RAPD应用于遗传多样性和系统学研究中的问题

在研究银杉（Ｃａｔｈａｙａ ａｒｇｙｒｏｐｈｙｌｌａ）的遗传多样性时，对ＲＡＰＤ 产物的影响因素进行了大量的实验探索，结果表明：逐级纯化的ＤＮＡ 模板的ＲＡＰＤ结果一致， 因而模板制备过程中的很多纯化步骤是不必要的； ＲＮＡ 对扩增产物无影响； 模板浓度在一个相当大的范围内不影响扩增结果； 从干叶和鲜叶中提取的ＤＮＡ 可获得一致的扩增产物； 从而证明ＲＡＰＤ 产物具有很好的重复性。进而讨论了ＲＡＰＤ产物分析及数据分析中的一些问题。通过对升麻属（Ｃｉｍ ｉｃｉｆｕｇａ） ５ 种、类叶升麻（Ａｃｔａｅａ ａｓｉａｔｉｃａ）及松潘乌头（Ａｃｏｎｉｔｕｍ ｓｕｎｇｐａｎｅｎｓｅ）的ＲＡＰＤ 结果分析，认为ＲＡＰＤ 方法可用于种间乃至近缘属间的系统学研究， 但有一定的局限性  

新型标记SRAP在棉花F2分离群体及遗传多样性评价中的适用性分析

将新型分子标记SRAP(Sequence-related Amplified Polymorphism)应用于棉花的遗传研究，并建立了完整的PCR反应体系，此体系稳定可靠、扩增效果好、可重复性强。采用30个SRAP引物组合对海岛棉品种“Pima90”和陆地棉品种“邯郸208”进行比较扩增，29个引物组合可以获得多态性扩增，显示了较高的多态性。对上述两个品种的F2群体进行检测，共产生149个多态性条带，平均每个组合产生5．14个，单引物组合最多可产生13个多态性条带。用SRAP标记对11份陆地棉材料进行遗传多样性检测，30个引物组合中15个组合有多态性，得到22个多态性条带，显示了较高的多态性比率。研究结果表明，SRAP标记可在棉花分子生物学领域中广泛应用。  

Genomic control for association studies

A dense set of single nucleotide polymorphisms (SNP) covering the genome and an efficient method to assess SNP genotypes are expected to be available in the near future. An outstanding question is how to use these technologies efficiently to identify genes affecting liability to complex disorders. To achieve this goal, we propose a statistical method that has several optimal properties: It can be used with case control data and yet, like family-based designs, controls for population heterogeneity; it is insensitive to the usual violations of model assumptions, such as cases failing to be strictly independent; and, by using Bayesian outlier methods, it circumvents the need for Bonferroni correction for multiple tests, leading to better performance in many settings while still constraining risk for false positives. The performance of our genomic control method is quite good for plausible effects of liability genes, which bodes well for future genetic analyses of complex disorders.  

鱼类线粒体DNA研究新进展

线粒体DNA是分子生物学研究中的一个热门领域，已成为鱼类进化生物学和群体遗传学研究的重要分子遗传标记。本文对鱼类线粒体DNA分子生物学的最新研究进展进行了较详细的阐述。重点介绍鱼类线粒体DNA全序列的研究进展、组成及特征，鱼类线粒体DNA非编码区结构研究进展，鱼类线粒体DNA多态性及其主要的检测方法；综述了最近有关鱼类线粒体DNA在鱼类系统学、种间杂交渐渗、种群识别、起源和进化、地理分化等研究中的应用情况。  

The comparison of RFLP,RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis

The utility of RFLP (restriction fragment length polymorphism), RAPD (random-amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSR (simple sequence repeat, microsatellite) markers in soybean germplasm analysis was determined by evaluating information content (expected heterozygosity), number of loci simultaneously analyzed per experiment (multiplex ratio) and effectiveness in assessing relationships between accessions. SSR markers have the highest expected heterozygosity (0.60), while AFLP markers have the highest effective multiplex ratio (19). A single parameter, defined as the marker index, which is the product of expected heterozygosity and multiplex ratio, may be used to evaluate overall utility of a marker system. A comparison of genetic similarity matrices revealed that, if the comparison involved both cultivated (Glycine max) and wild soybean (Glycine soja) accessions, estimates based on RFLPs, AFLPs and SSRs are highly correlated, indicating congruence between these assays. However, correlations of RAPD marker data with those obtained using other marker systems were lower. This is because RAPDs produce higher estimates of interspecific similarities. If the comparisons involvedG. max only, then overall correlations between marker systems are significantly lower. WithinG. max, RAPD and AFLP similarity estimates are more closely correlated than those involving other marker systems.Abbreviations RFLP restriction fragment length plymorphism - RAPD random-amplified polymorphic DNA - AFLP amplified fragment length polymorphism - SSR simple sequence repeat - PCR polymerase chain reaction - TBE Tris-borate-EDTA buffer - MI marker index - SENA sum of effective numbers of alleles  

小尾寒羊五个微卫星基因座遗传多态性研究

小尾寒羊是我国优良的地方绵羊品种，具有极高的繁殖力，平均每胎产羔2．6只。利用与绵羊高繁殖力主效基因Fec^B和FecX^1连锁的5个微卫星标记（OarAE101,BM1329,BMS2508,TGLA54t TGLA68)对244小尾寒羊母羊进行了遗传检测。用非变性（中性）聚丙烯酰胺凝胶电泳检测同卫星的PCR扩增产物，计算了5个同卫星基因座的等位基因频率，多态信息含量，基因纯合度和杂合度。在小尾寒羊中检测到BM1329有6个等位基因，片段大小为160－180bp,164bp等位基因频率最高（0．6320）；检测到OarAE101有9个等位基因，片段大小为97－135bp,97bp等位基因频率最高（0．7930）；检测到TGLA54有5个等位基因，片段大小为116－136bp,134bp等位基因频率最高（0．8500）；检测到TGLA68有2个等位基因，片段大小为98－100bp，2个等位基因频率相近，检测到BMS2508有6个等位基因，片段大小为93－115bp,99bp等位基因频率最高（0．4795）。BM1329，OarAE101,TGLA54,TGLA68,BMS2508的多态信息含量／基因纯合度／杂合度分别为0．4481／0．4840．0．5160，0．3516／0．6375／0．3625，0．2528／0．7326／0．2674，0．3733／0．5034／0．4966，0．5809／0．3581／0．6419。可见BMS2508的遗传变异最大，TGLA54的遗传变异最小。这些结果可为小尾寒羊种质特性研究提供分子基础数据。  

Molecular marker heterozygosity and hybrid performance in indica and japonica rice

An essential assumption underlying markerbased prediction of hybrid performance is a strong linear correlation between molecular marker heterozygosity and hybrid performance or heterosis. This study was intended to investigate the extent of the correlations between molecular marker heterozygosity and hybrid performance in crosses involving two sets of rice materials, 9 indica and 11 japonica varieties. These materials represent a broad spectrum of the cultivated rice gene pool including landraces, primitive cultivars, historically important cultivars, modern elite cultivars and parents of superior hybrids. Varieties within each set were intermated in all possible nonreciprocal pairs resulting in 36 crosses in the indica set and 55 in the japonica set. The F₁s and their parents, 111 entries in total, were examined for performance of seven traits in a replicated field trial. The parents were surveyed for polymorphisms using 96 RFLP and ten SSR markers selected at regular intervals from a published molecular marker linkage map. Molecular marker genotypes of the F₁ hybrids were deduced from the parental genotypes. The analysis showed that, with very few exceptions, correlations in the indica dataset were higher than in that of their japonica counterparts. Among the seven traits analyzed, plant height showed the highest correlation between heterozygosity and hybrid performance and heteorsis in both indica and japonica datasets. Correlations were low to intermediate between hybrid performance and heterozygosity (both general and specific) in yield and yield component traits in both indica and japonica sets, and also low to intermediate between specific heterozygosity and heterosis in the indica set, whereas very little correlation was detected between heterosis and heterozygosity (either general or specific) in the japonica set. In comparison to the results from our previous studies, we concluded that the relationship between molecular marker heterozygosity and heterosis is variable, depending on the genetic materials used in the study, the diversity of rice germplasms and the complexity of the genetic basis of heterosis.  

Abundance, variability and chromosomal location of microsatellites in wheat

The potential of microsatellite sequences as genetic markers in hexaploid wheat (Triticum aestivum) was investigated with respect to their abundance, variability, chromosomal location and usefulness in related species. By screening a lambda phage library, the total number of (GA)_n blocks was estimated to be 3.6 x 10⁴ and the number of (GT)_n blocks to be 2.3 x 10⁴ per haploid wheat genome. This results in an average distance of approximately 270 kb between these two microsatellite types combined. Based on sequence analysis data from 70 isolated microsatellites, it was found that wheat microsatellites are relatively long containing up to 40 dinucleotide repeats. Of the tested primer pairs, 36% resulted in fragments with a size corresponding to the expected length of the sequenced microsatellite clone. The variability of 15 microsatellite markers was investigated on 18 wheat accessions. Significantly, more variation was detected with the microsatellite markers than with RFLP markers with, on average, 4.6 different alleles per microsatellite. The 15 PCR-amplified microsatellites were further localized on chromosome arms using cytogenetic stocks of Chinese Spring. Finally, the primers for the 15 wheat microsatellites were used for PCR amplification with rye (Secale cereale) and barley accessions (Hordeum vulgare, H. spontaneum). Amplified fragments were observed for ten primer pairs with barley DNA and for nine primer pairs with rye DNA as template. A microsatellite was found by dot blot analysis in the PCR products of barley and rye DNA for only one primer pair.  

中国部分黄牛品种mtDNA遗传多态性研究

对我国8个黄牛品种22个个体的mtDNA D-loop区910bp全序列进行了分析。结果表明：8个黄牛品种D-loop区序列中，A T平均含量为61．65％；经比对，共检测到66个核苷酸多态位点，约占核苷酸总数的7．25％；D-loop全序列突变类型有5种，即转换、颠换、插入、缺失及转换与颠换共存，它们分别占核苷酸多态位点的81．82％、6．06％、7．57％、3．03％及1．52％。以欧洲牛mtDNA D-loop全序列为标准，8个黄牛群体D-loop的平均核苷酸变异率分3个层次：西镇牛、蒙古牛、黑白花牛及秦川牛的核苷酸变异率最低，分别为0．37％、0．44％、0．52％和0．66％；南阳牛与郏县红牛的核苷酸变异率居中，分别为1．91％和2．02％；晋南牛与岳阳牛的核苷酸变异率最高，分别为4．47％和4．73％。中国黄牛品种内D-loop区序列歧异度为0．55％～5．39％，品种间序列歧异度为1．21％～6．59％。在所测黄牛个体中，mtDNA D-loop序列由19种单倍型组成，单倍型比例为86．36%，说明中国黄牛mtDNA遗传多态性很丰富。由此构建了中国8个黄牛品种的NJ分子系统树，聚类分析表明：所测黄牛的mtDNA D-loop序列表现为3个单倍型组，从而揭示中国黄牛可能有3个母系起源，以普通牛起源和瘤牛起源为主。  

Target region amplification polymorphism: A novel marker technique for plant genotyping

The advent of large-scale DNA sequencing technology has generated a tremendous amount of sequence information for many important organisms. We have developed a rapid and efficient PCR-based technique, which uses bioinformatics tools and expressed sequence tag (EST) database information to generate polymorphic markers around targeted candidate gene sequences. This target region amplification polymorphism (TRAP) technique uses 2 primers of 18 nucleotides to generate markers. One of the primers, the fixed primer, is designed from the targeted EST sequence in the database; the second primer, the arbitrary primer, is an arbitrary sequence with either an AT-or GC-rich core to anneal with an intron or exon, respectively. PCR amplification is run for the first 5 cycles with an annealing temperature of 35°C, followed by 35 cycles with an annealing temperature of 50°C. For different plant species, each PCR reaction can generate as many as 50 scorable fragments with sizes ranging from 50–900 bp when separated on a 6.5% polyacrylamide sequencing gel. The TRAP technique should be useful in genotyping germplasm collections and in tagging genes governing desirable agronomic traits of crop plants.