A new framework marker-based linkage map and SDPs for the Rat HXB/BXH strain set

A new contiguous genetic linkage map of the HXB/BXH set of rat recombinant inbred (RI) strains was constructed to enhance QTL mapping power and precision, and thereby make the RI strain set a better genomics resource. The HXB/BXH rat RI strains were developed from a cross between the hypertensive SHR/OlaIpcv and normotensive BN-Lx/Cub rat strains and have been shown useful for identifying quantitative trait loci (QTL) for a variety of cardiovascular, metabolic, and behavioral phenotypes. In the current analysis, the DNAs from 31 existing strains, 1 substrain, and 4 extinct strains were genotyped for a selection of polymorphic microsatellite marker loci, predominantly polymorphic framework markers from high-density integrated rat genome maps. The resulting linkage map consists of 245 microsatellite markers spanning a total length of 1789 cM with an average inter-marker distance of ~8.0 cM. This map covers the rat genome contiguously and completely with the exception of two locations on Chromosomes (Chrs) 11 and 16. The new genotypic information obtained also permitted further genetic characterization of the RI strain set including strain independence, genetic similarity among the individual strains, and non-syntenic associations between loci.     

微卫星DNA标记在近交系大鼠HFJ和MIJ遗传监测中的应用

目的 用24对引物对近交系HFJ和MIJ大鼠的微卫星位点进行多态性分析,并选用近交系Lewis和F344大鼠作为对照,进行比较分析.方法 用传统的酚-氯仿法分别提取4个近交系大鼠MIJ、HFJ、Lewis和F344 的基因组DNA,选取大鼠24个微卫星位点,通过PCR扩增,扩增产物经过非变性聚丙烯酰胺凝胶电泳和银染,根据电泳结果,比较分析4种品系近交系大鼠之间微卫星多态性.结果 4种品系及品系内不同个体的近交系大鼠在24个微卫星位点上的扩增产物均出现一个条带,MIJ和HFJ大鼠在品系间和品系内均表现为单态性,同Lewis 和F344的扩增结果比较,14个位点显示多态性,有10个位点显示单态性.结论 两个近交系大鼠品系MIJ和HFJ符合近交系要求,筛选出的14个多态性微卫星位点可用于有关近交系大鼠的遗传背景监测.     

三个近交系C57BL/6J小鼠群体微卫星遗传变异分析(英文）

应用微卫星遗传标记对近交系C57BL/6J(B6)小鼠遗传稳定性进行分析。用FAM标记的引物PCR扩增了来自北京和上海三个实验动物生产单位提供的三个B6小鼠群体共15个微卫星位点并进行分型。结果显示,所有位点均处于纯合状态,其中7个位点为多态位点。研究表明各B6群体虽然为高度近交群体,但不同生产单位维持的B6群体之间存在遗传分化。     

羊肚菌不同单孢及不同萌发孔菌丝间的遗传多样性

本研究对来自不同单孢和不同萌发孔菌丝的166份羊肚菌菌株进行形态研究、交配型基因检测、基于ISSR的遗传多样性分析和菌株杂交选育。结果表明,来自不同单孢及其不同萌发孔菌丝培养的菌株间均存在不同程度的形态和遗传差异。4条ISSR引物共扩增出条带清晰的22条多态性谱带,多态性比率为88%。基于遗传相似性系数（GS）、不加权成对群算术平均法（UPGMA）构建的系统树,可将供试菌株分为梯棱羊肚菌Morchella importuna和六妹羊肚菌M. sextelata两大类群。聚类分析发现不同物种间的单孢菌株和单丝菌株的遗传差异显著;同一单孢不同萌发孔菌丝的菌株间存在较大的遗传分化,遗传多样性丰富。交配型基因检测证实羊肚菌是异宗结合型真菌,同一单孢的不同萌发孔菌丝体含相同的交配型基因（MAT 1-1-1或MAT 1-2-1）。遗传多样性结果表明：梯棱羊肚菌比六妹羊肚菌的遗传背景更广泛。此外,ISSR分子标记也表明仅依靠菌丝和菌核的形态特征并不能准确衡量羊肚菌菌株间的亲缘关系。研究羊肚菌单孢菌株、单丝菌株间的形态和遗传特征,将为羊肚菌优质菌种的精准选育提供理论参考。     

AFLP analysis for examining genetic differences in cultivated strains and their single-spore isolates and for confirming successful crosses in <Emphasis Type="Italic">Agaricus blazei</Emphasis>

Amplified fragment length polymorphism (AFLP) analysis was used to examine genetic differences in Agaricus blazei cultivated strains and their single-spore isolates (SSIs). AFLP analysis with five primer combinations identified a total of 267 AFLP bands from nine cultivated strains (one from Brazil and eight from Japan), of which 165 were polymorphic between the nine strains. An AFLP data dendrogram grouped the eight Japanese strains, with the Brazilian strain acting as an outlier, suggesting that the Brazilian and Japanese strains are genetically quite different. Twelve SSIs derived from each of four cultivated strains were subjected to AFLP analysis. All the AFLP bands detected in the cultivated strains were also found in at least one SSI, but some unique bands were detected in SSIs. The total number of AFLP bands from individual SSIs was clearly less than those from their parental strains, and many of polymorphic AFLP bands from the parental strains segregated in SSIs at a ratio of 1 : 1, suggesting that the SSIs are homokaryotic. Distance values based on presence or absence of individual AFLP bands among SSIs from different strains were clearly higher than those among SSIs from a single strain. In addition, AFLP analysis was shown to be useful in confirming hybrid formation in crosses between SSIs.     

Genetic analysis of Helicobacter pylori strain populations colonizing the stomach at different times postinfection

Genetic diversity of the human gastric pathogen Helicobacter pylori in an individual host has been observed; whether this diversity represents diversification of a founding strain or a mixed infection with distinct strain populations is not clear. To examine this issue, we analyzed multiple single-colony isolates from two to four separate stomach biopsies of eight adult and four pediatric patients from a high-incidence Mexican population. Eleven of the 12 patients contained isolates with identical random amplified polymorphic DNA, amplified fragment length polymorphism, and vacA allele molecular footprints, whereas a single adult patient had two distinct profiles. Comparative genomic hybridization using whole-genome microarrays (array CGH) revealed variation in 24 to 67 genes in isolates from patients with similar molecular footprints. The one patient with distinct profiles contained two strain populations differing at 113 gene loci, including the cag pathogenicity island virulence genes. The two strain populations in this single host had different spatial distributions in the stomach and exhibited very limited genetic exchange. The total genetic divergence and pairwise genetic divergence between isolates from adults and isolates from children were not statistically different. We also analyzed isolates obtained 15 and 90 days after experimental infection of humans and found no evidence of genetic divergence, indicating that transmission to a new host does not induce rapid genetic changes in the bacterial population in the human stomach. Our data suggest that humans are infected with a population of closely related strains that vary at a small number of gene loci, that this population of strains may already be present when an infection is acquired, and that even during superinfection genetic exchange among distinct strains is rare.     

瓜类枯萎病菌遗传多样性和亲缘关系的SRAP分析

尖孢镰刀菌可造成不同瓜类的枯萎病.为明确不同寄主、不同地区的瓜类枯萎病菌菌株间的遗传多样性及亲缘关系,采用相关序列扩增多态性(SRAP)分子标记技术,对来源于不同地区、不同寄主的95株尖孢镰刀菌的基因组DNA进行多态性扩增.以筛选出的19对引物共扩增出238条带,多态性比率为100%,平均每对引物扩增出12.5个位点和12.5个多态性位点;尖孢镰刀菌苦瓜专化型共扩增出166条带,其中145条为多态性条带,多态性比率为87.4%,平均每对引物扩增出8.7个位点和7.7个多态性位点,说明尖孢镰刀菌的遗传变异较为广泛.瓜类枯萎病菌株间的遗传相似系数范围为0.68～0.99,样品间的平均Nei遗传多样性指数和Shannon指数分别为0.2390和0.3718.在遗传相似系数为0.74时,可将供试的95株尖孢镰刀菌划分为苦瓜、黄瓜、西瓜、甜瓜4个专化群.在SRAP聚类树中,同一寄主的尖孢镰刀菌聚在一个分支上,其中尖孢镰刀菌苦瓜专化型菌株间的遗传相似系数范围为0.78～0.99,Nei遗传多样性指数为0.1811,平均Shannon指数为0.2750,表明尖孢镰刀菌苦瓜专化型的遗传变异较大,且菌株的聚群与地理来源存在相关性.     

茯苓种质资源的RAPD分析

为探讨国内茯苓人工栽培的主要品种和贵州野生茯苓菌株亲缘关系,利用RAPD技术对供试菌株的基因组DNA进行了分析。从41个随机引物中筛选出17个有效引物,共检测到101个RAPD标记位点,其中39个位点(38.6%)具有多态性,通过PAUP软件进行数据处理,采用最大简约法(MP法)进行聚类分析,并建立系统树。结果表明:不同来源的茯苓菌株亲缘关系非常相近,仅在某些引物的扩增物上存在较小的差异。     

A genetic analysis of the London strain of rainbow trout

The London strain of rainbow trout (Oncorhynchus mykiss) was created by interbreeding three other strains of rainbow trout and therefore was expected to have higher levels of genetic variation than other strains of rainbow trout. We examined 129 London strain rainbow trout from Indiana by allozyme electrophoresis to assess levels of genetic variation and to examine the relationship between the London strain and other hatchery strains. When using the same loci to compare with other hatchery strains the London strain showed levels of genetic variation within the range of other hatchery strains: mean heterozygosity of 0.053 (0.031-0.099), 1.27 (1.20-1.60) alleles per locus and 20.0% (20.0-40.0%) of the loci were polymorphic. The London strain is somewhat distinct from other hatchery strains (D=0.009-0.072), in part because of the high frequency of the sIDHP*40 allele.     

Heritability of flight distance for Cydia pomonella

Cydia pomonella L. (Lepidoptera: Tortricidae) is considered to be rather sedentary, but some individuals undertake flights of several kilometres in the field. This paper investigates the genetic influence on this variability. The flight capacity was measured in the laboratory by a flight mill and its heritability was estimated for two different strains. The laboratory strain was kept for more than 45 generations and the field strain from Embrach (northern Switzerland) was recently collected in the field.The multiple-trait-restricted-maximum-likelihood method was used for the estimation of genetic variances and covariances. A mixed full-sib/half-sib design was applied for the field strain and a full-sib design for the laboratory strain. The heritability of total distance was 0.57 for the field strain and 0.37 for the laboratory strain (both sexes). In addition, a heritability of 0.38 for total distance was estimated by parent-offspring regression for the laboratory strain. All three values were significantly different from zero P<0.05 and show that there is a significant additive genetic influence on flight capacity.The genetic correlations between total distance and other flight traits (total duration, flight velocity, longest flight) were between 0.84 and 1.00 for both strains and suggest that these traits actually belong to a single one. High genetic correlations were also found between total distance and the morphological traits body weight and wing length for the field strain, whereas a negative correlation was found between total flight distance and body weight for the laboratory strain. This difference between the two strains was interpreted as a possible trade-off between flight capacity and fecundity.     

Application of SNPs for assessing biodiversity and phylogeny among yeast strains

We examined the efficacy of single-nucleotide polymorphism (SNP) markers for the assessment of the phylogeny and biodiversity of Saccharomyces strains. Each of 32 Saccharomyces cerevisiae strains was genotyped at 30 SNP loci discovered by sequence alignment of the S. cerevisiae laboratory strain SK1 to the database sequence of strain S288c. In total, 10 SNPs were selected from each of the following three categories: promoter regions, nonsynonymous and synonymous sites (in open reading frames). The strains in this study included 11 haploid laboratory strains used for genetic studies and 21 diploids. Three non-cerevisiae species of Saccharomyces (sensu stricto) were used as an out-group. A Bayesian clustering-algorithm, Structure, effectively identified four different strain groups: laboratory, wine, other diploids and the non-cerevisiae species. Analysing haploid and diploid strains together caused problems for phylogeny reconstruction, but not for the clustering produced by Structure. The ascertainment bias introduced by the SNP discovery method caused difficulty in the phylogenetic analysis; alternative options are proposed. A smaller data set, comprising only the nine most polymorphic loci, was sufficient to obtain most features of the results.     

Interspecific hybridization and genetic variability of Phlebotomus sandflies

The first successful hybridization is reported between Phlebotomus papatasi and P. duboscqi, two important Old World sandfly vectors of leishmaniasis and other diseases. Laboratory strains of P. papatasi and P. duboscqi were separable by six diagnostic enzyme loci: Est-3, Idh-1, Mdh-2, Mpi, Tre-1 and Tre-3. Hybrids between the two species were verified by the recovery of heterozygous isozyme patterns for the diagnostic loci. No F2 or backcross progeny were obtained. P. papatasi was separated from P. bergeroti by three diagnostic enzyme loci: Est-3, Mpi and Pgd. The isozyme patterns of P. bergeroti contain elements of both P. duboscqi and P. papatasi, although seven diagnostic loci (Est-3, Idh-1, Me, Mpi, Pgd, Tre-1 and Tre-3) separated P. bergeroti from P. duboscqi. Genetic variability profiles of the three species were established for 20 enzyme loci. Three geographically distant strains of P. papatasi from Calcutta, Maharashtra and Israel had isozyme genetic distances of < 0.05. The recently established Calcutta strain showed an unexpectedly low genetic variability with only one (Idh-2) of 20 loci being polymorphic (average heterozygosity of 1.9%) in contrast to 5-8 polymorphic loci (10-12% heterozygosity) in the Maharashtra and Israel strains. Mass and single pair crosses between the three P. papatasi strains were fertile with normal progeny numbers. Thus we found no signs of speciation in P. papatasi.     

Microsatellite DNA variation in wild populations and farmed strains of turbot from Ireland and Norway: a preliminary study

Turbot Scophthalmus maximus is the focus of a rapidly expanding aquaculture industry, while at the same time wild catches appear to be in decline. As a preliminary investigation into the effects of hatchery rearing, genetic variation at three polymorphic microsatellite loci was assessed in two wild populations and two farmed strains of turbot, from Ireland and Norway. Although a considerable loss of rare alleles was observed in the Irish farmed strain, no statistically significant reductions were found in mean heterozygosity or allelic diversity in farmed strains compared to wild populations. Significant genetic heterogeneity was found between wild and farmed samples from each country but not between the two wild populations. Genetic differentiation between the farmed strains was presumed to be caused by drift in the hatcheries. The utility of these particular microsatellite loci in comparing these samples and the importance of molecular genetic testing of farmed strains is stressed.     

微卫星标记对WHBE兔封闭群、日本大耳白兔和新西兰兔的遗传分析

目的分析比较大耳白黑眼兔（WHBE兔）封闭群与日本大耳白兔（Jw兔）、新西兰兔（NZW兔）基因组存在的微卫星结构,研究WHBE兔封闭群的微卫星多态性。方法利用21个微卫星位点,通过微卫星分子标记技术对WHBE兔封闭群、Jw兔和NZW兔进行遗传多样性检测和对比。结果根据初步结果,在21对微卫星引物中筛选出扩增产物稳定并且具有多态性的11对引物。WHBE兔封闭群在每个位点上的等位基因数为3～8个不等,11个位点的平均有效等位基因数为2．0402个,平均杂合度为0．4810;Jw兔在每个位点上的等位基因数为2～8个不等,11个位点的平均有效等位基因数为3．6077个,平均杂合度为0．5039;NZW兔在每个位点上的等位基因数为3～9个不等,11个位点的平均有效等位基因数为2．6537个,平均杂合度为0．5334。WHBE兔封闭群在11个微卫星位点上的平均多态信息含量（PIC）为0．6005,多位点累积个体识别率达到100％,多位点累积非父排除概率（CPE）在双亲信息都是未知情况下的为0．9613,而在得知任一亲本信息的情况下,CPE值高达0．9973。在11个微卫星座位中,9个位点上出现了WHBE兔封闭群特有等位基因,其中在Sat2、Sat5、Sat7、Sat12、Sat13、Sat16、S0144和INRACCDDV0003八个位点上WHBE兔封闭群的特有等位基因为一个,在sat8位点上为两个。结论WHBE兔8个位点的平均杂合度、平均有效等位基因数均比JW兔及NZW兔低,说明WHBE兔群体的基因纯合度高于其他两个品系,具有更优的遗传稳定性。9个WHBE兔特有的等位基因可作为区分WHBE兔封闭群和其它两个品系实验兔的分子标记。     

Microsatellite loci for genetic mapping in the turkey (Meleagris gallopavo)

New microsatellite loci for the turkey (Meleagris gallopavo) were developed from two small insert DNA libraries. Polymorphism at these new loci was examined in domestic birds and two resource populations designed for genetic linkage mapping. The majority of loci (152 of 168) was polymorphic in domestic turkeys and informative in two mapping resource populations and thus will be useful for genetic linkage mapping.     

Development of microsatellite markers for the bracken fern, Pteridium aquilinum

We isolated eight novel polymorphic microsatellite loci from Pteridium aquilinum. These loci were characterized in 30 individuals, one from Bolivia, two from Peru, one from the USA, one from Japan, and 25 from Northeast China to Southwest China. The number of alleles per locus ranged from two to seven. The observed heterozygosity (H(O) ) ranged from 0.000 to 0.600 with an average of 0.3051, and the expected heterozygosity (H(E) ) ranged from 0.0966 to 0.7780 with an average of 0.4267. One locus deviated from Hardy-Weinberg equilibrium and four pairs of loci were found to be in linkage disequilibrium. These polymorphic loci will be useful in the study of the population genetic structure of Pteridium.     

Isolation and characterization of 16 novel microsatellite loci in two inbred strains of the Chinese hamster (Cricetulus griseus)

The Shanyi inbred A and E strains of the Chinese hamster are widely used in biomedical research, but detailed genetic characterization has been lacking. We developed microsatellite markers that could be used for genetic diversity analysis and linkage map construction. We isolated and characterized 16 novel microsatellite loci from a microsatellite-enriched genomic DNA library. These loci were genotyped in 48 animals from the two strains, and the polymorphic information content was determined. In the Shanyi A and E populations, 14 and 15 loci were found to be polymorphic, respectively, with polymorphic information content ranging from 0.1393 to 0.8082 and from 0.1109 to 0.7397, respectively. A total of 115 alleles were found for the 16 microsatellite loci in the two populations; the mean observed heterozygosity (H(O)) was 0.5191 and 0.4333 for the A and E populations, respectively, indicating marked genetic variation within the two populations. Correspondingly, the F(ST) values ranged from 0.002 to 0.9253, with an overall mean of 0.1935, indicating significant genetic difference between the two strains. The population differentiation levels were substantiated by Nei's genetic distance and full Bayesian analyses computed with STRUCTURE. Despite the genetic diversity and differentiation within and between the two inbred populations, the 48 individuals were correctly allocated into their original populations with high statistical confidence based on these 16 microsatellite loci. These novel microsatellite loci should be useful genetic markers for these two Chinese hamster inbred strains.     

Genetic differentiation among common and selected hatchery populations of flounder: Evidence from RAPD markers

Randomly amplified polymorphism DNA (RAPD) analysis was performed in order to evaluate one common population and two selected hatchery populations of flounder Paralichthys olivaceus. A total of 90 individuals belonging to three populations were screened using 12 different RAPD primers. A total of 71 loci were produced in the three studied populations, and 43.5%, 42.4% and 42.2% of these loci were polymorphic over all the genotypes tested in common, susceptible and resistant populations, respectively. The number of loci detected by single primers ranged from four to eight. The average heterozygosites of common, susceptible and resistant populations were 0.112, 0.103 and 0.111, respectively. Compared with the common population, the two selected hatchery populations, susceptible and resistant, showed some genetic differences including a smaller number of loci, a smaller number of polymorphic loci, a smaller number of genotypes and a smaller Shannon index. The present study confirmed that it is important to detect the genetic variability of the selected hatchery population for the conservation of natural flounder resources.     

Allozyme genetics in permanent translocation heterozygotes of the Oenothera biennis complex

Allozyme inheritance and transmission genetics of 11 enzyme systems were determined in the permanent translocation heterozygotes Oenothera biennis, Oe. strigosa, and Oe. parviflora. Electrophoretic variation was examined first among 164 strains of structural heterozygotes. Allelic configurations were then judged from inheritance patterns in reciprocal F1 hybrids between each of 22 ring-forming strains and tester strains of the related bivalent-formers, Oe. hookeri and Oe. grandiflora. Allozymes are inherited as codominant markers, and, as dictated by the genetic system, within a strain individual allelic variants are generally transmitted through only one germ line. Of the 20 loci resolved, only eight are polymorphic in any species, and, within species, generally only two alleles are present at each polymorphic locus. Despite the relatively meager allelic array, each of the 22 strains whose chromosome complexes were characterized is genotypically unique. Generally, within taxa, alpha (egg) and beta (sperm) complexes differ in allele frequency at several polymorphic loci. Such variability is correlated with differences in the phylogenetic origins of complexes and not with differences in segmental arrangement within a group of related complexes.     

草鱼基因组DNA一些RAPD位点的遗传分析及分子标记筛选

RAPD技术的实验结果很容易因实验条件和反应参数的不同而造成差异。为了建立能通用的草鱼基因组多态性分析RAPD分子标记体系,需要利用RAPD位点按照孟德尔共显性规律遗传的特点,用不同遗传背景的材料对多态性的RAPD位点进行统计遗传学比较分析以判断其真实性。为此,本实验选择具有遗传多态性的湘江流域草鱼群体和经连续两代人工诱导雌核发育获得的雌核发育草鱼品系,对一些可能作为草鱼基因组DNA分子标记的RAPD位点进行了遗传学比较分析。所用的10条多态性随机引物共检测到30个多态性RAPD位点。两个不同遗传背景群体的遗传统计对比分析结果表明:这30个多态位性位点在湘江流域草鱼群体和雌核发育草鱼群体中的分布符合孟德尔遗传规律,可以作为草鱼基因组DNA分析的可靠分子标记。本实验的观察结果还表明:在人工诱导雌核发育过程中,存在RAPD位点的快速丢失现象,两次人工诱导雌核发育过程中共丢失了17个多态性位点。因此,加强对自然水体中草鱼种质资源多样性的保护和利用各种现代生物学技术纯化、筛选和组合优良性状基因,是草鱼遗传育种中同样重要和不可或缺的两个方面。