Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P<0.05)and seven haplotypes(r2>0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.

Effect of ChREBP on carbohydrate feeding regulation in mandarin fish Siniperca chuatsi

Carnivorous fish have poor tolerance to carbohydrate in feed and low utilization rate of carbohydrate.Therefore,the balance of carbohydrate and lipids in the nutrient metabolism of carnivorous fish,the ef fective conversion and utilization of carbohydrate and lipids,and the feedback regulation of feeding are the key links for the e fficient utilization of carnivorous fish feed.Carbohydrate response element binding protein(ChREBP)is a new transcription factor found in recent years in the glucose signaling pathway,and can also participate in feeding regulation.We performed in-vivo and in-vitro experiments to reveal the role of ChREBP in the glucose metabolism and feeding in mandarin fish.The mRNA expression of ChREBP and appetite regulatory factors were measured after intraperitoneal injection of glucose in mandarin fish Siniperca chuatsi and cotransfection with glucose and glucose+siRNA in the hypothalamic cells in mandarin fish.The results reveal that at hour 2 and 4 post intraperitoneal injection with 1 mg/g BW glucose,the blood glucose level of the mandarin fish increased significantly,but food intake decreased significantly,and it also displayed a significantly increased ChREBP mRNA expression levels in liver.At hour 4 post injection,hypothalamic ChREBP mRNA level was significantly increased,whereas the mRNA expression levels of appetite genes neuropeptide Y(npy)and agouti-related peptide(AgRP)were decreased significantly.When the glucose concentration was 40 mmol/L,the expression level of ChREBP mRNA in mandarin fish hypothalamic cells was significantly up-regulated,but the expression level of appetite gene npy mRNA was down-regulated.When siRNA and glucose were co-transfected into mandarin fish brain cells,the expression level of chrebp mRNA was significantly decreased,and the appetite gene npy mRNA was significantly increased.The results indicated that glucose regulated food intake through the modulation of appetite gene npy by ChREBP.

Morphological characteristics and genetic differentiation of Lutraria maxima in coast waters off southeast China

To explore genetic diversity and estimate the genetic differences among populations of Lutraria maxima in the coastal waters off south to southeast China,the morphology of the species of five different geographical populations(Beihai,Weizhou Island,Zhanjiang,Xiamen,and Fuzhou)in Guangxi,Guangdong,and Fujian provinces was studied statistically in combination with the microsatellite markers.As revealed by morphological principal component analysis(PCA),the cumulative contribution rate of the first three principal components was 72.596%.The discrimination accuracy ranged from 47.5%to 80.0%,and the scatter plots of principal component and discriminant analysis were consistent in overall,showing that the Xiamen and Fuzhou populations were overlapped obviously.For microsatellite markers,10 pairs of polymorphic primers were obtained by high-throughput transcriptome sequencing,and used for genetic diversity analysis.It was showed that the average number of alleles and eff ective alleles observed in each population ranged from 8.100 to 10.900,and from 3.497 to 4.228,respectively.The average observed heterozygosity(H_(o))and expected heterozygosity(H_(e))in the five populations ranged from 0.541 to 0.615,and from 0.642 to 0.733,respectively.The genetic distance(DA)ranged from 0.078 to 0.523,and the population genetic differentiation index(F_(ST))ranged from 0.027 to 0.139.The unweighted pair-population method with arithmetic means(UPGMA)and structure analysis showed that the five populations could be divided into two main clusters,the Beibu Gulf group(Beihai and Weizhou Island)and the Southeast China Sea group(Zhanjiang,Xiamen,and Fuzhou),suggesting that L.maxima has been separated geographically by the barrier of the Leizhou Peninsula into two groups in evolution,which provided us with a scientific clue to better protect the bioresource and establish an appropriate fishery management stocks for L.maxima populations in south China.

Application of Gray Metabolic GM (1,1) Model in Prediction of Annual Total Yields of Chinese Aquatic Products

To predict the annual total yields of Chinese aquatic products in future five years ( 2011-2015) ,based on the theory and method of gray system,this paper firstly establishes a conventional GM ( 1,1) model and a gray metabolic GM ( 1,1) model respectively to predict the annual total yields of Chinese aquatic products in 2006-2009 and compare the prediction accuracy between these two models. Then,it selects the model with higher accuracy to predict the annual total yields of Chinese aquatic products in future five years. The comparison indicates that gray metabolic GM ( 1,1) model has higher prediction accuracy and smaller error,thus it is more suitable for prediction of annual total yields of aquatic products. Therefore,it adopts the gray metabolic GM ( 1,1) model to predict annual total yields of Chinese aquatic products in 2011-2015. The prediction results of annual total yields are 55. 32,57. 46,59. 72,62. 02 and 64. 43 million tons respectively in future five years with annual average increase rate of about 3. 7% ,much higher than the objective of 2. 2% specified in the Twelfth Five-Year Plan of the National Fishery Development ( 2011 to 2015) . The results of this research show that the gray metabolic GM ( 1,1) model is suitable for prediction of yields of aquatic products and the total yields of Chinese aquatic products in 2011-2015 will totally be able to realize the objective of the Twelfth Five-Year Plan.

The genetic basis of the leafy seadragon's unique camouflage morphology and avenues for its efficient conservation derived from habitat modeling

The leafy seadragon certainly is among evolution’s most“beautiful and wonderful”species aptly named for its extraordinary camouflage mimicking its coastal seaweed habitat.However,limited information is known about the genetic basis of its phenotypes and conspicuous camouflage.Here,we revealed genomic signatures of rapid evolution and positive selection in core genes related to its camouflage,which allowed us to predict population dynamics for this species.Comparative genomic analysis revealed that seadragons have the smallest olfactory repertoires among all ray-finned fishes,suggesting adaptations to the highly specialized habitat.Other positively selected and rapidly evolving genes that serve in bone development and coloration are highly expressed in the leaf-like appendages,supporting a recent adaptive shift in camouflage appendage formation.Knock-out of bmp6 results in dysplastic intermuscular bones with a significantly reduced number in zebrafish,implying its important function in bone formation.Global climate change-induced loss of seagrass beds now severely threatens the continued existence of this enigmatic species.The leafy seadragon has a historically small population size likely due to its specific habitat requirements that further exacerbate its vulnerability to climate change.Therefore,taking climate change-induced range shifts into account while developing future protection strategies.

Self-fertilization in a gonochoristic fish yellow catfish

Sex control techniques are in great demand for aquaculture because of the huge benefits of mono-sex production.In a previous study on yellow catfish(Tachysurus fulvidraco),intersex individuals were produced by administrating 17α-methyltestosterone(MT)or aromatase inhibitor letrozole(LZ).The ovarian and testicular portions of intersexual gonads developed well and were completely separated,arousing our interest in producing self-fertilizable fish and clone-like fish populations.In this study,yellow catfish fry were treated with a combination of MT and LZ at a low dose(5 mg kg^(-1)MT,300 mg kg^(-1)LZ)at a low water temperature(27.0℃,mixed sex-producing temperature,LL group)and a high temperature(33.5◦C,male-producing temperature,HL group),and with a high dose(10 mg kg^(-1) MT,600 mg kg^(-1) LZ)at a low water temperature(LH group),during 12-65 days post-hatching,the critical period of sex differentiation.Both XX and XY intersex were produced with different percentages at the same time through co-treatment with MT and LZ,with or without the help of male-producing temperature.The highest percentage of XY intersex(53%in XY,36%in XX and XY)and XX intersex(47%in XX,25%in XX and XY)was produced in LH and HL groups,respectively.Results of gonadal morphology,histology,and sperm dynamic analysis indicate that some XX and XY intersex individuals were capable of self-fertilization through artificial insemination.The reproductive performance of these intersex individuals was then investigated by injecting spawning agents,dissecting gonads,and artificially fertilizing eggs with their own sperm.The XX,XY,and YY genotypic individuals were produced by the self-fertilization of XY intersex individuals.The present study successfully produced high percentages of XX and XY intersex and conducted self-fertilization by mating the eggs and sperm of a single intersex individual.Self-fertilization in fish will show great potential in aquaculture genetics and breeding,for example,generating highly homozygous(or"clonal")genetic material,producing mono-sex populations,and identifying unknown sex determination modes.In particular,the cloning method of producing genetic materials will be greatly beneficial for maintaining advantageous traits through self-fertilization generation after generation.

Molecular Characterization and Expression Analysis of ftr01, ftr42,and ftr58 in Zebrafish(Danio rerio)

Tripartite motif(TRIM)proteins were shown to play an important role in innate antiviral immunity.FinTRIM(ftr)is a new subset of TRIM genes that do not possess obvious orthologs in higher vertebrates.However,little is known about its function.In this study,we used bioinformatic analysis to examine the phylogenetic relationships and conserved domains of zebrafish(Danio rerio)fir01,fir42,and fir58.as well as qualitative real-time PCR to examine their expression patterns in zebrafish embryonic fibroblast(ZF4)cells and zebrafish tissues.Sequence analysis showed that the three finTRIMs are highly conserved,and all contain a RING domain.B-box domain,and SPRY-PRY domain.In addition,fr42 and fir58 had one coiled-coil domain(CCD),whereas ftrol had two CCDs.Tissue expression analysis revealed that the mRNA level of ftr01 was the highest in the liver,whereas those of ftr42 and ftr58 were the highest in the gill;the expression of thesefinTRIMs was clearly upregulated not in the eyes,but in the liver,spleen,kidney,gill,and brain of zebrafish following spring viremia of carp virus(SVCV)infection.Similarly,the expression of these three finTRIM genes also increased in ZF4 cells after SVCV infection.Our study revealed that fir01,fr42,and fir58 may play an important role in antiviralimmune responses,and these findings validate the need for more in-depth research on the finTRIM family in the future.

Morphometric analysis and fluorescent microsatellite markers to evaluate the genetic diversity of five populations of Penaeus japonicus in China

To understand the current status of germplasm resources of Penaeus japonicus,in this study,genetic diversity was analyzed based on morphometric analysis and fluorescent microsatellite markers.For morphometric analysis,the cumulative ratios of the PC1 and PC2(85.90%)were greater than 75%,which can explain the morphological variation among populations.For microsatellite analysis,the allele number in 10 microsatellite loci ranged from 27 to 53,and the effective allele number ranged from 21 to 42.The observed heterozygosity ranged from 0.463 to 0.983,whereas expected heterozygosity ranged from 0.932 to 0.966,and the average polymorphism information content was 0.947,which indicated a high level of genetic diversity.The unbiased genetic distance among populations ranged from 0.230 to 0.431,and the genetic similarity coefficient ranged from 0.654 to 0.782.Analysis of molecular variance(AMOVA)showed that the genetic variation within individuals was the main source of variation,accounting for 88.55%,and only 1.49%of the genetic variation came from among populations.

Sex reversal and the androgenic gland (AG) in Macrobrachium rosenbergii: A review

The male giant freshwater prawn(Macrobrachium rosenbergii)generally exhibit faster growth rates compared to females of similar age.Consequently,the practice of culturing monosex(all-male)prawn can increase both the production yield and income.Manually selecting males for culture during the grow-out period has long been practiced in commercial prawn farming,but is labor-intensive and generally unsuccessful in producing a male monoculture.The androgenic gland(AG)is essential for sexual differentiation in prawn and development of male primary and secondary sexual characteristics.Microsurgical removal of the AG(andrectomy)from male prawn at an early development stage will transform the male into a fully-functioning neo-female.The M.rosenbergii androgenic gland-specific insulin-like hormone(Mr-IAG)plays critical roles in male spermatogenesis and male sexual development.RNA interference(RNAi)is a highly specific post-transcriptional interference or silencing of gene expression in cells.Silencing Mr-IAG had induced full and functional sex reversal of male to neo-female(genetic male with a female phenotype).Microsurgical removal of AG and RNAi are two different approaches to producing neo-females and both methods target the manipulation of AG for efficient sex-reversal.Neo-females can mate with normal males to produce all-male prawn progeny,which can be used for commercial prawn farming and to improve production efficiency and profitability.This article reviewed recent research related to the development and functions of AG and the testis and their interactions with morphological differentiation at various stages for male M.rosenbergii,aiming to increase understanding on this topic and facilitate discovery of new techniques for advancing M.rosenbergii aquaculture.