Ctenophyngodon idella is one of the most important aquaculture species in the world, and suffered from local adaptation during the process of introduction and aquaculture. However, most studies of C. idella local adaptation were based on genetic variation, and the effect of epimutation was still widely unknown. In order to explore how DNA methylation affects the domestication and environmental adaptation of the C. idella populations in Asia.A whole-genome bisulfite sequencing was performed between 5 farmed populations and the wild background population, followed by further differential methylation analysis and enrichment analysis. A total of 308.15 Gb sequencing data were generated with a sequencing depth of 31× and a mapping rate of 62.97 % in average, where76 422 differentially methylated loci（DML）, 3 737 differentially methylated regions（DMR）, and 1 950 differentially methylated genes（DMG） were identified. Gene Ontology enrichment analysis showed that the DMGs were significantly enriched in development process, such as angiogenesis, neural crest cell migration, and cranial skeletal system development. Annotation with the KEGG pathway database exhibited these genes were mainly involved in adhesion junction, Notch signaling pathway, and Wnt signaling pathway. Among the DMG, some might be functional in the developmental process of neural, immunity, bone, and muscle tissues, like sema3d,sema5bb and nrg2a. This study enhances the understanding of the epigenetic mechanism of domestication and environmental adaption during the process of aquaculture and provides valuable data for the conservation and utilization of the C. idella germplasm resources.

In this paper, we studied the structure, expression and function of black carp insulin gene. The complete Mylopharyngodon piceus insulin (Mp-Ins) gene is 1,965 bp long and includes a 1,499 bp 5ʹ-untranslated region (UTR), a 139 bp 3′-UTR with a poly(A) tail, and an open reading frame (ORF) of 327 bp. The predicted molecular weight of the recombinant Mp-Ins(rMp-Ins) protein is 11.87 kDa. The mRNA expression of Mp-Ins is upregulated in the brain and liver. After the injection of rMp-Ins, Mp-Ins mRNA transcript abundance was significantly upregulated in the liver. The rMp-Ins protein could inhibit the concentration of glycogen phosphorylase (GP), growth hormone (GH), fatty acid synthase (FAS), and insulin-like growth factors-1 (IGF-1), and it also significantly increased the concentration of PI3K. Additionally, the injection of rMp-Ins did not have a significant impact on the glucose-6-phosphatase (G6Pase) content in blood. In situ hybridization results showed that the positive signal of the Mp-Ins gene was mainly concentrated in the cell nucleus of brain tissue and the cell membrane of liver tissue and muscle tissue. Together, these results demonstrated that Mp-Ins plays an important role in growth and metabolism in M. piceus.

MicroRNAs (miRNAs) are integral to many biological functions, including autophagy, a process recently proven to be closely linked to innate immunity. In this study, we present findings on miR-22a, a teleost homolog of mammalian miR-22, illustrating its capacity to target the autophagy adaptor p62, subsequently inducing downregulation at both mRNA and protein levels. Utilizing Western blot analyses, we demonstrated that miR-22a inhibits the autophagy flux of CIK cells, correlated with an elevated presence of LC3 II. Additionally, the overexpression of miR-22a resulted in the suppression of NF-κB signaling, leading to reduced cellar antimicrobial abilities and increased apoptosis. These findings provide novel insights into the role of miR-22a as an autophagy-related miRNA and its immune mechanisms against pathogens via p62 in teleost, enriching our understanding of the interplay between autophagy and innate immunity.

Beclin1 is one of the first genes to be proven to positively regulate autophagy. It also connects immunization with autophagy in mammals. In this study, we reported that grass carp Beclin1 gene expression could be upregulated by bacterial infection. Overexpression of Beclin1 could increase the autophagy level of CIK cells by raising the ratio of LC II/I, and decrease the number of adhesive bacteria. Beclin1 could promote cellular migration, proliferation abilities, and vitality, but not anti-apoptosis. Besides, the expression of Beclin1 could activate the NF-κB signaling pathway by strengthening inflammatory cytokines Our finding indicated that Beclin1 participated in Ctenopharyngodon idella innate immune progress and autophagy. This study provides evidence of the positive regulation of Beclin1 in teleost innate immunity with its multiple functions. It thus may provide important information on the defenses and immune mechanisms of teleoskeletal fish against pathogens.

为了解长江水系青鱼不同地理群体肌肉营养品质的差异,用国标生化法测定了湖南湘江群体(XJ)、湖北石首群体(SS)、江苏邗江群体(HJ)青鱼肌肉的常规营养成分、氨基酸和脂肪酸的含量,并按FAO/WHO建议的标准进行了营养品质评价.结果显示:3个群体青鱼肌肉的水分质量分数为81.08％～82.20％,粗蛋白质质量分数为16.86％～17.94％,粗脂肪质量分数为0.46％～0.52％,粗灰分质量分数为1.26％～1.34％,3个群体间常规营养成分无显著性差异(P>0.05);在3个群体青鱼的肌肉中均检测出16种氨基酸,其中人体必需氨基酸7种,半必需氨基酸2种,非必需氨基酸7种,必需氨基酸占总氨基酸的39.24％～40.22％,鲜味氨基酸占总氨基酸的38.54％～39.37％;在脂肪酸组成和含量上,石首群体、邗江群体中均检测到18种脂肪酸,其中饱和脂肪酸9种,单不饱和脂肪酸3种,多不饱和脂肪酸6种,以上两个群体的脂肪酸组成种类均多于湘江群体,邗江群体在饱和脂肪酸总量和多不饱和脂肪酸总量上均显著高于石首群体和湘江群体(P<0.05),而在单不饱和脂肪酸总量上,3个群体间差异不显著(P>0.05),3个群体都含有高水平的DHA+EPA.结果表明,青鱼3个群体的蛋白质含量均较高,氨基酸组成合理,富含多种不饱和脂肪酸,均具有较高的营养价值,其中邗江群体营养价值最高,可作为青鱼良种选育的主要对象.

为掌握中国青鱼(Mylopharyngodon piceus)种质资源分布特征,揭示青鱼种质资源的遗传变异情况,研究通过对9个青鱼群体271个样本线粒体CO Ⅰ区设计引物并进行PCR扩增,运用软件分析了群体内部遗传多样性和各群体之间的进化关系.分析结果表明:长度为1003 bp的9个群体CO Ⅰ基因区域序列GC含量低于AT含量,共检测到6个突变位点,7种单倍型,其中Hap4单倍型在9个群体中都有分布.AMOVA分子方差分析显示271个青鱼样本的变异90.33％来自群体内部,9.67％来自群体间.青鱼总体核苷酸多样性(π)偏低,在0.00109-0.00244.单倍型多样(Hd)性较高,在0.403-0.847.遗传分化系数(Fst)在-0.0033-0.23445,保持在低度至高度分化,主要集中在低度和中度分化.分析得到广东佛山群体可能经历过瓶颈效应,其余8个群体可能经历过快速的种群扩张事件.研究结果揭示了中国目前青鱼种质资源的遗传背景,可以为中国青鱼种质资源的保护和创新利用提供重要的参考依据.

为了分析草鱼(Ctenopharyngodon idella)选育群体不同世代的遗传变异和遗传结构,本研究利用了已建立的一套标准微卫星标记对草鱼长江选育群体F0、F3、F4进行了遗传变异的评估,并与黑龙江选育群体和珠江选育群体进行了遗传变异的比较分析.实验结果表明长江选育群体的各世代均具有高度的遗传多样性(PIC＞0.05),且长江选育群体的遗传多样性相对于黑龙江和珠江选育群体的遗传多样性水平更高(P＜0.05).遗传分化指数(Fst)分析结果表明,长江选育群体F0、F3、F4之间遗传分化的水平较低(0＜Fst＜0.05);长江选育群体,与黑龙江和珠江选育群体之间都具有中等程度的遗传分化水平(0.05＜Fst＜0.15).分子方差分析(AMOVA)显示了长江选育群体各世代之间4.05％的变异来自于群体间,95.95％的变异来自于群体内;而对于草鱼5个群体,AMOVA显示了 8.46％的变异来自于群体间,91.54％的变异来自于群体内.Structure分析显示出草鱼5个群体可以划分为3个聚类簇.通过基于Fst距离矩阵构建的5个草鱼群体的UPGMA系统发育树,结果显示长江选育群体F0、F3聚为一支后与长江选育群体F4聚类为一支,再与黑龙江选育群体聚为一支,最后与珠江选育群体聚为一支.该研究结果将为草鱼选育工作的进一步开展提供参考.

为了评估青鱼(Mylopharyngodon piceus)不同群体的生长性能,对湖南湘江(XJ)、湖北石首(SS)、江苏邗江(HJ)的青鱼采用PIT标记和网箱同池混养法,比较三个不同地理群体生长差异性.通过单因素方差分析、相关性分析、多重比较分析不同青鱼群体间生长差异性和性状间的相关性.结果显示:三个群体中,HJ群体在增重率、增长率、生长指数等表现良好.XJ群体体重增重率以及生长指数都较低,表明XJ群体生长较为缓慢.SS群体在体重增重率上与HJ群体不具有显著性差异,但在体宽和体高上SS群体生长离散程度最大.性状相关性分析中,体长、体宽、体高与体重的相关系数也均达到极显著水平.综合以上研究,HJ群体的生长性能最好,可以作为良种选育的主要对象.

为了评估养殖条件下青鱼(Mylopharygodon piceus)不同组织的状态和分析青鱼不同肠段的功能分化,使用组织学半定量系统对青鱼的鳃、肝、脾和肠进行评估,并使用酶活检测分析青鱼不同肠段中消化酶和抗氧化酶的分布.结果 表明:青鱼的鳃、肝和脾的状况良好,处于Ⅰ级和Ⅱ级变化,肠道是最受影响的器官,达到Ⅲ级变化,在肠道的组织学分析中发现肠黏膜上皮细胞增生和固有层易碎和坏死.青鱼的Fulton状态指数(fulton's conditional factor,CF)介于1.01到2.30之间,均值为1.19;肝体指数(hepatic somatic index,HSI)介于0.29到0.93之间,均值为0.58,表明被检测的青鱼状态良好.在青鱼的肠道中,消化酶和抗氧化酶在不同肠段的分布存在显著差异,前肠淀粉酶、脂肪酶和胰蛋白酶的活性显著高于后肠,后肠中超氧化物歧化酶(superoxide dismutase,SOD)、谷胱甘肽还原酶(glutathione reductase,GR)、过氧化氢酶(catalase,CAT)活性和总抗氧化能力(total antioxidant capacity,T-AOC)显著高于前肠.结果 可以为养殖鱼类组织状态评估和肠道不同部分功能差异分析提供一定的参考资料.

安徽省黄山市发展泉水鱼养殖产业,带动旅游、渔家乐等产业延伸发展,使很多贫困人口脱贫,探索了一条山区精准脱贫的新路子,在当地产业扶贫中发挥了重要作用.2019年初,农业农村部等十部委印发《关于加快推进水产养殖业绿色发展的若干意见》,水产养殖在"十四五"时期面临绿色高质量发展的历史性机遇.2020年底,黄山市人民政府办公室印发《黄山市山泉流水养鱼产业高质量发展实施方案》,为黄山泉水鱼养殖产业绿色高质量发展奠定了基础.如何进一步提高黄山泉水鱼养殖产业发展质量,在乡村振兴中再立新功,面临着诸多新的课题.

Singapore is a small island country with limited land and sea space for aquaculture. Foodfish production in Singapore is mainly from cage aquaculture in sea and supplied about 10% of total fish consumed. The major cultured species are Asian seabass, milk fish, grey mullet, snappers, golden pompanos, hybrid groupers and shrimps. Although small scale of its aquaculture, constrained by limited available land and coastal areas and high cost for aquaculture, the industry is thriving and transferring from low-tech to high-tech. With the strong support of the government for food security, aquaculture R&D are geared towards developing novel hatchery technologies, marker-assisted and genomic selection to accelerate genetic improvement, the establishment of high-tech aquaculture farms and ensuring biosecurity. Singapore is fast becoming global aquaculture hotspot. In this review, we summarized the status of Singapore's aquaculture production, R&D, training and education and its challenges, and suggested some ideas on the future development of Singapore's aquaculture. Singapore is well-positioned to serve as a R&D and education hub for tropical aquaculture. Its R & D on aquaculture should focus on fish reproduction, genetic improvement and high-tech aquaculture systems to improve local fish production and to supply superior fry for culture in other countries.

As one of the most critical pathogens, Aeromonas hydrophila (AH) can cause motile aeromonad septicemia (MAS) in freshwater fish. In recent decades, a myriad of studies had been done for bacterial infect fish. However, the mechanism of bacterial infects fish especially freshwater fish was scanty. This study was conducted for investigating the invasion pathway of A. hydrophila in vivo of black carp. We have performed A. hydrophila 4332 transformed with a plasmid encoding the green fluorescent protein (pGFPuv) (AH4332GFPuv) in black carp. The AH4332GFPuv had similar growth properties and virulence as the wild‐type strains under the simulated natural condition. In this study, black carp were divided into five groups: IM (challenged via immersion), IBD (increased stocking density), SAW (skin artificially wounded by scalpel), MR (mucus removed from the body surface), and C0 (control group). The number of AH4332GFPuv in gill, liver, spleen, intestine, mid kidney, head kidney, muscle, eye, brain, heart, and blood were examined after 72 h post-infection from all groups. Significantly high bacterial numbers were observed in the gills and intestine. The number of bacteria was significantly higher in IBD group than IM group. In conclusion, the gill, intestines, and injured skin are likely to be the primary infection routes.

To investigate the health status of farmed Ctenopharyngodon idella, haematology, serum biochemistry, and histology analyses were carried out. Growth performance measurement shows Fulton's condition factor is 1.69. The hepatic somatic index (0.42 +/- 0.09) was markedly lower than the reference values (1.2-2.55 +/- 0.24). The white blood cell counts (1.57 x 10(8) +/- 0.37 x 10(7) cell/ml) were approximately 10 times higher than reference values (0.2974 +/- 0.00315) x 10(7) - (1.457 +/- 0.69) x 10(7) cell/ml, as was mean corpuscular volume. The percentage of neutrophil (5.29%) was lower than the reference values (11.59%-39.97%), but thrombocyte proportion (32.32%) was higher than the reference (4.31 +/- 7.7%). Activities of plasma alanine transaminase (2.38 +/- 1.10 U/L) and aspartate aminotransferase (3.72 +/- 1.25 U/L) were lower than reference values (ALT: 4.96-15.84 U/L; AST: 40.66-116.47 U/L). Combined, all reference value of complement C3 content indicates a negative correlation with body size, but C4 and immunoglobulin M was positively correlated. Peroxidase activity was 500 times higher than the reference, possibly due to fish size. Histological diagnosis showed that the Organ indexes (OI) of gill (12.0 +/- 8.9) and liver (11.9 +/- 12.9) were higher than kidney (7.1 +/- 5.5) and intestine (5.0 +/- 5.5). Moderate and pronounced histological differences were observed in gills and livers, but the kidney and intestine were mostly normal. This preliminary study has found the difference of health in farmed grass carp and try to reflect the potential health status of farmed fish.

The Chinese lake gudgeon is a small benthopelagic freshwater fish. It is presently threatened by human activities and environmental factors in China. Understanding the genetic diversity and population structure is fundamental for implementation of appropriate conservation measures and a sustainable management program. However, little is reported about the current genetic diversity and population structure. Here, we used ten microsatellite markers to genotype 175 individuals from six populations. Low levels of genetic diversity were found in all six tested populations. The Xiang river population showed the highest level of genetic diversity. Genetic differentiation was very low but significant among the Changyang, Changqidang and Mayang populations, but the Qiandao lake, Gan river, Xiang river populations all showed significant and strong differentiation from the other three populations. Contemporary gene flow was observed in among Changyang, Changqidang and Mayang populations and between Gan and Xiang river populations, respectively. This is the first genetic study to report the genetic diversity and population structure of S. sinensis and the results will be used to develop management and conservation strategies.

Grass carp has the highest production yield among all the farmed fish species around the world. But the molecular and genetic basis of growth traits is inadequately understood in this fish. In the present study, we apply whole-transcriptome sequencing to identify genes whose expression is different between fast and slow growing grass carp. We identified 1178 differentially expressed genes (DEGs), among which 270 were upregulated in the fast growing group and 908 upregulated in the slow growing group. The GO enrichment analysis revealed that DEGs was significantly enriched in protein synthesis and export machinery, cell division and development and metabolism, suggesting that cell division and metabolism may play key roles in development processes of fish. KEGG pathway analysis showed that MAPK signaling pathway may play a prominent role in growth difference. In addition, the majority of genes in immune responses related pathway were upregulated in the slow growing individuals. These results provide some valuable resources for understanding the molecular mechanisms of growth traits in fish.

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.

Background Genetic diversity within a species reflects population evolution, ecology, and ability to adapt. Genome-wide population surveys of both natural and introduced populations provide insights into genetic diversity, the evolutionary processes and the genetic basis underlying local adaptation. Grass carp is the most important freshwater foodfish species for food and water weed control. However, there is as yet no overall picture on genetic variations and population structure of this species, which is important for its aquaculture. Results We used 43,310 SNPs to infer the population structure, evidence of local adaptation and sources of introduction. The overall genetic differentiation of this species was low. The native populations were differentiated into three genetic clusters, corresponding to the Yangtze, Pearl and Heilongjiang River Systems, respectively. The populations in Malaysia, India and Nepal were introduced from both the Yangtze and Pearl River Systems. Loci and genes involved in putative local selection for native locations were identified. Evidence of both positive and balancing selection was found in the introduced locations. Genes associated with loci under putative selection were involved in many biological functions. Outlier loci were grouped into clusters as genomic islands within some specific genomic regions, which likely agrees with the divergence hitchhiking scenario of divergence-with-gene-flow. Conclusions This study, for the first time, sheds novel insights on the population differentiation of the grass carp, genetics of its strong ability in adaption to diverse environments and sources of some introduced grass carp populations. Our data also suggests that the natural populations of the grass carp have been affected by the aquaculture besides neutral and adaptive forces.

研究利用自主开发的12个微卫星标记,对来自于长江水系4个野生群体(湖北石首、湖南湘江、江苏邗江、浙江嘉兴)和1个养殖群体(江苏吴江)青鱼(Mylopharyngodon piceus)进行遗传多样性和遗传结构分析.遗传多样性分析结果显示这12个位点多态信息含量(PIC)介于0.660—0.923,表明这12个位点均具有高度多态性(PIC>0.5).5个群体的平均等位基因数(Na)介于7.917—11.667,平均有效等位基因数(Ne)介于4.837—6.035;平均观测杂合度介于0.713—0.861;平均期望杂合度介于0.749—0.819;平均多态信息含量介于0.711—0.788,表明这5个群体均具有较高的遗传多样性.遗传距离分析结果表明4个野生群体之间遗传距离较近,养殖群体与这4个野生群体遗传距离均较远.UPGMA系统进化树显示,湘江群体和石首群体首先聚为一支,然后与邗江群体和嘉兴群体聚为一支,最后与吴江养殖群体聚为一支.这12个微卫星位点具有较为丰富的遗传多样性特征,可以用于青鱼不同群体的种质资源的评估和遗传多样性的分析.

The ISGA (International Symposium on Genetics in Aquaculture) is an important conference in the field of aquaculture genetics, which is held every three years. This year, the meeting was hosted by James Cook University, in Cairns. The conference sessions included biotechnology and functional genomics, sex control, genomic prediction, selective breeding and quantitative genetics, industrial use of genetics, genome technology, genetics of diseases and stress, genetics of nutrition, epigenetics, genomics and metabolomes, population genetics and ethics, food safety, as well as environmental risks. Many new and interesting unpublished data, including those for new aquaculture species, marker-assisted selection, genomic selection and genome editing using Crispr/Cas9 technologies, were reported at the conference. In this brief review, we highlight the novel and interesting researches on aquaculture genetics and genomics to give readers an overview of the current status and trends of aquaculture genetics and genomics research.

Grass carp is one of the most important cultured fishes all over the world. The genetic diversity of grass carp plays an important role whatever in selective breeding progress or ecological conservation purposes. However, some genetic diversity researches were not accuracy and cannot be compared with each other due to different molecular markers, sample size and detection methods. In this study, we constructed five multiplex PCR assays contained 20 microsatellites with highly polymorphism and heterozygosity for evaluating genetic information of grass carp. We used nine cultured populations consisting of 507 individuals to detect stability of the five multiplex PCR assays. The results showed that the number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He) and polymorphism information content (PIC) of the 20 microsatellite loci were relative high compared with the genetic diversity parameters of microsatellite loci developed by other researchers. Six loci were significantly deviated from Hardy-Weinberg equilibrium (P < 0.01). And with exception of the Shaoguan, Indian and Nepal cultured population, all other cultured populations showed very high genetic diversity. Through the test of grass carp populations, we developed an effective and accurate multiplex SSR-PCR assays that can be as statistical powerful tool for detecting genetic information of grass carp.