大黄鱼生长速率差异个体肌肉组织的转录组比较分析

为了探究大黄鱼生长性状的分子调控机制,实验从同一个网箱内养殖的大黄鱼中选取生长速率较快的体重均值为(527.1±83.6) g的个体182尾、生长速率较慢的体重均值为(238.4±52.3) g的个体230尾,共412尾进行研究。对其肌肉组织进行总RNA提取和转录组测序,并对2组进行基因差异表达分析。以Padj <0.05、abs[log₂(FoldChange)]> 1为标准,共筛选到227个差异表达基因,包括125个上调基因、102个下调基因。差异表达基因在NCBI-nr和Uniprot (Swiss-Prot)数据库的注释率分别为99.12%、81.94%。通过差异表达基因的功能注释结果,初步筛选出了可能与肌肉生长相关的候选功能基因,如gdf9、ckm、tnni2和des等。GO和KEGG分析预测出部分与肌肉生长相关的信息,如GO term有肌动蛋白丝组织、肌动蛋白细胞骨架组织、肌动蛋白丝基过程、微管组织中心和发育生长等,KEGG通路有细胞和生长因子、脂肪酸生物合成、转化生长因子-β信号通路(TGF-β信号通路)、胰岛素信号通路和肌动蛋白细胞骨架...     

基于转录组测序筛选乌苏里白鲑肌肉生长关键候选基因研究

为了挖掘调控乌苏里白鲑(Coregonus ussurinsis Berg)肌肉生长的关键候选基因,本研究对不同生长速度乌苏里白鲑的肌肉组织进行转录组测序,以期为乌苏里白鲑群体选育提供基础数据。首先,在同等条件下(从混合池中)随机选择乌苏里白鲑F2个体进行实验分组(快长组和慢长组)。接着分别从快长组[体重为(219.20±38.66) g]和慢长组[体重为(74.30±17.86) g]中随机选取10尾样本,取其背部肌肉进行转录组测序。以FDR (false discovery rate)<0.05且|log2(FC)|>1 (FC, fold change)为条件筛选差异表达基因并对其进行GO (gene ontology)和KEGG (Kyoto encyclopedia of genes and genomes)富集分析,并通过qPCR验证转录组数据的准确性。转录组测序结果显示,共筛选出2 211个差异表达基因,与慢长组相比,快长组中583个差异基因表达上调及1 628个基因表达下调。GO功能注释结果显示,差异基因主要参与细胞过程和结合过程,差异基因显著富集到251条KEGG通路(P<0.05),其中,MAPK信号通路(MAPK signaling pathway)、PI3K-Akt信号通路(PI3K-Akt signaling pathway)、紧密连接(tight junction)、胰岛素信号通路(insulin signaling pathway)、糖酵解/糖异生(glycolysis/gluconeogenesis)和PPAR信号通路(PPAR signaling pathway)参与细胞生长。之后结合功能注释结果和KEGG,鉴定出肌浆/内质网钙ATP酶基因atp2a1和atp2a2、葡萄糖-6-磷酸脱氢酶基因g6pc、生长因子结合蛋白1基因igfbp1以及肌球蛋白重链基因myh1、myh4、myh6、myh7、myh9和myh13等可能与肌肉生长密切相关的基因。本研究共筛选出10个可能与乌苏里白鲑肌肉生长相关的关键候选基因,为今后乌苏里白鲑分子标记辅助育种提供了基础数据。     

全同胞家系中生长差异翘嘴鳜肌肉转录组分析

翘嘴鳜(Siniperca chuatsi)是中国重要的经济水产养殖品种,对翘嘴鳜基因表达模式进行研究有助于筛选优势个体,培育生长特性优良的品种。为了解体重明显差异翘嘴鳜个体的差异基因表达信息,为翘嘴鳜培育提供基因指导,本研究从同一家系中挑选体重明显差异的3月龄翘嘴鳜(Siniperca chuatsi)个体进行肌肉转录组测序,研究不同体型个体间基因表达模式差异。结果显示,来自同一家系的翘嘴鳜个体在相同养殖条件下仍出现明显体重差异,养殖3个月后,极大个体(overweight)平均体重可达到极小个体(underweight)的4倍。分别对极大个体和极小个体的肌肉组织进行转录组测序,共获得73353个非重复序列基因(unigenes),通过基因表达量比较共获得8942个差异基因,对差异表达基因进行定义发现,GHR2、IGFR1、4ebp、Mhc、Mlc、Troponin等基因在极小个体中具有更高的表达水平。通过KEGG通路富集显示,蛋白质生成、蛋白质消化、RNA转运通路富集了大量差异表达基因。本研究发现体重差异明显的翘嘴鳜个体具有不同基因表达模式,转录组测序获得了大量差异表达基因信息,为翘嘴鳜生长研究提供了丰富的基因资源。     

大黄鱼高温适应的转录组学分析

为了探究大黄鱼高温胁迫条件下基因表达水平的变化,实验利用Illumina Hiseq 2500的125 pair-ended测序模式分别对大黄鱼高温处理组和常温对照组进行了转录组测序。对照组(3个生物学重复)和高温处理组(3个生物学重复)分别获得15.28和13.92 Gb测序数据,GC含量平均值约为51%。过滤后的高质量测序reads使用Bowtie2软件比对到大黄鱼参考转录组序列上估计基因表达量,进而进行基因表达差异统计学检验。以常温对照组为参比,高温处理组中阈值设为|log2(FC)|2和FDR0.05,共检测到1 259条显著差异表达基因。其中,821条基因为高表达,438条基因为低表达。随机选取12条差异表达基因,运用实时荧光定量PCR(qRT-PCR)进行了验证,结果证实转录组分析可靠。进一步将所有差异表达的基因进行GO功能注释和KEGG通路富集分析,结果发现大量差异表达基因的功能与氧化还原反应、蛋白质折叠和去折叠、糖和脂代谢以及某些疾病的发生相关。该研究结果为下一步深入研究大黄鱼高温适应的调控机制提供了重要的参考材料。     

不同体色福瑞鲤2号肌肉品质分析

为探究鲤不同体色个体肌肉品质的差异,本研究以福瑞鲤2号(Cyprinus carpio)青灰色个体(BG)和全红个体(WR)为研究对象,通过检测其肌肉色泽、氨基酸、脂肪酸和质构指标,来评价这2种体色福瑞鲤2号肌肉品质的差异。结果表明：BG的b*^{值显著高于}WR(P<0.05);出肉率以及肌肉的水分、粗脂肪、粗蛋白和灰分无显著差异(P>0.05);不同体色福瑞鲤2号的肌肉中均能检测出17种氨基酸,其中人体必需氨基酸7种,非必需氨基酸10种。甘氨酸(Gly)、脯氨酸(Pro)、组氨酸(His)和半胱氨酸(Cys)在2组间差异不显著(P>0.05),其它氨基酸在2组间存在显著(P<0.05)或极显著差异(P<0.01),两种体色福瑞鲤2号之间ΣEAA/ΣTAA没有显著差异(P>0.05);BG肉豆蔻酸(C14:0)显著高于WR(P<0.05),BG的饱和脂肪酸含量较WR稍高,WR的单不饱和脂肪酸含量较BG稍高,两者多不饱和脂肪酸含量相近;WR的弹性和咀嚼性显著高于BG(P<0.05)。研究结果显示体色对福瑞鲤2号的肌肉品质有影响,本研究为鱼类肉质性状改良提供基础数据和参照依据。     

鲤在阿维菌素胁迫下肝胰腺组织的转录组分析

为了探究阿维菌素胁迫对鲤机体的响应机制,在水温(22±2.0)℃,将体质量(150±30)g的鲤(Cyprinus carpio)分别暴露在阿维菌素浓度0μg·L^-1(对照组)、1.5μg·L^-1和3.0μg·L^-1下5 d,采用转录组学测序分析方法,探究阿维菌素胁迫对鲤肝胰腺转录组学的影响,解析其对鲤的分子毒理机制。通过对所得基因的功能注释发现,被注释的差异基因主要与结合、催化和代谢等功能有关。KEGG通路富集分析结果显示,差异表达基因在药物代谢-细胞色素P450、药物代谢-其他酶、淀粉和蔗糖代谢等通路中显著富集,涉及药物代谢、氨基酸代谢、碳水化合物代谢、脂质代谢以及辅助因子和维生素的代谢等多个代谢过程。这些功能基因和预测通路为理解阿维菌素胁迫鲤体内解毒和免疫系统奠定了基础。本研究获得的转录组数据可为深入研究鱼类应对杀虫剂污染物的分子机制提供丰富的基因资源。     

透明草金鱼的皮肤转录组分析

采用Illumina HiSeq技术对体长(45.00±5.42)mm的透明草金鱼和不透明草金鱼皮肤组织透明性状相关基因进行转录组测序.6个组织共产生309364078条过滤序列,组装后获得72083个unigene,平均长度为1321 bp.DESeq分析共筛选出181个差异表达基因(DEGs),其中上调基因66个、...     

长吻鮠雌雄性腺转录组比较分析

长吻鮠(Leiocassislongirostris)是淡水特色经济鱼类,其雄性生长速度快于雌性,培育全雄苗种可显著提高养殖效益。为加快长吻鮠全雄苗种培育进程,需深入了解长吻鮠性别分化及性腺发育的调控机制。本研究通过Illumina高通量测序平台对长吻鮠卵巢和精巢进行转录组测序分析。结果显示,共有10872个雌雄差异表达基因,其中上调基因9375个,下调基因1497个。通过功能注释,筛选出71个与性别相关的重要候选基因,包括50个精巢高表达基因(dmrt1、cyp17a1、samd7、wnt6、wt1等)和21个卵巢高表达基因(foxl2、gdf9、zp3、zp1、figla、bmp15等)。KEGG通路富集分析发现,差异表达基因显著富集到16条与性别决定与分化及性腺发育相关的信号通路,包括Wnt信号通路、TGF-β信号通路、MAPK信号通路、卵巢类固醇通路、GnRH信号通路等。本研究筛选出与长吻鮠性别决定和分化相关差异表达基因,揭示参与其雌雄个体性腺发育的信号通路,为今后长吻鮠性别决定和分化机制的研究积累重要数据,从而为其全雄苗种的培育提供理论支撑。     

青海湖裸鲤盐碱耐受过程中的渗透、免疫、代谢相关基因筛选和分析

为探究青海湖裸鲤在盐碱耐受过程中的基因表达变化,对青海湖河口水域以及入湖淡水河——泉吉河中的青海湖裸鲤的鳃、肾脏组织进行转录组测序,筛选青海湖裸鲤耐盐碱过程中发挥作用的免疫、代谢、渗透相关基因.结果显示,使用Trinity对所有样本质控数据(clean data)进行从头组装后共得到 541 429 个非冗余的序列(unigene),N50 平均长度达 612 bp.经差异表达分析发现,共有 832 个基因在 2 个区域中的青海湖裸鲤鳃、肾脏中共表达.经GO功能注释分析,注释到结合(binding)、细胞过程(cellular process)、代谢过程(metabolic process)、单一生物过程(single-organism process)的DEGs占比较多.KEGG通路分析结果表明,与免疫、代谢、渗透相关的通路得到了富集.根据差异表达基因的GO注释和KEGG信号通路富集分析,实验初步筛选到了青海湖裸鲤渗透相关基因,主要包括钠/钾转运ATP酶(sodium/potassium-transporting,ATPase)、钙/钙调蛋白依赖性蛋白激酶(calcium/calmodulin-dependent protein kinase)、丝裂原活化蛋白激酶(mitogen-activated protein kinase)、溶质载体家族(solute carrier family)等;免疫相关基因主要包括白细胞介素(interleukin)、补体(complement)、整合素(integrin)等;代谢相关基因主要有一氧化氮合酶(nitric oxide synthase)、1,25-二羟基维生素 D(3)24-羟化酶(1,25-dihydroxyvitamin D(3)24-hydroxylase)、细胞色素P450(cytochrome P450)等.本实验为青海湖裸鲤的组学研究提供了相关数据,同时也为青海湖裸鲤在盐碱耐受方面的适应性研究奠定了基础.     

绿鳍马面鲀雌雄性腺转录组比较分析

为探明绿鳍马面鲀(Thamnaconus septentrionalis)性腺发育相关基因表达特征,优化亲本生殖调控技术,本研究对绿鳍马面鲀雌雄亲体的精巢和卵巢进行了转录组测序分析,经de novo拼装,最终获得119 219个单基因(unigene),N50长度为1 255 bp。在NR、NT、KO、SwissProt、PFAM、GO及KOG数据库分别注释到24 009、35 057、18 453、26 971、30 294、11 420和21 613个unigene。绿鳍马面鲀精巢和卵巢转录组中存在18 954个差异表达基因(DEG),相对于精巢,在卵巢中上调表达的基因有11 265个,下调表达的有7 689个。选取bmp2、sox3、figla、hsd17b1、cyp19a、cyp17、foxl2、star和amh 9个DEGs进行实时荧光定量PCR (qRT-PCR)验证,结果显示,qRT-PCR结果与RNA-Seq分析相一致。GO和KEGG富集结果分析发现,amh、cyp17和star可能在绿鳍马面鲀雄性精子发生过程中起关键作用;bmp2、foxl2、cyp19a、figla和hsd17b1在雌性卵子发生和卵巢类固醇生成过程中发挥重要作用。本研究通过比较绿鳍马面鲀精巢和卵巢的转录组表达差异,初步阐明了精巢和卵巢的基因表达特征,为进一步研究绿鳍马面鲀的性腺发育机制奠定了基础。     

First year growth and survival of common carp in two glacial lakes

Abstract  Cohorts of common carp, Cyprinus carpio Linnaeus, were monitored from hatch through the next spring in two South Dakota, USA lakes to identify factors affecting year-class strength. Hatching occurred over 37- and 47-day periods in the two lakes. Common carp that hatched earlier achieved greater total lengths at the end of the first growing season (Brant Lake: r  = −0.84, d.f. = 77, P  <   0.001; Campbell Lake: r  = −0.87, d.f. = 78, P  <   0.001). Mean daily growth rates were approximately 1.0 mm day⁻¹ and similar between lakes. Total length was positively related to daily growth rate in the two lakes, indicating that members of the cohort that grew faster achieved greater total lengths by time of capture. Hatch date was inversely related to daily growth (fish hatched earlier grew faster) in one lake ( r  = −0.44, d.f. = 77, P  < 0.001) but not the other ( r  = −0.04, d.f. = 78, P  = 0.678), suggesting that length at the end of the growing season can be affected by length of growing season and growth rate. Overwinter survival of age-0 fish appeared to be size dependent because age-1 common carp length–frequency distributions from both lakes comprised only of the larger cohort members present the previous autumn.     

低温胁迫对鲤血清生化指标的影响

本研究主要报道了荷包红鲤抗寒品系(Cyprinus．carpio var．wuyuanensis)与大头鲤(Cyprinus．pellegrini pellegrini)杂交F_2在温度骤降过程中,温度对其血清中的总蛋白、白蛋白、总胆红素、胆固醇、尿素氮、血糖和甘油三酯等血清生化指标的影响。骤降试验以2℃为降幅,每次间隔1h,依次将10℃、8℃、6℃和4℃,对应编号为A组、B组、C组和D组。数据经SAS8．0统计软件单因素方差分析。结果发现,除温度对尿素氮有显著性影响外{F0．05(3,28)=3.99,P=0．0175(P＜0．05)},温度与其它指标的变化无显著性关联。再对4组样本血清的各项指标进行Ducan式多重范围比较分析。结果表明,D组(4℃)与B组(8℃)总胆红素存在显著性差异(P＜0．05);C组(6℃)与A(10℃)、B (8℃)组尿素氮存在显著性差异(P＜0．05)。     

Effects of dietary medium-chain triacylglycerols (tricaprylin and tricaproin) and phospholipid supply on survival, growth and lipid metabolism in common carp (Cyprinus carpio L.) larvae

The present study investigated the interaction of dietary medium-chain fatty acids (MCFA) and phospholipids (PL) on survival, growth and lipid metabolism in common carp larvae. Nine diets based on casein and dextrin and with a variable lipid part were tested in triplicate for 22 days post first feeding. The 3×3 design consisted of three triacylglycerols (3% of diet) combined with three different lipid supplements. Tested triacylglycerols were triolein (TOL), tricaprylin (TC8) and tricaproin (TC6), and lipid supplements were 2% soybean oil (low-fat diets without PL), 2% soybean lecithin (low-fat diets with 2% PL) or both 2% soybean lecithin and 6% TOL (high-fat diets with 2% PL).

In the first step, both TC6 and TC8 resulted in improved survival and growth rates compared to TOL, irrespective of the PL supply. In the second step, TC8 decreased survival and growth rates, whereas the difference between TC6 and TOL became less. Histological signs of impaired intestinal absorption of neutral lipids were evidenced in larvae fed TOL without PL and also in high-fat diets with 2% PL. The latter diets also resulted in poorer growth rates compared to low-fat diets with 2% PL. These results suggest that the quantitative PL requirement of larvae increases as the dietary level of long-chain triacylglycerols increases. Larvae fed TC6 or TC8 showed enlarged liver and hepatocyte volume and a decreased level of body neutral lipids. Based on β-hydroxybutyrate (β-HBA) measurements in whole larvae, TC8 was found to be more ketogenic than TC6. TC6 and TC8 affected differently the fatty acid profile of larval body neutral lipids. TC6 did not induce the appearance of MCFA, whereas TC8 feeding resulted in a low level of 8:0 and relatively high levels of 10:0 (3.8% of total fatty acids). Neither 8:0 nor 10:0 were found in larval polar lipids.

This study confirmed the essentiality of PL in common carp larval diets and underlines differences in the utilization of TC6 and TC8, which both initially stimulate growth during the first week, but only temporarily in the case of TC8.     

Influence of management protocols on carp growth under nursery conditions: relative importance of food and water quality

Twenty outdoor holding tanks (10 m–3 each), were filled with ground water and grouped into five feeding schemes: live zooplankton cultured outside the fish growing tank (LFS); direct nursery pond fertilization schedule in static (MS) as well as in exchanged water (EMS); intermediate conditions between the LFS and MS (IS); and supplementary food system using mixture (1:1) of finely ground mustard oilcake and boiled rice (SFS). Two hundred common carp (Cyprinus carpio) fry were introduced into each of the twenty outdoor tanks maintained at ambient temperature outside the laboratory. After 90 days of rearing, the fish were harvested and analysed for various growth parameters and food conversion efficiency. The average weight of carp attained in the LFS was significantly higher than that in the other four feeding schemes. The frequency distribution of final body weight of common carp showed the preponderance of large and small fish in the LFS and MS, respectively. Likewise, plankton intake by the carp fry was highest in the LFS. The rate of survival was much higher in the LFS as compared with the rest of the treatments. The water quality remained far better in the former than the latter. © Rapid Science Ltd. 1998     

鲤低氧适应性状的全基因组关联分析

低氧适应是水产养殖物种的重要性状,筛选用于改良低氧适应性状的分子标记及候选基因有助于鱼类耐低氧品种选育.在数量性状和质量性状的遗传研究中,全基因组关联分析(GWAS)广泛应用于性状相关标记和基因的发掘.本研究对鲤(Cyprinus carpio)养殖群体开展了低氧胁迫实验,选取了低氧敏感和低氧耐受的极端性状个体作为研究...     

Effect of d-Lys6 salmon sGnRH alone and in combination with domperidone on the spawning of common carp during the late spawning season

The effect of [d-Lys6] salmon gonadotropin-releasing hormone alone (sGnRH) and in combination with domperidone, a dopamine antagonist, on the spawning of common carp, Cyprinus carpio, was investigated during the late spawning season (when mature fish stop spawning under natural conditions when males and females are put together). Fish were induced to spawn by [d-Lys6]-sGnRH salmon gonadotropin-releasing hormone analogue (sGnRH-X) only when injected in combination with domperidone at doses of 10 g kg-1 and 20 mg kg-1 body weight respectively. [d-Lys6]-sGnRH-X alone did not induce spawning at a dose as high as 100 g kg-1 body weight. Fish injected with domperidone alone did not spawn either. These results demonstrate that [d-Lys6]-sGnRH-X in combination with a dopamine antagonist is effective in inducing spawning during the late spawning season.     

Dietary lysine requirement of juvenile Jian carp (cyprinus carpio var. Jian)

This study was designed to determine the dietary lysine requirement of juvenile Jian carp (cyprinus carpio var. Jian). A total of 990 juvenile Jian carps (initial weight 7.89 ± 0.04 g) were randomly allocated six groups of each three replicates, feeding isonitrogenous (320 g kg^?1 crude protein) and isolipidic (50 g kg^?1 crude fat) diets containing graded levels of coated l ‐lysine, with dietary lysine content ranging from 22 to 69 g kg^?1 of protein, respectively, for 80 days. Final weight, protein deposition and protein production value were significantly improved in response to the increasing levels of dietary lysine up to 59 g kg^?1 of protein and remained nearly constant thereafter. Whole‐body protein content followed a similar pattern as growth parameters in relation to dietary lysine level. Hepatopancreas and intestine protein content, hepatopancreas index (HSI) and intestine index (ISI) were positively affected by dietary lysine level. The dietary lysine requirement of juvenile Jian carp estimated by broken line analysis based on weight gain was 59 g kg^?1 of protein.     

红鲤4群体间红细胞免疫功能及其差异

应用红细胞C3b受体花环试验和红细胞天然免疫粘附肿瘤细胞花环试验方法,证实兴国红鲤(Cyprinuscarpio.var.singguonensis)、玻璃红鲤(C.carpio.var.wananensis)、荷包红鲤(C.carpio.var.wananensis)及瓯江彩鲤(C.carpio.var.color)的红细胞表面都存在C3b补体受体,均可形成花环;红鲤的红细胞免疫粘附能力存在着种群间差异,上述2种花环试验的花环率大小的顺序均是：兴国红鲤＞荷包红鲤＞瓯江彩鲤＞玻璃红鲤,差异都极显著(P＜0．01);4群体红鲤的红细胞均具有吞噬作用。结果证实,鱼类红细胞免疫功能在机体防御病原的过程中占有重要地位。     

建鲤生长性状QTL区间及其与镜鲤同源性比对

以建鲤(Cyprinus carpio var. jian)F₁群体的94尾个体为材料, 利用254个微卫星标记构建了建鲤的遗传图谱, 并对体长、体高和体厚性状进行了QTL定位, 共检测到17个生长相关性状QTL, 分布在10个连锁群上, 解释表型变异为10.8%~35.2%。以相同的分子标记, 构建建鲤与镜鲤(Cyprinus carpio L.)的比较图谱, 分析了建鲤和镜鲤群体生长性状QTL的同源性关系。结果表明, 建鲤与镜鲤图谱具有广泛的共线性或同线性关系, 建鲤每个连锁群在镜鲤图谱中均找到了对应的同源连锁群, 其中建鲤10个生长性状QTL与镜鲤13个相同性状QTL具有同源性, 同源比例高达58.8%。同时发现, 建鲤QTL置信区间相对较大, 与之同源的镜鲤QTL置信区间较小, 通常位于建鲤QTL子区间内, 定位结果更精细。此外, 建鲤与镜鲤连锁群上都存在QTL的富集区域, 而这些富集区域常常存在于同源连锁群的共线性区域, 可作为标记辅助选择的重点区域。鲤通用QTL的发掘, 为分子标记辅助育种和更进一步的精细定位打下基础。