A common variant in the FTO gene is associated with body mass index and predisposes to childhood and adult obesity

Obesity is a serious international health problem that increases the risk of several common diseases. The genetic factors predisposing to obesity are poorly understood. A genome-wide search for type 2 diabetes-susceptibility genes identified a common variant in the FTO (fat mass and obesity associated) gene that predisposes to diabetes through an effect on body mass index (BMI). An additive association of the variant with BMI was replicated in 13 cohorts with 38,759 participants. The 16% of adults who are homozygous for the risk allele weighed about 3 kilograms more and had 1.67-fold increased odds of obesity when compared with those not inheriting a risk allele. This association was observed from age 7 years upward and reflects a specific increase in fat mass.     

The structure of haplotype blocks in the human genome

Haplotype-based methods offer a powerful approach to disease gene mapping, based on the association between causal mutations and the ancestral haplotypes on which they arose. As part of The SNP Consortium Allele Frequency Projects, we characterized haplotype patterns across 51 autosomal regions (spanning 13 megabases of the human genome) in samples from Africa, Europe, and Asia. We show that the human genome can be parsed objectively into haplotype blocks: sizable regions over which there is little evidence for historical recombination and within which only a few common haplotypes are observed. The boundaries of blocks and specific haplotypes they contain are highly correlated across populations. We demonstrate that such haplotype frameworks provide substantial statistical power in association studies of common genetic variation across each region. Our results provide a foundation for the construction of a haplotype map of the human genome, facilitating comprehensive genetic association studies of human disease.     

广西邕宁普通野生稻(Oryza rufipogon Griff.)种群遗传多样性及核心种质构建研究

[目的]研究广西邕宁普通野生稻种群的遗传多样性和核心种质构建,为普通野生稻种群保护提供依据。[方法]从水稻12条染色体上均匀选取24对SSR标记对243份样本进行遗传多样性分析。[结果]结果表明,24对引物均表现出多态性,多态位点比率为100%;24个多态位点共检测出103个等位变异,平均等位基因数A为4.291 7,平均有效等位基因数E是2.511 2,平均期望杂合度He为0.573 2,平均多态信息含量PIC为0.572 0。根据聚类结果分析,从243份材料中筛选出31份核心种质,包含了24个SSR位点检测到的所有的遗传变异,其平均期望杂合度He是0.595 8,平均多态信息含量PIC是0.586 3,基本上可以代表广西邕宁普通野生稻种群的遗传多样性。[结论]广西邕宁普通野生稻资源具有丰富的遗传多样性,建议对该地区普通野生稻种群的遗传多样性进行重点保护和利用     

Regulation of food intake and obesity

This is not the place to consider the medical significance of obesity in terms of conditions such as heart disease and hypertension, diabetes, and arthritis. These very complex interrelationships have been dealt with elsewhere (69). We hope that enough evidence has been presented to demonstrate that energy balance is normally maintained by a precise and reliable physiologic mechanism, and that the energy surplus represented by obesity may reflect direct failure of this mechanism or some combination from a variety of neurological, endocrine, enzymatic, and psychological disorders. Environmental conditions as well as genetic and traumatic factors may contribute to the development of obesity. If increasing mechanization brings tus below the level of energy expenditure at which food intake is properly regulated, appropriate habits of exercise will have to be established and maintained.     

Genome-wide association analysis identifies loci for type 2 diabetes and triglyceride levels

New strategies for prevention and treatment of type 2 diabetes (T2D) require improved insight into disease etiology. We analyzed 386,731 common single-nucleotide polymorphisms (SNPs) in 1464 patients with T2D and 1467 matched controls, each characterized for measures of glucose metabolism, lipids, obesity, and blood pressure. With collaborators (FUSION and WTCCC/UKT2D), we identified and confirmed three loci associated with T2D-in a noncoding region near CDKN2A and CDKN2B, in an intron of IGF2BP2, and an intron of CDKAL1-and replicated associations near HHEX and in SLC30A8 found by a recent whole-genome association study. We identified and confirmed association of a SNP in an intron of glucokinase regulatory protein (GCKR) with serum triglycerides. The discovery of associated variants in unsuspected genes and outside coding regions illustrates the ability of genome-wide association studies to provide potentially important clues to the pathogenesis of common diseases.     

运用RAPD技术对云南省魔芋软腐病菌系进行类群划分的初步研究*

 引起魔芋发生病害的病菌有很多种,其中软腐病是对云南魔芋生产和产量影响最为严重的病害。本试验运用RAPD技术对从云南省部分地区采集并分离得到的26个病菌进行遗传多样性的分析,从而对所分离得到的病菌进行病菌类群的初步划分。用已筛选出的7条引物对26个菌进行RAPD扩增后,发现7条随机引物共得到64条电泳带。在71.8%的相似水平上,将其分成3个类群：a,b和c。c组是SM-2（嵩明）;b组为HZ-2(会泽)和CYA(姚安县);其余的为a组。a组在73.0%的相似水平上,又分为a1和a2两个亚组。RAPD结果表明该病原菌在种内明显的分化,且与形态鉴定的结果基本一致。     

中国328个玉米品种（组合）SSR标记遗传多样性分析

【目的】从育成年份、种植区域角度分析中国328个玉米品种的遗传多样性,在分子水平上分析各适宜种植区域品种的遗传分化特点,为玉米品种区域试验、审定管理以及育种策略提供一定的理论依据。【方法】利用均匀分布于玉米基因组的40对核心SSR引物,采用10重荧光毛细管电泳检测技术对328个代表性育成品种进行基因分型;通过Power-Marker ver.3.25软件评估40对SSR引物多态性,对参试品种按年份、区试组分析遗传多样性情况;利用多变量统计分析软件MVSP ver.3.13对328个品种按区试组进行主坐标分析。【结果】基于328个玉米品种数据,检测到40对SSR引物等位基因变异范围为3-16个,平均8.10个,多态信息指数（PIC）值变化范围为0.18-0.85,平均为0.63。参试品种不同年份间遗传多样性变化不大,PIC值在0.60左右摆动;8个区试组品种的总等位基因和总基因型变异范围为170-262和200-511,京津唐和西南组分别表现出了最低值和最高值,京津唐组PIC值最低为0.51,其余组均接近于0.60,平均杂合度均在0.60左右。8个区试组主坐标分析显示鲜食、极早熟品种遗传分布偏离普通玉米区域,具有明显的种质特异性;青贮玉米由于早期对照品种为普通玉米导致遗传分布向普通玉米延伸,仅有少数品种分布偏离普通玉米;京津唐、西南、东北早熟三组品种遗传分布相对集中;极早熟、京津唐、西南三组之间品种遗传分布几乎无重叠区域;东华北和黄淮海两组参试品种遗传分布具有明显的分化但也有部分重叠,原因与对照品种曾经相同、育种同质化有关。【结论】利用SSR标记分析328份玉米品种的遗传多样性及遗传分化特点,表明近年来育成品种遗传多样性指数在不同年份间变化不大,除京津唐组之外在其它区试组间差异性也不大。参试品种主坐标分析显示各区试组划分、对照品种设置起到了育种导向的作用。     

元江鲤种群遗传多样性

选择12对微卫星标记检测了于2011年采集自元江(红河上游中国江段)5个样点192尾鲤的群体遗传多样性。共检测到201个等位基因,每个位点等位基因2-27个。各群体各位点平均等位基因(N_A)12.25-14.67个,平均有效等位基因(N_E)8.28-9.73个,平均观察杂合度(H_O) 0.7765-0.8037,平均期望杂合度(H_E)0.7761-0.8080,平均多态信息含量(PIC) 0.7534-0.7843。元江鲤种群192个个体各位点N_A、N_E、H_O、H_E、PIC分别为16.50、11.26、0.7927、0.8049、0.7966,种群遗传多样性水平高。元江鲤群体之间遗传分化小,可作为一个种群管理单元进行管理。增殖放流要防止遗传多样性丧失。     

Whole-genome patterns of common DNA variation in three human populations

Individual differences in DNA sequence are the genetic basis of human variability. We have characterized whole-genome patterns of common human DNA variation by genotyping 1,586,383 single-nucleotide polymorphisms (SNPs) in 71 Americans of European, African, and Asian ancestry. Our results indicate that these SNPs capture most common genetic variation as a result of linkage disequilibrium, the correlation among common SNP alleles. We observe a strong correlation between extended regions of linkage disequilibrium and functional genomic elements. Our data provide a tool for exploring many questions that remain regarding the causal role of common human DNA variation in complex human traits and for investigating the nature of genetic variation within and between human populations.     

福建省烟粉虱自然种群遗传多样性的RAPD和ISSR分析

采用RAPD和ISSR 2种分子标记分别对福建省7个地区8个烟粉虱自然种群的80份样品进行遗传多样性分析.筛选出4条RAPD引物和4条ISSR引物,从80份样品的DNA中分别扩增2 240和1 776条带,其中多态性条带分别为2 000和1 728条,说明福建地区烟粉虱自然种群遗传多样性较为丰富;聚类分析表明,福建地区8个自然烟粉虱种群可分为2大类群,采自龙海变叶木种群单独聚为1类,说明与其他种群存在较远亲缘关系,推测为不同生物型;遗传距离分析说明福建不同种群在遗传相似性上与地理分布有一定的相关性.     

中国4个牛种MSTN基因外显子2多态性分析与其系统发生关系研究

[目的]解决牛亚科动物近缘物种的分类归属问题,了解牛亚科各种群遗传多样性。[方法]采用酚-氯仿抽提法从4个中国牛种中提取基因组DNA,对MSTN基因进行PCR扩增和测序,构建系统发育树,探讨4个牛种间MSTN基因外显子2的系统发生关系。[结果]MSTN基因外显子2编码区为372 bp。蒙古牛、牦牛和独龙牛的MSTN基因外显子2具有丰富的多态性。在所测66个样本中存在3个核苷酸多态位点,定义了6种单倍型。雷琼牛、蒙古牛、独龙牛与巴州牦牛享有共同的单倍型。巴州牦牛独自聚成一支,而雷琼牛与一部分独龙牛、大部分蒙古牛和引用瘤牛聚成一支。[结论]蒙古牛、雷琼牛、独龙牛种间存在着基因交流。牦牛与普通牛、瘤牛的分化较明显,比瘤牛与普通牛的亲缘关系要远。     

Plant regeneration and genetic transformation in switchgrass——A review

Switchgrass is native to the tallgrass prairie of North America. It is self-incompatible and has varied ploidy levels from diploid(2x) to dodecaploid(12x) with tetraploid and octoploid being the most common. The high yielding potential and the ability to grow well in marginal lands make switchgrass an ideal species as a dedicated biomass producer for lignocellulosic ethanol production. Genetic transformation is an important tool for studying gene function and for germplasm improvement in switchgrass, the genome of which has been sequenced recently. This paper intends to provide a comprehensive review on plant regeneration and genetic transformation in switchgrass. We first reviewed the effect of explants, basal medium and plant growth regulators on plant regeneration in switchgrass, which is a prerequisite for genetic transformation. We then reviewed the progresses on genetic transformation with either the biolistic or Agrobacterium-mediated method in switchgrass, and discussed various techniques employed to improve the transformation efficiency. Finally we reviewed the recent progresses on the use of genetic transformation in improving biomass quality such as the reduction of lignin, and in increasing biomass yield in switchgrass. We also provided a future perspective on the use of new genome editing technologies in switchgrass and its potential impact on regulatory processes.     

基于COI基因构建西北太平洋常见鱼类DNA条形码参考数据库

西北太平洋以其独特的地理位置和复杂的海洋环境,孕育了极为丰富的渔业资源,成为全球海洋生物多样性保护和渔业资源管理的热点区域。为了更有效地进行鱼类种类识别和多样性的调查,本研究建立了西北太平洋常见鱼类DNA条形码本地数据库。基于线粒体COI基因,对2023年6-8月在西北太平洋海域所采集的307份样品进行扩增和测序,共获得7目13科20属25种鱼类的COI基因序列。77.96%的COI序列在公共数据库中都能比对到高相似度序列。种间平均遗传距离为0.233,种内平均遗传距离为0.003,种间遗传距离是种内遗传距离的77.67倍,且能够形成明显的条形码间隙,不存在物种区分困难的现象。基于COI基因序列构建的系统发育树显示,同一属的鱼类首先聚为一支,随后与同一科的鱼类聚为一支,最后,同目不同科的鱼类聚为一支。综上所述,COI基因具有物种特异性,能够有效的区分西北太平洋常见鱼类物种,本数据库的初步建立,有利于后期利用环境DNA技术进行西北太平洋鱼类多样性的监测和调查,为西北太平洋海域生物多样性保护、资源管理和种群动态监测提供了技术支持。     

Hemophilia A: polymorphism detectable by a factor 8 antibody

Plasma from 54 patients with hemophilia A was tested for neutralizing activity with a human antibody to factor VIII. The plasma from 52 patients had no demonstrable neutralizing activity. Two plasma samples had neutralizing activity equivalent to that of normal plasma despite the lack of factor VIII clotting activity. Apparently, most patients with hemophilia A do not synthesize factor VIII, whereas a few synthesize an inactive molecule with a presumed genetic structural mutation of the active site but with antigenic determinants in common with normal factor VIII. Thus, hemophilia A is a disease caused by more than a single genetic mechanism.     

广西普通野生稻遗传多样性中心的确定与核心种质构建

【目的】确定广西普通野生稻Oryza rufipogon Griff.遗传多样性中心,构建普通野生稻核心种质资源,为广西普通野生稻资源保护利用提供参考资料。【方法】利用24对微卫星标记分析来自郁江流域、红水河流域、南流江流域和桂北山区的普通野生稻623份材料的遗传多样性;采用逐步聚类法构建10%和5%的广西普通野生稻核心种质。【结果】24个SSR位点总共检测到114个等位基因。平均等位基因数为4.75,平均有效等位基因数为3.000 1,Shannon信息指数为1.180 1,平均期望杂合度为0.638 8。9个居群遗传多样性指数为:邕宁居群临桂居群扶绥居群容县居群贵港居群平南居群古棚居群五里塘居群博白居群。4个区域的多样性指数为:郁江流域桂北山区南流江流域红水河流域。广西普通野生稻资源5%的核心样本共31份,其中邕宁居群有14份,扶绥居群有12份;邕宁居群和扶绥居群分别占本居群分析样本的5.76%和18.75%,是核心样本的主要来源。【结论】郁江流域是广西普通野生稻多样性中心;邕宁居群的普通野生稻地理分布广、种类丰富,而扶绥居群遗传多样性异常丰富,它们是核心样本的主要来源,也是值得特别关注和重点保护的重要区域。     

西南牡丹品种起源的ISSR研究

【目的】通过对西南牡丹21个品种、中原牡丹18个品种、江南牡丹1个品种和1个野生种之间的亲缘关系进行研究,了解西南牡丹品种群的遗传背景,为品种选育奠定基础。【方法】通过改良的CTAB法对41份材料抽提总基因组DNA,采用ISSR分子标记的方法,通过优化的ISSR-PCR反应体系,从60个哥伦比亚大学（UBC）开发的通用引物中筛选27个进行PCR扩增差异比较,利用POPGENE软件计算多态位点百分率（%）;依据Nei’s遗传距离,运用NTSYSPC进行UPGMA聚类构建不同品种群和品种间亲缘关系。【结果】利用27个ISSR引物对41个牡丹样本扩增,共获得的317个条带,其中304个为多态性条带,多态性条带比率为95.41%,平均每个引物扩增条带为11.74;41个样本的遗传相似性系数为0.483-0.811,云南牡丹‘丽江紫5’和‘大关粉4’的遗传相似性系数最大,为0.811;云南牡丹‘大关粉4’和中原牡丹‘彩绘’的遗传相似性系数最小,为0.483;UPGMA聚类结果显示41个样本在阈值为0.625时,聚为四支：第一支由19份样本组成,其中包括5个中原牡丹品种和14个西南牡丹品种,其中,云南牡丹‘丽江紫5’与‘大关粉4’亲缘关系最近,而云南牡丹‘丽江紫5’与中原牡丹‘首案红’的亲缘关系最远,其遗传相似性系数仅为0.609;第二支包括10份样本：有‘乌龙捧盛’、‘豆绿’等5个中原品种和‘四川粉紫’、‘昭通粉’、‘丽江粉1’等5个西南牡丹品种,其中天彭牡丹‘紫金荷2’与‘四川粉紫’的亲缘关系最近,遗传相似性系数最大为0.770;天彭牡丹‘紫金荷2’与中原牡丹‘罗婺现瑞’亲缘关系最远,其遗传相似性系数为0.625;第三支包括11个样本：1个江南品种,8个中原牡丹品种;3个西南牡丹品种。亲缘关系最近的是中原牡丹‘菱花湛露’与‘朱砂垒’,其遗传相似性系数为0.779;亲缘关系最远的是‘朱砂垒’和‘凤丹白’;第四支为黄牡丹单独聚为一支。多数花色相同的供试中原品种表现出近缘关系,红色系的天彭牡丹‘胭脂楼’与紫红色系的中原牡丹品种有着较近的亲缘关系,而供试的紫红色系的天彭牡丹分别紫红色、粉色、紫色和红色的中原品种有近缘关系;云南紫牡丹品种与紫色、紫红色系的中原品种有一定关系,粉牡丹则与紫红、浅红、浅紫红、浅紫色等不同色系的中原牡丹和天彭牡丹都有一定的亲缘关系。天彭牡丹总是先与中原牡丹品种相聚,再与云南牡丹相聚;云南牡丹品种除‘狮山皇冠’、‘香玉板’外,不同产地、株型相似和花色相同的云南牡丹品种间遗传相似性较高,总是先聚为一分支后,才与其他中原品种相聚。【结论】西南牡丹品种栽培起源较复杂,天彭牡丹比云南牡丹与中原牡丹有着较近缘关系,云南牡丹不可能是天彭牡丹直接引种驯化产物,推测云南牡丹品种可能是由几个祖先品种演化的产物,但本地黄牡丹参与起源的可能性较小。     

基于SSR标记的楸树遗传多样性及核心种质构建

利用SSR标记对192个楸树种质资源进行遗传多样性和亲缘关系研究。试验筛选出13对引物对192份供试材料进行扩增,共获得89个等位基因位点,有效等位基因平均为3.795 9,Shannon’s多样性指数平均值为0.506 6;Nei’s遗传多样性平均值为0.667 7。用MEGA6.0软件对192份楸树材料进行遗传距离分析,通过聚类分析构建出供试材料楸树种质资源间的聚类图。利用SSR分子标记,采用多次聚类结合位点优先的取样策略,比较了样本数不同的4个核心样本群的等位基因数、有效等位基因数、Shannon’s指数和Nei’s遗传多样等参数,初步构建了192份楸树种质材料的46份核心种质。核心种质保留了初始种质23.96%的样品。     

利用FTIR和化学计量学对牛肝菌亲缘关系的研究

采用傅里叶变换红外光谱结合化学计量学对不同种牛肝菌亲缘关系进行研究,为该种群亲缘关系鉴定提供依据,同时为人工栽培牛肝菌奠定理论基础。采集12个种类72份牛肝菌样品的红外光谱,采用二阶导数(2D)、标准正态(SNV)变量和小波压缩(WC)等方法对牛肝菌的原始红外光谱进行优化处理,结合偏最小二乘判别分析(PLS-DA)建立鉴别模型。将PLS-DA得到的前8个主成分数据作为提取数据代入系统聚类分析(HCA),获得亲缘关系树状图。结果显示:12种牛肝菌的原始红外光谱较为相似,共有峰主要归属为蛋白质、多糖、纤维素和氨基酸等物质中OH、C=O、C-O-H、C=O、C-C等官能团的吸收峰。对比不同优化处理的鉴别结果,发现2D+WC预处理方法对不同种类牛肝菌区分效果较好。HCA亲缘关系树状图表明,按照物种层面划分,中华牛肝菌和远东疣柄牛肝菌亲缘关系最近,且2种牛肝菌与圆花孢牛肝菌亲缘关系较近;深褐牛肝菌和美味牛肝菌亲缘关系较近;小美牛肝菌和美柄牛肝菌亲缘关系较近,且2种牛肝菌与栗色牛肝菌亲缘关系较近。傅里叶变换红外光谱法可应用于牛肝菌的亲缘关系分析,能为野生食用菌的亲缘关系研究提供一种新方法。     

山东省猪种mtDNA CytB基因遗传多样性及系统进化研究

 【目的】利用mtDNA CytB基因为标记,从分子水平探讨12个猪种166个样本（8个山东省猪种,3个引进猪种和梅山猪种）的遗传多样性和各猪种间的亲缘关系,为山东省猪种合理利用以及生物多样性保护提供基础资料。【方法】对各猪种样本mtDNA CytB基因进行PCR扩增和测序,采用现代生物信息学方法进行数据处理分析。【结果】山东8个猪种种内遗传变异和种间遗传距离均较小,有共享单倍型。山东各猪种和梅山猪与大约克的遗传距离也较小,但与引进猪种杜洛克和长白的遗传距离较大。利用分子系统进化树和CytB基因4个SNP位点的分类方法将上述样本分为2个独立的支系,第一支以中国猪种为主,将除鲁烟白猪的一种单倍型在内的所有山东猪种、梅山猪和大约克的两种单倍型聚为一类,第二支以引进猪种为主,将长白、杜洛克、大约克的一种单倍型和鲁烟白猪的一种单倍型聚为一类。【结论】山东猪种有共同的母系祖先,品种内母系遗传多样性较贫乏;外来猪种引入山东后主要是用作父本以提高生产速度和瘦肉率等,对本地猪种未有母系贡献;利用CytB基因4个SNP位点对欧洲单倍型和亚洲单倍型的分类方法,可以方便地估测利用中外猪种结合培育的猪新品种（配套系）的母系血统情况。     

河南主栽枣品种遗传关系的ISSR分析

利用ISSR分子标记,对河南主栽的9个枣品种进行了遗传关系分析.结果表明,10个引物共扩增出96个条带,多态性条带82个.9个枣品种45个样本的Nei’s基因遗传多样度(He)为0.272 0,Shannon信息指数(I)为0.415 2.利用UPGMA构建了9个品种的聚类树状图,在相似系数取0.63时,9个枣品种聚为2类:冬枣、无核枣和鸡心枣聚为1类;灰枣、灵宝大枣、广洋枣、扁核酸、桐柏大枣和长红枣聚为1类.河南的栽培枣群体有着较高的遗传变异,存在着较大的选育潜力.