天女木兰遗传多样性微卫星标记的研究

以中国7个省份9个天女木兰种群为研究对象,采用微卫星技术(SSR)探讨天女木兰分子遗传多样性。结果显示:(1)9个天女木兰种群间存在较低的遗传多样性,种群平均Nei基因多样性指数(H)0.098 5,平均Shannon信息指数(I)0.146 8;种群间基因流为0.597 9(1),处于很低的水平。(2)天女木兰不同种群在长期进化过程中发生了一定的遗传分化,9个天女木兰种群的遗传距离为0.068 8~0.214 2,遗传相似度介于0.82~0.93之间。(3)聚类分析结果显示,9个天女木兰种群在进化上形成2个主要分枝,贵州麻江种群为一支,其他地区的种群为另一支,其中贵州麻江的天女木兰生存状况较差。(4)天女木兰的遗传多样性与种群分布的经度呈正相关。研究表明,天女木兰种群间的遗传多样性低,缺乏基因交流,可能是导致其濒危的主要遗传学机制。     

亚历山大藻属微卫星标记的筛选

采用生物信息学方法,从塔玛亚历山大藻的ESTs数据库中筛选微卫星(Simple Sequence Repeat, SSR)位点,设计SSR引物,利用毛细管电泳对4株塔玛亚历山大藻(Alexandrium tamarense)、2株相关亚历山大藻(Alexandrium affine)和1株链状亚历山大藻(Alexandrium catenella)进行种内、种间遗传多样性分析,获得以下主要结果:(1)从6830条非冗余的ESTs中共查找到222个SSR,平均每18.5kb就有一个SSR,三核苷酸重复在所有的重复类型中所占比例最大,达到48.2%,重复单元CTG/CAG出现频率最高.进一步筛选出12条SSR引物,用于遗传多样性分析.(2)种内遗传多样性水平整体偏低,多态性引物比率仅为41 67%,Nei's基因多样性平均为0.2130.种间遗传多样性水平较高,多态性引物比率为75%,Nei's基因多样性平均水平为0 4643;另外,种间遗传分化系数较高,平均水平为0.7051.(3)对7个样品的聚类图分析发现,A. tamarense CCMP116 与A. affine CCMP112遗传距离极为接近;A. tamarense ATHK9301、CCMP1598和ATDH01相互聚在一起;A. catenella ACDH01与A. tamarense分属两枝.以上结果表明,SSR标记在亚历山大藻种内遗传多样性分析方面是一种非常有用的工具.     

基于微卫星标记的中国东北地区灰飞虱遗传变异及种群遗传结构分析

【目的】本研究旨在明确我国东北地区灰飞虱Laodelphax striatellus种群遗传变异及种群遗传结构,阐明种群间遗传分化与基因流。【方法】利用9对微卫星引物对采自我国东北地区15个地理种群的375头灰飞虱样品进行测序与分析;利用GeneAlex6.51,GENEPOP4.0.9和STRUCTURE 2.3.4等软件分析灰飞虱地理种群间的遗传多样性、遗传分化、基因流及种群遗传结构。【结果】在所分析的375头灰飞虱个体中,各位点平均有效等位基因数Na=6.898;总体上,灰飞虱不同地理种群遗传多样性较高(平均观测杂合度Ho=0.548;平均期望杂合度He=0.582),各种群间基因流较低(Nm=0.660)。UPGMA聚类树、PCoA及STRCTURE分析结果表明,东北地区灰飞虱种群分为两分支:吉林(JL)和沈阳(SY2012,SY2013和SY2014)种群聚为一支;其余种群聚为一支。AMOVA分析结果表明,灰飞虱遗传变异主要来自种群内(87%),种群间变异水平较低(13%)。【结论】中国东北地区灰飞虱遗传多样性较高,不同地理种群存在一定程度的遗传分化,且基因交流较低,存在一定的种群遗传结构。     

利用ISSR标记分析红脂大小蠹微生境中球孢白僵菌遗传多样性

针对红脂大小蠹危害程度不同的3个地区的球孢白僵菌种群,利用ISSR（inter-simple sequence repeat）分子标记分析了各个种群的遗传多样性。从19条引物中筛选出10条多态性高、稳定性好的ISSR引物用于扩增分析。68株球孢白僵菌的Nei’s基因多样性（h）为0.2973,Shannon指数（Is）为0.4488。旬邑、宜君、古交3地白僵菌种群间的基因分化系数（GST）为0.0525,基因流（Nm）为9.0255;而来源于土壤、红脂大小蠹、蛀屑和树皮的白僵菌种群间的基因分化系数为0.1449,基因流为2.9508。各球孢白僵菌种群表现出不同的多样性水平,旬邑种群和红脂大小蠹虫种群的遗传多样性相对较高;地理分布种群间的差异不如分离基质种群间的差异明显,地理分布种群间存在明显的基因交流,而分离基质种群间的基因流较低,遗传分化明显。     

中国桔小实蝇种群的微卫星多态性分析

为了研究桔小实蝇种群的遗传结构,本文采用微卫星分子标记技术,对中国南方9省区、越南和泰国的11个桔小实蝇地理种群共224个个体的遗传多样性水平及种群遗传结构进行了研究。用9对微卫星引物共检测到48个等位基因, 平均每个微卫星位点的等位基因数为5.33个。GENEPOP分析结果表明：11个桔小实蝇种群在9个微卫星位点上的多态位点百分率平均为94.45%。种群的Nei's基因多样性指数平均为0.4371,Shannon信息指数平均为0.7870,表明桔小实蝇种群具有非常丰富的遗传多样性。Nei's遗传多样性分析发现,各地理种群间产生了一定程度的遗传分化,种群间平均遗传分化系数F_st=0.2370。种群间一定程度的遗传分化可能是由地理隔离和基因流障碍（N_em = 0.8049）所引起。UPGMA聚类分析可知, 中国的桔小实蝇地理种群可分为华南支和西南支两大分支,华南分支包括福建、台湾、广东和海南4个种群,西南分支包括四川、云南、广西、贵州和湖南5个种群。由此推测, 中国桔小实蝇种群结构的形成与演变是在地理演化与经贸交流加强这两种因素的影响下不断进行的动态过程。     

内蒙古扁蓿豆遗传多样性的ISSR分析

应用ISSR分子标记对分布于内蒙古不同地区的扁蓿豆(Medicago ruthenica)8个地理种群进行了遗传多样性研究.结果表明:扁蓿豆具有较高的遗传多样性;15个引物共扩增出363个位点,物种水平上Nei s基因多样性指数为0.198 9,Shannon多样性指数为0.303 7;种内总基因多样性为0.308 6,种群内基因多样性为0.198 9,64.45%的遗传变异存在于种群内,35.55%的遗传变异存在于种群间,种群间的遗传分化系数为0.355 5,基因流为0.906 4,8个种群间基因交流较少,遗传分化较强.UPGMA遗传距离聚类结果表明,生态地理条件相似的种群优先聚集.     

蒙古沙葱萤叶甲种群遗传多样性的微卫星分析

【目的】沙葱萤叶甲 Galeruca daurica (Joannis)是一种近年来在内蒙古草原上猖獗成灾的新害虫,本研究旨在明确内蒙古沙葱萤叶甲不同地理种群间的遗传分化和基因交流程度。【方法】应用5对微卫星引物分析了沙葱萤叶甲8个地理种群的遗传多样性、基因流和遗传分化。【结果】5个位点等位基因数为10~18,有效等位基因数为9.2796~16.0388,多态信息含量值为0.6760~0.8985,期望杂合度为0.3430~0.5284,说明所选5个微卫星位点均为高度多态性位点。8个种群的期望杂合度为0.2216~0.3701,平均值为0.2680;种群间遗传分化系数为0.1244~0.4116,平均值为0.2521;种群间基因流为0.3574~1.7596,平均值为0.9622。8个地理种群根据遗传距离聚为3个分支,遗传距离与地理距离呈显著的正相关关系 (r=0.4854,P=0.0180)。【结论】沙葱萤叶甲种群遗传多样性低,不同地理种群之间基因流较小,遗传分化程度高;沙葱萤叶甲迁移能力弱和地理阻碍可能是限制其基因交流和导致遗传高度分化的主要原因。     

内蒙古沙葱萤叶甲种群遗传多样性的微卫星分析

【目的】沙葱萤叶甲Galeruca daurica(Joannis)是一种近年来在内蒙古草原上猖獗成灾的新害虫,本研究旨在明确内蒙古沙葱萤叶甲不同地理种群间的遗传分化和基因交流程度。【方法】应用5对微卫星引物分析了沙葱萤叶甲8个地理种群的遗传多样性、基因流和遗传分化。【结果】5个位点等位基因数为10~18,有效等位基因数为9.2796~16.0388,多态信息含量值为0.6760~0.8985,期望杂合度为0.3430~0.5284,说明所选5个微卫星位点均为高度多态性位点。8个种群的期望杂合度为0.2216~0.3701,平均值为0.2680;种群间遗传分化系数为0.1244~0.4116,平均值为0.2521;种群间基因流为0.3574~1.7596,平均值为0.9622。8个地理种群根据遗传距离聚为3个分支,遗传距离与地理距离呈显著的正相关关系(r=0.4854,P=0.0180)。【结论】沙葱萤叶甲种群遗传多样性低,不同地理种群之间基因流较小,遗传分化程度高;沙葱萤叶甲迁移能力弱和地理阻碍可能是限制其基因交流和导致遗传高度分化的主要原因。     

保护生物学中若干术语的理解和辨析(2)

7 Gene Flow（基因流）、Genetic Drift（遗传漂变）和Gene Fixation（基因固定） GeneFlow（基因流,也写作基因流动）,是指由于迁移和杂交等原因导致一个种群的基因进人到另一个种群（同种或不同种）的基因库,使接受者的基因频率发生改变。其他种群基因的流人可以直接改变种群原有的基因频率,影响遗传结构,并使基因交流频繁的种群间在遗传上趋于一致。基因流可以使具有不同等位基因的种群间产生新的遗传组合;不同品种间的基因交流可能形成新种。而且这些新的基因组合也可能具有更强的生存力和适应力,从而在进化上起到很大作用。但事实上,即使种群间有相当多的基因流,由于强有力的选择,种群间仍然会存在一定的遗传分化,并保持各自的属性。     

濒危植物翅果油树种群的遗传多样性和遗传分化研究

利用微卫星（SSR）标记对来自山西和陕西两省的7个翅果油树（Elaeagnus mollisDiels）种群进行遗传多样性和遗传结构研究。10对SSR标记共检测到126个位点,其中多态位点114个。在物种水平上,平均多态位点百分率为90.79%,有效等位基因数（Ne）、Nei基因多样性指数（H）和Shannon多样性指数（I）分别为1.6072、0.3166、0.4603;在种群水平上,多态位点百分率为61.99%,有效等位基因数（Ne）、Nei’s基因多样性指数（H）、Shannon多样性指数（I）分别为1.5445、0.2683、0.3815。遗传分化系数GST为0.2074,表明了翅果油树种群的遗传变异主要存在于种群内。基因流Nm为1.9111〉1,说明种群间基因交流可以阻止由于遗传漂变导致的遗传分化。聚类结果表明,翅果油树种群间的遗传距离与地理距离有一定的相关性,经Mantel检验,种群的地理距离与遗传距离之间呈正相关,但未达到显著水平（p〉0.05）。结果表明,遗传多样性水平与物种本身特性和不同干扰生境有关,濒危植物并不一定表现为遗传变异水平的降低。     

Differentiation and phylogenetic relationship among different cultivars of asparagus bean (Vigna unguiculata ssp. sesquipedalis) assessed using ISSR markers

Asparagus bean, one of the three subspecies of Vigna unguiculata, has a long cultivation history in China. The genetic diversity was analyzed based on the 66 landraces and cultivars cultivated in China by using ISSR molecular markers, with which 192 amplification loci were obtained 32.3% of them being polymorphic. The genetic differentiation analysis revealed a very high genetic diversity in the Chinese landraces, which confirmed that China is the secondary origin centre of the asparagus bean. The commercial cultivars bred in China were genetically highly homogenous, suggesting that the breeding process has resulted in disappearance of some of the genetic variation. A cluster analysis at 0.17 of Nei genetic distance divided the 66 landraces and cultivars into 9 groups. Their clustering pattern basically matches the phylogeny of those cultivars, and also corresponds to their geographical origin and morphological traits.     

Evaluation of Genetic Diversity and Population Structure Analysis among Germplasm of Agaricus bisporus by SSR Markers

Agaricus bisporus is a popular edible mushroom that is cultivated worldwide. Due to its secondary homothallic nature, cultivated A. bisporus strains have low genetic diversity, and breeding novel strains is challenging. The aim of this study was to investigate the genetic diversity and population structure of globally collected A. bisporus strains using simple sequence repeat (SSR) markers. Agaricus bisporus strains were divided based on genetic distance-based groups and model-based subpopulations. The major allele frequency (MAF), number of genotypes (NG), number of alleles (NA), observed heterozygosity (HO), expected heterozygosity (HE), and polymorphic information content (PIC) were calculated, and genetic distance, population structure, genetic differentiation, and Hardy–Weinberg equilibrium (HWE) were assessed. Strains were divided into two groups by distance-based analysis and into three subpopulations by model-based analysis. Strains in subpopulations POP A and POP B were included in Group I, and strains in subpopulation POP C were included in Group II. Genetic differentiation between strains was 99%. Marker AB-gSSR-1057 in Group II and subpopulation POP C was confirmed to be in HWE. These results will enhance A. bisporus breeding programs and support the protection of genetic resources.     

Mitochondrial Genetic Variation in Chinese Pigs and Wild Boars

The mitochondrial DNAs (mtDNAs) from 30 pig breeds (29 Chinese native breeds and 1 European breed) and wild boars were investigated for restriction fragment length polymorphisms (RFLPs) to determine the phylogenetic relationships and genetic diversity among pig breeds and wild boars. Of the 24 enzymes used, 8 (AvaI, BclI, BglII, EcoRI, EcoRV, ScaI, StuI, and XbaI) detected polymorphisms. By combining the cleavage patterns for each enzyme, 108 individuals were sorted into eight mtDNA mitotypes. There are two haplotype lineages in domestic pigs, i.e., Chinese and European lineages. The pairwise nucleotide sequence divergence was calculated to be 0.56% between Chinese pigs and European pigs, suggesting that they might have diverged from a common ancestor approximately 280,000 years ago. The wild boars showed more extensive genetic variation, four mitotypes were detected in six wild boars. In addition, one of the Zhejiang wild boars was found to share the same mitotype with Chinese native pigs. A UPGMA tree based on genetic distance among mitotypes indicated that mtDNAs of Chinese pigs and European pigs are clearly divided into two clusters, and Chinese wild boars are more closely related to the Chinese pigs. Our results provide molecular evidence to support the previous hypothesis that pigs may be derived from two maternal origins, Asian and European wild boars. Chinese native pig breeds may have a single origin.     

Origin, genetic diversity, and population structure of Chinese domestic sheep

To characterize the origin, genetic diversity, and phylogeographic structure of Chinese domestic sheep, we here analyzed a 531-bp fragment of mtDNA control region of 449 Chinese autochthonous sheep from 19 breeds/populations from 13 geographic regions, together with previously reported 44 sequences from Chinese indigenous sheep. Phylogenetic analysis showed that all three previously defined lineages A, B, and C were found in all sampled Chinese sheep populations, except for the absence of lineage C in four populations. Network profiles revealed that the lineages B and C displayed a star-like phylogeny with the founder haplotype in the centre, and that two star-like subclades with two founder haplotypes were identified in lineage A. The pattern of genetic variation in lineage A, together with the divergence time between the two central founder haplotypes suggested that two independent domestication events have occurred in sheep lineage A. Considerable mitochondrial diversity was observed in Chinese sheep. Weak structuring was observed either among Chinese indigenous sheep populations or between Asian and European sheep and this can be attributable to long-term strong gene flow induced by historical human movements. The high levels of intra-population diversity in Chinese sheep and the weak phylogeographic structuring indicated three geographically independent domestication events have occurred and the domestication place was not only confined to the Near East, but also occurred in other regions.     

Genetic diversity and population structure in French populations of Mycosphaerella graminicola

Mycosphaerella graminicola populations were examined in France with microsatellite markers and PCR-SSCP analysis of partial actin and β-tubulin encoding sequences. A total of 363 isolates was sampled in 2005 from 17 provinces, and genotypes from corresponding strains were characterized. Unique haplotypes comprised 84% of the population, and gene diversity was high nationwide (0.70) and locally. A moderate genetic differentiation (G(ST) = 0.18) was found and indicated that in France the M. graminicola population was more structured than in other previously studied European countries. Bayesian structure analysis identified three genetic clusters distributed among the 17 provinces. Our results highlighted the potential for the adaptation of the fungus to local conditions, leading to genetic clusters among the French population of the fungus as well as genotype flow between regional clusters.     

Application of High-Throughput Sequencing to Evaluate the Genetic Diversity Among Wild Apple Species Indigenous to Shandong,China, and Introduced Cultivars

The Taiyi mountainous region of Shandong province in eastern China has an abundance of wild Malus species. We evaluated the genetic diversity of 88 Malus accessions (45 Asian apple cultivars, 10 American apple cultivars, 12 European apple cultivars, 19 Chinese wild apples, and two apple cultivars with unknown origins) based on single-nucleotide polymorphism (SNP) markers. A total of 38,364 SNPs were obtained with an average of 2256 SNPs per chromosome. The average of the polymorphism information content (PIC), gene diversity, and allele frequency for SNPs was 0.268, 0.306, and 0.364, respectively. A circular phylogenetic tree constructed based on SNP data revealed that the 88 Malus accessions could be divided into three groups. However, a population structure analysis suggested the 88 Malus accessions could be divided into four groups. A principal component analysis (PCA) revealed some population stratification. The first three PCs accounted for 41.62% of the population-wide SNP variation, with PC1 accounting for 33.9%. Moreover, the kinship values of the 88 Malus accessions ranged from 0 to 2.36, with 96.42% of the kinship values between 0 and 0.2. A phylogenetic tree and a PCA indicated the Chinese wild apples widely distributed among the cultivated apples had a diverse genetic background. Characterizing the genetic relationships between cultivated apples and Chinese wild apples is essential for increasing the genetic diversity of the germplasms used by apple breeders.

     

中国与欧洲高卢蜜环菌的遗传多样性

高卢蜜环菌(Armillaria gallica)为北半球广布种,不同大陆间的菌株遗传相似性和多样性水平能反映出该种在洲际大陆尺度上的地理遗传变异关系。作者用ISSR(inter-simple sequence repeat)分子标记技术,对从中国和欧洲收集到的高卢蜜环菌79个菌株进行了遗传多样性分析。用6个ISSR引物扩增得到210个位点,其中多态性位点(频率<0.95)为202个,占96.2%,平均每个引物多态位点多达33.6个,表明ISSR标记在蜜环菌中存在较高的多态性。根据非加权类平均法(UPGMA)聚类分析,中国53个菌株中的49个在0.773的相似性水平上聚成了中国类群(China group);而欧洲26个菌株遗传分化较大,分别在0.775和0.763的相似性水平上聚成了欧洲类群A(Europe group A)和B(Europe group B);2个欧洲类群间的相似性水平仅为0.738,而欧洲类群A与中国类群间的相似性却达到了0.770;两个大陆均有少数菌株表现出较为明显的遗传分化,个别菌株的种内遗传相似性甚至低于蜜环菌种间的遗传相似性。结果表明,中欧两个大陆间的A.gallica菌株因地理隔离已经表现出明显的遗传分化,处于异域物种形成过程中;欧洲大陆的菌株遗传分化更为明显,可能是两个大陆A.gallica菌株的起源地。     

Russian ethnic history inferred from mitochondrial DNA diversity

With the aim of gaining insight into the genetic history of the Russians, we have studied mitochondrial DNA diversity among a number of modern Russian populations. Polymorphisms in mtDNA markers (HVS-I and restriction sites of the coding region) of populations from 14 regions within present-day European Russia were investigated. Based on analysis of the mitochondrial gene pool geographic structure, we have identified three different elements in it and a vast "intermediate" zone between them. The analysis of the genetic distances from these elements to the European ethnic groups revealed the main causes of the Russian mitochondrial gene pool differentiation. The investigation of this pattern in historic perspective showed that the structure of the mitochondrial gene pool of the present-day Russians largely conforms to the tribal structure of the medieval Slavs who laid the foundation of modern Russians. Our results indicate that the formation of the genetic diversity currently observed among Russians can be traced to the second half of the first millennium A.D., the time of the colonization of the East European Plain by the Slavic tribes. Patterns of diversity are explained by both the impact of the native population of the East European Plain and by genetic differences among the early Slavs.     

Genetic structure and colonization processes in European populations of the common vole, Microtus arvalis

The level of genetic differentiation within and between evolutionary lineages of the common vole (Microtus arvalis) in Europe was examined by analyzing mitochondrial sequences from the control region (mtDNA) and 12 nuclear microsatellite loci (nucDNA) for 338 voles from 18 populations. The distribution of evolutionary lineages and the affinity of populations to lineages were determined with additional sequence data from the mitochondrial cytochrome b gene. Our analyses demonstrated very high levels of differentiation between populations (overall FST: mtDNA 70%; nucDNA 17%). The affinity of populations to evolutionary lineages was strongly reflected in mtDNA but not in nucDNA variation. Patterns of genetic structure for both markers visualized in synthetic genetic maps suggest a postglacial range expansion of the species into the Alps, as well as a potentially more ancient colonization from the northeast to the southwest of Europe. This expansion is supported by estimates for the divergence times between evolutionary lineages and within the western European lineage, which predate the last glacial maximum (LGM). Furthermore, all measures of genetic diversity within populations increased significantly with longitude and showed a trend toward increase with latitude. We conclude that the detected patterns are difficult to explain only by range expansions from separate LGM refugia close to the Mediterranean. This suggests that some M. arvalis populations persisted during the LGM in suitable habitat further north and that the gradients in genetic diversity may represent traces of a more ancient colonization of Europe by the species.     

Using mitochondrial nucleotide sequences to investigate diversity and genealogical relationships within common carp (Cyprinus carpio L.)

Direct sequencing of mitochondrial DNA (mtDNA) D-loop (745 bp) and MTATPase6/MTATPase8 (857 bp) regions was used to investigate genetic variation within common carp and develop a global genealogy of common carp strains. The D-loop region was more variable than the MTATPase6/MTATPase8 region, but given the wide distribution of carp the overall levels of sequence divergence were low. Levels of haplotype diversity varied widely among countries with Chinese, Indonesian and Vietnamese carp showing the greatest diversity whereas Japanese Koi and European carp had undetectable nucleotide variation. A genealogical analysis supports a close relationship between Vietnamese, Koi and Chinese Color carp strains and to a lesser extent, European carp. Chinese and Indonesian carp strains were the most divergent, and their relationships do not support the evolution of independent Asian and European lineages and current taxonomic treatments.