Accuracy of pairwise methods in the reconstruction of family relationships, using molecular information from turbot (Scophthalmus maximus)

Many estimators and algorithms have been developed to infer the genealogical relationships from molecular marker data when there is no pedigree information. Most pairwise methods provide estimates in a continuous range that needs to be converted into genealogical relationships (namely full-sibs, half-sibs and unrelated) if there is a previous knowledge of the population structure. Transformations are usually based on arbitrary thresholds, but the possibility of correcting the coancestry estimates via explicit pedigree reconstruction methods has been suggested. Using molecular data for ten highly polymorphic microsatellite loci on a population of turbot (Scophthalmus maximus) with a known genealogy, the behaviour of four pairwise marker-based coancestry estimators and the molecular coancestry has been evaluated. The population consisted on 138 families with 4 full-sib individuals each and one family with 8 full-sib individuals (up to 15 half-sib families were also present due to the sharing of parents between some of the full-sibs families). Our results suggested that transforming the pairwise estimators and the molecular coancestry to family relationships through the establishment of thresholds performs slightly better than the explicit pedigree reconstruction method, when accuracy is measured in a pairwise basis. However, if joint relationships between more than two individuals were tested at a time, the threshold methods led to a high percentage of incongruous triads of full-sib individuals, with Mendelian incompatibilities appearing in congruous full-sib families (more than 70% and 60% in our study, respectively). The explicit pedigree reconstruction approach, due to its nature, is free from such problems. Therefore, the pedigree reconstruction approach seems to be a valuable tool to provide a congruent and compatible pedigree when the pairwise marker-based coancestry matrices or the molecular coancestry need to be transformed.     

微卫星标记在海洋经济贝类中的应用

微卫星标记是一种DNA分析手段,是种群遗传学研究中广泛应用的分子遗传标记。本文探讨了海洋贝类微卫星DNA的开发现状,介绍了微卫星的特点。阐述了微卫星标记技术应用于海洋贝类遗传多样性研究、遗传连锁图谱的构建、杂交子代的鉴定及杂种优势和繁殖成功率分析以及物种鉴定等方面的情况,并说明了微卫星标记技术存在的问题和发展趋势。     

应用RAPD标记对东方(鱼屯)属进行种类鉴别及其聚类分析

利用RAPD技术对红鳍东方、假睛东方、暗纹东方和从日本引进的红鳍东方4个种进行了遗传标记鉴别研究.在事先优化的条件下,20个随机引物共扩增出134条谱带清晰、重复性高的DNA片段,其中多态性片段77条.结果证实每一种均有其特异性扩增图谱,可作为种鉴定的依据;用UPGMA和NJ等方法进行聚类,构建的系统树与借助形态学和生化特征进行的传统分类结果一致.研究表明,RAPD作为一种新的分子标记,在海洋动物遗传鉴定方面具有巨大的潜力.     

Microsatellite marker isolation and cultured strain identification in <Emphasis Type="Italic">Carassius auratus gibelio</Emphasis>

Microsatellites have become the preferred molecular markers for strain selection and genetic breeding in fish. In this study a total of 105 microsatellites were isolated and identified in gibel carp (Carassius auratus gibelio) by microsatellite sequence searches in GenBank and other databases and by screening and sequencing of positive clones from the genomic library enriched for AG and GATA repeats. Moreover, nineteen microsatellites were randomly selected to design locus-specific primer pairs, and these were successfully used to identify and discriminate different cultured strains of gibel carp including strains A, D, L, and F. Three different types of microsatellite pattern were distinguished by the number and length of fragments amplified from the 19 primer pairs, and some microsatellite primer pairs were found to produce different microsatellite patterns among strains and strain-specific fragments. In addition, some duplicated alleles were also detected in two microsatellite patterns. Therefore, the current study provides direct molecular markers to discriminate among different cultured strains for selective breeding and aquaculture practice of gibel carp.     

A method to determine protein digestibility of microdiets for larval and early juvenile fish

A method to evaluate protein quality using in vivo methods was developed for larval fish. FluoSpheres^® fluorescent microspheres (10 μm) were incorporated into two test diets, our standard zein microdiet (ZMD) and a microdiet with identical ingredients except for the replacement of high quality fish meal with the same product cooked for 24 h at 80 °C (ZMD-CF). Several trials were performed to design a reliable method to test digestibility using FluoSpheres^® as a marker. The developed in vivo technique was tested on 35 days posthatch (dph) larval Atlantic cod ( Gadus morhua L.) and two tropical fish species in the early juvenile stage. The method took into account loss of total protein to the faecal pellet and water column. Apparent digestibility of protein in larval cod fed ZMD was significantly higher than that of larvae fed ZMD-CF ( P  < 0.05). A growth study to validate differences between the two diets showed significant differences in growth and survival of larvae fed ZMD versus ZMD-CF ( P  < 0.05). Further validation of our results was indicated through the use of a pH-stat method using enzymes extracted from 35 dph larval cod guts. This novel technique will be advantageous for researchers to evaluate feed ingredients for larval marine fish and is adaptable to many different areas of larval fish nutrition.     

栉孔扇贝×虾夷扇贝单对杂交子一代幼虫ISSR标记的分离方式

通过对栉孔扇贝Chlamys farreri×虾夷扇贝Patinopecten yessoensis正反单对杂交子一代幼虫进行ISSR(Inter Simple Sequence Repeats)标记,分析了双亲位点在杂交子一代中的传递分离方式。从20个ISSR引物中筛选出引物807和834进行扩增,正交家系和反交家系均统计了70条清晰稳定的扩增带。正交家系中双亲和F_1共有位点占总位点数的38.6%,仅由母本或父本传递给F_1的位点分别占总位点数的27.1%和21.4%。反交家系中双亲和F_1共有位点占总位点数的34.3%,仅由母本或父本传递给F_1的位点分别占总位点数的25.7%和22.9%,表明双亲的遗传物质皆传递给了F_1代,证实属间杂交成功。实验结果表明,两家系中F_1均偏向各自的母本。另外,在F_1中还出现了较高比例的非孟德尔分离位点和非亲位点。     

牙鲆3个养殖群体遗传结构的微卫星分析

采用微卫星标记分析技术,用5个多态性的微卫星标记对来自3个不同国家（中国、日本和韩国）的牙鲆养殖群体进行了遗传多样性研究。研究结果表明,3个牙鲆群体平均等位基因在4．8～5．6之间,平均观测杂合度（H0）在0．3917～0．5643之间,平均期望杂合度（HE）在0．5981～0．6264之间。有多个位点在不同的群体中偏离哈代-温伯格平衡。遗传距离分析表明,中国群体与日本群体遗传距离最近,韩国群体与日本群体遗传距离最远。分子方差分析（AMOVA）表明,群体内遗传变异与群体间遗传变异分别占总遗传变异的92．44％和7．56％,固定系数（R）为0．0752（P〈0．001）,表明牙鲆3个养殖群体遗传分化显著。     

我国五个青蛤地理群体遗传变异的RAPD分析

本文利用RAPD方法对我国浙江、江苏、辽宁、天津和福建沿海青蛤地理群体的遗传变异和遗传结构进行了分析。从60条随机引物中,筛选出其中12条扩增效果好、条带清晰的引物进行扩增。结果表明,青蛤遗传多样性较丰富,五个群体的多态度在0.249～0.307之间,平均为0.278,按递减依次为江苏>福建>辽宁>浙江>天津;经分子方差分析(AMOVA),10.69%的遗传变异来自于群体间,89.31%来自于群体内,遗传分化除辽宁与江苏、天津群体间不显著外,其它群体间分化显著;根据遗传距离,用UPGMA法进行聚类分析表明,浙江群体与江苏群体,辽宁群体与天津群体分别先聚在一起,最后与福建群体聚类;S11、S424、S228、S4254个引物可以区分这五个青蛤地理种群,作为群体特征标记。     

异型雄性罗氏沼虾遗传多样性的微卫星分析

利用微卫星DNA标记研究3种近亲交配形态型雄性罗氏沼虾遗传多样性,所用虾样均采自国家级(南宁)罗氏沼虾良种场,共150尾成年近亲交配的雄虾,其中蓝色长臂型、橙色长臂型、小个体型各50尾。研究结果表明,3组样品的生长发育差异显著,蓝色长臂型、橙色长臂型、小个体型各组中微卫星位点的总等位基因分别为24、28和22,3组样品所有位点的平均观察杂合度为0.474～0.556。其平均群体内近交系数为-0.0189,说明杂合子过剩,对比分析和群体间分化系数表明,3组雄虾遗传差异明显,最大遗传间距位于蓝色长臂型和小个体型,最小的遗传间距位于蓝色长臂型和橙色长臂型。研究结果将为罗氏沼虾优质父本选育和调控雄性遗传发育提供基础性遗传信息。     

中国大陆沿海六水系绒螯蟹_中华绒_省略__群体亲缘关系_RAPD指纹标记

用 4 8个具有丰富多态性的 10碱基随机引物对辽河、黄河、长江、瓯江、珠江和南流江的中华绒螯蟹和日本绒螯蟹的 6个群体进行RAPD分析。结果发现 :(1)两个引物具有群体特异性带 ,其中Z2扩增的 880bp片段为珠江蟹和南流江蟹群体中所特有 ,而 70 0bp片段为长江蟹、辽河蟹、黄河蟹和瓯江蟹所特有 ,可作为区别日本绒螯蟹和中华绒螯蟹的分子遗传标记 ;(2 )Opp17扩增的 94 7bp片段的出现频率 ,在长江、黄河和辽河群体显著地从南到北递减 ,长江蟹 87.50 %、黄河蟹4 1.66%、辽河蟹 10 .83%。这一遗传渐变的度量可作为区别这三个水系的中华绒螯蟹种群的判据 ;(3) 6水系群体内的平均遗传相似度依次为 :辽河蟹 0 .90 8>南流江蟹 0 .897>瓯江蟹和珠江蟹 0 .895>黄河蟹 0 .890 >长江蟹 0 .850 ;6群体间遗传距离及其UPGMA、NJ聚类分析进一步表明 ,南流江蟹、珠江蟹同长江蟹、辽河蟹及黄河蟹在基因组之间存在明显的歧化。 更多还原