复杂遗传性状连锁不平衡基因定位的理论基础

复杂遗传疾病基因的定位克隆要求首先获得疾病位点与遗传标记位点间的高分辨率连锁图谱。本文报道在不可没基因型复杂疾病的细微定位理论与方法方面所得的研究成果。     

家畜育种中MAS的遗传标记与QTL

简要评述了在家畜育种中标记辅助选择（ＭＡＳ）所适用的遗传标记系统及对数量性状位点（ＱＴＬ）和标记的基本要求．对ＭＡＳ中遗传标记与ＱＴＬ的紧密连锁之意义进行了讨论，认为遗传标记与ＱＴＬ间的连锁程度是决定ＭＡＳ效能的关键因素．并简述了获得与ＱＴＬ紧密连锁之遗传标记的一般方法     

Bt/CpTI抗虫转基因水稻及其非转基因亲本与普通野生稻杂种F2群体的等位基因偏态分离

了解水稻转基因是否影响野生稻基因传递的频率,对于评价转基因逃逸及其生态影响有重要意义.本研究构建了不含转基因和含转基因的栽培稻与普通野生稻杂种F2群体,利用分子标记检测了F2群体各位点的基因型和基因频率.以连续卡方分析了F2群体相关位点的基因型和基因频率观察值是否符合理论分离比,同时对各位点进行了连锁不平衡分析,并对实验群体所需的最小样本量进行理论探索.结果表明两个F2群体分别有25.93%与33.33%的位点出现了显著的非随机分离,非转基因与转基因F2群体分别在偏态分离位点数与偏离亲本方向上出现一定差异,并观察到连锁不平衡位点.实验个体数应不少于280个才能保证实验结果准确.外源转基因在杂种后代群体中会因为选择而影响基因分离,进而影响杂种群体的进化潜力.     

肢带型肌营养不良一家系致病基因排除性定位

为了定位一个常染色体显性遗传肢带型肌营养不良家系的致病基因（ADLGMD）,采用13个荧光微卫星标记对收集到的一个包括4代33人的ADLGMD家系进行连锁分析,所选择的标记覆盖了3个已知ADL—GMD致病基因位点和4个已报道的致病基因定位区段．通过Linkage 5．1软件包计算连锁概率,各位点连锁分析所得的LOD值均小于-3,显示该家系致病基因与这7个位点均不连锁．该家系的肌营养不良症致病基因不在已知的位点内,很可能是一个新致病基因．     

苦荞重组自交系群体F_5代SSR遗传图谱的构建

以"小米荞×晋荞2号"杂交组合,通过单粒传获得的245个F_5代重组自交系(命名为SJ-RILs)群体为作图材料,构建SSR遗传连锁图谱。结果显示:350对SSR引物在亲本间有多态性的为59对,多态率为16.9%;多态性引物在SJ-RILs群体共扩增出80个等位变异位点;来自小米荞和晋荞2号等位基因分别占群体总基因型的51.5%和48.5%;采用作图Jionmap4.0软件构建的遗传连锁图总长度为1 106.74cm,含11个连锁群,80个分子标记,其中偏分离标记27个,相邻标记的平均间距为13.83cm。结论:该图谱可为苦荞遗传图谱构建、重要性状QTL的定位和基因组学研究隆奠定基础。     

SSR标记分离技术的研究概况

SSR标记是植物中目前运用的最广泛的分子标记之一，广泛地运用于植物种质鉴定、分子标记连锁图的构建和群体遗传学等诸多领域．由于SSR为共显性标记，可以区分纯合、杂合基因型，因而得到更广泛的应用．目前出现了有筛选文库、筛选富集文库、与其他现有技术结合、STMP技术等SSR标记方法．在这些技术中，目前运用最广泛而且比较成熟的方法是筛选富集文库的方法，STMP技术是目前效率最高的分离单个微卫星位点的方法，可以开发SSR标记．本文对这些技术的原理作了论述．     

石刁柏雄性连锁的AFLP及SCAR标记的建立

目的:对石刁柏雌雄株基因组差异进行分析,筛选雄性或雌性连锁的分子标记.方法:利用限制性片段长度多态性技术,设计了多个引物组合,分别对石刁柏雌雄株基因组进行扩增.结果:在使用的72个引物组合中,引物组合E-AAG+M-CAT从雄性基因组中扩增出了一个雄性连锁的标记(MLDA555),该序列长度为555bp,AT含量为59%.Blast检索未发现相似序列.根据该片段序列设计的引物将该标记转化为雄性连锁的大小为523bp的稳定的SCAR标记,经过不同基因型雄性个体的验证证明该标记广泛存在于不同基因型石刁柏雄性个体中.结论:通过AFLP扩增筛选得到了石刁柏雄性连锁的AFLP和SCAR标记,为石刁柏性别决定机制的理解及石刁柏的分子标记辅助育种提供理论资料和技术支持.     

石刁柏雄性连锁的AFLP及SCAR标记的建立

目的:对石刁柏雌雄株基因组差异进行分析,筛选雄性或雌性连锁的分子标记.方法:利用限制性片段长度多态性技术,设计了多个引物组合,分别对石刁柏雌雄株基因组进行扩增.结果:在使用的72个引物组合中,引物组合E-AAG+M-CAT从雄性基因组中扩增出了一个雄性连锁的标记(MLDA555),该序列长度为555bp,AT含量为59%.Blast检索未发现相似序列.根据该片段序列设计的引物将该标记转化为雄性连锁的大小为523bp的稳定的SCAR标记,经过不同基因型雄性个体的验证证明该标记广泛存在于不同基因型石刁柏雄性个体中.结论:通过AFLP扩增筛选得到了石刁柏雄性连锁的AFLP和SCAR标记,为石刁柏性别决定机制的理解及石刁柏的分子标记辅助育种提供理论资料和技术支持.     

基于神经网络和粒子群算法的遗传位点与患病信息的关联性分析

基于遗传疾病与某些遗传基因位点存在的较强关联性，并考虑到位点间存在交互作用的情形，提出了关联性最强的位点组合的筛选方法。将每个候选位点组合对应的基于神经网络的预报准确率作为评价标准，用粒子群算法（PSO）通过迭代逼近找出最优的位点组合，并与神经网络权重分析法进行比较。结果表明，由本文方法得到的位点组合预报精度更高，对患病情况有着较好的识别效果，可为遗传疾病诊断等提供参考方法。     

利用位点信息分析遗传疾病与基因的关联性

人体的许多遗传疾病都与其基因包含的多个位点(SNPs)相关联。因此定位与遗传疾病相关联基因在染色体中的位置,能帮助研究人员了解疾病的遗传机理,预防某些遗传病的发生。利用全基因组关联分析方法,对两类样本(患病,未患病)各个位点上的碱基进行卡方检验,找出某种遗传病最有可能的致病位点,定位其所在的致病基因。利用连锁不平衡系数,得出最可能相关的致病基因,并通过聚类算法检验结论的合理性。     

Theoretical strategies for high-resolution mapping of complex genetic disorders in humans

Positional cloning of gene(s) underlying a complex disease trait poses requirement of a highresolution linkage map between the disease locus and genetic marker loci. Recent researches have shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. However, these models were restricted to the circumstances where genotyping at the disease locus was feasible. The major limitations of pedigree-based linkage analyses were addressed in the light of positional cloning and positional candidate gene identification in humans. It summarizes the recent efforts in developing theories for fine-scale mapping of genes underlying complex genetic variations where the one-to-one relationship no longer exists between phenotype of the genetic disorders and the corresponding genotype. Dedicated to Dr. C. C. Tan for his 90th birthday.     

Genetic mechanisms of floral trait correlations in a natural population

Genetic correlations among traits are important in evolution, as they can constrain evolutionary change or reflect past selection for combinations of traits. Constraints and integration depend on whether the correlations are caused by pleiotropy or linkage disequilibrium, but these genetic mechanisms underlying correlations remain largely unknown in natural populations. Quantitative trait locus (QTL) mapping studies do not adequately address the mechanisms of within-population genetic correlations because they rely on crosses between distinct species, inbred lines or selected lines (see ref. 5), and they cannot distinguish moderate linkage disequilibrium from pleiotropy because they commonly rely on only one or two episodes of recombination. Here I report that after nine generations of enforced random mating (nine episodes of recombination), correlations between six floral traits in wild radish plants are unchanged, showing that pleiotropy generates the correlations. There is no evidence for linkage disequilibrium despite previous correlational selection acting on one functionally integrated pair of traits. This study provides direct evidence of the genetic mechanisms underlying correlations between quantitative traits in a natural population and suggests that there may be constraints on the independent evolution of pairs of highly correlated traits.     

Genetic mapping of complex discrete human diseases by discriminant analysis

The objective of the present study is to propose and evaluate a novel multivariate approach for genetic mapping of complex categorical diseases. This approach results from an application of standard stepwise discriminant analysis to detect linkage based on the differential marker identity-by-descent (IBD) distributions among the different groups of sib pairs. Two major advantages of this method are that it allows for simultaneously testing all markers, together with other genetic and environmental factors in a single multivariate setting and it avoids explicitly modeling the complex relationship between the affection status of sib pairs and the underlying genetic determinants. The efficiency and properties of the method are demonstrated via simulations. The proposed multivariate approach has successfully located the true position(s) under various genetic scenarios. The more important finding is that using highly densely spaced markers (1～2 cM) leads to only a marginal loss of statistical efficiency of the proposed methods in terms of gene localization and statistical power. These results have well established its utility and advantages as a fine-mapping tool. A unique property of the proposed method is the ability to map multiple linked trait loci to their precise positions due to its sequential nature, as demonstrated via simulations.     

On the origin of species by sympatric speciation.

Understanding speciation is a fundamental biological problem. It is believed that many species originated through allopatric divergence, where new species arise from geographically isolated populations of the same ancestral species. In contrast, the possibility of sympatric speciation (in which new species arise without geographical isolation) has often been dismissed, partly because of theoretical difficulties. Most previous models analysing sympatric speciation concentrated on particular aspects of the problem while neglecting others. Here we present a model that integrates a novel combination of different features and show that sympatric speciation is a likely outcome of competition for resources. We use multilocus genetics to describe sexual reproduction in an individual-based model, and we consider the evolution of assortative mating (where individuals mate preferentially with like individuals) depending either on an ecological character affecting resource use or on a selectively neutral marker trait. In both cases, evolution of assortative mating often leads to reproductive isolation between ecologically diverging subpopulations. When assortative mating depends on a marker trait, and is therefore not directly linked to resource competition, speciation occurs when genetic drift breaks the linkage equilibrium between the marker and the ecological trait. Our theory conforms well with mounting empirical evidence for the sympatric origin of many species.     

Assignment of multiple endocrine neoplasia type 2A to chromosome 10 by linkage

Multiple endocrine neoplasis type 2A (MEN2A) is one of several kinds of cancers that appear to be inherited in an autosomally dominant fashion. We have assigned the MEN2A locus to chromosome 10 by linkage with a new DNA marker (D10S5). The linkage led us to investigate other chromosome 10 markers and demonstrate linkage between the disease locus and the interstitial retinol-binding protein (IRBP) gene. The D10S5 locus was sublocalized to 10q21.1 by hybridization in situ and the IRBP gene to p11.2----q11.2 with a secondary site at q24----q25. The linkages were established using 292 members of five families, three different restriction fragment length polymorphisms (RFLPs) at D10S5 and two RFLPs recognized by the IRBP probe. The recombination frequencies from pairwise linkage analysis between the disease and two marker loci D10S5 and IRBP were 0.19 and 0.11, with maximum lod scores of 3.6 and 8.0 respectively. Ordering of the three loci by multipoint analysis placed the IRBP gene approximately midway between the disease and D10S5 loci.     

Dissecting the architecture of a quantitative trait locus in yeast

Most phenotypic diversity in natural populations is characterized by differences in degree rather than in kind. Identification of the actual genes underlying these quantitative traits has proved difficult. As a result, little is known about their genetic architecture. The failures are thought to be due to the different contributions of many underlying genes to the phenotype and the ability of different combinations of genes and environmental factors to produce similar phenotypes. This study combined genome-wide mapping and a new genetic technique named reciprocal-hemizygosity analysis to achieve the complete dissection of a quantitative trait locus (QTL) in Saccharomyces cerevisiae. A QTL architecture was uncovered that was more complex than expected. Functional linkages both in cis and in trans were found between three tightly linked quantitative trait genes that are neither necessary nor sufficient in isolation. This arrangement of alleles explains heterosis (hybrid vigour), the increased fitness of the heterozygote compared with homozygotes. It also demonstrates a deficiency in current approaches to QTL dissection with implications extending to traits in other organisms, including human genetic diseases.     

Gene for chronic proximal spinal muscular atrophies maps to chromosome 5q

Proximal spinal muscular atrophies represent the second most common fatal, autosomal recessive disorder after cystic fibrosis. The childhood form is classically subdivided into three groups: acute Werdnig-Hoffmann (type I), intermediate Werdnig-Hoffmann disease (type II) and Kugelberg-Welander disease (type III). These different clinical forms have previously been attributed to either genetic heterogeneity or variable expression of different mutations at the same locus. Research has been hindered because the underlying biochemical defect is unknown, and there are insufficient large pedigrees with the most common and severe form (type I) available for study. Therefore, we have undertaken a genetic linkage analysis of the chronic forms of the disease (types II and III) as an initial step towards the ultimate goal of characterizing the gene(s) responsible for all three types. We report here the assignment of the locus for the chronic forms to the long arm of chromosome 5 (5q12-q14), with the anonymous DNA marker D5S39, in 24 multiplex families of distinct ethnic origin. Furthermore, no evidence for genetic heterogeneity was found for types II and III in our study, suggesting that these two forms are allelic disorders.     

Mapping of mutation causing Friedreich's ataxia to human chromosome 9

Friedreich's ataxia is an autosomal recessive disease with progressive degeneration of the central and peripheral nervous system. The biochemical abnormality underlying the disorder has not been identified. Prompted by the success in localizing the mutations causing Duchenne muscular dystrophy, Huntington's disease and cystic fibrosis, we have undertaken molecular genetic linkage studies to determine the chromosomal site of the Friedreich's ataxia mutation as an initial step towards the isolation and characterization of the defective gene. We report the assignment of the gene mutation for this disorder to chromosome 9p22-CEN by genetic linkage to an anonymous DNA marker MCT112 and the interferon-beta gene probe. In contrast to the clinical variation seen for the disorder, no evidence of genetic heterogeneity is observed.     

Localization of cystic fibrosis locus to human chromosome 7cen-q22

Cystic fibrosis (CF) is the most common genetic disease in Caucasian populations, with an incidence of 1 in 2,000 live births in the United Kingdom, and a carrier frequency of approximately 1 in 20. The biochemical basis of the disease is not known, although membrane transport phenomena associated with CF have been described recently. Consanguinity studies have shown that the inheritance of CF is consistent with it being a recessive defect caused by a mutation at a single autosomal locus. Eiberg et al. have reported a genetic linkage between the CF locus and a polymorphic locus controlling activity of the serum aryl esterase paraoxonase (PON). The chromosomal location of PON, however, is not known. Linkage to a DNA probe, DOCR1-917, was also recently found at a genetic distance of approximately 15 centimorgans (L.-C. Tsui and H. Donnis-Keller, personal communication), but no chromosomal localization was given. Here we report tight linkage between the CF locus and an anonymous DNA probe, pJ3.11, which has been assigned to chromosome 7cen-q22.