The environmental analysis and site selection of mussel and large yellow croaker aquaculture areas based on high resolution remote sensing

Mussel aquaculture and large yellow croaker aquaculture areas and their environmental characteristics in Zhoushan were analyzed using satellite data and in-situ surveys.A new two-step remote sensing method was proposed and applied to determine the basic environmental characteristics of the best mussel and large yellow croaker aquaculture areas.This methodology includes the first step of extraction of the location distribution and the second step of the extraction of internal environmental factors.The fishery ranching index(FRI1,FRI2)was established to extract the mussel and the large yellow croaker aquaculture area in Zhoushan,using Gaofen-1(GF-1)and Gaofen-6(GF-6)satellite data with a special resolution of 2 m.In the second step,the environmental factors such as sea surface temperature(SST),chlorophyll a(Chl-a)concentration,current and tide,suspended sediment concentration(SSC)in mussel aquaculture area and large yellow croaker aquaculture area were extracted and analyzed in detail.The results show the following three points.(1)For the extraction of the mussel aquaculture area,FRI1 and FRI2 are complementary,and the combination of FRI1 and FRI2 is suitable to extract the mussel aquaculture area.As for the large yellow croaker aquaculture area extraction,FRI2 is suitable.(2)Mussel aquaculture and the large yellow croaker aquaculture area in Zhoushan are mainly located on the side near the islands that are away from the eastern open waters.The water environment factor template suitable for mussel and large yellow croaker aquaculture was determined.(3)This two-step remote sensing method can be used for the preliminary screening of potential site selection for the mussels and large yellow croaker aquaculture area in the future.the fishery ranching index(FRI1,FRI2)in this paper can be applied to extract the mussel and large yellow croaker aquaculture areas in coastal waters around the world.

Spatial-temporal dynamics of bacterioplankton communities in the breeding area of large yellow croaker Larimichthys crocea in Sansha Bay,China

As an important spawning ground for large yellow croaker Larimichthys crocea,Sansha Bay,South China Sea has been a research hotspot.However,studies on the influence of the bacterioplankton community and assessments of its seasonal succession of bacterioplankton in different sea areas in Sansha Bay are still limited.To address the issue,we use 16S rRNA gene amplicon sequencing and functional prediction to investigate the spatial-temporal dynamics of the bacterioplankton community in three distinct areas,i.e.,Breeding Area(BA),Yantian Harbor(YH),and Bay Margin(BM)of Sansha Bay.Results show that the structure of the bacterioplankton community in Sansha Bay had a significant seasonal succession.Moreover,the representative zero-radius Operation Taxon Units in different seasons were significantly different among the three selected sea areas.Specifically,during the breeding season,bacterioplankton communities in BA were characterized by compound-degrading bacteria,such as Rhodococcus and Owenweeksia,while in YH and BM,animal parasites or symbionts such as Vibrio and Arcobacter were dominant.Furthermore,the redundancy analysis and Spearman correlation analysis further explained that water temperature,dissolved oxygen,and ammonia nitrogen were the main environmental factors responsible for the difference.In addition,the bioindicator functions screened by Functional Annotation of Prokaryotic Taxa and random forest machine learning mainly relied on compound degradation,nitrite oxidation,and photoheterotrophy.The compound-degradationcorresponded bacterioplankton genera such as Rhodococcus had relatively higher abundance in BM,while Nitrospina corresponding to nitrite oxidation tended to be abundant in YH and BA.Based on the spatial and temporal variation in the composition and function of bacterioplankton,our findings provide a basis for understanding the theory of bacterioplankton community structure in the inner-bay habitat of the large yellow croaker in Sansha Bay.

Environmental hypoxia induces apoptosis in large yellow croaker Larimichthys crocea via both intrinsic and extrinsic pathways

Hypoxia has become an unfavorable factor affecting the sustainable development of the large yellow croaker Larimichthys crocea,an economically important mariculture fish in China.Apoptosis is a consequence of hypoxia on fish.However,the effects of hypoxia stress on apoptosis in L.crocea remain largely unknown.We investigated the effect of environmental hypoxia on apoptosis in L.crocea.Results show that hypoxia induced apoptosis in L.crocea both in vivo and in vitro.The mitochondrial membrane potential was significantly reduced in large yellow croaker fry(LYCF)cells.The expression levels of Bcell lymphoma/leukemia-2(Bcl-2)m RNA and protein were also significantly decreased in the liver and LYCF cells during 96 h and 48 h of hypoxia stress,respectively,whereas the expression level of Bcl-2 associated X(Bax)mRNA,Casp3 mRNA,and activity of caspase-3/7/9 were significantly increased,indicating that hypoxia induced caspase-dependent intrinsic apoptosis in L.crocea.The expression level of the apoptosis-inducing factor(AIF)protein was significantly increased in the liver and LYCF cells.The level of AIF protein was significantly decreased in the cytoplasm but increased in the nuclei of L.crocea,demonstrating that hypoxia induced the AIF-mediated caspase-independent intrinsic apoptosis.In addition,the activity of caspase-8 was significantly increased,indicating that hypoxia stress induced extrinsic apoptosis in L.crocea.Therefore,hypoxia induced apoptosis in L.crocea through both the intrinsic and extrinsic pathways.The present study accumulated basic biological information to help elucidate the mechanism of hypoxia response in marine fish.

Replacement of Dietary Fish Oil with Vegetable Oils Improves the Growth and Flesh Quality of Large Yellow Croaker(Larmichthys crocea)

We investigated the effect of the replacement of dietary fish oil with vegetable oils on the growth and flesh quality of large yellow croaker(Larmichthys crocea). The basal diet(FO) was formulated to contain 66.5% fish meal and 6.4% menhaden fish oil; whereas the other 3 experimental diets were formulated by replacing the fish oil with 50% soybean oil(SO50), 100% soybean oil(SO100) and 100% palm oil(PO100), respectively. The 4 diets were randomly assigned to 4 floating sea cages(3.0 m × 3.0 m × 3.0 m), and each was stocked with 250 fish individuals with an initial average weight of 245.29 g ± 7.45 g. The fish were fed to apparent satiation twice a day at 5:00 and 17:00, respectively, for 12 weeks. Experimental analysis showed that the specific growth rate of fish fed SO50 or PO100 were significantly higher than that of fish fed FO or SO100(P<0.05), and crude lipid contents of ventral muscle and viscera were significantly lower in fish fed FO than in those fed the other 3 diets(P<0.05). No significant differences in condition factor, viscerosomatic index, hepatosomatic index, gutted yield and colorimetric values of fish among the dietary treatments were observed(P>0.05). Compared to FO diet, SO50, SO100 and PO100 diets led to substantial decreases in the liquid loss and water loss from fresh fillets(1 d, 4℃)(P<0.05). Similarly, thiobarbituric acid reactive substance(TBARS) values of fillets under different storage conditions(1 d, 4℃; 7 d, 4℃; 4 weeks,-20℃; 8 weeks,-20℃) decreased significantly after partial or complete replacement of fish oil with vegetable oils. These findings indicated that the growth performance and selected flesh quality properties(liquid holding capacity and TBARS value) of large yellow croaker were substantially improved by replacing dietary fish oil with vegetable oils.

Molecular characterization of an IL-1β gene from the large yellow croaker（Larimichthys crocea） and its effect on fish defense against Vibrio alginolyticus infection

Interleukin 1β（IL-1β）, the first interleukin to be characterized, plays a key role in regulating the immune response. In this study, we determined the c DNA and genomic DNA sequences of the IL-1β gene from the large yellow croaker, Larimichthys crocea. Phylogenetic analysis indicated that the IL-1β（Lc IL-1β） gene was most closely related to that of European seabass（Dicentrarchus labrax）, sharing 67.8% amino acid identity. In healthy large yellow croaker, Lc IL-1β transcription was detected in all tested tissues, with the highest level found in the head kidney. Upon Vibrio alginolyticus infection, Lc IL-1β transcription in all tested tissues was significantly upregulated. Intraperitoneal injection of recombinant Lc IL-1β（r Lc IL-1β） improved the survival rate and reduced the tissue bacterial load after V. alginolyticus infection. In addition, r Lc IL-1β induced monocytes/macrophages（MO/MΦ） chemotaxis and increased phagocytosis and bactericidal activity in vitro. These results suggest that Lc IL-1β plays an important role in the large yellow croaker immune response against V. alginolyticus.

Cloning and mRNA expression of macrophage migration inhibitory factor (MIF) gene of large yellow croaker (P seudosciaena crocea)

Mammalian macrophage migration inhibitory factor （MIF） plays an important role as an indispensable mediator in the pathogenesis of inflammatory disease like septicemia, but little is known about the role of MIF homologue in fish septicemia. The authors have cloned the MIF homologue in large yellow croaker Pseudosciaena crocea （LycMIF） using RACE approach. The full-length cDNA of LycMIF was 634 bases and contained an ORF of 345 bases encoding a protein of 115 amino acid residues. As demonstrated by RT-PCR and QRT-PCR assay, MIF mRNAs were constitutively expressed in 11 selected tissues and were abundant in brain and liver. Moreover, the LycMIF transcripts in the liver and head kidney were responsive to bacteria infection and could be significantly up-regulated. Our results provide the first direct evidence that fish MIF was implicated in pathogenesis of fish vibrosis and play an important role in response to bacteria infection.

Diagnosis of iridovirus in large yellow croaker by PCR

A rapid and sensitive PCR-based method for the detection of the large yellow croaker iridovirus (LYCIV) is described, which involves the amplification of a 295 bp fragment of the LYCIV ATPase gene from DNA isolated from naturally infected fish spleen. Sequencing of LYCIV ATPase gene fragment showed it shared 100% nucleotide sequence homology with the corresponding region of the ATPase gene of red sea bream iridovirus (RSIV) and sea bass iridovirus (SBIV), suggesting that LYCIV was homologous with RSIV and SBIV at least in part of the gemone. The specificity and sensitivity of the PCR procedure were tested on the iridovirus-infected fishes, the expected fragment was detected from spleen DNA samples of infected fishes, whereas no fragments were amplified from healthy fish spleen DNA, white spot syndrome baculoviruses (WSBV) DNA and pseudorabies virus (PRV) DNA. Detection limit of this method was 10(-7) ng positive plasmid DNA containing target sequence, equal to about 100 virions. In the infected experiment, first positive detection (1/4) appeared at Day 3 post-infection, all fish (4/4) tested positive at Day 7, however obvious symptoms were observed at Day 8, so LYCIV infection could be detected prior to the appearance of obvious symptoms. These results indicate that this PCR method could be used for early, rapid and specific detection of LYCIV infection.

Establishment of a Spleen Cell Line from Large Yellow Croaker Pseudosciaena crocea and its Primitive Application in Foreign Gene Transfection

A large yellow croaker,Pseudosciaena crocea,spleen(LYCS)cell line was established and the feasibility of using it for foreign gene transfection was evaluaed in this study.Primary culture of LYCS cells was initiated from spleen tissue pieces,which were cultured at 25℃ in Dulbecco's modiced Eagle medium/F12 medium(DMEM/F12,1:1)(pH7.2),supplemented with 20% fetal bovine serum,carboxymethyl chitosan,chondroitin sulfate,basic fibroblast growth factor(bFGF)and insulin-like growth factor-I(IGF-I).The cultured LYCS cells,in fibroblast shape,proliferated to 100% confluency 20 days later.Chromosome analyses indicated that the LYCS cells exhibited chromosomal aneuploidy with a modal chromosome number of 48 which displayed the normal diploid karyotype of P.crocea(6m+6sm+36t,NF=60).A LYCS cell line,with a population doubling time of 48.7 h at passage 60,has been established and subcultured to passage 70.Transgenic feasibility test demonstrated that positive green fluorescence protein(GFP)expression was observed in LYCS cells after pcDNA3.1-GFP plasmid transfection.In conclusion,a continuous foreign gene trans-fection feasible LYCS cell line has been established successfully.The cell line might serve as a valuable tool for studies of transgenic breeding and has potential applications for different kinds of cytotechnological studies.

Effect of Dietary Olaquindox on the Growth of Large Yellow Croaker(Pseudosciaena crocea R.) and the Distribution of Its Residues in Fish Tissues

Olaquindox(OLA), one of quinoxaline-N, N-dioxides, has been put under ban. However it was used as a medicinal feed additive early; it promotes the growth of livestock and prevents them from dysentery and bacterial enteritis. In this study, we evaluated the effect of dietary OLA on the growth of large yellow croaker(Pseudosciaena crocea R.) and the histological distribution of OLA and its metabolite 3-methyl-quinoxaline-2-carboxylic acid(MQCA) in fish tissues. Four diets containing 0(control), 42.5, 89.5 and 277.2 mg kg-1 OLA, respectively, were formulated and tested, 3 cages(1.0 m × 1.0 m × 1.5 m) each diet and 100 juveniles(9.75 ± 0.35 g) each cage. The fish were fed to satiation twice a day at 05:00 am and 17:00 pm for 8 weeks. The survival rate of fish fed the diet containing 42.5 and 89.5 mg kg-1 OLA was significantly higher than that of fish fed the diet containing 0 and 277.2 mg kg-1 OLA(P < 0.05), while the weight gain rate of fish fed the diet containing 42.5 and 89.5 mg kg-1 OLA was significantly higher than that of fish fed the diet without OLA(control)(P<0.05), but similar to that of fish fed the diet with 277.2 mg kg-1 OLA. Fish fed the diet with 277.2 mg kg-1 OLA had the highest content of OLA and MQCA in liver(3.44 and 0.39 mg kg-1, respectively), skin(0.46 and 0.09 mg kg-1, respectively) and muscle(0.24 and 0.06 mg kg-1, respectively). In average, fish fed the diet containing OLA had the highest content of OLA and MQCA in liver which was followed by skin and muscle(P < 0.05), whereas OLA and MQCA were not detectable in control. Our findings demonstrated that OLA and MQCA accumulated in large yellow croaker when it was fed with the diet containing OLA, thus imposing a potential safety risk to human health.

Thermal tolerance evaluation and related microsatellite marker screening and identification in the large yellow croaker Larimichthys crocea

Thermal tolerance to high temperature was evaluated in the large yellow croaker Larimichthys crocea. The survival thermal maximum for L. crocea was 33.0℃, the 50% critical thermal maximum （50% CTMax） was 35.5℃, and the critical thermal maximum （CTMax） was 36.0℃. Three microsatellite markers （LYC0148, LYC0200 and LYC0435）, associated with thermal tolerance were screened and identified using a Bulked Segregation Analysis （BSA） method. These markers have six amplified fragments in which four are related to thermal tolerance. These fragments were cloned and sequenced, and the results showed the core motif were all ＂AC＂ repeats. For LYC0148 and LYC0200, the lengths of fragments are 18l bp and 197 bp, respectively. For LYC0435, which has two fragments, the fragment lengths are 112 bp and 100 bp. The results provide useful molecular markers for thermal-tolerance breeding of large yellow croaker in the near future.

Temperature Tolerance of Large Yellow Croaker,Pseudosciaena Crocea(Richardson)Associated with Summer Season

L ethal temperature tolerance was determined for about 8 cm, age 0 Pseudosciaena crocea using both slow heating and rapid transfer protocol. The acclimatization temperature was 28 ℃ with summer season, lethal temperature ( LT50 value ) of slow heating protocol ( CTMax ) was 35.0 ℃, and the upper and lower incipient lethal temperatures of rapid transfer protocol were 34.2 ℃ and 17.5 ℃ respectively.

Intragenic and intergenic sequences regulating the expression of the 5'-to-5' linked adult α-and β-globin genes from large yellow croaker Pseudosciaena crocea

One adult α-globin gene and one β-globin gene have been cloned from the large yellow croaker Pseudosciaena crocea. Linkage analysis indicated that the α- and β-globin genes were oriented head-to-head relative to each other. To identify the regulatory elements present in the intergenic and intragenic regions of the globin complex, the intergenic region alone or together with the β-globin gene first intron was cloned into the luciferase-reporter vector pGL3-Basic respectively, and the chimeric constructs were tran- siently transfected into Vero cells and primary fish erythrocytes. The intergenic region cannot support the high-level expression of luciferase. However, the promoter activity of the intergenic region was strongly stimulated by the positive regulatory elements （PRE） located in the β-globin gene intron 1. Thus, it is proposed that the intergenic promoters and intragenic PRE were necessary for the effective expression of the linked α- and β-globin genes.

Artificial induction of mito-gynogenetic diploids in large yellow croaker(Pseudosciaena crocea) by hydrostatic pressure

The present study investigated conditions for inducing mito-gynogenetic(endomitosis) diploids by hydrostatic pressure in the large yellow croaker Pseudosciaena crocea.In haploid control groups,the development of eggs was activated with ultraviolet radiated semen.All fry presented typical haploid syndrome in the haploid control groups,and were verified as haploids using cytometry.After hydrostatic pressure treatment,morphologically normal fry reappeared at different frequencies according to the intensity and time of pressure shock.Fry with normal appearance in the pressure treated groups were verified as gynogenetic double haploids(GDHs),containing only one allele from the female parent at all four diagnostic microsatellite loci.For a fixed duration of 3 min,the optimal intensity of blocking the first mitosis was determined to be 40 Mpa,which was similar to that of blocking the second meiosis.There was a "window" of starting time,from 36.1 min to 38.1 min post-insemination at 25.0±1.0°C,within which the production of GDHs was not significantly different.Maximum production of morphologically normal fries,9.36%±2.97% of developed eggs,was found when the eggs were shocked with hydrostatic pressure at 40 Mpa for 3 min,starting from 38.1 min post insemination at 25.0±1.0°C.

MicroRNAs identification and bioinformatics analysis in large yellow croaker Larimichthys crocea using an integrated comparative and ab initio approach

MicroRNAs(miRNAs) are a group of small, endogenous, single-stranded non-coding RNAs that post-transcriptionally regulate gene expression levels. Previous studies have revealed that miRNAs play key roles in multiple biological processes, such as growth and development in both animals and plants. Computational identification is an efficient method for miRNA prediction in organisms with a reference genome before high-throughput miRNA sequencing experiments. In this study, we employed an integrated strategy combining the homology-based and ab initio approaches to predict miRNAs from the genome and transcriptome of large yellow croaker, one of the most commercially important marine fish in China and East Asia. A total of 418 miRNA molecules, including 287 miRNAs by the homology-based method and 131 miRNAs by the ab initio approach, were identified for large yellow croaker. Additionally, 16 053 target genes were predicted and annotated for Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) databases. Meanwhile, we analysed single nucleotide polymorphisms(SNPs) around large yellow croaker miRNA and found that the miRNA seed regions were significantly less prone to mutations, indicating that the miRNA sequences were under strict natural selection based on their essential regulation functions in living cells. Twenty-two SNPs were identified in large yellow croaker miRNA seed regions, which dramatically influenced the miRNA-gene regulation networks. This is the first reported miRNA detection from both the genome and transcriptome using the integrated strategy for large yellow croaker species, and the miRNA and SNP analyses in this work provide important resources and a reference for subsequent miRNA functional investigations in large yellow croaker.

Population structure and genome‑wide evolutionary signatures reveal putative climate‑driven habitat change and local adaptation in the large yellow croaker

The large yellow croaker(Larimichthys crocea)is one of the most economically valuable marine fsh in China and is a notable species in ecological studies owing to a serious collapse of wild germplasm in the past few decades.The stock division and species distribution,which have important implications for ecological protection,germplasm recovery,and fshery resource management,have been debated since the 1960s.However,it is still uncertain even how many stocks exist in this species.To address this,we evaluated the fne-scale genetic structure of large yellow croaker populations distributed along the eastern and southern Chinese coastline based on 7.64 million SNP markers.Compared with the widely accepted stock boundaries proposed in the 1960s,our results revealed that a climate-driven habitat change probably occurred between the Naozhou(Nanhai)Stock and the Ming-Yuedong(Mindong)Stock.The boundary between these two stocks might have shifted northwards from the Pearl River Estuary to the northern area of the Taiwan Strait,accompanied by highly asymmetric introgression.In addition,we found divergent landscapes of natural selection between the stocks inhabiting northern and southern areas.The northern population exhibited highly agminated signatures of strong natural selection in genes related to developmental processes,whereas moderate and interspersed selective signatures were detected in many immune-related genes in the southern populations.These fndings establish the stock status and genome-wide evolutionary landscapes of large yellow croaker,providing a basis for conservation,fsheries management and further evolutionary biology studies.

Large yellow croaker(Larimichthys crocea)mitofusin 2 inhibits type I IFN responses by degrading MAVS via enhanced K48‑linked ubiquitination

In mammals,mitofusin 2(MFN2)is involved in mitochondrial fusion,and suppresses the virus-induced RIG-I-like receptor(RLR)signaling pathway.However,little is known about the function of MFN2 in non-mammalian species.In the present study,we cloned an MFN2 ortholog(LcMFN2)in large yellow croaker(Larimichthys crocea).Phylogenetic analysis showed that MFN2 emerged after the divergence of amphioxus and vertebrates.The protein sequences of MFN2 were well conserved from fsh to mammals.LcMFN2 was expressed in all the tissues/organs examined at diferent levels,and its expression was upregulated in response to poly(I:C)stimulation.Overexpression of LcMFN2 inhibited MAVS-induced type I interferon(IFN)promoter activation and antiviral gene expression.In contrast,knockdown of endogenous LcMFN2 enhanced poly(I:C)induced production of type I IFNs.Additionally,LcMFN2 enhanced K48-linked polyubiquitination of MAVS,promoting its degradation.Also,overexpression of LcMFN2 impaired the cellular antiviral response,as evidenced by the increased expression of viral genes and more severe cytopathic efects(CPE)in cells infected with spring viremia of carp virus(SVCV).These results indicated that LcMFN2 inhibited type I IFN response by degrading MAVS,suggesting its negative regulatory role in cellular antiviral response.Therefore,our study sheds a new light on the regulatory mechanisms of the cellular antiviral response in teleosts.

Effective CRISPR/Cas9-based genome editing in large yellow croaker (Larimichthys crocea)

The large yellow croaker (Larimichthys crocea) is an economically important marine species with the highest annual production among the farmed marine fishes in China. However, the aquaculture industry of this species is suffering from severe problems that include weakened disease resistance, decreased growth rate, and reduced meat quality due to frequent inbreeding. Genome editing, which has a huge potential for solving those problems by introducing favorable genetic changes, is not yet available for the large yellow croaker. Here, we pioneered the techniques of embryo microinjection and genome editing using the CRISPR/Cas9 system in this species. Recombinant plasmids encoding green fluorescent protein (GFP) were introduced into the fertilized eggs of L. crocea by microinjection before the chorion had hardened. A high survival rate (40%) and GFP-positive larvae rate (81.8%) were achieved, indicating that the microinjection technique in L. crocea was successfully established. On this basis, Cas9 mRNA and sgRNA targeting the tyrosinase a gene in L. crocea (Lc-tyra) were co-injected into fertilized eggs of L. crocea. Mutant individuals with insertion and deletion mutations of Lc-tyra were detected. These results indicated that the CRISPR/Cas9-based genome editing technology established herein could efficiently introduce mutations at a specific site in the L. crocea genome. This method provides the potential for genetic improvement and functional genomic study in this species. This is the first report on effective CRISPR/Cas9-based genome editing in L. crocea.

Fatty acid profiles of muscle from large yellow croaker (Pseudosciaena crocea R.) of different age

We investigated the fatty acid profiles of muscle from large yellow croaker （Pseudosciaena crocea R.） of different age. One- and two-year-old fish were cultured in floating net cages and sampled randomly for analysis. Moisture, protein, lipid and ash contents were determined by methods of Association of Analytical Chemist （AOAC） International. Fatty acid profile was deter- mined by gas chromatography. Crude protein, fat, moisture and ash contents showed no significant differences between the two age groups. The contents of total polyunsaturated fatty acids and docosahexaenoic acid （DHA） were significantly higher and eicosapentaenoic acid （EPA） content was significantly lower in the two-year-old large yellow croaker than in the one-year-old （/＇〈0.05）. No significant differences were observed in the contents of total saturated fatty acids and monounsaturated fatty acids, or the ratio ofn-3/n-6 fatty acids among the large yellow croakers of the two age groups. We conclude that large yellow croakers are good food sources of EPA and DHA.

Sex-biased gene discovery from the gonadal transcriptomes of the large yellow croaker(Larimichthys crocea)

The investigation of sex determination in fish is not only of great scientific value,but also has important practical significance,especially in fishes grown in aquaculture exhibiting obvious growth-related sexual dimorphism,such as the large yellow croaker(Larimichthys crocea).While growth of the female large yellow croaker is faster than that of the male,little information exists on the mechanisms that drive the differentiation of the testis and ovary in this species.In this study,the gene expression profiles of large yellow croaker testis and ovary were analysed using RNA-Seq technology.A total of 222 million reads were mapped to the reference genome(89.80%).The differential gene expression analysis identified 13 genes specifically expressed in ovary and 897 specific to testis.Among these,were candidate sex determining genes,such as Dmrt1,Gsdf,Sox9,Amh.This study explored gene expression profiles in large yellow croaker gonads at the transcriptome level by RNA-Seq technology.We found many DEGs related to the development of each specific organ,including the candidate testis differentiation genes Dmrt1,Gsdf,Sox9,Sox3,Amh and ovary differentiation gene Foxl2 by analogy with other fish species,providing essential foundation clarifying the molecular mechanism involved in early sex differentiation.

Genome-wide association study identifies loci for body shape in the large yellow croaker(Larimichthys crocea)

The large yellow croaker(Larimichthys crocea)is an important maricultured fish species in southeast China.Body shape is an important economic trait for this species,because consumers prefer to purchase fish that have a slender shape.Furthermore,investigating the genetic basis of this trait may be useful for understanding the evolution of fish body shape in general.This study randomly selected 500 large yellow croakers to perform genome-wide association study of this trait.We used Genotyping-By-Sequencing technology combined with a genome-wide prediction model(BayesC)to identify and test QTLs.We also compared the association results using BayesC and single-marker analysis,and found that BayesC outperformed single-marker analysis in detecting significant SNPs explaining a proportion of the total genetic variance in this experiment.Using 124,419 SNP markers,10 candidate genes,correspond to 4 QTL regions located around 3.5,1.8,23.9 and 10.8 Mb on chromosomes 2,4,8 and 22 respectively,were suggested to be relevant to the trait.All of these genes may directly or indirectly participate in bone development.These genes may provide a valuable reference for marker-assisted selective breeding and investigating the genetic basis of the evolution of fish body shape.