The Amount of DNA Polymorphism Maintained in a Finite Population When the Neutral Mutation Rate Varies among Sites

The expectations of the average number of nucleotide differences per site (π), the proportion of segregating site (s), the minimum number of mutations per site (s*) and some other quantities were derived under the finite site models with and without rate variation among sites, where the finite site models include Jukes and Cantor's model, the equal-input model and Kimura's model. As a model of rate variation, the gamma distribution was used. The results indicate that if distribution parameter α is small, the effect of rate variation on these quantities are substantial, so that the estimates of θ based on the infinite site model are substantially underestimated, where θ = 4Nv, N is the effective population size and v is the mutation rate per site per generation. New methods for estimating θ are also presented, which are based on the finite site models with and without rate variation. Using these methods, underestimation can be corrected.     

单核苷酸多态性技术在鸡遗传变异中的研究及应用

单核苷酸多态性(SNP)是继限制性片段长度多态性、微卫星标记之后的第三代分子标记,通常呈双等位基因多态。本文从SNP的特点、SNP的发现与检测、SNP数据库、SNP的频率及其与表型的关系等方面简述了SNP在鸡遗传变异中的研究及应用进展。     

拟南芥幼苗超低温保存后DNA甲基化的遗传变异

运用MSAP技术分析了拟南芥（Arabidopsis thaliana）幼苗超低温保存后DNA甲基化的遗传变异情况。结果表明,在扩增的662条带中,对照和2个处理及其第2代间完全一致的带型有598条：发生变化的带型有64条,其中能遗传给第2代的有48条,占变异条带的75％。与对照相比,经超低温保存的样品新产生的甲基化位点有14个,而去甲基化的位点有22个。经过处理但未冷冻的与冷冻处理组之间带型一致的有624条,差异条带有38条,占5.7％,而对照与未冷冻处理组的差异率是7．45％,对照与冷冻处理组之间的差异率是6。63％。可见,拟南芥在超低温保存中,无论是经液氮冷冻还是未经冷冻处理,对材料的甲基化状态均有影响,而这种甲基化变化大部分是可以遗传的。     

Genetic Variation and Discriminating Power of Four DNA Microsatellites in the Russian Population

The allele and genotype frequency distributions of four STRs (the LPL, vWA, FES/FPS, and F13B loci) commonly used in forensic medicine were studied with a sample of 200 ethnic Russians from Siberia. Genetic and molecular diversity of the four STRs was characterized in comparison with the American Caucasoid population. The set of the four STRs showed a high power of discrimination (PD = 0.99975). Comparison of the genetic variation at the four loci revealed a considerable difference between the Russian and American Caucasoid populations, precluding the use of data on allele frequencies in American Caucasoids for forensic testing in Russia. The results can be used as a reference in Siberia.     

Genetic variation of the bovine thyroglobulin gene studied at the DNA level

The bovine thyroglobulin gene has been analysed for variation using restriction endonucleases. Six independent restriction fragment length polymorphisms have been identified. One of these results most probably from a 2.5-kb deletion, the others being compatible with point mutations. We determined that an individual taken at random within the Belgian White and Blue breed is, on average, heterozygous for one out of 1700 nucleotides within the thyroglobulin gene.     

红腹锦鸡线粒体DNA控制区结构和遗传变异研究

红腹锦鸡(Chrysolophus pictus)是中国特有珍稀鸟类,仅见于中国中部和西部的山地,为国家二级重点保护动物.采用聚合酶链式反应和直接测序的方法测定了采自湖南新宁县和龙山县的28只红腹锦鸡线粒体DNA控制区序列.在获得的1 123 bp的碱基序列中,碱基含量为T 32.79%、C 26.07%、A 26.62%和G14.52%,共检测出20个多态性核苷酸变异位点,其中简约信息位点11个.对比其它已报导的雉类控制区结构,对红腹锦鸡控制区结构进行了分析,识别了其高变Ⅰ区、中间保守Ⅱ区和保守Ⅲ区,找到了与终止相关的序列TAS以及保守序列(F、E、D、C).28个样本共发现11种单倍型,其中单倍型hap1和hap2的比例很高.新宁种群的遗传多样性比龙山种群的高,两个种群存在基因流较频繁,未出现明显遗传分化.     

Microsatellite and Morphological Markers Reveal Genetic Variation within a Population of Sclerotinia sclerotiorum from Oilseed Rape in the Çanakkale Province of Turkey

The genetic variation among a population of Sclerotinia sclerotiorum collected from oilseed rape fields in the Çanakkale Province of Turkey was assessed using molecular and morphological markers. Seven microsatellite primer pairs (out of eight) revealed 32 clear polymorphic alleles among the 36 fungal isolates examined. An unweighted pair‐group mean analysis dendrogram was generated using the genetic distance matrix with the 32 microsatellite alleles. The level of similarity was as low as 15% between some isolates indicating a high level of genetic diversity within the fungal population; 23 distinct isolates were found (at a genotypic diversity level of 63%). Among the collection of 36 isolates, 19 mycelial compatibility groups (MCGs) were identified; 10 MCGs included at least two isolates. Molecular and morphological data suggest that most of the isolates within a single MCG were identical; however, the isolates belonging to the MCG2 and MCG4 had variable microsatellite haplotypes and were morphologically dissimilar. The data suggest that there is possibly a high rate of outcrossing as well as evolutionary potential within the population of the pathogen in oilseed rape fields. This is the first report demonstrating the genetic and morphological variation within a population of S. sclerotiorum in Turkey.     

基于DNA变异的中国汉族人群脱发表型推断及预测模型评估

目的 男性型脱发（male pattern baldness,MPB）,又称为雄激素性脱发（AGA）,是一种常见的男性脱发类型,大约80%的表型差异可以用遗传因素解释。目前的MPB遗传推断研究主要基于欧洲人群,东亚人群相关研究较少。本研究在中国人群中对欧洲人群MPB关联位点进行验证分析,并建立遗传推断模型。方法 本研究调查了486个与欧洲人群MPB相关单核苷酸多态性（SNP）位点在312名中国汉族男性中的关联性,分别使用逐步回归和Lasso回归方法对关联出的位点进行筛选。使用逻辑回归算法构建预测模型,通过十折交叉验证的方法评估。之后进一步比较了逻辑回归、k近邻分类器、随机森林、支持向量机4种常用分类器模型对MPB的预测准确性。结果 有174个SNP位点与中国汉族男性的MPB显著相关（P＜0.05）。通过不同的筛选方法,分别得到了22个SNP和25个SNP的位点集合。基于上述位点集合建立了22-SNP和 25-SNP两种逻辑回归预测模型。以AUC（ROC曲线下方的面积大小,area under curve）来衡量,两种模型对MPB预测的准确性分别为0.85和0.84;经十折交叉验证后预测准确性分别下降至0.81和0.77。当加入年龄作为预测因子后,两种模型的AUC均达到最大值0.89。从运行结果来看,逻辑回归预测模型较本研究中的其他分类器模型具有明显优势。结论 总体而言,虽然预测模型的准确性尚未达到临床期望水平,但SNP在MPB的遗传预测方面仍具备很大的潜力,可以为MPB的早期诊断、临床干预和法庭科学应用提供参考。     

Genetic Variation at the MHC in a Population of Introduced Wild Turkeys

Genetic variation in the major histocompatibility complex (MHC) is known to affect disease resistance in many species. Investigations of MHC diversity in populations of wild species have focused on the antigen presenting class IIβ molecules due to the known polymorphic nature of these genes and the role these molecules play in pathogen recognition. Studies of MHC haplotype variation in the turkey (Meleagris gallopavo) are limited. This study was designed to examine MHC diversity in a group of Eastern wild turkeys (Meleagris gallopavo silvestris) collected during population expansion following reintroduction of the species in southern Wisconsin, USA. Southern blotting with BG and class IIβ probes and single nucleotide polymorphism (SNP) genotyping was used to measure MHC variation. SNP analysis focused on single copy MHC genes flanking the highly polymorphic class IIβ genes. Southern blotting identified 27 class IIβ phenotypes, whereas SNP analysis identified 13 SNP haplotypes occurring in 28 combined genotypes. Results show that genetic diversity estimates based on RFLP (Southern blot) analysis underestimate the level of variation detected by SNP analysis. Sequence analysis of the mitochondrial D-loop identified 7 mitochondrial haplotypes (mitotypes) in the sampled birds. Results show that wild turkeys located in southern Wisconsin have a genetically diverse MHC and originate from several maternal lineages.     

山猪群体钙调蛋白酶抑制蛋白基因遗传变异研究

目的：研究猪钙调蛋白酶抑制蛋白（CAST）基因在山猪群体的遗传变异情况,为山猪肉质研究奠定基础。方法：应用PCR-SSCP技术和测序方法检测山猪及其杂种猪CAST基因的遗传多态性,并与其他品种猪相应序列进行比较。结果：用pCT1引物在山猪及其杂种群体中检测到2个多态位点（A,B）,用pCT2引物检测到3个多态位点（C,D,E）;序列分析表明,C和E位点共同拥有6处变异。结论：通过与其他猪品种比较,发现山猪的CASTMsp基因型分布与梅山猪的基因型分布完全一样,而与国外品种猪的基因型分布差异明显。     

Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis (Trin.) Tzvel.

Randomly amplified polymorphic DNA (RAPD) analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis (Trin.) Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% (P ＜ 0.04), and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% (P ＜ 0.002). A 21.06% RAPD variation among all 16 populations among two regions was found (P ＜ 0.001), as well as 72.59% variation within populations (P ＜ 0.001). Molecular variation within populations was significantly different among 16 populations.     

Molecular Genetic Variation in a Clonal Plant Population of Leymus chinensis （Trin.） Tzvel.

Randomly amplified polymorphic DNA （RAPD） analysis was used to investigate the genetic variation among populations, between populations, and within populations, relationships between genetic distance and geographic distance, and the molecular variation and population size. The effects of geographic and genetic distances, as well as of genetic differentiation and population size, on genetic variations of Leymus chinensis （Trin.） Tzvel. are discussed. The present study showed that there was significant RAPD variation between the Baicheng region population and the Daqing region population, with a molecular variance of 6.35% （P 〈 0.04）, and for differentiation among area populations of the Daqing region, with a molecular variance of 8.78% （P 〈 0.002）. A 21.06% RAPD variation among all 16 populations among two regions was found （P 〈 0.001）, as well as 72.59% variation within populations （P 〈 0.001）. Molecular variation within populations was significantly different among 16 populations.     

Genetic mapping of biomass yield in three interconnected Miscanthus populations

Improving biomass yield is a major goal of Miscanthus breeding. We conducted a study on one interspecific Miscanthus sinensis × Miscanthus sacchariflorus F₁ population and two intraspecific M. sinensis F₁ populations, each of which shared a common parent. A field trial was established at Urbana, IL during spring 2011, and phenotypic data were collected in 2012 and 2013 for fourteen yield traits. Six high‐density parental genetic maps, as well as a consensus genetic map integrating M. sinensis and M. sacchariflorus, were developed via the pseudotestcross strategy for noninbred parents with ≥1214 single‐nucleotide polymorphism markers generated from restriction site‐associated DNA sequencing. We confirmed for the first time a whole‐genome duplication in M. sacchariflorus relative to Sorghum bicolor, similar to that observed previously for M. sinensis. Four quantitative trait locus (QTL) analysis methods for detecting marker‐trait associations were compared: (1) individual parental map composite interval mapping analysis, (2) individual parental map stepwise analysis, (3) consensus map single‐population stepwise analysis and (4) consensus map joint‐population stepwise analysis. These four methods detected 288, 264, 133 and 109 total QTLs, which resolved into 157, 136, 106 and 86 meta‐QTLs based on QTL congruency, respectively, including a set of 59 meta‐QTLs common to all four analysis methods. Composite interval mapping and stepwise analysis co‐identified 118 meta‐QTLs across six parental maps, suggesting high reliability of stepwise regression in QTL detection. Joint‐population stepwise analysis yielded the highest resolution of QTLs compared to the other three methods across all meta‐QTLs. Strong, frequently advantageous transgressive segregation in the three populations indicated a promising future for breeding new higher‐yielding cultivars of Miscanthus.     

Ribosomal DNA Evolution at the Population Level: Nucleotide Variation in Intergenic Spacer Arrays of Daphnia Pulex

Nucleotide variation was surveyed in 21 subrepeat arrays from the ribosomal DNA intergenic spacer of three Daphnia pulex populations. Eighteen of these arrays contained four subrepeats. Contrary to expectations, each of the four positions within the array had a different consensus sequence. However, gene conversion, involving sequences less than the length of a subrepeat, had occurred between subrepeats in different positions. Three arrays had more than four subrepeats and were undoubtedly generated by unequal crossing over between standard-length arrays. The data strongly suggested that most unequal exchanges between arrays are intrachromosomal and that they occur much less frequently than unequal exchanges at the level of the entire rDNA repeat. Strong associations among variants at different positions allowed the recognition of five groups of arrays, two of which were found in more than one population. Five of the seven individuals surveyed had arrays from more than one group. Analysis of the distribution of nucleotide variation suggested that the populations were quite divergent, a result that is concordant with previous surveys of allozyme and mitochondrial DNA variation. It was suggested that some of the subrepeat array types are quite old, at least predating the recolonization of pond habitats in the midwestern United States after the last glaciation.     

Genetic Structure and Kinship Patterns in a Population of Black Howler Monkeys, Alouatta pigra, at Palenque National Park, Mexico

We investigated the genetic structure and kinship patterns of black howler monkeys (Alouatta pigra) at Palenque National Park, Mexico. Fecal samples from 49 individuals residing in eight social groups were successfully genotyped for 19 polymorphic microsatellite markers known to be variable in other ateline primates. Overall, genetic diversity was low (H_o = 0.588) with an average of 4.2 alleles per loci (range = 2–8). We found that intergroup genetic variation among adults was relatively high (mean between‐group F_ST = 0.119), largely due to the genetic divergence of one study group from the others. Intragroup kinship patterns showed that in most social groups, either adult males, adult females, or individuals of both sexes resided with same‐sexed adult kin, suggesting that some black howler males and females may not disperse from their natal group or may disperse with related individuals. Of the six sampled immigrant males, two males joined established groups by themselves, and four males formed two pairs that each took over the social group they joined after evicting the resident males. Males in both these coalitions were genetically closely related, while the two solitary immigrants were not closely related to any of the resident males present in the group they joined. Am. J. Primatol. 74:948‐957, 2012. © 2012 Wiley Periodicals, Inc.     

Genetic variations in the DNA replication origins of human papillomavirus family correlate with their oncogenic potential

Human papillomaviruses (HPVs) encompass a large family of viruses that range from benign to highly carcinogenic. The crucial differences between benign and carcinogenic types of HPV remain unknown, except that the two HPV types differ in the frequency of DNA replication. We have systematically analyzed the mechanism of HPV DNA replication initiation in low-risk and high-risk HPVs. Our results demonstrate that HPV-encoded E2 initiator protein and its four binding sites in the replication origin play pivotal roles in determining the destiny of the HPV-infected cell. We have identified strain-specific single nucleotide variations in E2 binding sites found only in the high-risk HPVs. We have demonstrated that these variations result in attenuated formation of the E2-DNA complex. E2 binding to these sites is linked to the activation of the DNA replication origin as well as initiation of DNA replication. Both electrophoretic mobility shift assay and atomic force microscopy studies demonstrated that binding of E2 from either low- or high-risk HPVs with variant binding sequences lacked multimeric E2-DNA complex formation in vitro. These results provided a molecular basis of differential DNA replication in the two types of HPVs and pointed to a correlation with the development of cancer.     

The Loss of Genetic Diversity in Sichuan Taimen as Revealed by DNA Fingerprinting

Species endangerment often derives from the “endangerment” of genetic diversity, thus loss of genetic diversity is an important cause of species extinction. Since historical specimens were unavailable, previous studies mainly described the genetic diversity status in the current population rather than the loss of genetic variation over time. In this study, we collected samples during1998–1999 and obtained historical specimens from 1957 to 1958. Based on the two sets of fish, we determined the changes in genetic diversity of Sichuan taimen using DNA fingerprinting. The differences in genetic parameters between the present samples and historical taimens revealed their loss of genetic variation. As a result, the existing populations have lower viability, and proper management has to be implemented to preserve genetic diversity.     

Molecular Characterization of a Mitochondrial DNA Segment from the Japanese Scallop (Patinopecten yessoensis): Demonstration of a Region Showing Sequence Polymorphism in the Population

A 1.3-kb mitochondrial DNA segment from the Japanese scallop Patinopecten yessoensis was cloned and sequenced. This segment contained the transfer RNA^Met gene and partial sequences of 2 ribosomal RNA genes, together with 2 separate noncoding regions (designated NcR1 and NcR2). The NcR regions derived from 78 individuals cultured in Lake Saroma or Matsu Bay, were sequenced, and we found 15 loci with sequence alterations including 13 substitutions, 1 deletion, and 1 insertion (1 locus in NcR1, 14 loci in NcR2), and 17 haplotypes. Of the 17 haplotypes, 10 were found in the Saroma population only, 3 in the Mutsu population only, and 4 in both populations. The gene diversity and nucleotide diversity values were, respectively, 0.87 and 0.0069 for the Saroma population, 0.63 and 0.0040 for the Mutsu population, and 0.83 and 0.0203 overall. Thus the NcR segment was considered to have sufficient sequence variation for population genetic studies. The 16 variants of the NcR2 sequence were separated successfully by denaturing gradient gel electrophoresis, confirming the sequence variation in NcR2. Received October 3, 2001; accepted February 19, 2001.     

Primate evolution at the DNA level and a classification of hominoids

Summary The genetic distances among primate lineages estimated from orthologous noncoding nucleotide sequences of -type globin loci and their flanking and intergenic DNA agree closely with the distances (delta T₅₀H values) estimated by cross hybridization of total genomic single-copy DNAs. These DNA distances and the maximum parsimony tree constructed for the nucleotide sequence orthologues depict a branching pattern of primate lineages that is essentially congruent with the picture from phylogenetic analyses of morphological characters. The molecular evidence, however, resolves ambiguities in the morphological picture and provides an objective view of the cladistic position of humans among the primates. The molecular data group humans with chimpanzees in subtribe Hominina, with gorillas in tribe Hominini, orangutans in subfamily Homininae, gibbons in family Hominidae, Old World monkeys in infraorder Catarrhini, New World monkeys in semisuborder Anthropoidea, tarsiers in suborder Haplorhini, and strepsirhines (lemuriforms and lorisiforms) in order Primates. A seeming incongruency between organismal and molecular levels of evolution, namely that morphological evolution appears to have speeded up in higher primates, especially in the lineage to humans, while molecular evolution has slowed down, may have the trivial explanation that relatively small genetic changes may sometimes result in marked phenotypic changes.