Consistent divergence times and allele sharing measured from cross‐species application of SNP chips developed for three domestic species

Recent advances in technology facilitated development of large sets of genetic markers for many taxa, though most often model or domestic organisms. Cross‐species application of genomic technologies may allow for rapid marker discovery in wild relatives of taxa with well‐developed resources. We investigated returns from cross‐species application of three commercially available SNP chips (the OvineSNP50, BovineSNP50 and EquineSNP50 BeadChips) as a function of divergence time between the domestic source species and wild target species. Across all three chips, we observed a consistent linear decrease in call rate (~1.5% per million years), while retention of polymorphisms showed an exponential decay. These results will allow researchers to predict the expected amplification rate and polymorphism of cross‐species application for their taxa of interest, as well as provide a resource for estimating divergence times.     

Cost-efficient selection of a marker panel in genetic studies

Genetic techniques are frequently used to sample and monitor wildlife populations. The goal of these studies is to maximize the ability to distinguish individuals for various genetic inference applications, a process which is often complicated by genotyping error. However, wildlife studies usually have fixed budgets, which limit the number of genetic markers available for inclusion in a study marker panel. Prior to our study, a formal algorithm for selecting a marker panel that included genotyping error, laboratory costs, and ability to distinguish individuals did not exist. We developed a constrained nonlinear programming optimization algorithm to determine the optimal number of markers for a marker panel, initially applied to a pilot study designed to estimate black bear abundance in central Georgia. We extend the algorithm to other genetic applications (e.g., parentage or population assignment) and incorporate possible null alleles. Our algorithm can be used in wildlife pilot studies to assess the feasibility of genetic sampling for multiple genetic inference applications. © 2011 The Wildlife Society.     

Estimation of the degree of self-fertilization in Porphyra yezoensis (Bangiales,Rhodophyta)

Crosses between genotypically distinct thalli of the monoecious species Porphyra yezoensis were carried out using immature thallus fragments from green- and red-type color mutants and also wild-type thalli. As the genes governing the mutants are monogenic, recessive to the wild-type, and belong to the same linkage group, the degree of self-fertilization could be estimated based on the pigmentation of the resultant diploid conchocelis. The degree of self-fertilization in the cross between the green-type and the wild-type was 48.5–55.0%, and in the cross between the red-type and the wild-type was 45.1–56.5%. In the cross between the green- and red-type mutants, the degree of self-fertilization was 46.0–54.5% when the green-type was the female parent, and was 44.8–55.6% when the red-type was the female parent.     

太白红杉群落优势种的生态位研究

应用Levins和Shannon-Wiener生态位宽度指数及Pianka生态位重叠指数,研究了太白红杉群落12个优势种的生态位宽度和生态位重叠。结果表明,乔木层中太白红杉的生态位宽度最大,对高海拔地区的环境适应能力较强,巴山冷杉对的低海拔地区的环境适应能力较强;灌木层中香柏的生态位宽度最大,华西忍冬、华西银腊梅、太白忍冬次之,头花杜鹃的生态位宽度最小。乔木层中太白红杉与巴山冷杉的生态位重叠较大,但二者只在低海拔分布范围有重叠;灌木层头花杜鹃的分布范围较大,与其它3个种的生态位重叠也最大,另外3个种的生态位重叠较小;草本层中毛状苔草、羊茅和嵩草的生态位重叠较大,而大叶碎米荠和太白银莲花的生态位重叠较小。     

Chlorimuron ethyl as a new selectable marker for disrupting genes in the insect-pathogenic fungus Metarhizium robertsii

A lack of selectable markers was a hindrance in investigating gene function in Metarhizium robertsii. A reliable Agrobacterium-mediated transformation system based on the use of chlorimuron ethyl as the selectable marker was developed which could serve as a useful tool to inactivate genes involved in insect pathogenicity.     

Development of nuclear microsatellite markers for the threatened wetland plant Geranium soboliferum var. kiusianum (Geraniaceae)

Nuclear microsatellite markers were developed for the threatened plant Geranium soboliferum var. kiusianum, which has decreased its population size as a result of loss of its wetland habitat in Kyushu, Japan. Utilizing RNA‐seq data obtained by next‐generation sequencing techniques, 10 polymorphic microsatellite markers with 3–16 alleles in a nuclear genome were developed and characterized. Two to 15 alleles were observed in G. soboliferum. These markers will be used to investigate the genetic circumstance of remnant populations of G. soboliferum var. kiusianum and their phylogenetic relationship with G. soboliferum.     

A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat

Lr19, one of the few widely effective genes conferring resistance to leaf rust in wheat, was transferred from the wild relative Thinopyrum ponticum to durum wheat. Since Lr19 confers a hypersensitive response to the pathogen, it was considered likely that the gene would be a member of the major nucleotide-binding site (NBS)-leucine-rich repeat (LRR) plant R gene family. NBS profiling, based on PCR amplification of conserved NBS motifs, was applied to durum wheat–Th. ponticum recombinant lines involving different segments of the alien 7AgL chromosome arm, carrying or lacking Lr19. Differential PCR products were isolated and sequenced. From one such sequence (AG15), tightly linked to Lr19, a 4,121-bp full-length cDNA was obtained. Its deduced 1,258 amino acid sequence has the characteristic NBS-LRR domains of plant R gene products and includes a coiled-coil (CC) region typical of monocots. The genomic DNA sequence showed the presence of two exons and a short intron upstream of the predicted stop codon. Homology searches revealed considerable identity of AG15 with the cloned wheat resistance gene Pm3a and a lower similarity with wheat Lr1, Lr21, and Lr10. Quantitative PCR on leaf-rust-infected and non-infected Lr19 carriers proved AG15 to be constitutively expressed, as is common for R genes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Identification of vhhP2, a novel genetic marker of Vibrio harveyi, and its application in the quick detection of V. harveyi from animal specimens and environmental samples

Aims:  To investigate the species-specific prevalence of vhhP2 among Vibrio harveyi isolates and the applicability of vhhP2 in the specific detection of V. harveyi from crude samples of animal and environmental origins.
Methods and Results:  A gene ( vhhP2 ) encoding an outer membrane protein of unknown function was identified from a pathogenic V. harveyi isolate. vhhP2 is present in 24  V. harveyi strains isolated from different geographical locations but is absent in 24 strains representing 17 different non- V. harveyi species, including V. parahaemolyticus and V. alginolyticus . A simple polymerase chain reaction method for the identification of V. harveyi was developed based on the conserved sequence of vhhP2 . This method was demonstrated to be applicable to the quick detection of V. harveyi from crude animal specimens and environmental samples. The specificity of this method was tested by applying it to the examination of two strains of V. campbellii , which is most closely related to V. harveyi . One of the V. campbellii strains was falsely identified as V. harveyi .
Conclusions:  vhhP2 is ubiquitously present in the V. harveyi species and is absent in most of the non- V. harveyi species; this feature enables vhhP2 to serve as a genetic marker for the rapid identification of V. harveyi . However, this method can not distinguish some V. campbellii strains from V. harveyi .
Significance and Impact of the Study:  the significance of our study is the identification of a novel gene of V. harveyi and the development of a simple method for the relatively accurate detection of V. harveyi from animal specimens and environmental samples.     

乌头及其同属近缘种的SSR指纹图谱研究

乌头(Aconitum carmichaeli Debx.)为中国重要的药用植物,种质资源丰富,同属近缘种繁多。该研究采用SSR分子标记技术对采自17个种群的51份乌头样本和13个同属近缘种的65份样本进行扩增和聚丙烯酰胺凝胶电泳检测,分析了乌头及其同属近缘种的遗传多样性、遗传分化和系统发育关系,筛选出稳定性好、多态性高的SSR引物构建乌头及其近缘种的指纹图谱。结果表明:(1)11对乌头微卫星引物均表现出高的多态性,共检测出109个复等位基因,平均每个位点9.91。(2)乌头在物种水平上遗传多样性丰富(A=3.090 9,I=0.889 7,h=0.540 2),种群间的遗传分化显著(Gst=0.277 4);乌头属14种植物表现出了较高的遗传多样性(A=9.909 1,I=1.526 2,h=0.690 5),物种间遗传分化显著(Fst=0.437),基因流微弱(Nm=0.451 8)。(3)聚类分析表明,同一种群的乌头样本首先聚在一起各自形成小支,17个小支聚为一支;13个乌头近缘种材料中,相同物种的样本分别聚为一支;乌头属14个物种聚为5个大支,与形态分类结果一致。(4)利用基因型丰富、多态性高的6对SSR引物(Tchin03、Tchin04Tchin20、Tchin26、Tchin29、Tchin32)可有效区分14种乌头属植物,并以此建立了乌头种质资源和近缘种的DNA指纹图谱。该研究为乌头的种质资源鉴定及混伪品鉴定提供了重要的技术支撑。     

Up-regulation of vimentin expression in low-density malignant glioma cells as immediate and late effects under irradiation and temozolomide treatment

Nervous system tumors are one of the leading causes of cancer related death. Specific mechanisms facilitating the invasive behavior of gliomas remain obscure. Advanced simulation models of the in vivo response to therapy conditions should potentially improve malignant glioma treatment. Expressional profiling of vimentin––one of reliable pro-invasive tumor makers––in those simulation models was the goal of this study, in order to estimate a pro-invasive response of surviving malignant glioma cells under clinically relevant therapeutic conditions. Human U87-MG malignant glioma cells were used. These cells are characterized by the wild p53-phenotype, which is relevant for the majority of primary malignant glioblastomas. Experimental design foresaw the cells to undergo either irradiation or chemo-treatment with temozolomide alone, or combined treatment. Expression profiling of vimentin was performed by quantitative “Real-Time”-PCR under all treatment conditions simulating diverse tumor regions. Here we demonstrated that vimentin expression patterns in human malignant glioma cells strongly depend on cellular density, algorithms of drug delivery and chemo/radio treatment. Substantial differences were recognized between immediate and late therapy effects. Significant increase in vimentin expression levels was detected particularly in low-density cell cultures under durable treatment with constant concentration levels of temezolomide. Simulation of variable intratumoral regional conditions (central intratumoral regions vs. disseminated malignant cells in peripheral regions) demonstrated differential response of vimentin expression in malignant glioma cell cultures treated under clinically relevant conditions. Slight ebbing of expression levels as late effects of the treatment in confluent cultures may correspond to necrotic processes clinically observed in central intratumoral regions. Contrary, in disseminated malignant cells of peripheral regions therapy resulted in vimentin-inducing effects. This is in agreement with the clinical observations of an increased aggressiveness and malignancy grade of post-operatively chemo/radio-treated malignant gliomas.