基于RAPD标记的南苍术居群遗传多样性分析

采用RAPD标记技术对分布于江苏小九华山、小汤山和湖山,安徽金寨和芜湖以及湖北保康和英山的7个南苍术〔Atractylodes lancea(Thunb.)DC.〕野生居群的28个单株基因组总DNA进行PCR扩增,在此基础上分析居群的遗传多样性及遗传分化,并采用聚类分析法对居群的遗传关系进行分析。结果表明:用18条RAPD引物共扩增出193条带,其中多态性条带111条,多态性条带百分率(PPB)为57.51%;平均每条引物扩增出10.72条带,其中多态性条带6.17条。从省级水平看,安徽居群的PPB、有效等位基因数(Ne)、Nei’s基因多样性指数(H)和Shannon信息指数(I)均最低,而湖北居群的Ne、H和I均最高,但江苏居群的PPB最高;从居群水平看,湖北保康居群的PPB、Ne、H和I均最高,而安徽金寨居群均最低。7个居群的基因分化系数和基因流分别为0.206 5和1.921 5,说明7个居群总遗传变异的20.65%存在于居群间、79.35%存在于居群内。7个居群间的遗传距离为0.150 7～0.252 1,其中,安徽金寨和芜湖居群间最小(0.150 7),江苏湖山和安徽芜湖居群间最大(0.252 1)。基于遗传距离的聚类分析结果表明:7个居群可分为2组,湖北保康居群单独成组,其他6个居群聚为另一组;来自同一居群的单株均聚在一起。研究结果提示:南苍术居群间的遗传多样性较低,居群间无明显的遗传分化。     

基于SSR标记的8个山荆子居群遗传多样性和遗传关系分析

采用10对SSR引物对8个山荆子[Malus baccata (L.) Borkh.]居群140个单株的基因组总DNA进行PCR扩增,并据此对8个居群的遗传多样性和遗传关系进行了分析.结果表明:用10对SSR引物共扩增出91条带,多态性条带百分率达100.00％.8个居群的遗传多样性参数差异较大,有效等位基因数为1.437 9～1.535 0,Nei's基因多样性指数为0.256 0～0.309 2,Shannon信息指数为0.376 7～0.459 2,多态性条带百分率为64.84％～85.71％.居群间的有效等位基因数为1.616 9,Nei's基因多样性指数为0.355 1,Shannon信息指数为0.528 5,均明显高于居群内;8个居群间的基因流为1.739 5,基因分化系数为0.223 3,显示居群间的基因交换较多.UPGMA聚类分析结果表明:在Nei's遗传距离0.148 6处,8个居群被分为3组,河北塞罕坝居群单独为一组,山西五台山居群和北京东灵山居群为一组,其余5个居群为一组.据此推测:山荆子起源于中国华北和东北地区,山西灵空山、黑龙江小兴安岭、吉林长白山和山西中条山居群可能是其遗传多样性的核心居群.     

中国杯萼海桑遗传多样性的ISSR研究

杯萼海桑(Sonneratia alba J.Smith.)是海桑科红树植物,在我国分布于海南岛的东海岸.本文采用简单序列霞复区间扩增(ISSR)分子标记技术对分布于海南岛的杯萼海桑的4个天然居群和东寨港红树林自然保护区引种的一人工居群共100个个体进行了遗传变异分析.11个引物共扩增出133条带,其中103条具多态性,多态位点百分率为77.44%.在居群水平上相对较低,多态位点百分率为51.88%～65.41%,平均为57.74%.期望杂合度、香农信息指数在物种水平上分别为0.227 1和0.348 9;在居群水平上分别为0.1 83 7和0.227 5.依据Gst值,杯萼海桑绝大多数遗传变异发生在居群内的个体间(81.02%),18.98%的遗传变异发生在居群间.AMOVA分析也表明了类似的遗传结构.居群间平均遗传一致度为0.934 2.依据Nei(1972)的遗传距离对不同居群进行UPGMA聚类,将居群分为两组,来自三亚(SY)和陵水(LS)的居群聚为一类;东寨港引种栽培的人工居群(DZ)和琼海(QH)、文昌(WC)的居群聚为另一类.Mantel检验表明,遗传距离与地理距离呈极显著相关.     

内蒙古中部地区小叶锦鸡儿天然居群表型多样性分析

对采自内蒙古中部地区的7个小叶锦鸡儿(Caragana microphylla Lam.)天然居群的207份材料进行了表型多样性分析.结果表明:小叶锦鸡儿种内表型性状存在丰富的变异,无论在居群间还是在居群内均表现出极显著差异(P<0.001);叶片、荚果、种子等11个表型性状居群间分化系数为16.90%,居群内表型性状分化系数为83.10%,是小叶锦鸡儿表型变异的主要来源;主成分分析显示荚果柄长、荚果长、关节长是造成小叶锦鸡儿表型变异的主要影响因子;依据小叶锦鸡儿表型性状,通过聚类分析将7个小叶锦鸡儿居群分为3类,第1类为多伦居群,第2类为西乌旗居群,第3类为四子王旗、察右后旗、化德、镶黄旗和正镶白旗5个居群.     

四个不同地理区域的库蚊复合组居群的遗传多样性研究

库蚊种群在农药强选择压下的生存及抗性进化是与其种群的遗传多样性密切相关的。本文主要从居群的遗传多样性角度出发 ,研究其抗性遗传行为。分别对采自 4个不同地理区域的库蚊复合组样群 ,采用水平切片淀粉凝胶电泳的方法 ,分析了 3个酶系统 (苹果酸酶Me、苹果酸脱氢酶Mdh、甘油醛-3-磷酸脱氢酶Gpd) ,获得了 5个位点共 2 7个等位基因的资料。并计算了 4个库蚊居群的遗传多样性指标为 (A ,P ,He,Ho) ,同时分析了 5种居群间的遗传距离。分析结果表明 :遗传多样性主要存在于各居群之内 (FIS=0 .5 4 37) ,但居群之间的遗传分化程度也相对较大 (Gst =0 .4 498)。     

中国卵叶海桑遗传多样性的ISSR研究

卵叶海桑 (Sonneratiaovata)是海桑科濒危红树植物 ,在我国仅分布于海南文昌清澜自然保护区内。采用简单序列重复区间扩增 (ISSR)分子标记技术对该天然居群和东寨港红树林自然保护区引种的人工居群共 3个居群 3 9个个体进行了遗传变异分析。 1 1个引物共扩增出 1 85条带 ,其中 1 2 7条具多态性 ,多态位点百分率为 68.65 %。在居群水平上相对较低 ,多态位点百分率 3 6.76%～ 5 4.5 9% ,平均值为 47.2 1 %。Nei的基因多样性、Shannon信息指数在物种水平上分别为 0 .1 41 1和 0 .2 2 92 ;在居群水平上平均值分别为 0 .1 2 0 9和0 .1 91 0。Nei的遗传分化系数Gst表明 :87.5 8%遗传变异分布在居群内 ,1 2 .42 %的遗传变异分布在居群间。居群间的遗传一致度达 0 .970 7。东寨港迁地保护的人工居群有效地保护了卵叶海桑的遗传多样性。     

基于RAPD标记的叉蕊薯蓣和粉背薯蓣不同居群遗传多样性研究

采用RAPD分子标记技术对6个叉蕊薯蓣(Dioscorea collettii Hook. f.)居群及5个粉背薯蓣[D. collettii var. hypoglauca (Palibin)C. T. Ting et al.]居群的遗传多样性进行了分析,并基于遗传相似系数采用UPGMA法对11个居群进行了聚类分析.用14个寡聚核苷酸引物共扩增出170条带,其中多态性条带161条,多态性条带百分率高达94.71%; 粉背薯蓣5个居群多态性条带百分率的变化幅度(81.25%～89.29%)略大于叉蕊薯蓣6个居群(82.00%～84.21%).粉背薯蓣居群间的有效等位基因数(Ne)、Nei's基因多样性指数(h)和Shannon多样性指数(I)分别为1.368 5、0.238 4和0.376 3,叉蕊薯蓣居群间的Ne、h和I分别为1.331 1、0.197 2和0.298 3;叉蕊薯蓣与粉背薯蓣间的基因分化系数(Gst)为0.122 8,基因流(Nm)为3.570 7.二者间的遗传相似系数为0.922 3, 遗传距离为0.080 9; 其中, 粉背薯蓣江西庐山居群和叉蕊薯蓣云南丽江居群间的遗传距离最远,达0.693 1;叉蕊薯蓣云南蒙自和云南景洪居群间的遗传距离最近,仅0.219 4.根据聚类分析结果可将参试的11个居群分成4组,其中,所有的叉蕊薯蓣居群和粉背薯蓣浙江临安居群聚成第1组,粉背薯蓣重庆南川居群和湖南衡山居群聚为第2组,粉背薯蓣湖南永顺居群和江西庐山居群则各自独立成组.研究结果证明,叉蕊薯蓣和粉背薯蓣这2个类群之间为原变种和变种的关系,并存在着变种水平上的分化不完全.     

基于AFLP分子标记技术的黑花韭与多星韭遗传多样性与亲缘关系分析

采用AFLP分子标记技术分析了分布在滇中、滇西、滇西北的3个黑花韭居群、3个二倍体多星韭居群和6个四倍体多星韭居群的遗传多样性与亲缘关系.结果表明,12个居群在DNA水平上已发生明显分化.居群间的基因分化系数(GST)为0.444.由GST计算的居群间基因流(Nm)为0.625,表明居群间部分基因流动受阻.12个居群间...     

油松天然次生林居群遗传多样性及与产地地理气候因子的关联分析

利用ISSR分子标记技术,分析了中国北部地区10个油松天然次生林居群的遗传多样性,以及与地理环境因子的相关性.研究结果表明:13条ISSR引物对250个个体扩增出137条谱带,平均多态位点百分率60.72％,不同居群的多态位点百分率差异明显;不同地理居群间的期望杂合度指数在0.2824-0.3702之间,平均为0.3210;Shannon多样性指数范围为0.1923-0.2490,平均为0.2165.居群间的遗传变异占居群总的遗传多样性的37.53％.经Mantel检验,居群间的地理距离和遗传距离间不存在显著相关性(r=0.069,p=0.360).聚类分析(UPGMA)表明,河南宝天曼(BTM)、承德大窝铺(DWP)、宁夏苏峪口(SYK)和甘肃冶力关(YLG)居群聚为一组,辽宁医巫闾山(YWL)、山西沁源灵空山(LKS)、陕西蔡家川林场(CJC)、山西和顺云龙公园(YLGY)和山西汶水三道川林场(SDC)居群为一组,山东蒙山(Ms)居群独立为一组.经分析发现,分布于我国地势二级、三级阶梯分界线区域的油松天然林( YWL、BTM、YLGY)遗传多样性水平高,位于分布区东西临界点居群(MS、YLG)遗传多样性水平低.经相关性分析,温度相关因子(年均温、1月均温、极端最低温)、海拔及年降雨量显著影响遗传多样性水平.油松天然居群分子变异存在一定的地理变异规律.     

云南泸定百合遗传多样性的表型与ISSR分析

用表型变异分析并结合ISSR分子标记对云南境内10个泸定百合(Lilium sargenttiae)居群进行遗传多样性分析。结果显示:(1)云南10个泸定百合居群的7个表型性状的居群间F值在3.26～19.1之间,表型的居群间差异均达到显著或极显著水平;平均表型分化系数为71.22%,居群间变异(59.92%)大于居群内变异(23.42%),说明居群间表型变异是泸定百合居群变异的主要来源。(2)13个ISSR引物共检测到248个多态位点,物种水平上多态位点率98.80%,Nei’s多样性指数和Shannon多样性指数分别为0.265 5和0.413 1;居群内基因多样度(Hs)为0.175 7,居群间基因分化系数(Gst)0.336 7,Mantel检验显示泸定百合居群在地理距离和遗传距离间具有显著相关性(r=0.804 4,P=0.009 9)。研究表明,云南泸定百合的居群间表型和分子水平均具有较高的遗传多样性,居群间的遗传分化较大,并且分化趋势具有明显的地域性。因此,可选择迁地种植对泸定百合进行有效保护。     

The influence of altitude and topography on genetic structure in the long-toed salamander (Ambystoma macrodactulym)

A primary goal of molecular ecology is to understand the influence of abiotic factors on the spatial distribution of genetic variation. Features including altitudinal clines, topography and landscape characteristics affect the proportion of suitable habitat, influence dispersal patterns, and ultimately structure genetic differentiation among populations. We studied the effects of altitude and topography on genetic variation of long-toed salamanders (Ambystoma macrodactylum), a geographically widespread amphibian species throughout northwestern North America. We focused on 10 low altitude sites (< 1200 m) and 11 high-altitude sites in northwestern Montana and determined multilocus genotypes for 549 individuals using seven microsatellite loci. We tested four hypotheses: (1) gene flow is limited between high- and low-altitude sites; and, (2) gene flow is limited among high-altitude sites due to harsh habitat and extreme topographical relief between sites; (3) low-altitude sites exhibit higher among-site gene flow due to frequent flooding events and low altitudinal relief; and (4) there is a negative correlation between altitude and genetic variation. Overall F(ST) values were moderate (0.08611; P < 0.001). Pairwise F(ST) estimates between high and low populations and a population graphing method supported the hypothesis that low-altitude and high-altitude sites, taken together, are genetically differentiated from each other. Also as predicted, gene flow is more prominent among low-altitude sites than high-altitude sites; low-altitude sites had a significantly lower F(ST) (0.03995; P < 0.001) than high altitude sites (F(ST) = 0.10271; P < 0.001). Use of Bayesian analysis of population structure (BAPS) resulted in delineation of 10 genetic groups, two among low-altitude populations and eight among high-altitude populations. In addition, within high altitude populations, basin-level genetic structuring was apparent. A nonequilibrium algorithm for detecting current migration rates supported these population distinctions. Finally, we also found a significant negative correlation between genetic diversity and altitude. These results are consistent with the hypothesis that topography and altitudinal gradients shape the spatial distribution of genetic variation in a species with a broad geographical range and diverse life history. Our study sheds light on which key factors limit dispersal and ultimately species' distributions.     

Genetic adaptation to high altitude in the Ethiopian highlands

Background

Genomic analysis of high-altitude populations residing in the Andes and Tibet has revealed several candidate loci for involvement in high-altitude adaptation, a subset of which have also been shown to be associated with hemoglobin levels, including EPAS1, EGLN1, and PPARA, which play a role in the HIF-1 pathway. Here, we have extended this work to high- and low-altitude populations living in Ethiopia, for which we have measured hemoglobin levels. We genotyped the Illumina 1M SNP array and employed several genome-wide scans for selection and targeted association with hemoglobin levels to identify genes that play a role in adaptation to high altitude.

Results

We have identified a set of candidate genes for positive selection in our high-altitude population sample, demonstrated significantly different hemoglobin levels between high- and low-altitude Ethiopians and have identified a subset of candidate genes for selection, several of which also show suggestive associations with hemoglobin levels.

Conclusions

We highlight several candidate genes for involvement in high-altitude adaptation in Ethiopia, including CBARA1, VAV3, ARNT2 and THRB. Although most of these genes have not been identified in previous studies of high-altitude Tibetan or Andean population samples, two of these genes (THRB and ARNT2) play a role in the HIF-1 pathway, a pathway implicated in previous work reported in Tibetan and Andean studies. These combined results suggest that adaptation to high altitude arose independently due to convergent evolution in high-altitude Amhara populations in Ethiopia.     

Gene Expression Variability within and between Human Populations and Implications toward Disease Susceptibility

Variations in gene expression level might lead to phenotypic diversity across individuals or populations. Although many human genes are found to have differential mRNA levels between populations, the extent of gene expression that could vary within and between populations largely remains elusive. To investigate the dynamic range of gene expression, we analyzed the expression variability of ∼18, 000 human genes across individuals within HapMap populations. Although ∼20% of human genes show differentiated mRNA levels between populations, our results show that expression variability of most human genes in one population is not significantly deviant from another population, except for a small fraction that do show substantially higher expression variability in a particular population. By associating expression variability with sequence polymorphism, intriguingly, we found SNPs in the untranslated regions (5′ and 3′UTRs) of these variable genes show consistently elevated population heterozygosity. We performed differential expression analysis on a genome-wide scale, and found substantially reduced expression variability for a large number of genes, prohibiting them from being differentially expressed between populations. Functional analysis revealed that genes with the greatest within-population expression variability are significantly enriched for chemokine signaling in HIV-1 infection, and for HIV-interacting proteins that control viral entry, replication, and propagation. This observation combined with the finding that known human HIV host factors show substantially elevated expression variability, collectively suggest that gene expression variability might explain differential HIV susceptibility across individuals.     

Major-histocompatibility-complex gene markers and restriction-fragment analysis of steroid 21-hydroxylase (CYP21) and complement C4 genes in classical congenital adrenal hyperplasia patients in a single population

The gene CYP21B, encoding the steroid 21-hydroxylase enzyme of adrenal steroid biosynthesis, has been mapped to the human major histocompatibility complex (MHC). Deficiency of this enzyme leads to congenital adrenal hyperplasia (CAH). We report the phenotypes of the HLA and complement C4 and Bf genes, which are closely linked to the CYP21B gene, together with a detailed analysis of the CYP21 and C4 RFLP, in 17 Finnish families with CAH. The RFLP analysis with six restriction enzymes suggested that, altogether, 35% of the affected chromosomes had a CYP21B + C4B gene deletion, 9% an obvious gene conversion of the CYP21B gene to a CYP21A-like gene, and 3% a CYP21A + C4B duplication. The remaining 53% gave the RFLP patterns also found in nonaffected chromosomes. We also found that a 14.0-kb EcoRI RFLP marker of the CYP21 genes was strongly associated with the presence of a short C4B gene, suggesting that some of the RFLP markers found with the CYP21 probe may actually derive from C4B gene polymorphism. Three particular MHC haplotypes, each with a characteristic RFLP pattern, were found in many unrelated families. These three haplotypes accounted for 59% of the affected chromosomes in our study group, the rest (41%) of the affected chromosomes being distributed among various subtypes. The results suggest that, within a single, well-defined population such as in Finland, only a few CYP21B gene defects may constitute a substantial part of the affected chromosomes. This finding will help in genetic studies of CAH in such populations.     

蒺藜苜蓿糖基转移酶基因SMALL AND EMERALD1的克隆和功能研究

类黄酮代谢对于植物生长发育和植物-环境互作至关重要,其中糖基转移酶介导的糖基化修饰在类黄酮代谢中发挥着重要作用。为了研究蒺藜苜蓿中糖基转移酶的生物学功能,通过定向筛选蒺藜苜蓿Tnt1逆转座子插入突变体库,获得了一类植株矮小、叶片深绿的突变体small and emerald1 (se1)。通过基因表型连锁性分析成功克隆了SE1基因,该基因编码1个糖基转移酶,与拟南芥中调控类黄酮生物合成的AtUGT84A1氨基酸同源性为52.8%。对野生型和se1突变体叶片的类黄酮含量进行测定发现类黄酮总量在se1突变体中显著降低(P<0.01)。进一步研究发现在se1突变体中类黄酮合成途径关键基因CHS、F3H和F3’H表达水平下降。亚细胞定位显示SE1可能在细胞质和细胞核中发挥生物学功能。研究表明糖基转移酶基因SE1可能参与蒺藜苜蓿类黄酮合成代谢调控,进而影响其生长发育。此外,研究还发现SE1基因对于叶绿素合成可能具有负向调控作用。