New genetic recombination in hypervariable regions of the white spot syndrome virus isolated from Litopenaeus vannamei (Boone) in northwest Mexico

The white spot syndrome virus (WSSV) is a pathogen of great concern to the worldwide shrimp culture. In comparative studies on the WSSV genome, regions such as the open reading frame (ORF) 14–15 and ORF 23–24, prone to deletions and recombination, had been useful to study the evolutive relationships among viral strains. When looking for the WSSV strains infecting Litopenaeus vannamei (Boone) in northwest Mexico, we found evidence of a genetic similarity in ORF 14–15 to a strain from India and a recombination involving ORFs 78, 79 and 80. Two genotypes were found involving the insertion of a 265 base‐pair segment of ORF 108 into ORF 78 with inversions and deletions within ORFs 78, 79 and 80. The WSSV has an Asian origin and the mutations found could be an adaptation strategy to infect L. vannamei and other crustacean species of the American continent.     

中国沿海6个花鲈群体的遗传多样性分析

利用8对微卫星或简单重复序列[microsatellite or simple sequence repeats(SSR)]标记对辽宁东港(DG)、绥中(SZ),河北秦皇岛(QHD),山东青岛(QD),浙江舟山(ZS)以及广东珠海(ZH)海域的6个花鲈(Lateolabrax maculatus)群体进行遗传多样性分析。结果表明,共检测到等位基因90个,每个位点的等位基因数(NA)为3~20;有效等位基因数(Ae)为1.7~11.4;观测杂合度(Ho)为0.355~0.971;期望杂合度(He)为0.398~0.912;多态信息含量(PIC)为0.365~0.906;6个群体的遗传多样性处于中等水平且群体间差异不显著(P0.05),其中舟山群体的遗传多样性最高(NA=11;He=0.762;PIC=0.734),绥中群体的遗传多样性最低(NA=9.8;He=0.721;PIC=0.692);哈代?温伯格平衡检验显示,除秦皇岛群体外,标记Lama18、Lama21和Lama29在其他5个群体中偏离HWE(P0.01)。位点Lama18与Lama42间存在极显著性的连锁不平衡(P0.01);分子方差(AMOVA)分析结果显示群体间、群体内个体间以及所有个体间的方差均达显著性水平(P0.01);群体间配对Fst(pair-wise Fst)和遗传距离分析结果显示,舟山群体与其他5个群体遗传分化最远,遗传距离最大,而北方的绥中、东港、青岛以及秦皇岛4个群体间分化不显著;聚类分析显示,珠海与秦皇岛群体先聚合,再与舟山群体聚为一支。绥中、东港、青岛群体聚为一支;遗传组分分析结果显示,6个花鲈群体中共包含3个主要遗传组分,其中舟山群体遗传混杂少,遗传信息保留完整,而绥中、东港和青岛3个群体遗传组分类似,遗传混杂严重。另外,秦皇岛与珠海群体约40%的遗传组分相同;研究结果表明,中国沿海的花鲈群体中除舟山群体外,绥中、东港、青岛、秦皇岛和珠海5个群体的遗传多样性已受到现有养殖模式与养殖逃逸的影响。     

Genetic variation in the growth traits of straight-bred and crossbred black bream (Acanthopagrus butcheri Munro) at 90 days of age

The current slow growth rate of black bream (Acanthopagrus butcheri Munro) impedes their widespread commercial aquaculture across inland southern Australia. We report initial estimates of genetic variation for growth traits at 90 days of age from a diallel cross using two black bream populations. Standard length, total length, and wet weight varied significantly among lines and among half‐sib groups within lines. Differences among half‐sib groups explained 6.8% of the total variance in standard length, 8.3% in total length, and 7.1% in wet weight, giving estimated heritabilities over all lines of 0.27±0.11 for standard length, 0.33±0.13 for total length, and 0.28±0.12 for wet weight. There was no evidence for heterosis in any traits when straight‐bred and crossbred lines were compared. There were high phenotypic (r_P=0.95–0.98) and genetic (r_G=0.63–0.69) correlations among all growth traits.     

三个不同养殖群体金鱼遗传多样性的RAPD分析

采用随机扩增多态性DNA(RAPD)方法对金鱼3个不同地区养殖群体-天津塘沽(TJ)、江苏苏州(JS)及福建福州(FZ)群体各20ind的DNA多态性进行了分析。在事先优化的反应条件下,所使用的100个随机引物中,有14个引物扩增出清晰稳定的片段,共计103条,大小在200~2500bp,其中多态性片段27条。金鱼总的DNA多态位点百分率为26.21%。数据分析结果显示,3个金鱼群体内遗传多样性偏低,遗传相似度为0.9519~0.9785。金鱼3个群体总的Nei基因多样性指数为0.1061,Shannon信息指数为0.1547。金鱼3个群体间平均遗传距离为0.0375,基因分化系数Gst为0.243,表明3个养殖群体间产生了一定程度的遗传分化。UPGMA法和NJ法的聚类分析显示,两者结果一致。TJ群体和JS群体优先聚类,再与FZ群体聚类。     

文蛤北方种群生化遗传结构与变异的研究

采用聚丙烯酰胺凝胶电泳技术,对文蛤5个北方种群进行了生化遗传分析。结果表明:文蛤5个天然种群的多态座位比例为0.475±0.064;平均杂合度为0.212±0.026,总体上遗传多样性较好,遗传变异水平较高。在各多态座位中有78.95%的座位符合Hardy-W e inberg平衡,有65.79%的座位d值为正,34.21%的座位为近交座位,存在近交,但近交程度不高。通过聚类分析可以初步判定,这5个群体同属于一个种,种群间由于地理隔离已形成了不同的地理种群。     

中国沿海脉红螺群体遗传多样性及其遗传结构

我国脉红螺自然资源日趋衰减，为制定相应保护措施需要对脉红螺遗传多样性及遗传结构进行分析研究。利用9个微卫星标记分析了我国沿海9个脉红螺群体的遗传多样性和遗传分化水平。遗传多样性分析结果显示，群体平均等位基因丰度（AR）为8.6~9.5，期望杂合度（HE）为0.705~0.777，观测杂合度（HO）为0.498~0.626。遗传分化分析结果显示，群体间遗传分化指数（FST）范围为0.012 2~0.093 6，各群体间没有显著的遗传分化，遗传距离（DC）为0.212~0.349。本研究结果表明，我国沿海脉红螺群体具有较高的遗传多样性，各群体间没有显著分化。     

伊犁河流域不同群体伊犁裂腹鱼遗传差异分析

伊犁裂腹鱼（Schizothorax pseudaksaiensis）仅分布于新疆伊犁河流域，是该流域典型的土著种和生态敏感种。近年来，过度捕捞及水利工程开发使栖息地环境改变，种群数量急剧减少。本研究分析了伊犁河流域4个采样点共计54尾伊犁裂腹鱼线粒体DNA细胞色素b基因（长度为1109bp）的序列，探讨了伊犁裂腹鱼遗传结构及其影响因素。54尾个体共定义了16种单倍型，其中雅玛渡采样点群体（YJ）享有单倍型的数量最多，而恰普其海水库群体（YQ）享有单倍型的数量最少。单倍型分子系统树和中介网络图均分为两支，不同群体间单倍型交叉出现。平均遗传距离表明，4个伊犁裂腹鱼群体的遗传分化为种内个体间差异，尚未达到亚种水平。伊犁裂腹鱼单倍型分布的分化可能与大坝的阻隔效应有关。建议对两个类群伊犁裂腹鱼采取不同的管理策略加以保护。     

广西沿海及其邻近海区拟穴青蟹群体遗传多样性的RAPD分析

采用随机扩增多态DNA（random amplified polymorphic DNA,RAPD）技术检测广西沿海及其邻近海区拟穴青蟹（Scylla paramamosain）6个地理群体的遗传变异和遗传结构,8条10 bp寡核苷酸随机引物扩增99个个体,分析其中的44个位点,31个位点表现出多态性,在种水平的多态位点百分率为70.45%。POPGENE分析结果显示,6个群体的多态位点百分率为29.55%～54.55%,平均为36.97%;群体的遗传多样性自高至低排列为钦州湾群体〉党江群体〉珍珠湾群体〉闸口群体〉清化群体〉流沙湾群体;群体内的遗传变异大于群体间的遗传变异,群体间的遗传分化程度较大。AMOVA分析显示,群体内遗传变异占87.03%,群体间遗传变异占12.97%,群体间发生中等程度遗传分化。Mantel检测结果表明,拟穴青蟹6个群体间的遗传距离与地理距离之间的相关性不显著。聚类分析表明,群体间聚类无明显的地域性分布格局。     

南海海域常见龙虾的遗传多样性分析

运用RAPD技术分析了南海海域黄斑龙虾、锦绣龙虾、密毛龙虾、杂色龙虾、波纹龙虾、中国龙虾、日本龙虾7种常见龙虾的种内和种间遗传多样性、种间亲缘关系及种质特异性标记。研究结果显示,7种龙虾的遗传多样性均较丰富,种质资源良好,其平均多态性位点比率为73.39%～89.12%,平均遗传距离为0.2134～0.4044,平均Nei基因多样性指数为0.0834～0.1990;对7个种的种间遗传距离进行聚类分析表明,日本龙虾与密毛龙虾的亲缘关系最近,与杂色龙虾的亲缘关系最远。     

Multiplex PCR for genotyping Flavobacterium columnare

Recent research has identified four distinct genetic groups among isolates of Flavobacterium columnare through multilocus phylogenetic analyses; however, there are no quick methods to determine the genotype of an isolate. The objective of this research was to develop a multiplex PCR to rapidly genotype F. columnare to genetic group. Comparative bacterial genomics was used to identify regions in the genomes unique to each genetic group, and primers were designed to specifically amplify different sized amplicons for each genetic group. The optimized assay was demonstrated to be specific for each genetic group and F. columnare, and no specific amplicons were generated using gDNA from a panel of other Flavobacterium spp. and bacterial fish pathogens. The analytical sensitivity of the assay ranged from 209 to 883 genome equivalents depending on the genetic group. The multiplex PCR was evaluated by genotyping a panel of 22 unknown F. columnare isolates and performing DNA sequencing of the dnaK gene in parallel. The results demonstrated 100% accordance between multiplex PCR results and assignment to genetic group via phylogenetic analysis. The multiplex PCR provides a useful tool for assigning an unknown isolate to genetic group and may be used to determine which genetic groups of F. columnare are circulating and most predominant in different aquaculture industries.