhas. Our first analysis of the piranha genome offers new insight and resources for the study of piranha biology and for feeding motivation and starvation in other organisms.

Construction of High-Density Genetic Map and Mapping of Sex-Related Loci in the Yellow Catfish (Pelteobagrus fulvidraco)

The yellow catfish (Pelteobagrus fulvidraco) is a very important aquaculture species distributed in freshwater area of China. All-male yellow catfish is very popular in aquaculture because of their significant sex dimorphism phenomena. The males grow much faster than females in full-sibling family. However, the sex dimorphism mechanism is still unclear in yellow catfish. In order to better understand the genetic basis of yellow catfish sexual dimorphism, it is vital to map the sex-related traits and localize the candidate genes across yellow catfish whole genome. Here, we constructed a high-density linkage map of yellow catfish using genotyping-by-sequencing (GBS) strategy. A total of 5705 single-nucleotide polymorphism (SNP) markers were mapped to 26 different linkage groups (LGs) using 184 F1 offspring. The total genetic map length was 3071.59 cM, with an average interlocus distance of 0.54 cM. Eleven significant sex-related QTLs in yellow catfish were identified. Six sex-related genes were identified from the region of reference genome near these QTLs including amh, gnrhr, vasa, lnnr1, foxl2, and bmp15. The high-density genetic linkage map provides valuable resources for yellow catfish molecular assistant breeding and elucidating sex differentiation process. Moreover, the comparative genomic study was analyzed among yellow catfish, channel catfish, and zebrafish. It revealed highly conserved chromosomal distribution between yellow catfish and channel catfish.

Construction of a High-Density Genetic Linkage Map and QTL Mapping for Growth-Related Traits in Takifugu bimaculatus

Takifugu bimaculatus is a euryhaline species, distributed ranging from the southern Yellow Sea to the South China Sea. Their tolerance to a wide range of salinity and temperature, coupled with a desirable firm texture, makes T. bimaculatus a strong candidate for Takifugu aquaculture in subtropics areas. Due to the increasing demand in markets and emerging of the Takifugu aquaculture industry, close attention has been paid to improvement on the T. bimaculatus production. In aquaculture, the great effort has been put into marker-assisted selective breeding, and efficient improvement was realized. However, few genetic resources on T. bimaculatus are provided so far. Aiming at understanding the genetic basis underlying important economic growth traits, facilitating genetic improvement and enriching the genetic resource in T. bimaculatus, we constructed the first genetic linkage map for T. bimaculatus via double digestion restriction-site association DNA sequencing and conducted quantitative traits locus (QTL) mapping for growth-related traits. The map comprised 1976 single nucleotide polymorphism markers distributed on 22 linkage groups (LG), with a total genetic distance of 2039.74 cM. Based on the linkage map, a chromosome-level assembly was constructed whereby we carried out comparative genomics analysis, verifying the high accuracy on contigs ordering of the linkage map. On the other hand, 18 QTLs associated with growth traits were detected on LG6, LG7, LG8, LG10, LG20, and LG21 with phenotypical variance ranging from 15.1 to 56.4%. Candidate genes participating in cartilage development, fat accumulation, and other growth-related regulation activities were identified from these QTLs, including col11a1, foxa2, and thrap3. The linkage map provided a solid foundation for chromosomes assembly and refinement. QTLs reported here unraveled the genomic architecture of some growth traits, which will advance the investigation of aquaculture breeding efforts in T. bimaculatus.

A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus)

Large-scale loach (Paramisgurnus dabryanus) is a commercially important species in East Asia; however, the cultured population that exhibited degradation of germplasm resource cannot meet the market needs, and the genome resources for P. dabryanus are still lacking. In this study, the first high-density genetic map of P. dabryanus was constructed using 15,830 SNP markers based on high-throughput sequencing with an improved SLAF-seq strategy. The quantitative trait locus (QTL) mapping for sex, growth, and morphology traits was performed for the first time. The genetic map spanned 4,657.64 cM in length with an average inter-marker distance of 0.30 cM. QTL mapping and association analysis identified eight QTLs of growth traits, nine QTLs of morphology traits, and five QTLs of sex-related traits, respectively. Interestingly, the most significant QTLs for almost all the traits were concentrated on the same linkage group LG11. Seven candidate markers and 12 potentially key genes, which were associated with sex determination and growth, were identified within the overlapped QTL regions on LG11. Further, the first genome survey analysis of P. dabryanus was performed which represents the first step toward fully decoding the P. dabryanus genome. The genome scaffolds were anchored to the high-density linkage map, spanning 960.27 Mb of P. dabryanus reference genome. The collinearity analysis revealed a high level of collinearity between the genetic map and the reference genome of P. dabryanus. Moreover, a certain degree of homology was observed between large-scale loach and zebrafish using comparative genomic analysis. The constructed high-density genetic map was an important basis for QTL fine mapping, genome assembly, and genome comparison. The present study will provide a valuable resource for future marker-assisted breeding, and further genetic and genomic researches in P. dabryanus.

An SNP-Based Genetic Map and QTL Mapping for Growth Traits in the Red-Spotted Grouper (Epinephelus akaara)

The red-spotted grouper (Epinephelus akaara) is one of the most commercially important aquatic species in China. However, its seedstock has low larval survival rates, and its stability is confronted with the danger of overexploitation. In this study, a high-density genetic map was constructed using 3435 single nucleotide polymorphisms (SNPs) from 142 first generation (F₁) full-sib offspring and two parents of a red-spotted grouper population. The total genetic length of the map was 2300.12 cM with an average intermarker distance of 0.67 cM. Seventeen genome-wide significant quantitative trait loci (QTLs) for growth-related traits were detected on 24 linkage groups, including 5 QTLs for full length, 7 QTLs for body length, and 5 QTLs for body weight. The contribution values of explained phenotypic variance ranged from 10.7% to 12.9%. Moreover, 13 potential candidate genes for growth-related traits were identified. Collectively, these findings will be useful for conducting marker-assisted selection of the red-spotted grouper in future studies.

The allotetraploid origin and asymmetrical genome evolution of the common carp Cyprinus carpio

Common carp (Cyprinus carpio) is an allotetraploid species derived from recent whole genome duplication and provides a model to study polyploid genome evolution in vertebrates. Here, we generate three chromosome-level reference genomes of C. carpio and compare to related diploid Cyprinid genomes. We identify a Barbinae lineage as potential diploid progenitor of C. carpio and then divide the allotetraploid genome into two subgenomes marked by a distinct genome similarity to the diploid progenitor. We estimate that the two diploid progenitors diverged around 23 Mya and merged around 12.4 Mya based on the divergence rates of homoeologous genes and transposable elements in two subgenomes. No extensive gene losses are observed in either subgenome. Instead, we find gene expression bias across surveyed tissues such that subgenome B is more dominant in homoeologous expression. CG methylation in promoter regions may play an important role in altering gene expression in allotetraploid C. carpio.

The common carp is derived from recent whole genome duplication and represents a model for polyploid genome evolution, rare in vertebrates. Here, the authors generate and analyse chromosome-level reference genomes for common carp, and describe subgenome gene expression changes.

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.

The sequence and de novo assembly of Takifugu bimaculatus genome using PacBio and Hi-C technologies

Takifugu bimaculatus is a native teleost species of the southeast coast of China where it has been cultivated as an important edible fish in the last decade. Genetic breeding programs, which have been recently initiated for improving the aquaculture performance of T. bimaculatus, urgently require a high-quality reference genome to facilitate genome selection and related genetic studies. To address this need, we produced a chromosome-level reference genome of T. bimaculatus using the PacBio single molecule sequencing technique (SMRT) and High-through chromosome conformation capture (Hi-C) technologies. The genome was assembled into 2,193 contigs with a total length of 404.21 Mb and a contig N50 length of 1.31 Mb. After chromosome-level scaffolding, 22 chromosomes with a total length of 371.68 Mb were constructed. Moreover, a total of 21,117 protein-coding genes and 3,471 ncRNAs were annotated in the reference genome. The highly accurate, chromosome-level reference genome of T. bimaculatus provides an essential genome resource for not only the genome-scale selective breeding of T. bimaculatus but also the exploration of the evolutionary basis of the speciation and local adaptation of the Takifugu genus.

Gonadal transcriptome analysis of the common carp, Cyprinus carpio: Identification of differentially expressed genes and SSRs

Common carp (Cyprinus carpio) is a world-wide freshwater fish of eutrophic waters. C. carpio, have various reproductive traits, including early sexual maturity, that may make them excellent, large, realistic, aquaculture model species. In the present work, de novo assembly of gonadal (testicular and ovarian) transcriptomes from juvenile common carp was performed to identify genes involved in gonadal development. A total of 81,757 and 43,257 transcripts with average lengths of 769 and 856 bp, were obtained from the immature testicular and ovarian transcriptomes, respectively. About 84,367 unigenes were constructed after removing redundancy involving representation of transcripts in both gonadal transcriptomes. Gene ontology (39,171 unigenes), clusters of orthologous group's analysis (6651 unigenes) and Kyoto encyclopedia of genes, and genomes automatic annotation server analysis (4783 unigenes) were performed to identify potential genes along with their functions. Furthermore, 18,342 (testis) and 8693 (ovary) simple sequence repeats were identified. About 298 differentially expressed genes were identified, of which 171 and 127 genes were up-regulated in testis and ovary, respectively. Quantitative real-time reverse transcription PCR was performed to validate differential expression of selected genes in testis and ovary. Nearly 809 genes related to reproduction were identified, sex-wise expression pattern of genes related to steroid synthesis, endocrine regulation, germ cell maintenance and others factors related to gonadal differentiation was observed, and expression analysis of nanos, ad4bp/sf-1, and gdf9 was performed. The present study identified certain important genes/factors involved in the gonadal development of C. carpio which may provide insights into the understanding of sex-differentiation and gonadal development processes.

Genome survey and high-resolution backcross genetic linkage map construction of the ridgetail white prawn Exopalaemon carinicauda applications to QTL mapping of growth traits

BACKGROUND

High-resolution genetic linkage map is critical for QTL mapping, genome sequence assembly and marker-assisted selection in aquaculture species. The ridgetail white prawn Exopalaemon carinicauda is one of the most economic shrimp species naturally distributed in the coasts of eastern China and western Korea. However, quite limited genomics and genetics information have been exploited for genetic improvement of economic traits in this species.

RESULTS

In the present study, we conducted genome survey and constructed high-resolution genetic linkage maps of the ridgetail white prawn with reciprocal-cross mapping family genotyped using next-generation sequencing approaches. The estimated genome size was 9.33 Gb with a heterozygosity of 0.26% and a repeat sequence ratio of 76.62%. 65,772 protein-coding genes were identified by genome annotation. A total of 10,384 SNPs were used to high-throughput genotyping and assigned to 45 linkage groups (LGs) from reciprocal backcross families of E. carinicauda, and the average marker distances were 0.73 cM and 0.55 cM, respectively. Based on the high-resolution linkage map, twenty-three QTLs related to five growth traits were detected. All QTLs could explain 8.8-15.7% of the total growth-traits variation.

CONCLUSIONS

The genome size of E. carinicauda was estimated more accurately by genome survey analysis, which revealed basic genomic architecture. The first high-resolution backcross genetic linkage map and QTLs related to growth traits will provide important information for QTL fine mapping, genome assembly and genetic improvement of E. carinicauda and other palaemon shrimps.

Genome Scan for Genomic Regions and Genes Associated with Growth Trait in Pacific White Shrimp Litopeneaus vannamei

The Pacific white shrimp Litopeneaus vannmei (L. vannmei) is a predominant aquaculture shrimp species worldwide, and it is considered as the aquaculture species with the highest single output value. Advances in selective breeding have accelerated the development of L. vannmei aquaculture. Recently, the genome-wide association studies (GWAS) have been applied in aquaculture animals and markers associated with economic traits were identified. In this study, we focused on the growth trait of L. vannamei and performed GWAS to identify SNPs or genes associated with growth. Genomic regions in linkage group 7, 27, 33, and 38 were identified to be associated with body weight and body length of the shrimp. Further, candidate gene association analysis was performed in two independent populations and the result demonstrated that the SNPs in the genes protein kinase C delta type and ras-related protein Rap-2a were significantly associated with the growth trait of L. vannamei. This study showed that GWAS analysis is an efficient approach for screening trait-related markers or genes. The genomic regions and genes identified in this study are essential for further fine mapping of growth-related genes. The identified markers will provide useful information for marker-assisted selection in L. vannamei.

Multiple interacting QTLs affect disease challenge survival in common carp (Cyprinus carpio)

With the steady growth of the human population, food security becomes a prime challenge. Aquaculture is the fastest growing sector providing proteins from an animal source, but outbreaks of infectious diseases repeatedly hamper the production and further development of this sector. Breeding of disease-resistant strains is a desired sustainable solution to this problem. Cyprinid herpes virus-3 (CyHV-3) is a dsDNA virus damaging production of common carp, an important food and ornamental fish. Previously, we have demonstrated successful introgression of CyHV-3 resistance from a feral strain to commercial strains. Here, we used genotyping by sequencing to identify two novel quantitative trait loci (QTLs) for disease survival that map to different linkage groups than two other QTLs that we previously identified. Effects of these four QTLs were validated and further studied in 14 families with various levels of disease resistance. CyHV-3 survival was found to be a quantitative trait conditioned by mild additive QTL effects and by intricate dominant allelic and epistatic QTL-QTL interactions. Both rare feral alleles and alleles common to feral and cultured strains contributed to survival. This and other advantages of feral alleles introgression were demonstrated. These QTLs, which affected survival of individuals within families, had no significant effect on variation in cumulative family % survival, suggesting that more between family variation remains to be explored. Unraveling the underlying genetics of survival is important for enhancing the breeding of resistant strains and our knowledge of disease resistance mechanisms.

A High-Density Genetic Linkage Map and QTL Mapping for Sex in Black Tiger Shrimp (Penaeus monodon)

The black tiger shrimp, Penaeus monodon, is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.

High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab (Scylla paramamosain)

Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.

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.

Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish (Ictalurus punctatus)

A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F₁ family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.

Genomic, Transcriptomic, and Epigenomic Features Differentiate Genes That Are Relevant for Muscular Polyunsaturated Fatty Acids in the Common Carp

Polyunsaturated fatty acids (PUFAs) are a set of important nutrients that mainly include arachidonic acid (ARA4), docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and α-linolenic acid (ALA). Recently, fish-derived PUFAs have been associated with cardiovascular health, fetal development, and improvement of brain functions. Studies have shown that fish muscular tissues are rich in PUFAs, which are influenced by various factors, including genetic variations, regulatory profiles, and methylation status of desaturase genes during fatty acid desaturation and elongation processes. However, the genetic mechanism and the pathways involved in fatty acid metabolism in fishes remain unclear. The overall aim of this study was to assess differences in gene expression responses among fishes with different fatty acid levels. To achieve this goal, we conducted genome-wide association analysis (GWAS) using a 250K SNP array in a population of 203 samples of common carp (Cyprinus carpio) and identified nine SNPs and 15 genes associated with muscular PUFA content. Then, RNA-Seq and whole genome bisulfite sequencing (WGBS) of different groups with high and low EPA, DHA, ARA4, and ALA contents in muscle, liver and brain tissues were conducted, resulting in 6,750 differentially expressed genes and 5,631 genes with differentially methylated promoters. Gene ontology and KEGG pathway enrichment analyses of RNA-Seq and WGBS results identified enriched pathways for fatty acid metabolism, which included the adipocytokine signaling pathway, ARA4 and linoleic acid metabolism pathway, and insulin signaling pathway. Integrated analysis indicated significant correlations between gene expression and methylation status among groups with high and low PUFA contents in muscular tissues. Taken together, these multi-level results uncovered candidate genes and pathways that are associated with fatty acid metabolism and paved the way for further genomic selection and carp breeding for PUFA traits.

Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain

Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.

A high-density genetic linkage map and QTL mapping for growth and sex of yellow drum (Nibea albiflora)

A high-density genetic linkage map is essential for the studies of comparative genomics and gene mapping, and can facilitate assembly of reference genome. Herein, we constructed a high-density genetic linkage map with 8,094 SNPs selected from 113 sequenced fish of a F1 family. Ultimately, the consensus map spanned 3818.24 cM and covered nearly the whole genome (99.4%) with a resolution of 0.47 cM. 1,457 scaffolds spanning 435.15 Mb were anchored onto 24 linkage groups, accounting for 80.7% of the draft genome assembly of the yellow drum. Comparative genomic analyses with medaka and zebrafish genomes showed superb chromosome-scale synteny between yellow drum and medaka. QTL mapping and association analysis congruously revealed 22 QTLs for growth-related traits and 13 QTLs for sex dimorphism. Some important candidate genes such as PLA2G4A, BRINP3 and P2RY1 were identified from these growth-related QTL regions. A gene family including DMRT1, DMRT2 and DMRT3 was identified from these sex-related QTL regions on the linkage group LG9. We demonstrate that this linkage map can facilitate the ongoing marker-assisted selection and genomic and genetic studies for yellow drum.

Shared Genomic Regions Underlie Natural Variation in Diverse Toxin Responses

Phenotypic complexity is caused by the contributions of environmental factors and multiple genetic loci, interacting or acting independently. Studies of yeast and Arabidopsis often find that the majority of natural variation across phenotypes is attributable to independent additive quantitative trait loci (QTL). Detected loci in these organisms explain most of the estimated heritable variation. By contrast, many heritable components underlying phenotypic variation in metazoan models remain undetected. Before the relative impacts of additive and interactive variance components on metazoan phenotypic variation can be dissected, high replication and precise phenotypic measurements are required to obtain sufficient statistical power to detect loci contributing to this missing heritability. Here, we used a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to detect loci underlying responses to 16 different toxins, including heavy metals, chemotherapeutic drugs, pesticides, and neuropharmaceuticals. Using linkage mapping, we identified 82 QTL that underlie variation in responses to these toxins, and predicted the relative contributions of additive loci and genetic interactions across various growth parameters. Additionally, we identified three genomic regions that impact responses to multiple classes of toxins. These QTL hotspots could represent common factors impacting toxin responses. We went further to generate near-isogenic lines and chromosome substitution strains, and then experimentally validated these QTL hotspots, implicating additive and interactive loci that underlie toxin-response variation.

Genetic Mapping of Head Size Related Traits in Common Carp (Cyprinus carpio)

Head size is important economic trait for many aquaculture fish which is directly linked to their carcass yield. The genetic basis of head size trait remains unclear in many widely cultured fish species. Common carp (Cyprinus carpio) is one of the most widely studied fish due to its importance on both economic and environmental aspects. In this study, we performed genome-wide association study using 433 Yellow River carp individuals from multiple families to identify loci and genes potentially associated with head size related traits including head length (HL), head length/body length ratio (HBR), eye diameter (ED), and eye cross (EC). QTL mapping was utilized to filter the effects of population stratification and improve power for the candidates identification in the largest surveyed family with a published genetic linkage map. Twelve SNPs showed significant for head size traits in GWAS and 18 QTLs were identified in QTL mapping. Our study combining both GWAS and QTL mapping could compensate the deficiency from each other and advance our understanding of head size traits in common carp. To acquire a better understanding of the correlation between head size and body growth, we also performed comparisons between QTLs of head size traits and growth-related traits. Candidate genes underlying head size traits were identified surrounding the significant SNPs, including parvalbumin, srpk2, fsrp5, igf1, igf3, grb10, igf1r, notch2, sfrp2. Many of these genes have been identified with potential functions on bone formation and growth. Igf1 was a putative gene associated with both head size and body growth in Yellow River carp. The teleost-specific igf3 was a candidate head size related gene, related to both HL and HBR. Our study also indicated the importance of Igf signaling pathway for both growth and head size determination in common carp, which could be potentially used in future selective breeding in common carp as well as other species.

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

Common carp (Cyprinus carpio) is one of the most widely studied fish species due to its great economic value and strong environmental adaptability. Scattered scale, a typical phenotype of the mirror carp that is derived from Europe, has never been observed in the Yellow River carp previously. We recently identified approximately one fourth of the F1 progenies displaying scattered scale in a full-sib Yellow River carp family in our breeding program, despite both parents that showed wild type with normal scale patterns. This family provides us unique materials to investigate the genetic basis underlying the abnormal scale mutant in Yellow River carp population. Genome-wide association study (GWAS) and association mapping were performed based on genome-wide single nucleotide polymorphisms (SNP) genotyped with common carp 250 K SNP genotyping array in 82 samples of the Yellow River carp family. We identified a 1.4 Mb genome region that was significantly associated with abnormal scattered scale patterns. We further identified a deletion mutation in fibroblast growth factor receptor 1 a1 (fgfr1a1) gene within this genome region. Amplification and sequencing analysis of this gene revealed a 311-bp deletion in intron 10 and exon 11, which proved that fgfr1a1 could be the causal gene responsible for abnormal scattered scale in the Yellow River carp family. Since similar fragment mutation with 306-bp and 310-bp deletions had been previously reported as causal mutation of scattered scale patterns in the mirror carp, we speculate that either the deletion mutation was introduced from Europe-derived mirror carp or the deletion independently occurred in the mutation hotspot in fgfr1a1 gene. The results provided insights into the genetic basis of scale pattern mutant in Yellow River carp population, which would help us to eliminate the recessive allele of the abnormal scale patterns in Yellow River carp population by molecular marker-assisted breeding.

Construction of a high-density genetic map and fine QTL mapping for growth and nutritional traits of Crassostrea gigas

BACKGROUND

Both growth and nutritional traits are important economic traits of Crassostrea gigas (C. gigas) in industry. But few work has been done to study the genetic architecture of nutritional traits of the oyster. In this study, we constructed a high-density genetic map of C. gigas to help assemble the genome sequence onto chromosomes, meanwhile explore the genetic basis for nutritional traits via quantitative trait loci (QTL) mapping.

RESULTS

The constructed genetic map contained 5024 evenly distributed markers, with an average marker interval of 0.68 cM, thus representing the densest genetic map produced for the oyster. According to the high collinearity between the consensus map and the oyster genome, 1574 scaffold (about 70%) of the genome sequence of C. gigas were successfully anchored to 10 linkage groups (LGs) of the consensus map. Using this high-qualified genetic map, we then conducted QTL analysis for growth and nutritional traits, the latter of which includes glycogen, amino acid (AA), and fatty acid (FA). Overall, 41 QTLs were detected for 17 traits. In addition, six candidate genes identified in the QTL interval showed significant correlation with the traits on transcriptional levels. These genes include growth-related genes AMY and BMP1, AA metabolism related genes PLSCR and GR, and FA metabolism regulation genes DYRK and ADAMTS.

CONCLUSION

Using the constructed high-qualified linkage map, this study not only assembled nearly 70% of the oyster genome sequence onto chromosomes, but also identified valuable markers and candidate genes for growth and nutritional traits, especially for AA and FA that undergone few studies before. These findings will facilitate genome assembly and molecular breeding of important economic traits in C. gigas.

A high-resolution genetic linkage map and QTL fine mapping for growth-related traits and sex in the Yangtze River common carp (Cyprinus carpio haematopterus)

Background

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection for economic traits in aquaculture species. The Yangtze River common carp (Cyprinus carpio haematopterus) is one of the most important aquacultured strains in China. However, quite limited genetics and genomics resources have been developed for genetic improvement of economic traits in such strain.

Results

A high-resolution genetic linkage map was constructed by using 7820 2b-RAD (2b-restriction site-associated DNA) and 295 microsatellite markers in a F2 family of the Yangtze River common carp (C. c. haematopterus). The length of the map was 4586.56 cM with an average marker interval of 0.57 cM. Comparative genome mapping revealed that a high proportion (70%) of markers with disagreed chromosome location was observed between C. c. haematopterus and another common carp strain (subspecies) C. c. carpio. A clear 2:1 relationship was observed between C. c. haematopterus linkage groups (LGs) and zebrafish (Danio rerio) chromosomes. Based on the genetic map, 21 QTLs for growth-related traits were detected on 12 LGs, and contributed values of phenotypic variance explained (PVE) ranging from 16.3 to 38.6%, with LOD scores ranging from 4.02 to 11.13. A genome-wide significant QTL (LOD = 10.83) and three chromosome-wide significant QTLs (mean LOD = 4.84) for sex were mapped on LG50 and LG24, respectively. A 1.4 cM confidence interval of QTL for all growth-related traits showed conserved synteny with a 2.06 M segment on chromosome 14 of D. rerio. Five potential candidate genes were identified by blast search in this genomic region, including a well-studied multi-functional growth related gene, Apelin.

Conclusions

We mapped a set of suggestive and significant QTLs for growth-related traits and sex based on a high-density genetic linkage map using SNP and microsatellite markers for Yangtze River common carp. Several candidate growth genes were also identified from the QTL regions by comparative mapping. This genetic map would provide a basis for genome assembly and comparative genomics studies, and those QTL-derived candidate genes and genetic markers are useful genomic resources for marker-assisted selection (MAS) of growth-related traits in the Yangtze River common carp.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4613-1) contains supplementary material, which is available to authorized users.

Whole Genome Sequencing of Greater Amberjack (Seriola dumerili) for SNP Identification on Aligned Scaffolds and Genome Structural Variation Analysis Using Parallel Resequencing

Greater amberjack (Seriola dumerili) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology. The assembled sequences were aligned onto a yellowtail (Seriola quinqueradiata) radiation hybrid (RH) physical map by sequence homology. A total of 215 of the longest amberjack sequences, with a total length of 622.8 Mbp (92% of the total length of the genome scaffolds), were lined up on the yellowtail RH map. We resequenced the whole genomes of 20 greater amberjacks and mapped the resulting sequences onto the reference genome sequence. About 186,000 nonredundant SNPs were successfully ordered on the reference genome. Further, we found differences in the genome structural variations between two greater amberjack populations using BreakDancer. We also analyzed the greater amberjack transcriptome and mapped the annotated sequences onto the reference genome sequence.

Accuracy of Genomic Evaluations of Juvenile Growth Rate in Common Carp (Cyprinus carpio) Using Genotyping by Sequencing

Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key production traits. In the current study, a population of 1,425 carp juveniles, originating from a partial factorial cross between 40 sires and 20 dams, was used for investigating the potential of genomic selection (GS) for juvenile growth, an exemplar polygenic production trait. RAD sequencing was used to identify and genotype SNP markers for subsequent parentage assignment, construction of a medium density genetic map (12,311 SNPs), genome-wide association study (GWAS), and testing of GS. A moderate heritability was estimated for body length of carp at 120 days (as a proxy of juvenile growth) of 0.33 (s.e. 0.05). No genome-wide significant QTL was identified using a single marker GWAS approach. Genomic prediction of breeding values outperformed pedigree-based prediction, resulting in 18% improvement in prediction accuracy. The impact of reduced SNP densities on prediction accuracy was tested by varying minor allele frequency (MAF) thresholds, with no drop in prediction accuracy until the MAF threshold is set <0.3 (2,744 SNPs). These results point to the potential for GS to improve economically important traits in common carp breeding programs.

Identification of novel genes significantly affecting growth in catfish through GWAS analysis

Growth is the most important economic trait in aquaculture. Improvements in growth-related traits can enhance production, reduce costs and time to produce market-size fish. Catfish is the major aquaculture species in the United States, accounting for 65% of the US finfish production. However, the genes underlying growth traits in catfish were not well studied. Currently, the majority of the US catfish industry uses hybrid catfish derived from channel catfish female mated with blue catfish male. Interestingly, channel catfish and blue catfish exhibit differences in growth-related traits, and therefore the backcross progenies provide an efficient system for QTL analysis. In this study, we conducted a genome-wide association study for catfish body weight using the 250 K SNP array with 556 backcross progenies generated from backcross of male F1 hybrid (female channel catfish × male blue catfish) with female channel catfish. A genomic region of approximately 1 Mb on linkage group 5 was found to be significantly associated with body weight. In addition, four suggestively associated QTL regions were identified on linkage groups 1, 2, 23 and 24. Most candidate genes in the associated regions are known to be involved in muscle growth and bone development, some of which were reported to be associated with obesity in humans and pigs, suggesting that the functions of these genes may be evolutionarily conserved in controlling growth. Additional fine mapping or functional studies should allow identification of the causal genes for fast growth in catfish, and elucidation of molecular mechanisms of regulation of growth in fish.