大鳞副泥鳅5个野生群体的遗传多样性分析

利用微卫星分子标记分析了天津地区于桥水库、大黄堡湿地、七里海湿地、团泊水库和潮白新河5个野生大鳞副泥鳅群体的遗传多样性。5个群体在12个微卫星位点共检测到98个等位基因,平均等位基因数为8.500;有效等位基因数为2.713;平均观测杂合度为0.526;平均期望杂合度为0.544。5个群体间的遗传分化指数介于0.021~0.106之间,平均遗传分化指数为0.059,属中低水平的遗传分化。AMOVA分析结果显示,在总的变异中,94.1%的遗传变异来自群体内,5.90%的遗传变异来自于群体间。根据Nei’s遗传距离所绘制的系统树显示,于桥水库、团泊水库、七里海湿地和大黄堡湿地4个群体的遗传距离相对较小聚为一支,潮白新河群体单独为一支。遗传瓶颈效应分析表明,该5个群体近期未经受遗传瓶颈效应,处于突变-漂移平衡。总体来看,天津地区5个野生大鳞副泥鳅群体的遗传多样性较高,可作为品种选育的基础群体。     

河北省华北落叶松河北群体遗传多样性分析

以来自河北8个群体共312个华北落叶松天然个体为材料,利用10对SSR引物对群体进行扩增,所得数据用于其遗传多样性和遗传结构的研究。结果表明:10对SSR位点共检测到42个位点,平均每个位点有4.2个等位基因,位点的等位基因数(Na)为2~6个。群体平均等位基因数为3.36,Shannon指数(I)平均为0.749,观察杂合度Ho为0.405、期望杂合度He为0.423,来自河北北部的围场台子水和吉字以及兴隆雾灵山的多样性水平最高,南部的阜平群体多样性水平最低。AMOVA分子差异分析显示3%的遗传变异存在于群体间,97%的遗传变异则存在于群体内,基因分化系数Gst仅为0.028,表明华北落叶松在河北的群体分化很低。聚类结果表明河北围场两个群体为一类,蔚县、隆化和涿鹿为一类,阜平和赤城为一类,兴隆雾灵山群体距离其他较远。多样性北部群体较高,南部较低,表明华北落叶松可能的衍化方向是从北向南,印证了北部可能是起源中心的结论。     

澜沧江中上游光唇裂腹鱼四个地理群体遗传多样性分析

利用简化基因组测序对澜沧江中上游的苗尾-功果桥库区、黄登-大华桥库区、里底江段和乌弄龙江段4个地理群体60个光唇裂腹鱼(Schizothorax lissolabiatus Tsao)样本进行了简化基因组测序, 平均测序深度255.26X, Q30为94.96%, 平均GC含量为39.80%; 测序获得多态性SLAF标签252623个, SNP标记1151083个, 其中, SNP平均完整度为36.66%, SNP平均杂合率为9.5%; 通过测序结果进行遗传多样性分析, 结果表明, 观测等位基因数均为2, 平均期望等位基因数为1.4211—1.5029, 平均观测杂合度为0.2381—0.3131, 平均期望杂合度为0.2690—0.3115, 平均多样性指数为0.2868—03248, 平均香浓指数为0.4269—0.481, 平均次要基因频率(MAF)为0.1854—0.2216, 平均多态信息含量(PIC)为0.2237—0.2553; AMOVA分析结果显示, 在总的变异中, 89.73%的遗传变异来自群体内部, 10.27%的遗传变异来自于群体间, 群体间遗传分化指数在–0.0150—0.1299(P<0.05), 表明群体间存在不同程度的分化。4个群体间遗传距离为0.05—0.15, UPGMA聚类表明, 苗尾-功果桥库区、黄登-大华桥库区和里底3个地理群体相互交叉聚类, 乌弄龙地理群体单独聚为一类。综上, 4个群体的遗传多样性处于中等水平, 遗传距离及聚类结果与试验群体地理距离基本相符, 研究结果将为光唇裂腹鱼种质资源评价与保护提供参考依据。     

基于SSR标记的紫花风铃木群体遗传多样性分析

为揭示紫花风铃木(Handroanthus impetiginosus)的群体遗传变异特征，对广东省6市12个群体72份种质材料进行遗传多样性和群体遗传结构分析。结果表明，9对引物共扩增出123个等位基因位点，引物的平均多态信息量为0.754，具有较高的多态性。12个群体均具有较高的遗传多样性，群体间平均有效等位基因数为3.272个，平均Shannon指数为1.159。AMOVA分析表明群体间遗传分化程度相对较低，群体内遗传分化程度较高。群体的总体遗传分化系数为0.077，处于中等程度。基于Structure分析、主坐标分析和NJ聚类分析均可将12个群体分为2大类群，分组结果具有一定相似性，表明供试紫花风铃木群体遗传结构较为简单。这为紫花风铃木优良种质资源的利用、遗传变异和科学育种提供了理论参考。     

北京市华北落叶松优树群体遗传多样性分析

利用SSR分子标记对北京市华北落叶松人工林5个群体的220棵优树进行遗传多样性和群体结构分析。20对SSR引物共检测到81个等位基因,每个位点等位基因数2~8个不等,平均4.05个。群体观测和期望杂合度平均值分别为0.429和0.440,Shannon信息指数和多态性信息含量分别为0.756和0.380。5个群体中,百花山和云蒙山遗传多样性水平最高,雾灵山遗传多样性水平最低。AMOVA分析结果显示,2.65%的遗传变异来自于群体间,剩余97.35%的遗传变异来自于群体内。遗传分化系数仅为0.023,表明北京市华北落叶松优树群体遗传分化程度很低。基于Nei's遗传距离可以将5个群体划分为3个类群,四海镇和雾灵山归为第Ⅰ类,松山归为第Ⅱ类,百花山和云蒙山归为第Ⅲ类。STRUCTURE群体结构分析结果与上述聚类分析结果大体一致。以上研究为华北落叶松人工林遗传多样性评价和优良种质资源收集、保护和利用提供理论依据。     

基于SSR标记的广东栽培益智群体遗传多样性分析

为了解广东栽培益智(Alpinia oxyphylla)群体的遗传多样性,采用SSR分子标记技术对166份种质的遗传差异进行研究。结果表明,14对SSR引物共检测到88个等位基因,每对引物检测的有效等位基因为1.198~3.279,平均2.599;Shannon多样性信息指数为0.736~1.890,平均1.107。方差分析表明20.87%的变异来自组间,79.13%的变异来自组内。基于主成分分析和遗传结构分析表明,供试166份益智样本可分为4大类群,但没有反映出形态特征的规律性。因此,益智种质资源具有较高遗传多样性,且遗传变异主要发生在群体内,群体间的遗传分化较低,且基于表型性状的类型划分和基于SSR分子标记的聚类未能实现一致性。     

湘江野鲤养殖群体和自然群体遗传多样性的微卫星分析

采用微卫星技术,用17对微卫星引物对湘江野鲤养殖群体和自然群体的的遗传多样性进行分析.结果表明:有15对引物扩增出清晰的条带,其中13对引物在群体间呈现多态性;2个群体中,13对多态性引物分别扩增等位基因2～12个,共90个,其中35个等位基因为2群体共有,55个等位基因具有群体特异性,引物平均等位基因数为6.92个,等位基因频率为0.0667～0.8333;养殖群体和自然群体的平均遗传杂合度和平均多态信息含量分别为0.5688、0.5152,0.5860、0.5347;2个群体间遗传相似性指数为0.6762,遗传距离为0.3238,表明湘江野鲤养殖和自然群体遗传多样性均较为丰富,2个群体间遗传变异程度较高.     

长江中下游黄鳝遗传多样性的微卫星分析

为了解我国长江中下游地区野生黄鳝(Monopterus albus)的种质资源现状,利用黄鳝微卫星分子标记分析我国长江中下游4个黄鳝野生群体(湖北群体、安徽群体、江苏群体和浙江群体)的遗传多样性水平.通过磁珠富集法获得50个黄鳝徽卫星序列,设计并合成了30对微卫星引物,经筛选得到8对多态性稳定的引物,均为高度多态位点.每对引物扩增得到等位基因数12 -26,平均等位基因数17.4个群体的平均多态信息含量分别为0.804、0.864、0.824和0.736,平均等位基因数分别为9.13、11.00、9.00和7.25,平均期望杂合度分别为0.865、0.918、0.882和0.813,表明4个黄鳝群体遗传多样性丰富,其中安徽群体遗传多样性水平最高,浙江群体相对较低.4个群体间遗传分化指数(FsT)为0.031 2-0.096 5,6.28％的遗传变异存在于群体间,表明4个群体间存在一定的遗传分化.聚类分析显示,浙江群体与安徽群体先聚在一起,再与江苏群体聚为一支,湖北群体单独聚为一支.     

我国沿海缢蛏群体遗传结构的mtDNA-COⅠ分析

采集了我国沿海共计9个缢蛏(Sinonovacula constricta)地理群体的197个样本,分别是北部组群的3个群体:辽宁省庄河群体(ZH),天津市汉沽群体(HG),山东省海阳群体(HY);中部组群的3个群体:江苏省盐城群体(YC),上海市崇明县东滩群体(DT)和堡镇群体(BZ);以及南部组群的3个群体:浙江省宁波群体(NB),浙江省台州群体(TZ)以及福建省宁德群体(ND)。利用线粒体COⅠ标记分析了9个群体的遗传多样性和遗传分化。结果表明,在共计197个个体中检测到125个单倍型和96个变异位点,核苷酸多样性指数位于2.1764～7.4970之间,其中中部组群的群体遗传多样性指数最高。AMOVA分析结果显示,组间遗传变异量占总变异的80.27%,18.74%来自于群体内,只有0.99%来自于组内群体间。群体间遗传分化系数位于0.0219～0.8706之间,不同群体间具有一定的遗传分化,尤其是中部群体与其他群体间遗传分化值达到了0.8以上,为极高度分化。遗传距离和聚类结果显示,北部3群体和南部3群体首先聚在一起,之后与中部3群体聚类。     

五个罗氏沼虾群体遗传多样性的微卫星分析

利用16对微卫星标记对来自泰国(CP)、缅甸(MN)、孟加拉(BD)和中国(MP和DP)的共5个罗氏沼虾群体进行了遗传多样性和遗传结构的分析。结果显示, 16个微卫星位点均具有较高的多态性, 平均等位基因数(N_a)、期望杂合度(H_e)、Shannon信息指数(I)和多态信息含量(PIC)分别为17.563、0.8316、2.1662和0.7328。5个群体的期望杂合度(H_e)介于0.7025—0.8594, 多态信息含量(PIC)介于0.6538—0.8048, 表明所有群体均具有高度遗传多样性, 遗传多样性水平CP>MP>BD>MN>DP。遗传分化指数(F_st)值介于0.03430—0.17333, 表明所有群体间均有不同程度的遗传分化。16个微卫星位点的F_st值均大于0.05, 均值为0.0977, 与群体间有遗传分化相符。AMOVA分析显示群体间变异占总变异的6.22%, 群体内个体间的变异占总变异的40.72%, 个体内部的遗传变异占总变异的53.07%。基于Nei氏遗传距离构建的UPGMA系统进化树显示, MN群体首先与MP群体聚为一类, 再与DP群体聚为一类, 之后再与BD群体聚为一类, 最后与CP群体聚为一类, 表明中国群体与泰国群体亲缘关系较远。遗传结构分析显示, 参试样本被划分为5个理论群体, 除MP群体中个体遗传结构混杂外, 其余群体中个体遗传结构相对独立。研究为罗氏沼虾种质资源的开发利用和优良品种的选育提供了参考数据。     

Genetic diversity and population structure of Elytrigia pycnantha (Godr.) (Triticeae) in Mont Saint-Michel Bay using microsatellite markers

During the last decade, an invasive wheatgrass species (Elytrigia pycnantha) has colonized the low salt marshes of the Mont Saint Michel Bay resulting in an accelerated change in the vegetation. This study was conducted using microgeographical genetic diversity in order to understand the genetic structure of this invasive and clonal species. Genetic variation and population structure of fifteen populations collected in high and low marsh habitats around the Bay were analyzed using five microsatellite loci. Because E. pycnantha is an allohexaploid, the application of standard genetic diversity statistics was not possible; we chose to summarize genetic diversity using statistics calculated from banding phenotypes. The mean number of alleles per locus was 10.2, the mean number of different alleles per sample was 6.87. The mean number of allelic phenotypes across all populations was 7.21. The mean value of genetic diversity for the species, calculated as the average number of alleles by which pairs of individuals differ, was H's = 1.91 and H't = 2.04. Little genetic differentiation among populations was detected (0.067). The association between pairwise genetic differentiation and geographic distances exhibited no evidence for isolation by distance. A geographical pattern of population differentiation, where a single population GI was clearly separated from the remaining population groups (considered as a metapopulation), was revealed by principal component analysis (PCA), and we propose that this is because GI represents a new genotype.     

Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers

To determine genetic diversity and evolutionary relationships among Chinese buffalo populations, 18 indigenous swamp buffalo populations and two introduced river buffalo breeds were genotyped for 30 microsatellite loci. The mean number of alleles across the 30 loci was 8.13, and the expected heterozygosity ranged from 0.517 (Yanjin) to 0.609 (Dehong). Although there was abundant genetic variation, genetic differentiation between Chinese buffalo populations was low, with only 2.8% of the total genetic variance among populations. The genetic differentiation pattern and genetic relationships among Chinese buffalo populations were consistent with their geographic distribution. The Dehong population was discerned as a distinct indigenous population, but suffered genetic admixture with river buffalo. The remaining populations were divided into four major clusters, i.e. the Upper and Middle Reaches of Yangtze Valley cluster (Guizhou, Guizhoubai, Yanjin, Fuling, Enshi and Jianghan), the Lower Reaches of Yangtze Valley cluster (Haizi, Shanqu and Dongliu), the South China cluster (Fuan and Xinfeng) and the Southwest China cluster (Xinglong, Xilin, Diandongnan and Dechang).     

Population genetic analysis of the domestic Bactrian camel in China by RAD‐seq

Restriction site‐associated DNA sequencing (RAD‐seq) is one of the most effective high‐throughput sequencing technologies for SNP development and utilization and has been applied to studying the origin and evolution of various species. The domestic Bactrian camels play an important role in economic trade and cultural construction. They are precious species resources and indispensable animals in China's agricultural production. Recently, the rapid development of modern transportation and agriculture, and the deterioration of the environment have led to a sharp decline in the number of camels. Although there have been some reports on the evolution history of the domestic Bactrian camel in China, the origin, evolutionary relationship, and genetic diversity of the camels are unclear due to the limitations of sample size and sequencing technology. Therefore, 47 samples of seven domestic Bactrian camel species from four regions (Inner Mongolia, Gansu, Qinghai, and Xinjiang) were prepared for RAD‐seq analysis to study the evolutionary relationship and genetic diversity. In addition, seven domestic Bactrian camel species are located in different ecological zones, forming different characteristics and having potential development value. A total of 6,487,849 SNPs were genotyped. On the one hand, the filtered SNP information was used to conduct polymorphism mapping construction, LD attenuation analysis, and nucleotide diversity analysis. The results showed that the number of SNPs in Dongjiang camel was the highest, the LD coefficient decayed the fastest, and the nucleotide diversity was the highest. It indicates that Dongjiang camel has the highest genetic diversity. On the other hand, the filtered SNPs information was used to construct the phylogenetic tree, and F_ST analysis, inbreeding coefficient analysis, principal component analysis, and population structure analysis were carried out. The results showed that Nanjiang camel and Beijiang camels grouped together, and the other five Bactrian camel populations gathered into another branch. It may be because the mountains in the northern part of Xinjiang and the desert in the middle isolate the two groups from the other five groups.     

华东地区中华蜜蜂六地理种群的遗传多样性及遗传分化

目的】利用23对微卫星标记对来自于南昌、黄山、桐庐、费县、宜兴、武夷山6个华东地区的中华蜜蜂Apis cerana cerana种群进行遗传多样性及遗传分化分析。【方法】通过计算多态信息含量、平均杂合度、等位基因数、遗传距离、基因流、F 统计量等参数, 评估各中蜂种群遗传多样性和各种群间遗传分化。【结果】各座位的等位基因数为5（A014）至30（AP043）。所有种群均显示较高水平的期望杂合度, 其中, 武夷山中蜂最低, 为0.4280; 南昌中蜂最高, 为0.6329。各中蜂种群间存在极显著的遗传分化, 平均分化系数(Fst)为0.344。基于Nei氏遗传距离运用NJ聚类法将6个中蜂种群划分为3类。【结论】华东6个中蜂种群的遗传多样性较高, 遗传分化显著; 分析遗传分化与地理距离的关系发现, 华东6个中蜂种群间的遗传分化与地理距离不存在显著相关。     

濒危灌木长叶红砂遗传多样性的RAPD分析

应用RAPD分子标记对濒危灌木长叶红砂(Reaumuria trigyna)种群遗传多样性进行了分析.应用18条随机引物对长叶红砂5个种群的95个个体进行扩增,检测到118个位点,其中多态位点105个.结果表明:长叶红砂种群的多态位点比率(P)为88.98%,显示出长叶红砂种群存在较高的遗传多样性.Shannon多样性指数(0.4966)、Nei基因多样性指数(0.3303)和基因分化系数(Gst=0.1425)的分析结果显示,长叶红砂种群遗传变异大多存在于种群内,种群间的遗传分化占14.25%.聚类分析表明,长叶红砂种群遗传距离与地理距离之间无直接相关关系.遗传多样性水平与物种特性和所处不同群落有关,濒危植物并不一定表现为遗传变异水平的降低.     

欧洲刺槐种源群体遗传结构和多样性

对来自欧洲和美国的 18个刺槐种源子代进行了等位酶分析。可进行遗传分析的 7个酶系统 (Amy,Fe,L ap,Idh,Mdh,6 Pgd,Skd)中有 14个基因位点 ,其中 12个位点具有多态性。每个多态位点平均等位基因数 (A/L )变化在 1.5 6～ 3.6 7之间 ,平均基因型数 (G/L)变化在 1.6 1～ 7.11之间 ,平均等位基因有效数目 (Ae)变化在 1.0 2～ 2 .5 0之间 ,预期杂合度 (H e)变化在0 .0 2～ 0 .5 6之间。不同种源群体之间也存在较大的遗传差异 ,在 8个德国种源中 ,各群体的 A、Ae、和 H e等相对较小 ,但不同群体间差异较大。各位点等位基因频率在不同种源群体间变化也较大 ,表明德国各种源群体内遗传变异相对较小 ,但群体间差异较大。来自匈牙利和斯洛伐克的 8个种源群则相反 ,各群体的 A、Ae、和 H e等相对较大 ,而不同种源群体间差异则较小 ,各位点等位基因频率在种源群体间变化相对一致 ,表明这两个国家的种源群体内变异较大 ,但不同种源群体间差异较小。欧洲的刺槐种源并未形成明显的地理变异模式 ,而且欧洲的种源和来自原产地的美国种源相比 ,没有发现明显的差异。经过 Hardy-Weinberg平衡检测证明 ,88.4 1%位点符合 H- W遗传平衡 ,表明各群体基因频率和基因型频率保持较高的稳定性 ,且种源内的变异大于种源间变异 ,94 .     

Identification of Bactrian camel cell lines using genetic markers

Iranian Bactrian camel population is less than 100 animals. Iranian biological resource center produced more than 50 Bactrian camel fibroblast cell lines as a somatic cell bank for conservation animal genetic resources. We compared two type markers performance, including 14 random amplified polymorphic DNA (RAPDs) (dominant) and eight microsatellite (co-dominant) for cell line identification, individual identification and investigation genetic structure of these samples. Based on clarity, polymorphism, and repeatability, four RAPD primers were selected for future analysis. Four RAPD primers and eight microsatellite markers have generated a total of 21 fragments and 45 alleles, respectively. RAPD primers revealed fragment size between 150 to 2000 bp and gene diversity since 0.27 (IBRD) to 0.46 (GC10), with an average of 0.37. Microsatellite markers generated number of alleles per locus ranged from 3 to 11, with an average of 5.62 alleles. The observed heterozygosity ranged from 0.359 (IBRC02) to 0.978 (YWLL08), and expected heterozygosity ranged from 0.449 (IBRC02) to 0.879 (YWLL08). Bottleneck analysis and curve showed that Bactrian camel population did not experience a low diversity. RAPD profiles were especially suitable for investigation population genetics. All primers generated novel and polymorphic fragments. Briefly, our results show that a multiplex PCR based on these markers can still be valuable and suitable for authentication of cell lines, investigating gene diversity and conservation genetic resources in Bactrian camel, while new technologies are continuously developed.     

西南地区麻疯树天然种群遗传多样性的等位酶变异

为了揭示麻疯树(Jatropha curcas)天然种群的遗传多样性和遗传结构, 采用聚苯烯酰胺凝胶垂直平板电泳技术, 对采自四川、云南、贵州3个省的10个麻疯树天然种群的叶片样本进行了同工酶分析。7个酶系统10个位点的检测结果表明: 麻疯树种群水平上的遗传多样性较高, 每位点平均等位基因数为2.428 6, 多态位点百分率为97.14%, 平均期望杂合度为0.396 4。种群间遗传分化系数为0.041 3, 种群间总的基因流较高, 为5.808 9, 种群间遗传一致度较高(Shannon信息指数为0.921 7- 0.995 3)。非加权类平均法(UPGMA)聚类结果显示, 10个种群的遗传距离与地理距离相关性不显著。麻疯树天然种群具有较低程度的遗传分化、较高的基因流, 种内及种群内多样性丰富, 这为麻疯树优良品种的选育提供了良好的遗传基础。     

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (<Emphasis Type="Italic">Oryza rufipogon</Emphasis> Griff.) in China

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.     

利用SSR分子标记分析秦岭冷杉自然居群的遗传多样性

利用10对SSR引物对濒危植物秦岭冷杉(Abies chensiensis)6个自然居群的120个个体进行了遗传多样性研究,旨在分析秦岭冷杉6个自然居群的遗传多样性、遗传结构及基因流变化.研究结果表明,120个个体在10个位点上共检测到149个等位基因,平均每个位点的等位基因数(A)为14.9,每个位点的有效等位基因数(e)为7.7,每个位点的平均预期杂合度(He)和平均观察杂合度(Ho)分别为0.841和0.243,Shannon多样性指数(Ⅰ)为2.13,自然居群杂合性基因多样度的比率(FsT)为6.7％,居群间的基因流(Nm)为3.45.利用Mantel检测到自然居群的遗传距离与地理距离间无显著相关性(r=0.490 6,P＞0.05).秦岭冷杉自然居群的遗传多样性水平较低,遗传变异主要存在于居群内部.结合研究数据、实地调查及相关资料,推测秦岭冷杉自然居群间基因流较原来增大可能是因为居群间发生了远交衰退.