An amino-acid substitution involved in phenylketonuria is in linkage disequilibrium with DNA haplotype 2

Phenylketonuria (PKU) is an autosomal recessive human genetic disorder caused by a deficiency of hepatic phenylalanine hydroxylase (PAH, phenylalanine 4-monooxygenase, EC 1.14.16.1). PKU is a common inborn error of amino-acid metabolism in caucasian populations and approximately 1 in 50 individuals are carriers of a PKU allele. To define the molecular basis of PKU, we characterized twelve restriction fragment-length polymorphism (RFLP) haplotypes of the PAH locus in the northern European population and observed that 90% of the PKU alleles in this population are confined to four common RFLP haplotypes. We have recently reported a splicing mutation in the PAH gene that is associated with RFLP haplotype 3 which is present at about 40% of mutant alleles. We now report the molecular lesion associated with the RFLP haplotype 2 mutant allele. This defect is caused by a C-to-T transition in exon 12 resulting in an amino-acid substitution (Arg to Trp) at residue 408 of PAH. Direct hybridization analysis of the point mutation using a specific oligonucleotide probe demonstrated that this mutation is also in linkage disequilibrium with RFLP haplotype 2 alleles that make up about 20% of mutant PAH genes.     

Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

An RNA virus population does not consist of a single genotype; rather, it is an ensemble of related sequences, termed quasispecies. Quasispecies arise from rapid genomic evolution powered by the high mutation rate of RNA viral replication. Although a high mutation rate is dangerous for a virus because it results in nonviable individuals, it has been hypothesized that high mutation rates create a 'cloud' of potentially beneficial mutations at the population level, which afford the viral quasispecies a greater probability to evolve and adapt to new environments and challenges during infection. Mathematical models predict that viral quasispecies are not simply a collection of diverse mutants but a group of interactive variants, which together contribute to the characteristics of the population. According to this view, viral populations, rather than individual variants, are the target of evolutionary selection. Here we test this hypothesis by examining the consequences of limiting genomic diversity on viral populations. We find that poliovirus carrying a high-fidelity polymerase replicates at wild-type levels but generates less genomic diversity and is unable to adapt to adverse growth conditions. In infected animals, the reduced viral diversity leads to loss of neurotropism and an attenuated pathogenic phenotype. Notably, using chemical mutagenesis to expand quasispecies diversity of the high-fidelity virus before infection restores neurotropism and pathogenesis. Analysis of viruses isolated from brain provides direct evidence for complementation between members in the quasispecies, indicating that selection indeed occurs at the population level rather than on individual variants. Our study provides direct evidence for a fundamental prediction of the quasispecies theory and establishes a link between mutation rate, population dynamics and pathogenesis.     

中国野猪核DNA SANDX-2位点遗传变异分析

研究测定了89个中国野猪和1个家猪未知功能核基因SANDX-2位点的序列.在序列比对后长510 bp左右,发现有2处4种类型碱基缺失,30个位点发生碱基替换,共定义了19种单元型.在野猪中共发现18种单元型,其中7种只在某一地方种群中发现,11种为地方种群间共享单元型.用邻接法基于核苷酸 Kimura 2-parameter模型构建系统发生树中,19种单元型被明显分为2大枝.尽管各枝得到的Bootstrap值均较低,且各地方种群中出现的单元型散布在不同的进化枝中,但单元型在野猪亚种内的分布已出现了一定的地理分布格局.若不考虑碱基的插入/缺失,用TCS构建19种单元型网络表明,HAP2单元型为一古老单元型,其他为衍生单元型.     

Construction of fine SNP haplotypes and haplotype blocks in 5 genes in the centromere of chromosome 15 in Chinese Han subjects

Recent advances have shown that the majorityof the nucleotide variation in human genome is single nucleo-tide polymorphisms (SNPs). Using SNPs each chromosomecan be divided into different haplotype blocks, and there arelimited common haplotypes in each block. This provides apowerful approach for whole genome scan for disease-asso-ciated genes/variants. However, most data available todayare based on the large-scale genomic analyses, data concern-ing individual genes for fine mapping with high density SNPsare relatively lacking. We have sequenced 7 genes and theirflanking regions, identified 34 novel SNPs, constructed highdensity SNP haplotypes and haplotype blocks in 5 genes inthe centromeric region of chromosome 15 in I00 ChineseHart subjects. Our results show that there is a great hetero-geneity in the haplotypes and haplotype block structureswithin and between these genes, which are in close physicalproximity. Data obtained in this study provide a useful toolfor candidate gene approach at the fine scale for identifyingdisease contributing variants in the genes/regions.     

Genome-wide detection and characterization of positive selection in human populations

With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.     

Polymorphism of human Ia antigens: gene conversion between two DR beta loci results in a new HLA-D/DR specificity

The polymorphic HLA-DR beta-chains are encoded within the human major histocompatibility complex (MHC) by multiple loci resulting from gene duplications. Certain DR haplotypes can be grouped into families based on shared structural factors. We have studied the molecular basis of HLA-DR polymorphism within such a group which includes the haplotypes DR3, DR5 and DRw6. Molecular mapping of the DR beta-chain region allows true allelic comparisons of the two expressed DR beta-chain loci, DR beta I and DR beta III. At the more polymorphic locus, DR beta I, the allelic differences are clustered and may result from gene conversion events over very short distances. The gene encoding the HLA-DR3/Dw3 specificity has been generated by a gene conversion involving the DR beta I and the DR beta III loci of the HLA-DRw6/Dw18 haplotype, as recipient and donor gene, respectively. Based on which allele is found at DR beta III, the less polymorphic locus, two groups of haplotypes can be defined: DRw52a and DRw52b. The generation of HLA-DR polymorphism within the DRw52 supertypic group can thus be accounted for by a succession of gene duplication, divergence and gene conversion.     

Functional epistasis on a common MHC haplotype associated with multiple sclerosis

Genes in the major histocompatibility complex (MHC) encode proteins important in activating antigen-specific immune responses. Alleles at adjacent MHC loci are often in strong linkage disequilibrium; however, little is known about the mechanisms responsible for this linkage disequilibrium. Here we report that the human MHC HLA-DR2 haplotype, which predisposes to multiple sclerosis, shows more extensive linkage disequilibrium than other common caucasian HLA haplotypes in the DR region and thus seems likely to have been maintained through positive selection. Characterization of two multiple-sclerosis-associated HLA-DR alleles at separate loci by a functional assay in humanized mice indicates that the linkage disequilibrium between the two alleles may be due to a functional epistatic interaction, whereby one allele modifies the T-cell response activated by the second allele through activation-induced cell death. This functional epistasis is associated with a milder form of multiple-sclerosis-like disease. Such epistatic interaction might prove to be an important general mechanism for modifying exuberant immune responses that are deleterious to the host and could also help to explain the strong linkage disequilibrium in this and perhaps other HLA haplotypes.     

A closely linked genetic marker for cystic fibrosis

Cystic fibrosis is a recessive genetic disorder, characterized clinically by chronic obstructive lung disease, pancreatic insufficiency and elevated sweat electrolytes; affected individuals rarely live past their early twenties. Cystic fibrosis is also one of the most common genetic diseases in the northern European population. The frequency of carriers of mutant alleles in some populations is estimated to be as high as 1 in 20, carrying a concomitant burden of about one affected child in 1,500 births. Because little is known of the essential biochemical defect caused by the mutant gene, a genetic linkage approach based on arbitrary genetic markers and family studies is indicated to determine the chromosomal location of the cystic fibrosis (CF) gene. We have now obtained evidence for tight linkage between the CF locus and a DNA sequence polymorphism at the met oncogene locus. This evidence, combined with the physical localization data for the met locus presented in the accompanying paper, places the CF locus in the middle third of the long arm of chromosome 7, probably between bands q21 and q31.     

Out of Africa again and again

The publication of a haplotype tree of human mitochondrial DNA variation in 1987 provoked a controversy about the details of recent human evolution that continues to this day. Now many haplotype trees are available, and new analytical techniques exist for testing hypotheses about recent evolutionary history using haplotype trees. Here I present formal statistical analysis of human haplotype trees for mitochondrial DNA, Y-chromosomal DNA, two X-linked regions and six autosomal regions. A coherent picture of recent human evolution emerges with two major themes. First is the dominant role that Africa has played in shaping the modern human gene pool through at least two--not one--major expansions after the original range extension of Homo erectus out of Africa. Second is the ubiquity of genetic interchange between human populations, both in terms of recurrent gene flow constrained by geographical distance and of major population expansion events resulting in interbreeding, not replacement.     

Pseudomonas brassicacearum的数量分布差异及生物防治小麦全蚀病和油菜根腐病

通过3种PCR技术测定基因特征和测定3种生化特征,对来自南澳洲两块对比小麦田土壤中的Pseudomonas brassicacearum种群的菌株进行了分析研究.结果显示,两种不同土壤和两种不同根部区域(根表和根际),该种群具有高度多样性,其基因型和基因组也具有显著差异(P<0.05).所分离到的菌株中,四分之三具有独特的基因组,90%以上的基因组是其原种群所独具有的.所有菌株的基因组的平均同源性比较低(22%),聚类分析不能证明来自不同小麦田和不同根部区域的菌株具有亲缘性.聚类分析显示,种群内的基因流动是受到限制的,菌株基因组的差异是由于基因的随机漂流引起的,由根表得到的基因型是与所采集的对比土壤相关联的.有三分之一的菌株检测到了2,4-二乙酰基均苯三酚(PhlD)生物合成基因,这些菌株形成了一相关联的组群(同源性为60%).4株产生PhlD的菌株(两种野生型,表型不同)对小麦全蚀病和腐霉引起的油菜根腐病具有显著的防治效果,展现出了对这类病原菌引起的根部病害的防治潜能.     

Y-SNP多态性揭示的海南岛黎族、回族和仡隆人群的起源

分析黎族、海南回族、仡隆人群中Y染色体单倍型(Y-SNP)的分布,从遗传学角度研究3个人群的起源。选取部分与东亚人群起源相关的Y染色体非重组区单核苷酸多态性位点,采用PCR-RPLF和geno-typing法分析其多态性,观察由这些多态性位点组成的单倍型在海南3个人群中的分布情况,并将结果与其他人群的分布进行比较。结果在黎族人群中发现4种Y染色体单倍型,其中单倍型O*-175为5个支系所共有,且分布频率都在95%以上。回族人群出现4种单倍型,仡隆人群有2种单倍型。由单倍型种类、频率分布及主成分分析均揭示,黎族与台湾原住民及百越最为接近,可能有共同的起源。海南回族与中国北方回族遗传关系较远;仡隆人群与汉族差异较大,而与百越的仡佬族、水族及黎族遗传关系接近。     

中国西北少数民族东乡族的Y染色体微卫星单倍型分析

运用国际法医学界推荐的"最小单倍型"共7个微卫星位点(DYS19,DYS389Ⅰ,DYS389Ⅱ,DYS390,DYS391,DYS392,DYS393)和1个高多态性微卫星位点DYS385,采用PCR结合银染显色技术,对采自临夏回族自治区东乡县的133个健康男性个体的DNA,进行了Y染色体8个微卫星的等位基因及单倍型分布状况遗传多态性分析.结果显示,东乡族保留着较高的Y-STR遗传多态性,在测出的66个等位基因中共构建了110种单倍型,单倍型多样性为98.9%,表明该系统有较强的个体识别能力.另外,我们的研究可以为东乡族这一穆斯林民族的起源提供有价值的遗传资料.     

福建近海蓝圆鲹群体遗传结构分析

测定了福建近海蓝圆鲹(Decapterus maruadsi Temminck&Schlegel)2个群体共60尾个体的线粒体DNA(mtDNA)控制区序列,探讨了闽东和闽南群体遗传结构和遗传多样性.结果显示:获得长度为834～838 bp的控制区部分序列,在所测的60个样本中,共检测到23个变异位点,定义了28个单倍型,平均单倍型多样性(h)为0.948±0.0145,核苷酸多样性(π)为0.004 99±0.002 79,核苷酸差异数(K)为4.173±2.104,提示了福建近海蓝圆鲹具有较高的遗传多样性水平.构建的单倍型邻接关系树没有明显的以地理群体为单位的家系式分支出现,单倍型网络图也未显示出单倍型和地理位置的对应关系.Tajima's D和Fu's Fs中性检验及核苷酸不配对分析暗示了蓝圆鲹闽南群体在63 000年前可能发生过扩张事件,而闽东群体符合中性理论进化,2个群体不同的历史动态可能是由于小冰河期海区间的气候差异和闽东群体的过度利用所致.分子方差分析(AMOVA)表明,遗传变异全部存在于群体内,2个群体间具有紧密的基因流和较低的遗传分化,群体问和群体内的Kimura双参数遗传距离均较小.可知:福建近海蓝圆鲹遗传多样性较高,闽东和闽南群体的遗传结构相似,不存在显著的遗传分化.因此,建议将闽南渔场和闽东渔场作为一个种质资源评估、管理和保护单元.     

Mechanism of antigen-driven selection in germinal centres

The high affinity of antibodies produced during responses to T-cell-dependent antigens is associated with somatic mutation in the variable region of the immunoglobulin. Indirect evidence indicates that: (1) this arises by a process of hypermutation, acting selectively on rearranged immunoglobulin variable-region genes, which is activated in centroblasts within germinal centres; and (2) centrocytes, the progeny of centroblasts, undergo selection on the basis of their ability to receive a positive signal from antigen. We have now performed experiments analysing this selection process, and found that, on culture, centrocytes isolated from human tonsil kill themselves within a few hours by apoptosis. This is not a feature of other tonsillar B cells. Centrocytes can be prevented from entering apoptosis if they are activated both through their receptors for antigen and a surface glycoprotein recognized by CD40 antibodies.     

上海原住民的Y染色体遗传分析

Y染色体是继线粒体之后的研究人类进化的又一热点,通过对其上的多态性位点研究也证实了非洲起源说.Y染色体上的各单核苷酸多态(SNP)位点组合成的单倍型与民族系统的时间发生尺度比较一致,所以是鉴别民族迄今最恰当的遗传材料.M119C这一SNP突变是百越民族的特色,M119C-M110C和M95T-M88G更是百越的特有种.良渚文化的族属是考古学界的一个争议焦点,有百越和三苗两种说法.良渚文化与马桥文化之间差异极大,其居民遗传上是否继承也是有问题的.本项研究通过对马桥地区良渚时期、马桥时期、战国、明代及现代居民Y染色体若干SNP位点的检测,重点考察了M119位点,发现马桥地区各时期的居民都有较高的M119C和M95T类型,具有典型的百越特征,而没有苗瑶的特征.这说明自古以来马桥地区居民都是越人,并且一脉传承至今.现代上海的原住民"宕傣"人与台湾原住民的遗传结构最接近,其次接近西南部的侗傣民族.主成分分析及主成分与Y染色体单倍型的相关分析发现,单倍型H9和H11区分了东越与西越,H7区分了苗瑶,H8区分出了氐羌,H11与H5区分了濮越系统与非濮越系统.各单倍型能对各民族系统较清晰地区分和代表,是族属分析的良好材料,值得深入研究.     

中国人十四个群体中Gm和Km因子的分布

本文研究了中国昆明汉族、贵州汉族、广西侗族、大连汉族、山东汉族、沈阳朝鲜族、宁夏回族的Gm和Km因子的表型频率及四川、广西、武汉、上海、长春汉族和广西壮族、新疆维吾尔族共十四个群体的Gm单倍型频率、Km基因频率,并用Gm单倍型频率计算了中国14个群体与其他人种国家的3个群体间的遗传距离和这些群体的系统树。结果表明Gm分布不均一,提示早先大陆上存在的两个群体曾发生过迁移和混杂,在新疆维吾尔族和宁夏回族中均发现白种人和黄种人血缘融合的现象。群体中Km频率呈随机分布。     

9个地方鸡种MHC B-G座位多态性及其分子系统进化分析

以我国9个地方鸡为研究对象,对其MHC B-G座位全基因序列进行测序,以揭示这9个地方鸡种MHC B-G基因的遗传多样性,并构建其系统进化树.结果表明,9个地方鸡种MHC B-G基因序列具有较高的遗传多样性,在9个地方鸡种中共存在666个突变位点,其中单一位点突变554个,简约信息112个,共缺失782 bp.核苷酸多样度(Pi)为0.030 79±0.004 39,平均核苷酸差异(K)为182.639.9个地方鸡品种为9个单倍型,单倍型多样度为1.00±0.052.9个鸡种MHC B-G基因Kiumura双参数遗传距离范围为0.010～0.070,鹿苑鸡与新狼山鸡的遗传距离最小,为0.010;茶花鸡与东乡绿壳蛋鸡遗传距离最大,为0.070.根据9个鸡品种MHC B-G基因全序列构建的NJ树和ME树,茶花鸡单独聚为1类,其他8个品种被聚为2大类.Tajima's D值为-1.554 6,且差异不显著(0.10>P>0.05),说明MHC B-G基因为负向选择,不遵循中性进化理论,MHC B-G基因多态性不是遗传漂变的结果,而是自然选择和人工选择的结果.     

Evolutionary relationships of human populations from an analysis of nuclear DNA polymorphisms

The genetic relationships of human populations have been studied by comparing gene frequency data for protein and blood-group loci of different populations. DNA analysis now promises to be more informative since not only do the DNA coding sequences have more variation than their corresponding proteins but, in addition, noncoding DNA sequences display more extensive polymorphism. We have now studied the frequency of a group of closely linked nuclear DNA polymorphisms (haplotypes) in the beta-globin gene cluster of normal (beta A) chromosomes of individuals from eight diverse populations. We have found that all non-African populations share a limited number of common haplotypes whereas Africans have predominantly a different haplotype not found in other populations. Genetic distance analysis based on these nuclear DNA polymorphisms indicates a major division of human populations into an African and a Eurasian group.     

花粉愈伤组织群体偏态分离的SSR标记鉴定

利用水稻花粉育性基因S-b的SSR分子标记RMl3，鉴定籼粳稻杂种Fl的花粉愈伤组织的基因型，以确定每块愈伤组织在S-b座位的遗传来源，结果表明该座位的等位基因S^i或S^j在愈伤组织群体中分离比不符合1：1的规律，出现偏态分离现象．选择不同培养基及增加预冷处理不会改变偏态分离的方向，但预冷处理会增大偏分离的趋势．为进一步解释DH群体构建中的某些基因的偏态分离现象提供了依据，同时讨论了将SSR标记引入组织培养体系的可行性．