Construction of a high-density linkage map and mapping of sex determination and growth-related loci in the mandarin fish (Siniperca chuatsi)

Genome-wide identification, evolution and expression of TGF-β signaling pathway members in mandarin fish (Siniperca chuatsi)

Members of the transforming growth factor β (TGF-β) signaling pathway regulate diverse cellular biological processes in embryonic and tissue development. We took mandarin fish (Siniperca chuatsi) as the research object to identify all members of the TGF-β signaling pathway, measure their expression pattern in the key period post hatching, and further explore their possible role in the process of sex regulation. Herein, we identified eighty-three TGF-β signaling pathway members and located them on chromosomes based on the genome of mandarin fish. TGF-β signaling pathway members were highly conserved since each TGF-β subfamily clustered with orthologs from other species. Transcriptome analysis, qRT-PCR and in situ hybridization demonstrated that most mandarin fish TGF-β signaling pathway members presented stage-specific and/or sex-dimorphic expression during gonadal development, and different members of the TGF-β signaling pathway participated in different stages of gonadal development. Taken together, our results provide new insight into the role of TGF-β signaling pathway members in the sex regulation of mandarin fish.

Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita

In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.

Master-Key Regulators of Sex Determination in Fish and Other Vertebrates-A Review

In vertebrates, mainly single genes with an allele ratio of 1:1 trigger sex-determination (SD), leading to initial equal sex-ratios. Such genes are designated master-key regulators (MKRs) and are frequently associated with DNA structural variations, such as copy-number variation and null-alleles. Most MKR knowledge comes from fish, especially cichlids, which serve as a genetic model for SD. We list 14 MKRs, of which dmrt1 has been identified in taxonomically distant species such as birds and fish. The identification of MKRs with known involvement in SD, such as amh and fshr, indicates that a common network drives SD. We illustrate a network that affects estrogen/androgen equilibrium, suggesting that structural variation may exert over-expression of the gene and thus form an MKR. However, the reason why certain factors constitute MKRs, whereas others do not is unclear. The limited number of conserved MKRs suggests that their heterologous sequences could be used as targets in future searches for MKRs of additional species. Sex-specific mortality, sex reversal, the role of temperature in SD, and multigenic SD are examined, claiming that these phenomena are often consequences of artificial hybridization. We discuss the essentiality of taxonomic authentication of species to validate purebred origin before MKR searches.

Screening of Genes Related to Sex Determination and Differentiation in Mandarin Fish (Siniperca chuatsi)

Mandarin fish has an XX/XY sex-determination system. The female mandarin fish is typically larger than the male. Sex identification and the discovery of genes related to sex determination in mandarin fish have important theoretical significance in the elucidation of the regulation and evolutionary mechanism of animal reproductive development. In this study, the chromosome-level genome of a female mandarin fish was assembled, and we found that LG24 of the genome was an X chromosome. A total of 61 genes on the X chromosome showed sex-biased expression. Only six gonadal genes (LG24G00426, LG24G003280, LG24G003300, LG24G003730, LG24G004200, and LG24G004770) were expressed in the testes, and the expression of the other gene LG24G003870 isoform 1 in the ovaries was significantly higher than that in the testes (p < 0.01). Five (except LG24G003280 and LG24G003300) of the seven aforementioned genes were expressed at the embryonic development stage, suggesting their involvement in early sex determination. The expression of LG24G004770 (encoding HS6ST 3-B-like) was also significantly higher in female muscles than in male muscles (p < 0.01), indicating other functions related to female growth. ZP3 encoded by LG24G003870 isoform 1 increased the C-terminal transmembrane domain, compared with that encoded by other fish zp3 isoforms, indicating their different functions in sex determination or differentiation. This study provides a foundation for the identification of sex-determining genes in mandarin fish.

Comparative Analysis of the Gut Microbiota of Mandarin Fish (Siniperca chuatsi) Feeding on Compound Diets and Live Baits

Siniperca chuatsi feeds on live fry throughout their life. The sustainable development of its farming industry has urgently necessitated the development of artificial diets to substitute live baits. It has been demonstrated that gut microbiota assists in feed adaptation and improves the feed conversion rate in fish. Therefore, this study aimed to understand the potential role of intestinal microorganisms in the domestication of S. chuatsi with a compound diet. Accordingly, we performed 16S rRNA sequencing of the gut microbial communities in S. chuatsi groups that were fed a compound diet (including large and small individuals) and live baits. A total of 2,471 OTUs were identified, and the large individual group possessed the highest number of unique OTUs. The α-diversity index of the gut microbiota in groups that were fed a compound diet was significantly higher (p < 0.05) than that in the live bait group. There were no significant differences in the α-diversity between the large and small individual groups. However, relatively higher numbers of Lactococcus, Klebsiella, and Woeseia were observed in the intestines of the large individual group. Prediction of the metabolic function of the microbiota among these three fish groups by Tax4Fun revealed that most metabolic pathways, such as glycan metabolism and amino acid metabolism, were typically more enriched for the larger individuals. The results indicated that certain taxa mentioned above exist in large individuals and may be closely related to the digestion and absorption of compound diets. The present study provides a basis for understanding the utilization mechanism of artificial feed by S. chuatsi.

Application of Untargeted Metabolomics to Reveal the Taste-Related Metabolite Profiles during Mandarin Fish (Siniperca chuatsi) Fermentation

Spontaneous fermentation is a critical processing step that determines the taste quality of fermented mandarin fish (Siniperca chuatsi). Here, untargeted metabolomics using ultra-high-performance liquid chromatography coupled with Q Exactive tandem mass spectrometry was employed to characterize the taste-related metabolite profiles during the fermentation of mandarin fish. The results demonstrated that the taste profiles of mandarin fish at different stages of fermentation could be distinguished using an electronic tongue technique. Sixty-two metabolites, including amino acids, small peptides, fatty acids, alkaloids, and organic acids, were identified in fermented mandarin fish samples. Additional quantitative analysis of amino acids revealed glutamic acid and aspartic acid as significant contributors to the fresh flavor. Furthermore, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that amino acid metabolism was the dominant pathway throughout the fermentation process. This study provides a scientific and theoretical reference for the targeted regulation of the quality of fermented mandarin fish.

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

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

Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus

Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.

Identification and expression analysis of sixteen Toll-like receptor genes, TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR7-9, TLR13a-c, TLR14, TLR21-23 in mandarin fish Siniperca chuatsi

Toll-like receptors (TLRs), as a family of pattern recognition receptors (PRRs), possess specific pathogen-related molecular pattern (PAMP) recognition spectrum in inducing immune responses. In this study, sixteen TLRs were identified and characterized in mandarin fish (Siniperca chuatsi). All these TLRs consist of leucine-rich repeats (LRRs), a transmembrane domain and a Toll/interleukin-I receptor (TIR) domain, with the exception of TLR5S which lacks TIR domain, and they can be clustered into five branches, i.e. TLR1 subfamily, TLR3 subfamily, TLR5 subfamily, TLR7 subfamily and TLR11 subfamily in phylogenetic tree. These TLR genes were expressed in all tested tissues and had high expression levels in immune-related tissues such as head-kidney and spleen or mucosa-related tissues such as intestine and pyloric caecum. The transcripts of TLR2a, TLR2b, TLR3, TLR13a, TLR14, TLR22 and TLR23 were all significantly up-regulated after stimulation with poly(I:C); TLR1, TLR2a, TLR2b, TLR3, TLR5M, TLR5S, TLR13a and TLR13b transcripts were all significantly up-regulated after stimulation with PGN; and TLR2a, TLR2b, TLR5M, TLR5S, TLR7, TLR8, TLR9, TLR13c, TLR14 and TLR22 transcripts were all significantly up-regulated after stimulation with LPS in isolated head kidney lymphocytes of mandarin fish. The findings in this study may provide a valuable basis for functional study on TLR genes in mandarin fish.

A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi)

The mandarin fish, Siniperca chuatsi, is an economically important perciform species with widespread aquaculture practices in China. Its special feeding habit, acceptance of only live prey fishes, contributes to its delicious meat. However, little is currently known about related genetic mechanisms. Here, we performed whole-genome sequencing and assembled a 758.78 Mb genome assembly of the mandarin fish, with the scaffold and contig N50 values reaching 2.64 Mb and 46.11 Kb, respectively. Approximately 92.8% of the scaffolds were ordered onto 24 chromosomes (Chrs) with the assistance of a previously established genetic linkage map. The chromosome-level genome contained 19,904 protein-coding genes, of which 19,059 (95.75%) genes were functionally annotated. The special feeding behavior of mandarin fish could be attributable to the interaction of a variety of sense organs (such as vision, smell, and endocrine organs). Through comparative genomics analysis, some interesting results were found. For example, olfactory receptor (OR) genes (especially the beta and delta types) underwent a significant expansion, and endocrinology/vision related npy, spexin, and opsin genes presented various functional mutations. These may contribute to the special feeding habit of the mandarin fish by strengthening the olfactory and visual systems. Meanwhile, previously identified sex-related genes and quantitative trait locis (QTLs) were localized on the Chr14 and Chr17, respectively. 155 toxin proteins were predicted from mandarin fish genome. In summary, the high-quality genome assembly of the mandarin fish provides novel insights into the feeding habit of live prey and offers a valuable genetic resource for the quality improvement of this freshwater fish.

A high-density genetic linkage map for Chinese perch (Siniperca chuatsi) using 2.3K genotyping-by-sequencing SNPs

Chinese perch, Siniperca chuatsi (Basilewsky), is one of the most commercially important cultured fishes in China. In the present study, a high-density genetic linkage map of Chinese perch was constructed by genotyping-by-sequencing technique with an F1 mapping panel containing 190 progenies. A total of 2328 SNPs were assigned to 24 linkage groups (LGs), agreeing with the chromosome haploid number in this species (n = 24). The sex-averaged map covered 97.9% of the Chinese perch genome, with the length of 1694.3 cM and a marker density of 0.7 cM/locus. The number of markers per LG ranged from 57 to 222, with a mean of 97. The length of LGs varied from 43.2 to 108.2 cM, with a mean size of 70.6 cM. The recombination rate of females was 1.5:1, which was higher than that of males. To better understand the distribution pattern of segregation distortion between the two sexes of Chinese perch, the skewed markers were retained and used to reconstruct the sex-specific maps. The 16 segregation distortion regions were identified on 10 LGs of the female map, while 12 segregation distortion regions on eight LGs of the male map. Among these LGs, six LGs matched between the sex-specific maps. This high-density linkage map could provide a solid basis for identifying QTL associated with economically important traits, and for implementing marker-assisted selection breeding of Chinese perch.

A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli

BACKGROUND

A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits.

RESULTS

By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map' length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation.

CONCLUSIONS

We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.

Genomics to accelerate genetic improvement in tilapia

Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.

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.

Identification of male heterogametic sex-determining regions on the Atlantic herring Clupea harengus genome

The sex determination system of Atlantic herring Clupea harengus L., a commercially important fish, was investigated. Low coverage whole-genome sequencing of 48 females and 55 males and a genome-wide association study revealed two regions on chromosomes 8 and 21 associated with sex. The genotyping data of the single nucleotide polymorphisms associated with sex showed that 99.4% of the available female genotypes were homozygous, whereas 68.6% of the available male genotypes were heterozygous. This is close to the theoretical expectation of homo/heterozygous distribution at low sequencing coverage when the males are factually heterozygous. This suggested a male heterogametic sex determination system in C. harengus, consistent with other species within the Clupeiformes group. There were 76 protein coding genes on the sex regions but none of these genes were previously reported master sex regulation genes, or obviously related to sex determination. However, many of these genes are expressed in testis or ovary in other species, but the exact genes controlling sex determination in C. harengus could not be identified.

Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis

The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.

ddRADseq-assisted construction of a high-density SNP genetic map and QTL fine mapping for growth-related traits in the spotted scat (Scatophagus argus)

BACKGROUND

Scatophagus argus is a popular farmed fish in several countries of Southeast Asia, including China. Although S. argus has a highly promising economic value, a significant lag of breeding research severely obstructs the sustainable development of aquaculture industry. As one of the most important economic traits, growth traits are controlled by multiple gene loci called quantitative trait loci (QTLs). It is urgently needed to launch a marker assisted selection (MAS) breeding program to improve growth and other pivotal traits. Thus a high-density genetic linkage map is necessary for the fine mapping of QTLs associated with target traits.

RESULTS

Using restriction site-associated DNA sequencing, 6196 single nucleotide polymorphism (SNP) markers were developed from a full-sib mapping population for genetic map construction. A total of 6193 SNPs were grouped into 24 linkage groups (LGs), and the total length reached 2191.65 cM with an average marker interval of 0.35 cM. Comparative genome mapping revealed 23 one-to-one and 1 one-to-two syntenic relationships between S. argus LGs and Larimichthys crocea chromosomes. Based on the high-quality linkage map, a total of 44 QTLs associated with growth-related traits were identified on 11 LGs. Of which, 19 significant QTLs for body weight were detected on 9 LGs, explaining 8.8-19.6% of phenotypic variances. Within genomic regions flanking the SNP markers in QTL intervals, we predicted 15 candidate genes showing potential relationships with growth, such as Hbp1, Vgll4 and Pim3, which merit further functional exploration.

CONCLUSIONS

The first SNP genetic map with a fine resolution of 0.35 cM for S. argus has been developed, which shows a high level of syntenic relationship with L. crocea genomes. This map can provide valuable information for future genetic, genomic and evolutionary studies. The QTLs and SNP markers significantly associated with growth-related traits will act as useful tools in gene mapping, map-based cloning and MAS breeding to speed up the genetic improvement in important traits of S. argus. The interesting candidate genes are promising for further investigations and have the potential to provide deeper insights into growth regulation in the future.

Fine Mapping of the High-pH Tolerance and Growth Trait-Related Quantitative Trait Loci (QTLs) and Identification of the Candidate Genes in Pacific White Shrimp (Litopenaeus vannamei)

High-pH tolerance and growth are important traits for the shrimp culture industry in areas with saline-alkali water. In the present study, an F1 full-sib family of Pacific white shrimp (Litopenaeus vannamei) was generated with a new "semidirectional cross" method, and double-digest restriction site-associated DNA sequencing (ddRAD-Seq) technology was applied to genotype the 2 parents and 148 progenies. A total of 3567 high-quality markers were constructed for the genetic linkage map, and the total map length was 4161.555 centimorgans (cM), showing 48 linkage groups (LGs) with an average interlocus length of 1.167 cM. With a constrained logarithm of odds (LOD) score ≥ 2.50, 12 high-pH tolerance and 2 growth (body weight) QTLs were located. L. vannamei genomic scaffolds were used to assist with the detection of 21 stress- and 5 growth-related scaffold genes. According to the high-pH transcriptome data of our previous study, 6 candidate high-pH response genes were discovered, and 5 of these 6 genes were consistently expressed with the high-pH transcriptome data, validating the locations of the high-pH tolerance trait-related QTLs in this study. This paper is the first report of fine-mapping high-pH tolerance and growth (body weight) trait QTLs in one L. vannamei genetic map. Our results will further benefit marker-assisted selection work and might be useful for promoting genomic research on the shrimp L. vannamei.

QTL Fine Mapping for Sex Determination Region in Bighead Carp (Hypophthalmichthys nobilis) and Comparison with Silver Carp (Hypophthalmichthys molitrix)

Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix) are genetically close aquaculture fish in the Cyprinidae, which have been confirmed to hold XX/XY sex determination. However, genomic locations of potential sex-related loci in these two fishes are still unknown. In this study, a high-resolution genetic linkage map was constructed by using 2976 SNP and 924 microsatellite markers in a F1 full-sib family of bighead carp, the length of which spanned 2022.34 cM with an average inter-marker distance of 0.52 cM. Comparative genomics revealed a high level of genomic synteny between bighead carp and zebrafish as well as grass carp. QTL fine mapping for sex trait was performed based on this linkage map of bighead carp and an unpublished linkage map of silver carp. A map distance of 3.863 cM (69.787-73.650 cM) on LG19 of bighead carp and 4.705 cM (79.096-83.801 cM) on LG21 of silver carp was significantly associated with sex phenotypes, and these two LGs are homologous between two fish species. Fourteen markers harboring in these regions were in strong linkage disequilibrium with the sex phenotype variance explained (PVE) varying from 89 to 100%. Two common markers were mapped on the QTL regions of bighead carp and silver carp, suggesting that these two carp species may have similar genetic bases for sex determination. Eleven potentially sex-related genes were identified within or near the sex QTL markers in two species. This study provided insights into elucidating mechanisms and evolution of sex determination in cyprinid fishes.

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.

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.

High-Density Linkage Map and Mapping for Sex and Growth-Related Traits of Largemouth Bass (Micropterus salmoides)

The largemouth bass is an important species, and its culture has risen sharply with the surge in fish aquaculture in China. Due to the lack of selective breeding technology for the largemouth bass, the growth rate and disease resistance are low, its sexual maturation is slow, and other serious problems are contributing to a sharp decline in the safety and quality of largemouth bass products in recent decades. Therefore, comprehensive breeding programs to improve the economic performance and promote the modern industrial development of largemouth bass must be considered a priority. Here, a total of 152 adult largemouth bass, including two parents and 150 progenies, were selected to produce the genetic mapping family. Then, a high-density linkage map was constructed based on restriction site–associated DNA sequencing using 6,917 single-nucleotide polymorphisms (SNPs) located in 24 linkage groups (LGs). The total genetic length of the linkage map was 1,261.96 cM, and the length of each LG varied from 24.72 cM for LG02 to 117.53 cM for LG16, with an average length of 52.58 cM and an average SNP number of 286. Thirteen significant quantitative trait loci (QTLs) for sex determination were located on LG04, LG05, LG08, LG12, LG15, LG21, and LG23. An informative QTL cluster that included six QTLs was detected on LG12. However, one notable QTL, which accounted for 71.48% of the total phenotypic variation, was located in the region of 1.85 cM on LG05. In addition, 32 identified QTLs were related to growth, including body weight, body length, body height, and head length. The QTLs for these growth-related traits are located in 13 LG regions and have little effect on phenotypic variation. This high-density genetic linkage map will enable the fine-mapping of economic traits and support the future genome assembly of the largemouth bass. Additionally, our study will be useful for future selective culture of largemouth bass and could potentially be used in molecular-assisted breeding of largemouth bass for aquaculture.

Mapping and Validating QTL for Fatty Acid Compositions and Growth Traits in Asian Seabass

Asian seabass is an important food fish species. While improving growth, increasing the nutritional value is important, omega-3 fatty acids are indispensable to human health. Identifying and validating DNA markers associated with traits is the first step towards marker-assisted selection (MAS). We quantified 13 different fatty acids and three growth traits in 213 F₂ Asian seabass from a family at the age 270 days post hatch, and screened QTL for these traits. The content of total fatty acids in 100 g flesh was 2.57 ± 0.80 g, while the proportions of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) were 16.96 ± 2.20% and 5.42 ± 0.90%, respectively. A linkage map with 2424 SNPs was constructed and used for QTL mapping. For fatty acid compositions, 14 significant QTL were identified on three linkage groups (LG5, LG11 and LG14), with phenotypic variance explained (PVE) from 12.8 to 24.6%. Thirty-nine suggestive QTL were detected on 16 LGs. Two significant QTL for EPA were identified on LG5 and LG14, with PVE of 15.2% and 15.1%, respectively. No significant QTL was identified for DHA. For growth traits, six significant and 13 suggestive QTL were identified on two and seven LGs, respectively. Only a few significant QTL for fatty acids overlapped with previously mapped QTL for these traits, suggesting that most QTL detected in a family are family-specific and could only be used in MAS in the family per se. To facilitate population-wide molecular breeding, more powerful methods (e.g. GWAS) should be used to identify SNPs for genomic selection.

Constructing High-Density Genetic Maps and Developing Sexing Markers in Northern Snakehead (Channa argus)

High-density genetic maps are essential for mapping QTL, improving genome assembly, comparative genomics, and studying sex chromosome evolution. The northern snakehead (Channa argus) is an economically important foodfish species with significant sexual dimorphism, where the males grow much faster and bigger than the females. However, to date, the sex determination pattern is still not clear, limiting identification of sex chromosomes, even sex determination genes and development of monosex populations that are valuable for both sex evolution of vertebrates and aquaculture practices. Here, a sex-averaged map and two sex-specific genetic maps were constructed with 2974, 2323, and 2338 SNPs, respectively. Little difference was observed in the pattern of sex-specific recombination between female- and male-specific genetic maps. Genome scan identified a major locus for sex determination at LG16. Females and males are, respectively, homogametic and heterogametic, suggesting an XY sex determination system for this species. By resequencing genomes, InDels in the sex-associated QTL region were discovered and used for developing sex-specific PCR assays for fast sexing of snakehead. These high-density genetic maps provide useful resources for future genomic studies in snakehead and its related species. The PCR assays for sexing are of importance in developing all male populations for aquaculture.

Correlation analysis of mandarin fish (Siniperca chuatsi) growth hormone gene polymorphisms and growth traits

Screening of trait-associated molecular markers can be used to enhance the efficiency of selective breeding. Previously, we produced the first high-density genetic linkage map for the mandarin fish (Siniperca chuatsi) and identified 11 quantitative-trait loci significantly associated with growth, of which one is located within the growth hormone (GH) gene. To investigate the GH gene polymorphisms and their correlation with growth, the complete sequence was cloned and 32 single-nucleotide polymorphisms (SNPs) and one simple-sequence repeat (SSR) were identified. Of which, eight SNPs (G1-G8) and the SSR (GH-AG)were selected for genotyping and correlation analysis with growth traits in a random population. The results showed that the four novel polymorphicloci (G1, G2, G3 and GH-AG) were significantly correlated with growth traits of mandarin fish (P < 0.05). Of these, G1, G3 and GH-AG showed highly significant correlations with multiple growth traits (P < 0.01) and the combined SNP analysis showed that G1-G3 formed four effective diplotypes (D1-D4), among which D1 was highly significantly greater than D4 (P < 0.01) for some important growth traits. In conclusion, our results show that the four polymorphic loci G1-G3 and GH-AG within the mandarin fish GH gene are significantly correlated with growth traits and could be used as candidate molecular markers for selective breedingof superior varieties of mandarin fish.

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.

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.

A European Whitefish Linkage Map and Its Implications for Understanding Genome-Wide Synteny Between Salmonids Following Whole Genome Duplication

Genomic datasets continue to increase in number due to the ease of production for a wider selection of species including non-model organisms. For many of these species, especially those with large or polyploid genomes, highly contiguous and well-annotated genomes are still rare due to the complexity and cost involved in their assembly. As a result, a common starting point for genomic work in non-model species is the production of a linkage map. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g., chromosome number and type or sex-related structural differences, to fine scale patterns e.g., recombination rate variation and co-localization of differentiated regions. Here we present both sex-averaged and sex-specific linkage maps for Coregonus sp. "Albock", a member of the European whitefish lineage (C. lavaretus spp. complex), containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring. We discuss the differences between our sex-averaged and sex-specific maps and identify genome-wide synteny between C. sp. "Albock" and Atlantic Salmon (Salmo salar), which have diverged following the salmonid-specific whole genome duplication. Our analysis confirms that many patterns of synteny observed between Atlantic Salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily. We also show that regions known for their species-specific rediploidization history can pose challenges for synteny identification since these regions have diverged independently in each salmonid species following the salmonid-specific whole genome duplication. The European whitefish map provided here will enable future studies to understand the distribution of loci of interest, e.g., FST outliers, along the whitefish genome as well as assisting with the de novo assembly of a whitefish reference genome.

Highly dense linkage maps from 31 full-sibling families of turbot (Scophthalmus maximus) provide insights into recombination patterns and chromosome rearrangements throughout a newly refined genome assembly

Highly dense linkage maps enable positioning thousands of landmarks useful for anchoring the whole genome and for analysing genome properties. Turbot is the most important cultured flatfish worldwide and breeding programs in the fifth generation of selection are targeted to improve growth rate, obtain disease resistant broodstock and understand sex determination to control sex ratio. Using a Restriction-site Associated DNA approach, we genotyped 18,214 single nucleotide polymorphism in 1,268 turbot individuals from 31 full-sibling families. Individual linkage maps were combined to obtain a male, female and species consensus maps. The turbot consensus map contained 11,845 markers distributed across 22 linkage groups representing a total normalised length of 3,753.9 cM. The turbot genome was anchored to this map, and scaffolds representing 96% of the assembly were ordered and oriented to obtain the expected 22 megascaffolds according to its karyotype. Recombination rate was lower in males, especially around centromeres, and pairwise comparison of 44 individual maps suggested chromosome polymorphism at specific genomic regions. Genome comparison across flatfish provided new evidence on karyotype reorganisations occurring across the evolution of this fish group.

Ultrahigh-Density Linkage Map Construction Using Low-Coverage Whole-Genome Sequencing of a Doubled Haploid Population: Case Study of Torafugu (Takifugu rubripes)

Next-generation sequencing enables genome-wide genotyping of a large population and further facilitates the construction of a genetic linkage map. Low-coverage whole-genome sequencing has been employed for genetic linkage map construction in several species. However, this strategy generally requires available high-quality reference genomes and/or designed inbred pedigree lines, which restrict the scope of application for non-model and unsequenced species. Here, using torafugu (Takifugu rubripes) as a test model, we propose a new strategy for ultrahigh-density genetic linkage map construction using low-coverage whole-genome sequencing of a haploid/doubled haploid (H/DH) population without above requirements. Low-coverage (≈1×) whole-genome sequencing data of 165 DH individuals were used for de novo assembly and further performed single nucleotide polymorphisms (SNPs) calling, resulting in the identification of 1,070,601 SNPs. Based on SNP genotypes and de novo assembly, genotypes were associated with short DNA segments and an ultrahigh-density linkage map was constructed containing information of 802,277 SNPs in 3090 unique positions. Comparative analyses showed near-perfect concordance between the present linkage map and the latest published torafugu genome (FUGU5). This strategy would facilitate ultrahigh-density linkage map construction in various sexually reproducing organisms for which H/DH populations can be generated.

Development of F1 hybrid population and the high-density linkage map for European aspen (Populus tremula L.) using RADseq technology

BACKGROUND

Restriction-site associated DNA sequencing (RADseq) technology was recently employed to identify a large number of single nucleotide polymorphisms (SNP) for linkage mapping of a North American and Eastern Asian Populus species. However, there is also the need for high-density genetic linkage maps for the European aspen (P. tremula) as a tool for further mapping of quantitative trait loci (QTLs) and marker-assisted selection of the Populus species native to Europe.

RESULTS

We established a hybrid F1 population from the cross of two aspen parental genotypes diverged in their phenological and morphological traits. We performed RADseq of 122 F1 progenies and two parents yielding 15,732 high-quality SNPs that were successfully identified using the reference genome of P. trichocarpa. 2055 SNPs were employed for the construction of maternal and paternal linkage maps. The maternal linkage map was assembled with 1000 SNPs, containing 19 linkage groups and spanning 3054.9 cM of the genome, with an average distance of 3.05 cM between adjacent markers. The paternal map consisted of 1055 SNPs and the same number of linkage groups with a total length of 3090.56 cM and average interval distance of 2.93 cM. The linkage maps were employed for QTL mapping of one-year-old seedlings height variation. The most significant QTL (LOD = 5.73) was localized to LG5 (96.94 cM) of the male linkage map, explaining 18% of the phenotypic variation.

CONCLUSIONS

The set of 15,732 SNPs polymorphic in aspen and high-density genetic linkage maps constructed for the P. tremula intra-specific cross will provide a valuable source for QTL mapping and identification of candidate genes facilitating marker-assisted selection in European aspen.

Influence of epistatic segregation distortion loci on genetic marker linkages in Japanese flounder

For genetic linkage analysis of Japanese flounder, 160 doubled haploids (DH) were artificially produced using mitotic gynogenesis and were genotyped for 458 simple sequence repeat (SSR) markers, 101 of which show distortional segregation. The genetic linkage map was constructed by modifying recombination fractions between the distorted markers. Between the corrected and uncorrected genetic maps, there were considerable differences in genetic distance, but not in relative locations among markers. Using a liability model, a segregation distortion locus (SDL), with an additive genetic effect of 1.772, was mapped between markers BDHYP387 and Poli56TUF of chromosome 24 in the corrected genetic map. Additionally, six pairs of epistatic SDLs were identified on chromosomes 1, 5, 8, 9, 23, and 24. Changes in genetic distances between markers did not occur on chromosome regions with main effect SDLs. However, most chromosome regions where genetic distances changed covered the detected epistatic SDLs. This study concluded that epistatic SDLs decrease linkages between markers and lengthen genetic distances in Japanese flounder. This finding has been partially validated in other DH populations derived from three female Japanese flounders.