高黎贡山旱冬瓜Frankia的IGS PCR-RFLP分析

在云南省高黎贡山自然保护区海拔1310～2400m的范围内,采集30个旱冬瓜根瘤样品,直接从根瘤中提取Frankia DNA,对其,nifD-nifK基因间隔区(intergenic spacer,IGS)和16S-23S rDNA IGS进行PCR—RFLP分析．结果表明,nifD-nifK IGS的PCR产物长度差异很大,经HaeⅢ和Afa I双酶切后,得到15种酶切带型,检测到多种基因型的菌株同时与同一株宿主植物共生;16S-23S rDNA IGS的PCR产物长度相似,酶切后亦区分出15种酶切带型．通过对两个基因间隔区的PCR-RFLP联合分析,发现高黎贡山旱冬瓜Frankia存在20种基因型．     

企鹅珍珠贝微卫星标记与生长性状的相关性研究

研究利用5个高度多态性的微卫星标记,对500个企鹅珍珠贝(Pteria penguin)的4个生长性状进行了关联分析。结果显示, QEB-D15和CL-232两个微卫星标记与企鹅珍珠贝的壳宽呈极显著相关(P<0.01);位点QEBD15基因型是239/263的个体壳宽为最大值,基因型是239/273的个体壳宽为最小值,推测263 bp等位基因与壳宽之间存在正相关关系,而273 bp等位基因与壳宽之间存在负相关关系;位点CL-232基因型为157/174的个体壳长、壳宽、总重的均值较同一位点的其他基因型均为最大值,该基因型推测为优势基因型;而基因型为177/192的个体壳长、壳宽、壳高和总重的均值较同一位点的其他基因型均为最小值,推测该基因型为劣势基因型,上述结果可为企鹅珍珠贝分子标记辅助选择育种提供理论依据和参考。     

家族传播的口腔白色念珠菌基因型多态性分析

目的检测家族传播的口腔白色念珠菌基因多态性。方法采集35个家庭（119个样本）的口腔牙菌斑,采用PCR ITS1-ITS2基因分型方法,检测、分析家族传播的口腔白色念珠菌基因多态性。结果 18个家庭（18/35,61%）,34个样本（34/119,28.6%）有白色念珠菌感染,11个家庭存在家族传播（11/18,61%）。在5个母子（父子）垂直传播的家庭成员中,白色念珠菌基因型均不一致。在3个呈水平传播的家庭成员中,两家基因型一致,1家不一致。在3个垂直-水平传播的家庭成员中,两家基因型一致,1家不一致。白色念珠菌家族传播基因型差异有显著统计学意义（χ2=26.571,P〈0.01）。白色念珠菌感染与年龄、性别、学历、吸烟、饮酒、义齿和龋病均无显著相关。结论白色念珠菌在口腔定植,受宿主自身遗传背景影响较大,在家族垂直传播中呈明显的基因多态性。呈水平传播的白色念珠菌菌种具有较高的传染性,基因型可保持不变。     

大口黑鲈生长相关标记的聚合及其效果分析

为了解与大口黑鲈(Micropterus salmoides)生长性状相关分子标记优势基因型的聚合效果, 研究选择先前已获得的13个与生长性状相关的分子标记, 位于PCK1、HSBP1、FOXO3b、MYH、HSC70-1、CTSB、HBP、POU1F1、PACAP、IGF-I、ghrelin、ApoproteinA1和MSTN基因上。在40尾亲本群体中对各标记的基因型进行检测, 选择可聚合优势基因型最多的2对亲本分别构建家系。在9月龄时, 从2个家系子代中分别采集305尾和266尾个体进行生长性状测量和各标记的基因型分析。家系1子代个体中含生长相关优势基因型的数量为0—6个, 对应的个体数依次为8、26、75、74、76、35和11, 对应的平均体质量依次为185.03、196.46、198.73、212.59、222.66、235.54和261.27 g。家系2子代个体中含生长相关优势基因型的数量为1—6个, 对应的平均体质量依次为184.43、213.17、243.77、249.98、252.11和266.00 g。个体中生长相关优势基因型聚合数量多少与生长性状呈正相关, 提示通过对生长相关优势基因型进行聚合可获得生长性状优良的大口黑鲈, 为大口黑鲈分子标记辅助育种的应用提供科学依据。     

印楝种子提取物对荔枝蝽的毒性及与其等位酶基因型之间的关系

用5.2 mg/mL（LC₅₀）的印楝种子提取物对荔枝蝽1龄若虫进行急性毒性处理,24 h死亡率为51.8%。通过等位酶分析检测了死亡与存活试虫两种酶（PGI和MDH）,两个基因座（Pgi和Mdh）上各基因型及等位基因与印楝种子提取物毒性之间的关系,进行致死性差异比较研究。结果表明,印楝种子提取物对具有不同基因型及等位基因个体的致死性存在差异。在Pgi基因座上,Pgi-bb基因型死亡率最高,为84%,Pgi-aa 和Pgi-cc基因型死亡率较低,分别为0和7%,且与死亡率最高的Pgi-bb基因型存在显著差异（P<0.05）。在基因座Mdh上,Mdh-aa基因型个体死亡率最高（93%）,而具有Mdh-cc基因型的个体全部存活了下来, 另外3个基因型Mdh-ab、Mdh-bb与Mdh-bc死亡率居中,都与Mdh-aa、Mdh-cc基因型死亡率之间存在显著差异。在等位基因上,Pgi-a和Mdh-c个体的死亡率都最低,与各自其他两个等位基因的死亡率之间存在显著差异。结果说明不同基因型个体对印楝提取物具有不同的反应,印楝种子提取物对荔枝蝽等位酶基因型及等位基因存在选择性致死作用。这种荔枝蝽对印楝种子提取物的敏感性与其等位酶基因型及等位基因之间显明的相关关系提示我们,可将荔枝蝽种群中对印楝种子提取物敏感性低的基因型及等位基因作为遗传标记去监测荔枝蝽对印楝种子提取物的抗性状况。     

建鲤ODC1基因型与增重的相关性分析

构建了建鲤（Cyprinus carpio var. jian）鸟氨酸脱羧酶（Ornithine decarboxylase,ODC）jlODC1a基因上6个和jlODC1b基因上4个SNP位点的PCR-RFLP方法,检测了这10个位点在12个家系约900尾建鲤选育群体中的基因型,各位点的基因型频率存在差异,最小等位基因频率（MAF）为0.140.48。各位点不同基因型与增重相关分析结果,其中7个SNPs与建鲤增重显性相关的位点,ODC1s基因上与雌鱼增重相关的SNP位点（7个）较雄鱼（4个）多。标记富集结果表明富集与建鲤增重相关的优势基因型的SNP个数越多的个体增重速度越快SNP个数越多的个体增重速度越快,富集4个的平均增重显著快于富集03的个体增重,且比0标记的快约14%,这反映出生长为数量性状。进一步对所检测位点进行双倍型分析,结果显示具有四个优势基因型且全部杂合优势基因型的4567（XXXXXXACCTCTCT）组的增重最快,比0优势基因型的增重快达26.6%,可以考虑用于今后的快增长建鲤的选育计划中。此外,双倍型分析结果还表明,不同位点之间可能存在或颉抗或协同的互作,如1和4之间存在拮抗关系,因此在今后的选育计划中,在考虑标记富集的情况下还应考虑标记之间的关系。宜在选择互为协同作用优势基因型的前提下,富集尽可能多的SNP标记。       

向日葵种质资源的随机扩增多态性ＤＮＡ（ＲＡＰＤ）研究

采用ＲＡＰＤ方法对我国２１个向日葵（Helianthus annuus L.)基因型和１１个国外引进向日葵因型进行分析,构建了它们的方图谱。从８０个随机引物中筛选出的２５个有效引物共产生１８８条ＤＮＡ片段,大小分布在０．２６－１．９８kb之间,其中１６４例带具有遗传多态性,约占总数的８７．２％,平均每个引物扩增的ＤＮＡ带数为７．５２条。３２个向日葵的遗传相似性分析表明,各基因型间的Ｎei氏相似性系数分布在０．３９８７．０８５３１之间,平均相似性系数为０．６２８１。１１个国外向日葵基因型的Ｎei氏相似性系数分布在０．７１３４－０．８５３１之间,平均相似性系数为０．７８２８,说明国外基因型之间的遗传基础比较狭窄。２１个国内向日葵基因型的Ｎei氏相似性系数分布在０．４７５０－０．８２０６,平均相似性系数为０．６４７８,说明国内向日葵基因型之间的遗传多态性较为丰富。通过非加权算术平均数聚类（ＵＰＧＭＡ）的方法,给制了３２个向日葵基因型之间的遗传关系树图。３２个向日葵基因明显地聚成Ａ、Ｂ两大类群。２１个国内向日葵基因型聚成了Ａ１、Ａ２两个亚类,Ａ１组包括：Ｘ１０、陕西向日葵、Ｄ－Ｓ１２、长岭向日葵６、黑２－Ｓ２－２、Ｔ－Ｃ０８、长岭葵花４、白葵３号、ＢＨ－１０、Ｊ－Ｓ－Ｂ１、张掖白子葵、Ｃ１０１－Ｓ４－３Ｓ４等１２个基因型;Ａ２组包括：ＬＫ３０５－Ｓ８、ＬＫ、ＣＳ－７、长岭葵花Ｓ２－Ｓ２、辉南７－Ｓ１－３、辉南、ＣＹ－ＸＸ１９－ＸＸ２、吉葵１１２、吉葵１１６等９个基因型。１１个国外向日葵基因型划分为Ｂ１、Ｂ２两个亚类,Ｂ１组包括ＬＧ１２０２８Ｑ、ＬＧ９０２３Ｒ、ＣＲＮ１４３、ＳＦ９９０３、ＳＦ９９０２、Ｓ－３３２２、ＳＨ３３２、ＳＨ４１、ＳＦＰ９００１、ＣＲＮ１４４５等１０个法国基因型;Ｂ２组织有来自美国的Ｇ１０１一个材料。     

生长相关分子标记在翘嘴鳜五代中的富集

为进一步了解人工选育对翘嘴鳜生长相关遗传标记的影响作用,研究以翘嘴鳜华康1号的5代选育群体为实验材料,对具有生长相关优势基因型的5个标记的6个位点进行扩增,通过直接测序和聚丙烯酰胺凝胶电泳两种方法分型后,统计其优势基因型个体数目在翘嘴鳜5代中的变化。结果显示,在5代群体中,2个单核苷酸多态性位点和4个微卫星位点优势基因型的数目的分布范围为0-4,从F1到F5代,这6个位点优势基因型的平均值分别为0.36、0.71、0.68、0.77和0.94,优势基因型的平均含量随选育世代的增加呈现递增趋势,从侧面反映了人工选育在一定程度上富集了优良基因。此外,对微卫星位点进行了遗传相似性和遗传距离分析,结果显示,随着选育的进行,后续世代与F1的遗传距离有明显的增大趋势,遗传相似性减小,这符合育种的客观规律。但相邻世代间的遗传距离则逐代减小,遗传相似性逐代增大,说明人工选育将遗传相似性较大的群体保留下来了,这种相似性表现在表型上包括生长快、体重大、体长增加等。F1到F5代处于中度遗传多样性的稳定状态,说明群体还存在选育空间。     

应用贝叶斯理论推断DNA分子标记基因型

引入贝叶斯理论用以从DNA分子标记的表现型（电泳谱带）推断其基因型（DNA来源）。结果表明,根据标记座位独立贫富而确定的遗传信息不完全标记的基因型概率,与根据令近的遗传信息完全标记的基因型和有关重组率算得的相应贝叶斯概率,通常都有很大的差异,所以在进行数量性状基因定位和标记辅助选择等工作之前,应当计算每一个体基因组上所有遗传信息不完全座位的有关基因型的贝叶斯概率。文中列出计算未知基因型的贝叶期概率的详细过程,也讨论了贝叶斯概率的若干推广应用。     

多巴胺通路的基因与精神分裂症风险的多位点关联研究

精神分裂症是一种严重的精神疾患, 全世界的群体发病率约为1%. 一般认为它是一种复杂的多基因疾病, 其致病因素是多个基因的联合作用. 有证据表明多巴胺递质系统的改变与精神分裂症有关. 为了发现多巴胺代谢通路中的精神分裂症易感基因, 收集了82个精神分裂症病例和108个与之匹配的正常对照, 分析了该人群位于多巴胺代谢通路上的24个基因中的59个单核苷酸多态性(SNPs)位点. 由于传统的单位点关联研究忽视了复杂疾病的多基因致病性的本质, 不考虑易感基因之间的相互作用, 因此提出了一个多位点的关联分析方法, 该方法用致病后验概率度量一个多位点基因型组合的致病风险, 并用一套基于扰动和平均的算法来检测易感的多位点基因型组合和抑制噪声, 避免在结果中包含假阳性位点. 发现了一个三位点的SNP组合, 相应的基因组合为COMT和ALDH3B1基因, 对精神分裂症高度易感.     

标记基因型中QTL基因型条件概率分布

随着分子数量遗传学的发展,人们提出了很多统计模型用于QTL定位分析。在这些模型中,首先得确定QTL在标记基因型中的条件概率分布,然后利用适当的统计方法对QTL在基因组中所处的位置进行估计。本文讨论了常见作图群体（如F2和回交群体）中在给定标记基因型下QTL的条件概率分布,提出了用Mathematics软件推导QTL基因型条件概率分布的方法。用该方法能够快速地、准确地推导出比较复杂的标记基因型中QTL基因型的条件概率分布。     

Genetic susceptibility to prostate, breast, and colorectal cancer among Nordic twins

To investigate the role of genetics in the development of cancer, we developed a new approach to analyze data on prostate, breast, and colorectal cancer from the Swedish, Danish, and Finnish twin registries on monozygotic (MZ) and same-sex dizygotic (DZ) twins. In the spirit of a sensitivity analysis, we modeled genetic inheritance as either an autosomal recessive or dominant cancer susceptibility (CS) genotype that involves either a single gene, many genes with equal allele frequencies, or three genes with a ninefold range of allele frequencies. We also modeled the joint probability of cancer incidence among five age categories, conditional on the presence or absence of the CS genotype. The main assumptions are: (1) The joint distribution of unobserved environmental effects in a twin pair conditional on the presence or absence of the CS genotype is the same for MZ and DZ twins, (2) the probability of cancer conditional on the presence or absence of the CS genotype and the unobserved environmental effects (i.e., the gene-environment interaction) is the same for MZ and DZ twins, and (3) the probability of cancer is independent between twins with the CS genotype. Estimation was maximum likelihood via a search over allele frequency and two levels of EM algorithms. Models had acceptable or good fits. Variability was estimated using a bootstrap approach, but only 50 replications were feasible. The 94th percentile of bootstrap replications for the estimated fraction of cancers with the CS genotype ranged, over the various genetic models, from 0.16 to 0.45 for prostate cancer, 0.12 to 0.30 for breast cancer, and 0.08 to 0.27 for colorectal cancer. We conclude that genetic susceptibility makes only a small to moderate contribution to the incidence of prostate, breast, and colorectal cancer.     

The probabilistic determination of identity-by-descent sharing for pairs of relatives from pedigrees.

Methods for detecting genetic linkage are more powerful when they fully use all of the data collected from pedigrees. We first discuss a method for obtaining the probability that a pedigree member has a given genotype, conditional on the phenotypes of his relatives. We then develop a rapid method to obtain the conditional probabilities of identity-by-descent sharing of marker alleles for all related pairs of individuals from extended pedigrees. The method assumes that the individuals are noninbred and that the relationship between genotype and phenotype is known for the marker locus studied. The probabilities of identity-by-descent sharing among relative pairs, conditional on marker phenotype information, can then be used in any of the model free tests for linkage between a trait locus and a marker locus.     

Plant tumor reversal associated with the loss of marker chromosomes in tobacco cells

Summary The determination of partial genotype, B/b and D/d, for coat colour in dogs, from phenotypic observations, is discussed. It is shown that the probability of a given genotype can be reliably determined where multiple observations on the mating of a given dog are available.     

Conditional genotypic probabilities for microsatellite loci

Modern forensic DNA profiles are constructed using microsatellites, short tandem repeats of 2-5 bases. In the absence of genetic data on a crime-specific subpopulation, one tool for evaluating profile evidence is the match probability. The match probability is the conditional probability that a random person would have the profile of interest given that the suspect has it and that these people are different members of the same subpopulation. One issue in evaluating the match probability is population differentiation, which can induce coancestry among subpopulation members. Forensic assessments that ignore coancestry typically overstate the strength of evidence against the suspect. Theory has been developed to account for coancestry; assumptions include a steady-state population and a mutation model in which the allelic state after a mutation event is independent of the prior state. Under these assumptions, the joint allelic probabilities within a subpopulation may be approximated by the moments of a Dirichlet distribution. We investigate the adequacy of this approximation for profiled loci that mutate according to a generalized stepwise model. Simulations suggest that the Dirichlet theory can still overstate the evidence against a suspect with a common microsatellite genotype. However, Dirichlet-based estimators were less biased than the product-rule estimator, which ignores coancestry.     

The genotype x environment-to-phenotype relationship

Summary Proceeding from the formal genotype x environment-to-phenotype functional relationship, a few common concepts essentially based upon this relationship have been reviewed and redefined. Particular attention was given to forming unambiguous representations. In summary, these concepts were: the reaction norm and phenotypic range of a genotype, the genetic control of traits, the general representation of genotypic and environmental contributions to a phenotype and the related problem of genotype x environment interaction, the fitness function, selective neutrality and superiority. The role of joint frequency distributions of genotypes and environmental situations for detecting and describing certain properties of the underlying genotype x environment-to-phenotype functional relationship has been demonstrated by means of models for genotype x environment interaction and the fitness function.     

Progeny testing for recessive genes: procedures and interpretations

Summary Methods for calculating the probability of detecting a carrier of a recessive gene by utilizing matings among related individuals are presented for single and litter bearing species. The confidence level for detection of heterozygosity depends upon: (1) the genetic relationship between mates, (2) the number of mates per male and the number of offspring per mate, (3) whether an estimate of recessive gene frequency before selection is available and (4) the magnitude of that frequency. Methods of computing probability of heterozygosity vs homozygosity utilizing Bayes theorem also are presented. In the conventional progeny test method, a sire initially is assumed heterozygous before calculations are made, but no prior information concerning his probable genotype is utilized. In the method using Bayes theorem, prior sources of information from relatives or from estimates of population allele frequency are utilized. This method gives the exact probability that a sire is not a carrier, given prior information and that he produces all normal offspring. These methods could be used in any sexually reproducing species to identify not only detrimental genes but beneficial genes as well.     

Testing for clonal propagation

The conceptual basis for testing clonal propagation is reconsidered with the result that two steps need to be distinguished clearly: (1) specification of the characteristics of multilocus genotype frequencies that result from sexual reproduction together with the kinds of deviations from these characteristics that are produced by clonal propagation, and (2) a statistical method for detecting these deviations in random samples. It is pointed out that a meaningful characterization of sexual reproduction reflects the association of genes in (multilocus) genotypes within the bounds set by the underlying gene frequencies. An appropriate measure of relative gene association is developed which is equivalent to a multilocus generalization of the standardized gametic disequilibrium (linkage disequilibrium). Its application to the characterization of sexually produced multilocus genotypes is demonstrated. The resulting hypothesis on the frequency of a sexually produced genotype is tested with the help of the (significance) probability of obtaining at least two copies of the genotype in question in a random sample of a given size. If at least two copies of the genotype are observed in a sample, and if the probability is significant, then the hypothesis of sexual reproduction is rejected in favor of the assumption that all copies of the genotype belong to the same clone. Common testing approaches rest on the hypothesis of completely independent association of genes in genotypes and on the (significance) probability of obtaining at least as many copies of a genotype as observed in a sample. The validity of these approaches is discussed in relation to the above considerations and recommendations are set out for conducting appropriate tests.     

Why are rare variants hard to impute? Coalescent models reveal theoretical limits in existing algorithms

Genotype imputation is an indispensable step in human genetic studies. Large reference panels with deeply sequenced genomes now allow interrogating variants with minor allele frequency < 1% without sequencing. Although it is critical to consider limits of this approach, imputation methods for rare variants have only done so empirically; the theoretical basis of their imputation accuracy has not been explored. To provide theoretical consideration of imputation accuracy under the current imputation framework, we develop a coalescent model of imputing rare variants, leveraging the joint genealogy of the sample to be imputed and reference individuals. We show that broadly used imputation algorithms include model misspecifications about this joint genealogy that limit the ability to correctly impute rare variants. We develop closed-form solutions for the probability distribution of this joint genealogy and quantify the inevitable error rate resulting from the model misspecification across a range of allele frequencies and reference sample sizes. We show that the probability of a falsely imputed minor allele decreases with reference sample size, but the proportion of falsely imputed minor alleles mostly depends on the allele count in the reference sample. We summarize the impact of this error on genotype imputation on association tests by calculating the r² between imputed and true genotype and show that even when modeling other sources of error, the impact of the model misspecification has a significant impact on the r² of rare variants. To evaluate these predictions in practice, we compare the imputation of the same dataset across imputation panels of different sizes. Although this empirical imputation accuracy is substantially lower than our theoretical prediction, modeling misspecification seems to further decrease imputation accuracy for variants with low allele counts in the reference. These results provide a framework for developing new imputation algorithms and for interpreting rare variant association analyses.     

Association models for a multivariate binary response

Models for a multivariate binary response are parameterized by univariate marginal probabilities and dependence ratios of all orders. The w-order dependence ratio is the joint success probability of w binary responses divided by the joint success probability assuming independence. This parameterization supports likelihood-based inference for both regression parameters, relating marginal probabilities to explanatory variables, and association model parameters, relating dependence ratios to simple and meaningful mechanisms. Five types of association models are proposed, where responses are (1) independent given a necessary factor for the possibility of a success, (2) independent given a latent binary factor, (3) independent given a latent beta distributed variable, (4) follow a Markov chain, and (5) follow one of two first-order Markov chains depending on the realization of a binary latent factor. These models are illustrated by reanalyzing three data sets, foremost a set of binary time series on auranofin therapy against arthritis. Likelihood-based approaches are contrasted with approaches based on generalized estimating equations. Association models specified by dependence ratios are contrasted with other models for a multivariate binary response that are specified by odds ratios or correlation coefficients.