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1.
本研究利用MISA软件挖掘长江刀鲚(Coilia ectenes)肌肉和肝脏转录组中的微卫星标记,为刀鲚选育群体的种质资源评估和分子标记辅助育种奠定基础。结果显示,从71869条Unigenes中共获得33896条重复单元长度为1~6碱基的微卫星序列;刀鲚转录组中不同类型微卫星的重复基序具有不同的分布特征,其中,单核苷酸重复、二核苷酸重复和三核苷酸重复为主要的微卫星重复类型,分别占总微卫星数目的34.94%、49.47%和13.34%;不同微卫星重复类型的优势重复基序亦有所不同,其中,A/T为单核苷酸重复基序的优势重复基序占86.25%,AC/GT为二核苷酸重复基序的为优势重复基序占75.25%,AGG/CCT为三核苷酸重复基序的优势重复基序占28.57%;不同微卫星重复基序核苷酸的数量和重复次数亦有所不同,重复次数伴随着重复单元中核苷酸数量的增加而呈现降低的趋势;从100对四核苷酸重复的SSR引物中筛选获得了16对多态性微卫星标记,并以此为基础,对长江刀鲚选育群体(F3)的遗传学特征进行了初步评估,结果显示,长江刀鲚选育群体F3的平均有效等位基因数(Ne)、平均观测杂合度(Ho)、平均期望杂合度(He)和Shannon多样性指数I分别为1.7580、0.3414、0.3977和0.6278。以上结果表明,基于刀鲚转录组数据批量开发微卫星是切实可行的,所开发的多态性微卫星标记能够应用于长江刀鲚选育群体的遗传背景评估和进一步的遗传育种研究。  相似文献   

2.
本研究采用MISA软件分析泥东风螺(Babylonia lutosa)转录组中微卫星信息。结果显示,从转录组中共获得16324个SSR,共有181种重复基元;泥东风螺转录组中不同类型微卫星的重复基元具有不同的分布特征,其中,二核苷酸重复基元中AC/GT(70.58%)重复基元以重复6次出现频率占优;长度为12~20 bp的SSR占63.95%,长度为21~25 bp的SSR占9.14%,总体的平均长度为18.4 bp。随机选取其中50条序列设计引物,通过对福建野生泥东风螺群体(WP)DNA样本进行PCR扩增和分型,结果获得23个多态性位点,等位基因数目为2~7个不等,期望杂合度(Ne)为0.190~0.937,观察杂合度(No)为0.065~0.936,多态性信息含量(PIC)为0.061~0.777,有4个位点显著偏离哈迪温伯格平衡(Hardy-Weinberg equilibrium, HWE) (P<0.05)。对野生群体和养殖群体(BP)遗传多样性分析显示,野生群体和养殖群体的平均Ne分别为0.491和0.544,平均No分别为0.477和0.564,平均PIC分别为0.541和0.407。Fis结果显示,野生群体和养殖群体分别有13个和9个位点杂合子过剩。群体间遗传分化指数(Fst)为0.001~0.655,平均值为0.053 (0.05相似文献   

3.
为更好地开发军曹鱼(Rachycentron canadum)高多态性微卫星分子标记,本研究基于军曹鱼全基因组测序结果,利用MISA1.0软件对其简单重复序列(simple sequence repeat, SSR)的位点信息进行检索及分析。结果显示,基因组中共筛选出1~6个核苷酸为重复单元的SSR位点344 820个,其中,以单核苷酸重复序列最多(174 146个),占SSR总数的50.50%;其次为二核苷酸重复和三核苷酸重复序列,分别占SSR总数的30.23%和14.02%。在SSR包含的重复单元中,单核苷酸重复以A/T类型为主,AC/GT是二核苷酸的优势重复单元类型。军曹鱼基因组SSR核心序列重复次数在4~275次范围内波动,单核苷酸SSR重复数为10的最多,二核苷酸SSR重复次数为6的最多。本研究设置长度≥12 bp为筛选高多态性SSR位点的标准,共获得361 684个位点。在上述位点中随机选取100个候选位点进行基因分型检测,利用从中筛选到多态性较高的10个SSR标记分别对北海、陵水、硇洲、徐闻和三亚5个养殖群体进行遗传多样性分析,145尾个体中共检测到69个等位基因,观测杂合度(Ho)、期望杂合度(He)和多态信息含量(PIC)平均值分别为0.628、0.706和0.653。相关研究表明,军曹鱼基因组中SSR位点类型较为丰富、多态性潜能较高,从中筛选获得的多态性SSR标记可为军曹鱼分子标记辅助育种、群体遗传多样性评价等研究提供有力支持。  相似文献   

4.
以金乌贼(Sepia esculenta)转录组测序获得的177,951条Unigene为对象,采用Micro Satellite (MISA)软件检测及分析其中的简单重复序列(Simple sequence repeat, SSR)的位点信息。结果显示,在金乌贼转录组中共检测出161,327个SSR位点,分布在64,933条Unigene中,SSR位点发生频率为36.49%,出现频率为90.66%。其中,最主要的重复类型为单核苷酸、二核苷酸和三核苷酸,分别占SSR总数的46.00%、39.93%和9.48%。SSR包含的重复基元中,A/T是单核苷酸的优势重复基元,AT/AT和AC/GT是二核苷酸的优势重复基元类型。66,004个重复基元长度≥20 bp,占SSR总数的40.91%,且其中含有低级重复基元(二、三核苷酸重复)的SSR位点数量占优。以上结果表明,金乌贼转录组中SSR位点出现频率较高且类型丰富、多态性潜能较高,研究结果可为更好地开发金乌贼SSR分子标记、种质资源保护利用、遗传多样性评价和分子标记辅助育种等提供参考。  相似文献   

5.
通过对长体圆鲹(Decapterus macrosoma)基因组进行RAD-Seq高通量测序,共获得58 180条微卫星序列,选取112条二、三核苷酸重复的微卫星序列设计引物,经筛选后,共获得27个具有多态性的微卫星标记。利用一个长体圆鲹群体对通过筛选的微卫星标记的种群遗传学特征进行评价。结果显示,27对引物扩增的序列中18个位点为二核苷酸重复,重复次数为9~14次,9个位点为三核苷酸重复,重复次数为6~10次,等位基因数(Na)为5~17 (平均10.6),表观杂合度(Ho)为0.342 9~0.857 1 (平均0.631 7),期望杂合度(He)为0.538 3~0.911 8(平均0.796 8),多肽信息含量(PIC)为0.497~0.886 (平均0.780 9),除1个位点外,其他位点PIC值均大于0.500,表明开发的微卫星位点具有较高的多态性。"哈迪-温伯格"平衡(HWE)检测结果显示,19个标记等位基因频率符合HWE。连锁不平衡检测表明各位点间无连锁不平衡现象。该研究开发的27个微卫星标记可为长体圆鲹种群遗传学研究提供基础。  相似文献   

6.
吕建建  王渝  高保全  李健  刘萍 《水产学报》2013,37(6):816-822
为发掘三疣梭子蟹Ⅰ型微卫星标记,实验运用生物信息学方法,从NCBI数据库已公开的13 985条三疣梭子蟹EST序列中搜索微卫星位点.结果显示,共搜索到287个微卫星位点,其中主要为二核苷酸重复序列(173个),占总数的60.3%;其次为三核苷酸重复序列(79个),占总数的27.5%;四、五、六核苷酸重复位点较少;在二核苷酸重复位点中,AC/GT重复位点最为丰富,占二核苷酸重复位点总数的53.8%,AG/CT重复次之,占二核苷酸重复位点总数的37.0%,AT和GC重复较少.挑选14个Ⅰ型微卫星标记在野生三疣梭子蟹群体中进行多态性检测,发现8个位点呈多态性,平均多态信息含量(PIC)和平均遗传杂合度(H)分别为0.57和0.63.其中6个多态性位点的PIC值大于0.5,呈现较高多态性特征.研究表明,基于三疣梭子蟹EST数据发掘Ⅰ型微卫星标记的方法切实可行.本研究发掘的Ⅰ型微卫星标记将为三疣梭子蟹遗传多样性评估、遗传连锁图谱构建和QTL分析提供有效的分子标记.  相似文献   

7.
采用Illumina高通量测序技术,对兴国红鲤(Cyprinus carpio var.singuonensis)垂体和性腺等组织进行转录组测序分析,筛选微卫星标记并分析其组成及特征。结果显示:共获得13 652个微卫星标记,对所得位点进行分类,单核苷酸重复类型占47.86%,二、三、四、五、六核苷酸重复类型所占比例分别为34.43%、16.32%、1.25%、0.12%以及0.02%。随机选取30个SSR位点进行PCR验证,有20对可以扩增出清晰稳定的条带。在24个兴国红鲤个体中对上述位点进行多态性分析,结果表明,具有多态性的微卫星引物为9对。不同位点得到的等位基因范围为2~4,平均等位基因数为3.111 1±0.993 8,观测杂合度(Ho)、期望杂合度(He)以及多态信息含量(PIC)平均值分别为0.597 2±0.233 2、0.539 7±0.178 0和0.467 2±0.172 1。9个微卫星位点中,有4个显著偏离哈代-温伯格平衡(Hardy-Weinberg equilibrium,HWE)(P0.05)。Illumina高通量测序提供了一种直观、高效开发微卫星标记的方法,所选兴国红鲤群体遗传多样性维持较好。  相似文献   

8.
基于牙鲆RNA-seq数据中SSR标记的信息分析   总被引:1,自引:0,他引:1  
通过对牙鲆(Paralichthys olivaceus)进行转录组测序(RNA-seq),利用Micro SAtellite(MISA)软件对1~6个碱基重复、碱基数在10 bp以上的微卫星进行鉴定。结果表明,牙鲆转录组水平上,共发现42 183个SSR位点,分布在26 457条Unigene上,发生频率为27.12%,平均密度为339个/Mbp。获得的SSR一共有216种重复基元,其中二核苷酸重复基元类型数量最多,共有17 570个,占所鉴定SSR总数的41.65%。同时用SPSS statistics 20.0软件对牙鲆转录组SSR的多态性进行了评估。  相似文献   

9.
采用Illumina高通量测序技术对银鲴(Xenocypris argentea)肝脏组织进行转录组测序分析,筛选微卫星标记并进行多态性检验。共获得7 272个微卫星位点。随机选取48个4碱基以上重复类型的SSR位点进行引物设计和PCR验证,有47对可以扩增出清晰稳定的条带。在上述47个位点中随机选择26对在洞庭湖银鲴群体中进行多态性分析,结果表明,具有多态性的微卫星引物为21对。不同多态位点得到的等位基因数范围为3~15,平均基因数为7.29±3.94,观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)以及香浓-威尔指数(H)平均值分别为0.532 7±0.211 4、0.613 6±0.196 4、0.564 6±0.198 0和1.302 0±0.577 9。21个微卫星位点中,有6个显著偏离哈代-温伯格平衡(Hardy-Weinberg equilibrium,HWE)。  相似文献   

10.
本研究以前期获得的栉江珧(Atrina pectinata)转录组数据为基础,筛选获得10550条微卫星标记(SSR),检出率为8.2%,平均9.01 kb出现1个SSR位点。设计并合成120对SSR引物,筛选得到36对能够稳定扩增的引物,并利用已获得的36对SSR引物对青岛海区栉江珧进行了群体遗传多样性分析。结果显示,12对引物的扩增片段表现出多态性,共产生42个等位基因,平均每个位点产生3.5个等位基因,平均观测杂合度(H_o)、平均期望杂合度(H_e)和平均多态信息含量(PIC)分别为0.417、0.604和0.526,表明青岛海区栉江珧群体的遗传多样性较高。本研究获得的EST-SSR标记和群体遗传信息为栉江珧的种质资源保护提供了重要的参考资料。  相似文献   

11.
Previously, we reported 10 PEGE types of 85 tilapia Streptococcus agalactiae(GBS), which shifted from Streptococcus iniae in China, by using PEGE method. Presently, larger and more representative tilapia GBS were isolated, for the ?rst time in China, to characterize their serotypes and genetic diversities more precisely than had done before. 168 GBS strains were distributed in ?ve provinces of China, in which Guangdong, Guangxi and Hainan were the major ones, holding36.9%(62/168), 37.5%(63/168) and 19.6%(33/168), respectively. Serotypes, Ia, Ib and III, were observed in these strains and the most predominant one was Ia(95.2%), which mainly distributed in Guangdong, Guangxi and Hainan. Ia initially occurred in 2009, it shoot up to 32.1% in 2010,but decreased to 16.1% in 2011 before went up to 45.2% in 2012. Ib sporadically occurred during2007–2011, III onlyoccurred in 2012. 14 different PFGE types, including 4 new types(N, O,P and Q), were observed, in which B, D, F and G were the predominant types, holding 83.9%(141/168) of the total GBS strains. Ia corresponded to 11 PFGE types(A–H, N–P), in which type D predominated(51%). Ib represented 3 genotypes(I, J and Q) and III harbored only 2genotypes(N and F). Type N and Fsynchronously presented in Ia and III. In summary, the genetic diversity of tilapia GBS varied by serotypes and changed with geographical locations and years.Although Iastillpredominated, new rareserotypeIII alreadyoccurred in China.  相似文献   

12.
Two gonadotropins (GtH; Qa and Qb) were purified by gel filtration and ion exchange chromatography from the pituitaries of Indian walking catfish (Clarias batrachus). The presence of GtH during purification was assessed by in vitro oocyte maturation and in vivo steroidogenic activity, and their identities were determined by elution profiles, molecular weight, biological activities and yield. The molecular weights of Qa and Qb were 37 and 42 kDa, respectively, and composed of distinct subunits (Qa: 20 and 14 kDa and Qb: 26 and 18 kDa). Polyclonal antibodies raised against Qa immunostained Qa, Qb and pituitary GtH cells. A competitive Qa‐ELISA was developed whose sensitivity was 6.25 ng mL?1 (1.25 ng well?1) with intra‐ (3.5%) and inter‐ (12.4%) assay coefficients of variation. Displacement curves parallel to the standard were obtained with plasma and pituitary extracts of catfish, Qb and carp GtHII. The assay was validated by measuring the plasma Qa levels after LHRH treatment and in relation to ovarian growth in the female catfish during different reproductive phases. Based on the results, Qa and Qb corresponded to fish LH and FSH respectively. The findings will increase the knowledge of the mechanisms controlling fish reproduction and identification of sensitive phases in fish in captivity for hormonal manipulation.  相似文献   

13.
Tetrahymena is a protozoan parasite, which infects guppy, Poecilia reticulata Peters, and causes substantial economical losses in commercial farms worldwide. Studies of guppy infected by Tetrahymena require standardized infection protocols. The LD50 for Tetrahymena infection of guppies by intraperitoneal (IP) injection was calibrated, and the level obtained was 946 parasites per fish. Guppy infection with Tetrahymena by immersion, imitating the natural route of infection via the integument, was studied under normal or stress conditions. Exposure to cold and netting (CNI) and to cold only (CI) followed by immersion exposure to 10 000 Tetrahymena per mL resulted in 22.5% and 19.2% mortality, respectively, as compared to 14.2% and 10% in groups that were netted only (NI) or non‐stressed (I). Histopathology revealed that immersion infection resulted in a systemic infection. Lysozyme levels, measured 3 weeks after infection, were significantly higher in the CNI group (288 μg per mg protein) compared with CI‐, NI‐ and I‐treated groups (94.5, 64 and 62.3 μg mg?1, respectively). There was no evident parasite immobilization activity in body homogenates, suggesting no development of acquired immunity. Re‐infection by IP injection revealed no increase in protection in any of the treatment groups, mortality range of 56.3–75%, higher than in the non‐exposed control (40.6% mortality).  相似文献   

14.
There has been growing concern about the overuse of antibiotics in the ornamental fish industry and its possible effect on the increasing drug resistance in both commensal and pathogenic organisms in these fish. The aim of this study was to carry out an assessment of the diversity of bacteria, including pathogens, in ornamental fish species imported into North America and to assess their antibiotic resistance. Kidney samples were collected from 32 freshwater ornamental fish of various species, which arrived to an importing facility in Portland, Oregon from Colombia, Singapore and Florida. Sixty‐four unique bacterial colonies were isolated and identified by PCR using bacterial 16S primers and DNA sequencing. Multiple isolates were identified as bacteria with potential to cause disease in both fish and humans. The antibiotic resistance profile of each isolate was performed for nine different antibiotics. Among them, cefotaxime (16% resistance among isolates) was the antibiotic associated with more activity, while the least active was tetracycline (77% resistant). Knowing information about the diversity of bacteria in imported ornamental fish, as well as the resistance profiles for the bacteria will be useful in more effectively treating clinical infected fish, and also potential zoonoses in the future.  相似文献   

15.
This study investigated the efficiency of iodophor disinfection (135 ppm active iodine for 15–30 min) of non‐hardened Salmo trutta eggs against different groups of bacteria and against fungus. Egg samples were taken from non‐disinfected and from disinfected eggs, microorganisms were cultured on specific nutrient media and their mass was measured by turbidimetric methods. Bacteria and fungus mass of non‐hardened eggs could be reduced but not eliminated by iodophor disinfection with 135 ppm active iodine for 15 min. The extent of reduction was 47–65% (Experiment 1). The efficiency of disinfection increased with disinfection time as the reduction in bacteria and fungus mass was 40–55% after 15 min and 58–74% after 30 min (Experiment 2). Disinfection efficiency of iodophor solution diluted in water (reduction 49–57%) and of iodophor solution diluted in sodium chloride solution iso‐osmolar to the oocytes (reduction 52–61%) was similar (Experiment 3). The reduction in bacteria and fungus mass was persistent as it was 39–72% lower in embryos deriving from disinfected eggs than in embryos deriving from non‐disinfected ones (Experiment 4). In conclusion, the tested disinfection method is inadequate to eliminate pathogens completely but it could positively influence immune defence of eggs and embryos.  相似文献   

16.
The indiscriminate use of antibiotics and chemicals in shrimp hatcheries has led to biomagnification and that in turn could lead to rejection of a whole consignment. The application of the bioencapsulation technique as a tool for curative treatment in shrimp larvae was investigated. Herbs having antibacterial properties such as Solanum trilobatum, Andrographis paniculata and Psoralea corylifolia (methanolic extracts) were bioencapsulated in Artemia and fed to Penaeus monodon post larvae PL 1–25. The post larvae were reared in a medium inoculated with pathogenic bacteria such as Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi and Vibrio sp. Post larvae reared in the non-inoculated water and fed with non-enriched Artemia exhibited 90% survival, highest specific growth rate (12.43%) and reduced bacterial load. P. monodon reared in the bacterial inoculated water and fed with the non-enriched Artemia exhibited the lowest survival (10–30%), specific growth rate (8.42–9.1%) and increased bacterial load (2.86 × 103 to 3.76 × 105 cfu/g). The methanolic extracts of the herbs helped to increase survival and specific growth rate and reduced bacterial load in the P. monodon culture system. Among the three herbal extracts, P. corylifolia enriched Artemia fed post larvae showed the tendency to higher survival (>50%), growth rate (11.5 averaged) and low bacterial load (1.12 × 105 cfu/g). This revised version was published online in August 2006 with corrections to the Cover Date.  相似文献   

17.
The sea raven, Hemitripterus americanus, is a sit-and-wait, low metabolic rate, marine teleost. The objective of this study was to determine i) whether cortisol implantation (50 mg. kg-1) for 7 days altered hepatocyte metabolism, and hepatocyte responsiveness to epinephrine, glucagon and insulin, and ii) whether 8 weeks of food-deprivation modified the above response. Cortisol implantation significantly increased hepatocyte total glucose production and oxidation from alanine compared to the sham group. There was no cortisol effect on glycogen breakdown, suggesting that the activation of other pathways, including gluconeogenesis, are required to account for the increased glucose production. Epinephrine-mediated (10-5M) glycogen breakdown and insulin-mediated (10-8M) total glucose production were enhanced in hepatocytes of cortisol implanted sea ravens, but there were no change in any glucagon (10-7M) effects. The enhanced glycogen breakdown in the absence of similar increases in total glucose production with epinephrine indicates mobilization of carbohydrate reserves for endogenous use by the liver. Food-deprivation for 8 weeks significantly decreased condition factor, plasma cortisol concentration and liver glycogen content in the sea raven, but had no effect on plasma glucose concentration. Hepatocyte total glucose production and flux rates from alanine increased significantly with food-deprivation. Moreover, food-deprivation increased responsiveness of total hepatocyte glucose production to the actions of glucagon and insulin, but not to epinephrine; none of these effects were modified by cortisol implantation. Our results indicate that cortisol in the sea raven exerts both a direct and an indirect or permissive effect on hepatocyte metabolism by modifying hepatocyte responsiveness to epinephrine and insulin stimulation. Cortisol implantation did not modify the effects of glucagon or food-deprivation in this species.  相似文献   

18.
Important environmental processes for the survival and recruitment of early life stages of pelagic fishes have been synthesized through Bakun's fundamental triad as enrichment, concentration and retention processes (A. Bakun, 1996, Patterns in the Ocean. Ocean Processes and Marine Population Dynamics. San Diego, CA, USA: University of California Sea Grant). This conceptual framework states that from favourable spawning habitats, eggs and larvae would be transported to and/or retained in places where food originating from enrichment areas would be concentrated. We propose a method for quantifying two of the triad processes, enrichment and retention, based on the Lagrangian tracking of particles transported within water velocity fields generated by a three‐dimensional hydrodynamic model. We apply this method to the southern Benguela upwelling ecosystem, constructing putative maps of enrichment and retention. We comment on these maps regarding main features of the circulation in the region, and investigate seasonal variability of the processes. We finally discuss the results in relation to available knowledge on the reproductive strategies of two pelagic clupeoid species abundant in the southern Benguela, anchovy (Engraulis encrasicolus) and sardine (Sardinops sagax). Our approach is intended to be sufficiently generic so as to allow its application to other upwelling systems.  相似文献   

19.
This study evaluated the effects of three levels of loading density (200, 300 and 400 g L−1) and four levels of duration (1, 3, 6 and 9 h) on the mortality, plasma cortisol and chloride levels and growth of rohu Labeo rohita fingerlings in a transport simulation. While total immediate mortality was low (4–12%), delayed mortality was high (27–49%). Initial capture and handling were found to constitute the most stressful phase as indicated by elevated plasma cortisol. The levels of cortisol continued to rise at 6 and 9 h after transport, with the highest level observed at 9 h after transport. The level of plasma chloride fell after transport across all density levels and treatment durations. Specific growth rate (SGR, %/day) and total bacterial density (cfu/g) were not different between and within treatments, and between treatments and the controls. This study demonstrates that transport has a profound effect on the stress responses of rohu fingerlings. Although the level of immediate mortality was low, the higher level of delayed mortality has serious implications in terms of production inefficiency for grow-out farmers.  相似文献   

20.
  • 1. The common name ‘tilapia’ refers to a group of tropical freshwater fish in the family Cichlidae (Oreochromis, Tilapia, and Sarotherodon spp.) that are indigenous to Africa and the southwestern Middle East. Since the 1930s, tilapias have been intentionally dispersed worldwide for the biological control of aquatic weeds and insects, as baitfish for certain capture fisheries, for aquaria, and as a food fish. They have most recently been promoted as an important source of protein that could provide food security for developing countries without the environmental problems associated with terrestrial agriculture. In addition, market demand for tilapia in developed countries such as the United States is growing rapidly.
  • 2. Tilapias are well‐suited to aquaculture because they are highly prolific and tolerant to a range of environmental conditions. They have come to be known as the ‘aquatic chicken’ because of their potential as an affordable, high‐yield source of protein that can be easily raised in a range of environments — from subsistence or ‘backyard’ units to intensive fish hatcheries. In some countries, particularly in Asia, nearly all of the introduced tilapias produced are consumed domestically; tilapias have contributed to basic food security for such societies.
  • 3. This review indicates that tilapia species are highly invasive and exist under feral conditions in every nation in which they have been cultured or introduced. Thus, the authors have concluded that, despite potential or observed benefits to human society, tilapia aquaculture and open‐water introductions cannot continue unchecked without further exacerbating damage to native fish species and biodiversity. Recommendations include restricting tilapia culture to carefully managed, contained ponds, although exclusion is preferred when it is feasible. Research into culture of indigenous species is also recommended.
Copyright © 2005 John Wiley & Sons, Ltd.  相似文献   

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