Number Of Single Nucleotide Polymorphisms Research Articles

LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

BackgroundGenome-wide association studies (GWAS) have successfully identified a large number of single nucleotide polymorphisms (SNPs) that are associated with a wide range of human diseases. However, many of these disease-associated SNPs are located in non-coding regions and have remained largely unexplained. Recent findings indicate that disease-associated SNPs in human large intergenic non-coding RNA (lincRNA) may lead to susceptibility to diseases through their effects on lincRNA expression. There is, therefore, a need to specifically record these SNPs and annotate them as potential candidates for disease.DescriptionWe have built LincSNP, an integrated database, to identify and annotate disease-associated SNPs in human lincRNAs. The current release of LincSNP contains approximately 140,000 disease-associated SNPs (or linkage disequilibrium SNPs), which can be mapped to around 5,000 human lincRNAs, together with their comprehensive functional annotations. The database also contains annotated, experimentally supported SNP-lincRNA-disease associations and disease-associated lincRNAs. It provides flexible search options for data extraction and searches can be performed by disease/phenotype name, SNP ID, lincRNA name and chromosome region. In addition, we provide users with a link to download all the data from LincSNP and have developed a web interface for the submission of novel identified SNP-lincRNA-disease associations.ConclusionsThe LincSNP database aims to integrate disease-associated SNPs and human lincRNAs, which will be an important resource for the investigation of the functions and mechanisms of lincRNAs in human disease. The database is available at http://bioinfo.hrbmu.edu.cn/LincSNP.

Interferon-λ Genetic Variations and Hepatitis C: Yet to be Discovered.

Dear Editor, The association of genetic factors with treatment induced hepatitis C clearance in Pakistani patients was recently demonstrated by Tipu et al. (1). They evaluated the impact of different genetic variants in interferon-λ (IFNL) genomic region on treatment induced hepatitis C clearance. The study was remarkable regarding the investigation of several numbers of single nucleotide polymorphisms (SNPs) in IFNL region. We would like to express our comments regarding the study. We observed that the patients in the study were treated with interferon (IFN) alpha 2b and ribavirin (RBV). Since the combination of pegylated IFN and RBV has been approved for treatment of chronic hepatitis C from 2002, the conventional regimen (IFN alpha 2b and RBV) for treatment of hepatitis C virus (HCV) infected patients is a debate point. Also, we have a concern regarding two terms through the article, first the authors defined the term sustained virologic response (SVR) as undetectable HCV RNA at the end of treatment course, whereas SVR must be defined as undetectable HCV RNA 24 weeks after treatment completion; second the term spontaneous clearance which refers to clearance of HCV from serum without treatment was misused through the article. Interestingly, the current study showed significant association between different IFNL polymorphisms and treatment response in HCV genotype 3 infected patients in our neighbor country (Pakistan). The results of previous studies searching for the association of IL28B SNPs and SVR in patients infected with HCV genotype 2/3 were conflicting and most of them did not find any association between IL28B SNPs and SVR (2, 3). Also, in this study, 50 SNPs were genotyped of which 25 of them were included in the final association analysis and 13 of them were found to be associated with the treatment response (1). The role of SNPs in the IFNL region remained mysterious and yet to be discovered. There are two main hypotheses for the role of these SNPs: Combined effect of SNPs which refers to independent impact of each SNP; Causal and Tag SNPs which is defined by the linkage disequilibrium (LD) between few tag SNPs and a causal SNP (sometimes undiscovered or untested). Most of the SNPs in IFNL region including the SNPs found by Tipu et al. (1) to be associated with treatment response are in linkage disequilibrium (LD) which favors the Causal and Tag SNPs hypothesis. On the other hand, Prokunina-Olsson et al. (4) discovered a new IFNL gene which was assigned as IFNL4 and its encoded protein was observed to possess antiviral activity. Also, in the latter study, a genetic variant called ss469415590 (TT/ΔG) found to be located in exon one of IFNL4 gene which its TT allele does not express the protein and was associated with favorable treatment outcome and its ΔG allele expresses the IFNL4 protein and was associated with treatment nonresponse. The results of most previous studies looked for the functional role of IFNL SNPs showed the pretreatment expression of interferon stimulated genes (ISG) to be lower in patients with SVR when compared to patients with treatment failure. The same finding was observed for the expression of ISGs and IL28B genotypes in which the expression of ISGs were lower in patients with IFNL favorable genotypes than in patients with IFNL unfavorable genotypes (5, 6). However, the results of studies investigated the association of IL28B genotypes with IL28B expression were inconsistent which makes it difficult to draw the final role map (5-9). Discovery of IFNL4 gene and the exon one TT/ΔG SNP was a clue for solving the puzzle of IFNL genetic variations and HCV treatment response. If we accept the ss469415590 as the casual variant, the association of the IFNL genetic variants, IFNL4 expression, the subsequent ISGs expression, and the ultimate differences in treatment response seems to be relevant. In conclusion, studies such the one by Tipu et al. can open new horizons in diagnosis, management, and evaluation of hepatitis C prognosis in near future.

Draft Genome Sequence of the First Isolate of Extensively Drug-Resistant Mycobacterium tuberculosis in New Zealand

Extensively drug-resistant (XDR) tuberculosis has now been described in >90 countries worldwide. The first case of XDR tuberculosis (XDR-TB) in New Zealand was recorded in 2010. We report the draft whole-genome sequence of the New Zealand isolate, NZXDR1, and describe a number of single-nucleotide polymorphisms that relate to drug resistance.

Interleukin-18 −607C/A Gene Polymorphism in Egyptian Asthmatic Children

Asthma is a multifactorial respiratory disease determined by interactions of multiple disease susceptibility genes and environmental factors. Interleukin (IL)-18 is an important cytokine for initiating and perpetuating the catabolic and inflammatory response in allergic asthma. A number of single nucleotide polymorphisms that influence IL-18 production are found in the gene promoter region. The aim of this study was to investigate the association of IL-18 -607C/A promoter polymorphism with asthma and whether this polymorphism influenced the severity of asthma in affected children. The influence of this promoter gene polymorphism on total serum IgE level in studied subjects was also investigated. This study was carried out at the Allergy Clinic of Abu El Reesh Children's Hospital at Cairo University, Egypt. This study included 40 asthmatic children, subdivided into four groups according to different degrees of asthma severity, and 20 apparently healthy subjects as the control group. All cases were subjected to history taking, clinical examination, and the following laboratory investigations: complete blood count, total serum IgE level assay by ELISA and genomic DNA extraction, and analysis for IL-18 -607C/A promoter gene polymorphism using the PCR-RFLP (restriction fragment length polymorphism) technique. In the present study the IL-18 -607AA genotype frequency was higher in cases (22.5 %) than in the control group (15 %); however, the difference was not statistically significant (p = 0.773). No statistically significant difference between the degree of asthma severity and IL-18 -607C/A polymorphism was found (p = 0.489). No significant association could be detected upon comparing the frequencies of C and A alleles among the two studied groups (p = 0.366). Also, no significant differences were demonstrated for the allele frequencies when the intermittent with mild [odds ratio (OR) = 2.72, 95 % CI 1.03-2.33, p = 0.067], intermittent with moderate, and severe (OR = 2.8, 95 % CI 1.01-8.5, p = 0.066) asthma groups were compared. The median value of the total serum IgE level in asthmatic cases with the mutant genotype (AA) was significantly higher [360 IU/L (96.6-1,340 IU/L)] than in the control group [119 IU/L (70.6-158.9 IU/L)] (p = 0.033). No significant statistical difference was encountered regarding the distribution of IL-18 -607C/A genotypes and allele frequencies in asthma patients and healthy controls. Also, there were no significant associations between asthma severity and different genotypes or alleles. The median value of the total serum IgE level in asthmatic cases with the mutant genotype (AA) was significantly higher than in the control group. Thus, IL-18 -607AA genotype frequency might be related to higher total serum IgE.

A PRIMER EXTENSION DENATURING HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY METHOD FOR THE IDENTIFICATION OF THREE ABCC2 GENETIC POLYMORPHISMS

Background. A number of single nucleotide polymorphisms have been described in the ABCC2 gene that alters drug disposition. The aim of the study was to develop a primer extension denaturing high-performance liquid chromatography (PE-dHPLC) assay to determine three common variants of the ABCC2 gene in the promoter region (−24C > T), exon 10 (1249 G > A), and exon 28 (3972C > T). Methods. Polymerase chain reactions (PCRs) were used to isolate the area of interest in the ABCC2 gene. A comparison of the PCR product was performed between sequencing and dHPLC. Results. A 100%identity match was achieved between groups and allowed for a quick and accurate method to determine three single nucleotide polymorphisms in a single extension reaction. This assay is the first of its type to determine three ABCC2 variants by dHPLC.

Use of VeraCode 384-plex assays for watermelon diversity analysis and integrated genetic map of watermelon with single nucleotide polymorphisms and simple sequence repeats

Watermelon (Citrullus lanatus var. lanatus) is one of the most important vegetable crops in the world. Molecular markers have become the tools of choice for resolving watermelon taxonomic relationships and evolution. Increased numbers of single nucleotide polymorphism (SNP) markers together with simple sequence repeat (SSR) markers would be useful for phylogenetic analyses of germplasm accessions and for linkage mapping for marker-assisted breeding with quantitative trait loci and single genes. We aimed to construct a genetic map based on SNPs (generated by Illumina Veracode multiplex assays for genotyping) and SSR markers and evaluate relationships inferred from SNP genotypes between 130 watermelon accessions collected throughout the world. We incorporated 282 markers (232 SNPs and 50 SSRs) into the linkage map. The genetic map consisted of 11 linkage groups spanning 924.72 cM with an average distance of 3.28 cM between markers. Because all of the SNP-containing sequences were assembled with the whole-genome sequence draft for watermelon, chromosome numbers could be readily assigned for all the linkage groups. We found that 134 SNPs were polymorphic in 130 watermelon accessions chosen for diversity studies. The current 384-plex SNP set is a powerful tool for characterizing genetic relatedness and for developing medium-resolution genetic maps.

Genome-wide polymorphisms and development of a microarray platform to detect genetic variations in Plasmodium yoelii

The rodent malaria parasite Plasmodium yoelii is an important model for studying malaria immunity and pathogenesis. One approach for studying malaria disease phenotypes is genetic mapping, which requires typing a large number of genetic markers from multiple parasite strains and/or progeny from genetic crosses. Hundreds of microsatellite (MS) markers have been developed to genotype the P. yoelii genome; however, typing a large number of MS markers can be labor intensive, time consuming, and expensive. Thus, development of high-throughput genotyping tools such as DNA microarrays that enable rapid and accurate large-scale genotyping of the malaria parasite will be highly desirable. In this study, we sequenced the genomes of two P. yoelii strains (33X and N67) and obtained a large number of single nucleotide polymorphisms (SNPs). Based on the SNPs obtained, we designed sets of oligonucleotide probes to develop a microarray that could interrogate ∼11,000 SNPs across the 14 chromosomes of the parasite in a single hybridization. Results from hybridizations of DNA samples of five P. yoelii strains or cloned lines (17XNL, YM, 33X, N67 and N67C) and two progeny from a genetic cross (N67×17XNL) to the microarray showed that the array had a high call rate (∼97%) and accuracy (99.9%) in calling SNPs, providing a simple and reliable tool for typing the P. yoelii genome. Our data show that the P. yoelii genome is highly polymorphic, although isogenic pairs of parasites were also detected. Additionally, our results indicate that the 33X parasite is a progeny of 17XNL (or YM) and an unknown parasite. The highly accurate and reliable microarray developed in this study will greatly facilitate our ability to study the genetic basis of important traits and the disease it causes.

Determining population structure and hybridization for two iris species

Identifying processes that promote or limit gene flow can help define the ecological and evolutionary history of a species. Furthermore, defining those factors that make up “species boundaries” can provide a definition of the independent evolutionary trajectories of related taxa. For many species, the historic processes that account for their distribution of genetic variation remain unresolved. In this study, we examine the geographic distribution of genetic diversity for two species of Louisiana Irises, Iris brevicaulis and Iris fulva. Specifically, we asked how populations are structured and if population structure coincides with potential barriers to gene flow. We also asked whether there is evidence of hybridization between these two species outside Louisiana hybrid zones. We used a genotyping-by-sequencing approach and sampled a large number of single nucleotide polymorphisms across these species' genomes. Two different population assignment methods were used to resolve population structure in I. brevicaulis; however, there was considerably less population structure in I. fulva. We used a species tree approach to infer phylogenies both within and between populations and species. For I. brevicaulis, the geography of the collection locality was reflected in the phylogeny. The I. fulva phylogeny reflected much less structure than detected for I. brevicaulis. Lastly, combining both species into a phylogenetic analysis resolved two of six populations of I. brevicaulis that shared alleles with I. fulva. Taken together, our results suggest major differences in the level and pattern of connectivity among populations of these two Louisiana Iris species.

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci

A highly polygenic aetiology and high degree of allele-sharing between ancestries have been well elucidated in genetic studies of rheumatoid arthritis. Recently, the high-density genotyping array Immunochip for immune disease loci identified 14 new rheumatoid arthritis risk loci among individuals of European ancestry. Here, we aimed to identify new rheumatoid arthritis risk loci using Korean-specific Immunochip data. We analysed Korean rheumatoid arthritis case-control samples using the Immunochip and genome-wide association studies (GWAS) array to search for new risk alleles of rheumatoid arthritis with anticitrullinated peptide antibodies. To increase power, we performed a meta-analysis of Korean data with previously published European Immunochip and GWAS data for a total sample size of 9299 Korean and 45,790 European case-control samples. We identified eight new rheumatoid arthritis susceptibility loci (TNFSF4, LBH, EOMES, ETS1-FLI1, COG6, RAD51B, UBASH3A and SYNGR1) that passed a genome-wide significance threshold (p<5×10(-8)), with evidence for three independent risk alleles at 1q25/TNFSF4. The risk alleles from the seven new loci except for the TNFSF4 locus (monomorphic in Koreans), together with risk alleles from previously established RA risk loci, exhibited a high correlation of effect sizes between ancestries. Further, we refined the number of single nucleotide polymorphisms (SNPs) that represent potentially causal variants through a trans-ethnic comparison of densely genotyped SNPs. This study demonstrates the advantage of dense-mapping and trans-ancestral analysis for identification of potentially causal SNPs. In addition, our findings support the importance of T cells in the pathogenesis and the fact of frequent overlap of risk loci among diverse autoimmune diseases.

Germline variants in IKZF1, ARID5B, and CEBPE as risk factors for adult-onset acute lymphoblastic leukemia: an analysis from the GMALL study group

Germline variants in IKZF1, ARID5B, and CEBPE as risk factors for adult-onset acute lymphoblastic leukemia: an analysis from the GMALL study group

Sequencing, De Novo Assembly and Annotation of the Colorado Potato Beetle, Leptinotarsa decemlineata, Transcriptome

BackgroundThe Colorado potato beetle (Leptinotarsa decemlineata) is a major pest and a serious threat to potato cultivation throughout the northern hemisphere. Despite its high importance for invasion biology, phenology and pest management, little is known about L. decemlineata from a genomic perspective. We subjected European L. decemlineata adult and larval transcriptome samples to 454-FLX massively-parallel DNA sequencing to characterize a basal set of genes from this species. We created a combined assembly of the adult and larval datasets including the publicly available midgut larval Roche 454 reads and provided basic annotation. We were particularly interested in diapause-specific genes and genes involved in pesticide and Bacillus thuringiensis (Bt) resistance.ResultsUsing 454-FLX pyrosequencing, we obtained a total of 898,048 reads which, together with the publicly available 804,056 midgut larval reads, were assembled into 121,912 contigs. We established a repository of genes of interest, with 101 out of the 108 diapause-specific genes described in Drosophila montana; and 621 contigs involved in insecticide resistance, including 221 CYP450, 45 GSTs, 13 catalases, 15 superoxide dismutases, 22 glutathione peroxidases, 194 esterases, 3 ADAM metalloproteases, 10 cadherins and 98 calmodulins. We found 460 putative miRNAs and we predicted a significant number of single nucleotide polymorphisms (29,205) and microsatellite loci (17,284).ConclusionsThis report of the assembly and annotation of the transcriptome of L. decemlineata offers new insights into diapause-associated and insecticide-resistance-associated genes in this species and provides a foundation for comparative studies with other species of insects. The data will also open new avenues for researchers using L. decemlineata as a model species, and for pest management research. Our results provide the basis for performing future gene expression and functional analysis in L. decemlineata and improve our understanding of the biology of this invasive species at the molecular level.

Evaluation and integration of genetic signature for prediction risk of nasopharyngeal carcinoma in Southern China.

Genetic factors, as well as environmental factors, play a role in development of nasopharyngeal carcinoma (NPC). A number of single nucleotide polymorphisms (SNPs) have been reported to be associated with NPC. To confirm these genetic associations with NPC, two independent case-control studies from Southern China comprising 1166 NPC cases and 2340 controls were conducted. Seven SNPs in ITGA9 at 3p21.3 and 9 SNPs within the 6p21.3 HLA region were genotyped. To explore the potential clinical application of these genetic markers in NPC, we further evaluate the predictive/diagnostic role of significant SNPs by calculating the area under the curve (AUC). Results. The reported associations between ITGA9 variants and NPC were not replicated. Multiple loci of GABBR1, HLA-F, HLA-A, and HCG9 were statistically significant in both cohorts (P combined range from 5.96 × 10−17 to 0.02). We show for the first time that these factors influence NPC development independent of environmental risk factors. This study also indicated that the SNP alone cannot serve as a predictive/diagnostic marker for NPC. Integrating the most significant SNP with IgA antibodies status to EBV, which is presently used as screening/diagnostic marker for NPC in Chinese populations, did not improve the AUC estimate for diagnosis of NPC.

Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio).

BackgroundA large number of single nucleotide polymorphisms (SNPs) have been identified in common carp (Cyprinus carpio) but, as yet, no high-throughput genotyping platform is available for this species. C. carpio is an important aquaculture species that accounts for nearly 14% of freshwater aquaculture production worldwide. We have developed an array for C. carpio with 250,000 SNPs and evaluated its performance using samples from various strains of C. carpio.ResultsThe SNPs used on the array were selected from two resources: the transcribed sequences from RNA-seq data of four strains of C. carpio, and the genome re-sequencing data of five strains of C. carpio. The 250,000 SNPs on the resulting array are distributed evenly across the reference C.carpio genome with an average spacing of 6.6 kb. To evaluate the SNP array, 1,072 C. carpio samples were collected and tested. Of the 250,000 SNPs on the array, 185,150 (74.06%) were found to be polymorphic sites. Genotyping accuracy was checked using genotyping data from a group of full-siblings and their parents, and over 99.8% of the qualified SNPs were found to be reliable. Analysis of the linkage disequilibrium on all samples and on three domestic C.carpio strains revealed that the latter had the longer haplotype blocks. We also evaluated our SNP array on 80 samples from eight species related to C. carpio, with from 53,526 to 71,984 polymorphic SNPs. An identity by state analysis divided all the samples into three clusters; most of the C. carpio strains formed the largest cluster.ConclusionsThe Carp SNP array described here is the first high-throughput genotyping platform for C. carpio. Our evaluation of this array indicates that it will be valuable for farmed carp and for genetic and population biology studies in C. carpio and related species.

The Role of Single Nucleotide Polymorphisms in Predicting Prostate Cancer Risk and Therapeutic Decision Making

Prostate cancer (PCa) is a major health care problem because of its high prevalence, health-related costs, and mortality. Epidemiological studies have suggested an important role of genetics in PCa development. Because of this, an increasing number of single nucleotide polymorphisms (SNPs) had been suggested to be implicated in the development and progression of PCa. While individual SNPs are only moderately associated with PCa risk, in combination, they have a stronger, dose-dependent association, currently explaining 30% of PCa familial risk. This review aims to give a brief overview of studies in which the possible role of genetic variants was investigated in clinical settings. We will highlight the major research questions in the translation of SNP identification into clinical practice.

Urevaling the Underlying Genetic Factor of Antisocial Behavior Using Genome-Wide Association Study Methodology

Although antisocial behavior is a complex condition with environmental and genetic etiologies, the single susceptibility gene such as the Monoamine oxidase A(MAOA) gene, the serotonin transporter promoter gene(5-HTT) and the catechol O-methyltransferase gene, can't completely interpret the molecular genetics mechanism of the antisocial behavior. The genome-wide association study(GWAS) methodology from molecular genetics views millions of large number of single nucleotide polymorphisms(SNPs) and copy number variation(CNVs) as genetic markers to search the genetic locus related to external phenotype on the level of entire genome by high-throughput genotyping technology and so it can provide important clues for the further understanding of hereditary factors of antisocial behavior.In order to achieve the analysis for the gene-psychology-environment mechanism of complex traits or behavior, future studies should combine the accurate genotyping techniques with mental and environment factors.

The application of network label propagation to rank biomarkers in genome-wide Alzheimer's data.

BackgroundRanking and identifying biomarkers that are associated with disease from genome-wide measurements holds significant promise for understanding the genetic basis of common diseases. The large number of single nucleotide polymorphisms (SNPs) in genome-wide studies (GWAS), however, makes this task computationally challenging when the ranking is to be done in a multivariate fashion. This paper evaluates the performance of a multivariate graph-based method called label propagation (LP) that efficiently ranks SNPs in genome-wide data.ResultsThe performance of LP was evaluated on a synthetic dataset and two late onset Alzheimer’s disease (LOAD) genome-wide datasets, and the performance was compared to that of three control methods. The control methods included chi squared, which is a commonly used univariate method, as well as a Relief method called SWRF and a sparse logistic regression (SLR) method, which are both multivariate ranking methods. Performance was measured by evaluating the top-ranked SNPs in terms of classification performance, reproducibility between the two datasets, and prior evidence of being associated with LOAD.On the synthetic data LP performed comparably to the control methods. On GWAS data, LP performed significantly better than chi squared and SWRF in classification performance in the range from 10 to 1000 top-ranked SNPs for both datasets, and not significantly different from SLR. LP also had greater ranking reproducibility than chi squared, SWRF, and SLR. Among the 25 top-ranked SNPs that were identified by LP, there were 14 SNPs in one dataset that had evidence in the literature of being associated with LOAD, and 10 SNPs in the other, which was higher than for the other methods.ConclusionLP performed considerably better in ranking SNPs in two high-dimensional genome-wide datasets when compared to three control methods. It had better performance in the evaluation measures we used, and is computationally efficient to be applied practically to data from genome-wide studies. These results provide support for including LP in the methods that are used to rank SNPs in genome-wide datasets.

Prostate Cancer Risk Alleles are Associated with Prostate Cancer Volume and Prostate Size

Genome-wide association studies have identified an increasing number of single nucleotide polymorphisms associated with prostate cancer risk. Some of these genetic variants are also associated with serum prostate specific antigen levels and lower urinary tract symptoms, raising the question of whether they are truly prostate cancer biomarkers or simply lead to detection bias. Therefore, we determined whether single nucleotide polymorphisms associated with prostate cancer risk are more strongly associated with tumor or prostate volume. The genotypes of 38 validated prostate cancer risk single nucleotide polymorphisms were determined in 1,321 white men who underwent radical prostatectomy. Univariate and multivariate analyses were performed to compare the relationship of single nucleotide polymorphism frequency with total prostate and tumor volumes. On multivariate analysis 2 single nucleotide polymorphisms on chromosome 8q24, rs16901979 (A) and rs6983267 (G), were significantly associated with increased tumor volume (p=0.01 and 0.02, respectively). In contrast, rs17632542 (T) near the PSA gene on 19q13 was associated with significantly lower tumor volume and rs10788160 (A) on 10q26 was associated with significantly larger prostate volume (p=0.02 and 0.01, respectively). Analysis of 38 single nucleotide polymorphisms associated with prostate cancer risk revealed a significant association between several on chromosome 8q24 and increased tumor volume but not prostate volume. This suggests that they are bona fide markers of prostate cancer susceptibility and possibly more aggressive disease. Other prostate cancer risk alleles are associated with prostate specific antigen and increased prostate or decreased tumor volume, suggesting detection bias due to their phenotypic influence.

Identification of novel genetic markers and evaluation of genetic structure in a population of Japanese crested ibis

Japanese population of the Japanese crested ibis Nipponia nippon was founded by five individuals gifted from the People's Republic of China. In order to exactly evaluate genetic structure, we first performed development of novel genetic makers using 89 microsatellite primer pairs of related species for cross-amplification. Of these, only three primer pairs were useful for the genetic markers. Additionally, we sequenced allelic PCR products of these three markers together with 10 markers previously identified. Most markers showed typical microsatellite repeat units, but two markers were not simple microsatellites. Moreover, over half of the markers did not have the same repeat units as those of the original species. These results suggested that development of novel genetic markers in this population by cross-amplification is not efficient, partly because of low genetic diversity. Furthermore, the cluster analysis by STRUCTURE program using 17 markers showed that the five founders were divided into two clusters. However, the genetic relationships among the founders indicated by the clustering seemed to be questionable, because the analysis relied largely on a small number of triallelic markers, in spite of the addition of the three useful markers. Therefore, more efficient methods for identifying large numbers of single nucleotide polymorphisms are desirable.

The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep

In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the presence of recombination, a severe reduction in sequence diversity is expected around a strongly beneficial allele. The site frequency spectrum is an important tool in genome scans for selection and is composed of the numbers , where is the number of single nucleotide polymorphisms (SNPs) present in from individuals. Previous work has shown that both the number of low- and high-frequency variants are elevated relative to neutral evolution when a strongly beneficial allele fixes. Here, we follow a recent investigation of genetic hitchhiking using a marked Yule process to obtain an analytical prediction of the site frequency spectrum in a panmictic population at the time of fixation of a highly beneficial mutation. We combine standard results from the neutral case with the effects of a selective sweep. As simulations show, the resulting formula produces predictions that are more accurate than previous approaches for the whole frequency spectrum. In particular, the formula correctly predicts the elevation of low- and high-frequency variants and is significantly more accurate than previously derived formulas for intermediate frequency variants.

The 18S rDNA gene discriminates between red-listed and unexplored ethnomedicinal species of Myristicaceae restricted to humid tropics of India

A potentially diagnostic 18S rDNA (ribosomal DNA) gene was amplified reliably from red-listed ethnomedicinal species of Myristica and its wild and related genera. Individuals from nine species of Myristicaceae were utilized for the study. The sequences ranged from 1,767 to 1,794 nucleotide (nt) in length. The GC content (%) varied from 52.77 to 51.04. The frequencies (%) of nt were A (23.31), T (23.82), C (24.48) and G (28.39). The alignment of all sequences produced 195/1,516 variable sites and 1,257/1,516 conserved sites. Total numbers of single nucleotide polymorphism (SNP) sites found in the alignment were 146/1,516. Knema andamanica (Warb.) W.J. de Wilde was the most distinct that included 18 variable regions and 15 InDel with 27 SNP sites, specific to this species. The identified regions from nine species of Myristica and its wild and closely related genera were deposited in the GenBank Database (Accession numbers JN228257-JN228265). Comparison of morphological identifications and phylogenetic analysis indicated that the specimens were correctly assigned on the basis of a short stretch of 18S rDNA (~1,600 bp) making this a potentially useful marker for the rapid molecular assignment of an unknown related species also. Significant sequence homology ranging from 72 to 99 % was observed on comparison with 18S rDNA genes of other plants in the public domain. A comparison of intraspecific data information of nine 18S with that of 73 matK and 86 rbcL sequences from GenBank revealed that polymorphism, divergence and conservation is higher in 18S locus for Myristicaceae. Hence these markers may be utilized for phylogenetic analysis, evaluation of species richness during ecological surveys or for environmental assessments. These molecular markers are especially important due to the fact that the species studied are mostly vulnerable and red-listed with limited availability in endangered ecological niches.