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At least 37 records · Page 2Linked to original sources
PubMed2000

Allele association studies with SSR and SNP markers at known physical distances within a 1 Mb region embracing the ALDH2 locus in the Japanese, demonstrates linkage disequilibrium extending up to 400 kb.

There has been considerable recent debate concerning the distances over which levels of allelic association useful for genomic quantitative trait locus (QTL) scans can be detected. We have examined simple sequence repeat (SSR) polymorphisms and two single nucleotide polymorphisms (SNPs) in the region flanking the aldehyde dehydrogenase 2 locus, ALDH2, in populations of Japanese alcoholics and controls. These groups differ significantly in the allele frequencies for the functional SNP in exon XII of this gene located on chromosome 12. The results obtained with SSR markers complement recent investigations with SNPs over similar distances at the TCR alpha/delta locus. Significant allelic association with this marker could be detected for SSRs over distances up to 400 kb and over 37 kb for the SNP thereby extending the distance over which LD at this locus could be detected by an order of magnitude. Furthermore, as a proof of principle, we show that comparisons of allele frequency differences for the SSR markers in the case (alcoholics) and control populations would have detected the ALDH2 marker as a putative QTL. Extending the tests to include alleles at two or three flanking loci suggests that the power to detect QTLs through association can be enhanced significantly.

Alcohol Dehydrogenase↗
PubMed2005

The effect of SNP marker density on the efficacy of haplotype tagging SNPs--a warning.

We investigate here the efficacy of selecting haplotype tagging SNPs at different marker densities (2kb-10kb). Our results are based on publicly available data on 5324 markers with a median spacing of 1kb from chromosome 20. We find that whatever density of SNPs is used, htSNP analysis indicates in most cases that at least 80% of the variation can be captured using a subset of SNPs. However, as marker density decreases these htSNPs become increasingly unreliable. In this dataset htSNPs were selected to capture at least 80% of the variation at every observed SNP. At an observed SNP density of 2kb, htSNP analysis suggests that the htSNPs capture on average 95% of the observed variation, when in fact they capture 88% of the unobserved variation. At a density of 10kb, htSNP analysis suggests that 93% of the observed variation was captured, when in fact they capture on average only 78%. Our results indicate that htSNP analysis is only reliable when markers are dense--a spacing of even 2kb shows a considerable loss of information. Such findings are important both for individual studies utilising htSNPs to reduce costs, and for projects such as HapMap which try to characterise human genomic variation using htSNPs.

Chromosomes, Human, Pair 20↗
PubMed2006

[SNP marker and allele-specific diagnostic PCR for authenticating herbs of Perilla].

AIM: To authenticate all the varieties of Perilla (single-species genus), to analyze sequences of rDNA ITS regions and single nucleotide polymorphism (SNP) within them and based on these, to design allele-specific diagnostic PCR primers. METHODS: The rDNA ITS regions of the perilla varieties were sequenced and analyzed by Clustal X 1.8, MEGA 3.0. Allele-specific diagnostic PCR primers that can authenticate all the perilla varieties were designed based on SNPs loci. RESULTS: The length of rDNA ITS sequences of perilla varieties ranged from 612 to 615 bp in size, including ITS1 (230 -232 bp), 5.8S (179 bp) and ITS2 (203 -204 bp). The GC content is about 61.5% - 61.9%. There is not only SNPs in non-coding region ITS1 and ITS2 (ncSNP), but also three coding SNPs (cSNP) loci in the conservative region of 5.8S. All the SNPs have only two allele loci polymorphism. The cSNP in 5.8S is related to the morphology variation among the varieties. Allele-specific diagnostic PCR primers have been designed according to SNPs loci to authenticate accurately all the seeds and leaves of Perilla varieties. CONCLUSION: SNPs in rDNA ITS region can be used as an effective molecular markers to authenticate all the varieties of Perilla.

Alleles↗
PubMed2001

Genetic mapping with SNP markers in Drosophila.

Map-based positional cloning of Drosophila melanogaster genes is hampered by both the time-consuming, error-prone nature of traditional methods for genetic mapping and the difficulties in aligning the genetic and cytological maps with the genome sequence. The identification of sequence polymorphisms in the Drosophila genome will make it possible to map mutations directly to the genome sequence with high accuracy and resolution. Here we report the identification of 7,223 single-nucleotide polymorphisms (SNPs) and 1,392 insertions/deletions (InDels) in common laboratory strains of Drosophila. These sequence polymorphisms define a map of 787 autosomal marker loci with a resolution of 114 kb. We have established PCR product-length polymorphism (PLP) or restriction fragment-length polymorphism (RFLP) assays for 215 of these markers. We demonstrate the use of this map by delimiting two mutations to intervals of 169 kb and 307 kb, respectively. Using a local high-density SNP map, we also mapped a third mutation to a resolution of approximately 2 kb, sufficient to localize the mutation within a single gene. These methods should accelerate the rate of positional cloning in Drosophila.

Animals↗
PubMed2006

Development of loop-mediated isothermal amplification (LAMP)-based SNP markers for shelf-life in melon (Cucumis melo L.).

In this study, LAMP markers linked to shelf-life in melon (Cucumis melo L.) were developed by converting a cleaved amplified polymorphic sequences (CAPS) marker (C2). The CAPS-PCR fragments from the long-shelf-life melon (O-3) and short-shelf-life melon (Nat-2) were cloned and sequenced to construct LAMP primers. A single nucleotide polymorphism (SNP) was identified between O-3 and Nat-2. LAMP primers were designed to detect the SNP. In the LAMP reaction to detect long-shelf-life melon, the turbidity of the templates using O-3, F1, homozygous long-shelf-life F2 lines and heterozygous long-shelf-life F2 lines started to increase after 40 min. In contrast, the turbidity of Nat-2 and homozygous short-shelf-life F2 lines did not increase even after 90 min. In the LAMP reaction to detect short-shelf-life melon, the turbidity of the templates using Nat-2, F1, homozygous short-shelf-life F2 lines and heterozygous long-shelf-life F2 lines started to increase after 40 min. But the turbidity of O-3 and homozygous long-shelf-life F2 lines did not increase after 90 min. This attests to the high reliability and usefulness of LAMP for marker-assisted selection.

Base Sequence↗
PubMed2002

SNP markers for black-grass ( Alopecurus myosuroides Huds.) genotypes resistant to acetyl CoA-carboxylase inhibiting herbicides.

Chloroplastic acetyl CoA-carboxylase (ACCase) is the target of widely used, specific graminicide herbicides: cyclohexanediones (CHDs) and aryloxyphenoxypropionates (APPs). Resistance to these compounds is a worldwide, increasing problem. Population genetic studies aimed at understanding the dynamics of this situation and the diffusion of resistance genes within and between weed populations are challenging because biological assays are not adequate for this purpose, and because different mechanisms of resistance confer a similar resistance phenotype. Molecular markers for specifically detecting resistance genes are therefore urgently needed to conduct such studies. For this purpose, we cloned and sequenced the whole gene encoding chloroplastic ACCase in Alopecurus myosuroides Huds. (Black-grass). We identified two point mutations at nucleotide 5,341 that both cause an isoleucine-leucine substitution at position 1,781. Three bi-directional allele-specific PCR assays were developed, each detecting two distinct ACCase alleles with a single PCR reaction. The sensitivity of 1,190 seedlings of A. myosuroides to one CHD and one APP was determined. Genotyping revealed that, although resistant plants were only selected by APPs, the (1,781)Leu ACCase allele is a widespread, dominant gene of resistance to both APPs and CHDs. No other ACCase allele associated with resistance could be identified in this work. Useful applications of allele-specific PCR markers are population genetic studies as well as routine molecular diagnosis of herbicide resistance.

Journal Article↗
PubMed2006

Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping.

Carotenoid pigments are important components of the human diet and carrots are the main dietary sources of the vitamin A precursors alpha- and beta-carotene. Carotenoids play essential biological roles in plants and the genes coding for the carotenoid pathway enzymes are evolutionarily conserved, but little information exists about these genes for carrot. In this study, we utilized published carrot sequences as well as heterologous PCR approaches with primers derived from sequence information of other plant species to isolate 24 putative genes coding for carotenoid biosynthesis enzymes in carrot. Twenty-two of these genes were placed on the carrot genetic linkage map developed from a cross between orange-rooted and white-rooted carrot. The carotenoid genes were distributed in eight of the nine linkage groups in the carrot genome recommending their use for merging maps. Two genes co-localized with a genomic region spanning one of the most significant quantitative trait loci (QTL) for carotenoid accumulation. Carotenoid biosynthesis cDNAs linked to root color mutations and to QTL for carotenoid accumulation may suggest a functional role for them as candidate genes. RACE PCR and reverse transcriptase PCR were used to amplify the full-length transcript for twenty expressed carotenoid biosynthesis genes and sequences were submitted to GenBank. The cloning and sequence information of these genes is useful for PCR-based expression studies and may point toward transgenic approaches to manipulate carotenoid content in carrot.

Base Sequence↗
PubMed2000

Association analysis with microsatellite and SNP markers does not support the involvement of BCL-2 in systemic lupus erythematosus in Mexican and Swedish patients and their families.

We have described suggestive linkage between microsatellite markers within the cytogenetic region 18q21-23 and SLE, a region where linkage with other autoimmune diseases has also been detected. The Bcl-2 gene located within this region, is a candidate gene because of its role in apoptosis, a physiological mechanism that could be deregulated in autoimmune disease. Furthermore, several studies have found abnormalities of Bcl-2 expression in SLE patients. We therefore sought to determine if the Bcl-2 gene is involved in SLE by studying members of a large cohort of Mexican SLE patients (n = 378) and 112 Swedish simplex families. Using a microsatellite marker and two single nucleotide polymorphisms located within the gene, we were unable to detect association between Bcl-2 and SLE in either population. We also tested whether combinations of alleles of the Bcl-2 and IL-10.G microsatellites would increase the risk for SLE. Our results do not support such hypothesis. Our findings suggest that linkage between SLE and the 18q21-23 region is due to a gene other than Bcl-2.

Alleles↗
PubMed2005

cDNA sequence of the horse (Equus caballus) LAMA3 gene and characterization of two intronic SNP markers.

Laminins are large heterotrimeric basement membrane glycoproteins composed of alpha, beta and gamma chains. The Laminin 5 isoform has an alpha3beta3gamma2 composition and is essential for the adhesion of basal keratinocytes to the underlying epithelial basement membrane where it is mainly located. Mutations in the genes coding for the 3 chains have been associated with a severe skin blistering disease, Herlitz's junctional epidermolysis bullosa (JEB), observed in different species as man, dog, cat and horse. In this study, we report the sequence of the 5.2 kb horse laminin alpha 3 cDNA (LAMA3) as well as the detection of two intronic SNPs. These data will be useful to further identify causal mutations for the disease in this gene.

Amino Acid Sequence↗
PubMed2006

Absence of significant associations between four AKT1 SNP markers and schizophrenia in the Taiwanese population.

AKT1 (V-akt murine thymoma viral oncogene homolog 1) is a protein kinase isoform of AKT. Five single-nucleotide polymorphisms, rs3803300, rs1130214, rs3730358, rs2498799 and rs2494732, at the genomic region of AKT1 have been reported to be significantly associated with schizophrenia. We tested for the presence of these five single-nucleotide polymorphisms in a Taiwanese population by genotyping 218 co-affected schizophrenia families. Both single locus and haplotypes analyses showed no association of these single-nucleotide polymorphisms with schizophrenia. These findings fail to support AKT1 as a susceptibility gene for schizophrenia in the Taiwanese population.

Genetic Markers↗
PubMed2006

Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP set.

We analyzed a global collection of Mycobacterium tuberculosis strains using 212 single nucleotide polymorphism (SNP) markers. SNP nucleotide diversity was high (average across all SNPs, 0.19), and 96% of the SNP locus pairs were in complete linkage disequilibrium. Cluster analyses identified six deeply branching, phylogenetically distinct SNP cluster groups (SCGs) and five subgroups. The SCGs were strongly associated with the geographical origin of the M. tuberculosis samples and the birthplace of the human hosts. The most ancestral cluster (SCG-1) predominated in patients from the Indian subcontinent, while SCG-1 and another ancestral cluster (SCG-2) predominated in patients from East Asia, suggesting that M. tuberculosis first arose in the Indian subcontinent and spread worldwide through East Asia. Restricted SCG diversity and the prevalence of less ancestral SCGs in indigenous populations in Uganda and Mexico suggested a more recent introduction of M. tuberculosis into these regions. The East African Indian and Beijing spoligotypes were concordant with SCG-1 and SCG-2, respectively; X and Central Asian spoligotypes were also associated with one SCG or subgroup combination. Other clades had less consistent associations with SCGs. Mycobacterial interspersed repetitive unit (MIRU) analysis provided less robust phylogenetic information, and only 6 of the 12 MIRU microsatellite loci were highly differentiated between SCGs as measured by GST. Finally, an algorithm was devised to identify two minimal sets of either 45 or 6 SNPs that could be used in future investigations to enable global collaborations for studies on evolution, strain differentiation, and biological differences of M. tuberculosis.

Algorithms↗
PubMed2005

Failure to confirm association between RGS4 haplotypes and schizophrenia in Caucasians.

The regulator of G-protein signaling (RGS) and RGS-like proteins are a diverse family of over 30 molecules that function as GTPase activating proteins for Galpha subunits of the Gq and Gi families of heterotrimeric guanine nucleotide-binding proteins (G proteins). By accelerating GTPase activity, RGS proteins drive G proteins into their inactive GDP-bound forms. G-protein coupled dopamine, metabotropic glutamate, and other neurotransmitter receptors can be modulated by RGS4, the predominant form in brain. The recent finding of decreased RGS4 mRNA expression in post-mortem brains from schizophrenic patients, coupled with the map position of RGS4 to a region previously linked to schizophrenia, as well as other biological data, prompted the investigation of the gene as a disease candidate. Multiple family-based and case-control association studies have been conducted, with modest and conflicting support for particular single nucleotide polymorphism (SNP) markers and SNP marker haplotypes. The present case-control analysis of 568 patients and 689 controls, one of the largest single studies to date, failed to confirm support for association of particular RGS4 SNP alleles, or for association of any particular four, three, or two SNP haplotype.

Adult↗
PubMed2005

Identification of genetic markers for fat deposition and meat tenderness on bovine chromosome 5: development of a low-density single nucleotide polymorphism map.

As genetic markers, SNP are well suited for the development of genetic tests for production traits in livestock. They are stable through many generations and can provide direct assessment of individual animal's genetic merit if they are in linkage disequilibrium and phase with functional genetic variation. Bovine chromosome 5 has been shown to harbor genetic variation affecting production traits in multiple cattle populations; thus, this chromosome was targeted for SNP-based marker development and subsequent association analysis with carcass and growth phenotypes. Discovery of SNP was performed in a panel of 16 sires representing two sires from each of seven beef breeds and two Holstein sires by PCR amplification and sequencing using primers designed from genomic sequence obtained by low-coverage sequencing of bacterial artificial chromosome (BAC) clones. From 550 SNP, 296 (54%) were tentatively identified as having a minor allele frequency >10%. Forty-five SNP derived from 15 BAC were chosen based on minor allele frequency and were genotyped in 564 steers and their sires. Production and carcass data were collected on the steers as a part of the Germplasm Evaluation (GPE), Cycle VII Project at the U.S. Meat Animal Research Center (Clay Center, NE), which involves of the evaluation of sires from seven of the most popular U.S. breeds. Haplotypes based on seven SNP derived from a BAC containing the bovine genes HEM1 and PDE1B were associated with traits related to carcass fat. Steers homozygous for the major haplotype had 0.15 +/- 0.04 cm less subcutaneous fat, 0.57 +/- 0.18 kg less rib fat, 0.18 +/- 0.07 lower yield grade, 1.11 +/- 0.35% less predicted fat yield, and 0.79 +/- 0.3% greater predicted retail product yield than heterozygotes. The frequency of the major haplotype was 0.70 in the steers, and it ranged from 0.44 (Limousin) to 0.98 (Simmental and Gelbvieh) in a panel consisting of an average of 20 purebred sires from each of the seven breeds. A second set of haplotypes based on four SNP derived from a BAC containing the genes NOL1 and CHD4 was associated with Warner-Bratzler shear force. Steers homozygous for the major haplotype had 0.27 +/- 0.11 kg greater shear force than those heterozygous for the major haplotype and one of two minor haplotypes. The frequency of the major haplotype was 0.59 in the steers and ranged from 0.27 (Hereford) to approximately 0.95 (Angus and Red Angus) in the panel of purebred sires. These results demonstrate the feasibility of targeting QTL regions for SNP-based marker development and that a low level of coverage can identify markers associated with phenotypic traits.

Adipose Tissue↗
PubMed2005

Comparison of single-nucleotide polymorphisms and microsatellite markers for linkage analysis in the COGA and simulated data sets for Genetic Analysis Workshop 14: Presentation Groups 1, 2, and 3.

The papers in presentation groups 1-3 of Genetic Analysis Workshop 14 (GAW14) compared microsatellite (MS) markers and single-nucleotide polymorphism (SNP) markers for a variety of factors, using multiple methods in both data sets provided to GAW participants. Group 1 focused on data provided from the Collaborative Study on the Genetics of Alcoholism (COGA). Group 2 focused on data simulated for the workshop. Group 3 contained analyses of both data sets. Issues examined included: information content, signal strength, localization of the signal, use of haplotype blocks, population structure, power, type I error, control of type I error, the effect of linkage disequilibrium, and computational challenges. There were several broad resulting observations. 1) Information content was higher for dense SNP marker panels than for MS panels, and dense SNP markers sets appeared to provide slightly higher linkage scores and slightly higher power to detect linkage than MS markers. 2) Dense SNP panels also gave higher type I errors, suggesting that increased test thresholds may be needed to maintain the correct error rate. 3) Dense SNP panels provided better trait localization, but only in the COGA data, in which the MS markers were relatively loosely spaced. 4) The strength of linkage signals did not vary with the density of SNP panels, once the marker density was approximately 1 SNP/cM. 5) Analyses with SNPs were computationally challenging, and identified areas where improvements in analysis tools will be necessary to make analysis practical for widespread use.

Alcoholism↗
PubMed2005

Which strategy is better for linkage analysis: single-nucleotide polymorphisms or microsatellites? Evaluation by identity-by-state-identity-by-descent transformation affected sib-pair method on GAW14 data.

The central issue for Genetic Analysis Workshop 14 (GAW14) is the question, which is the better strategy for linkage analysis, the use of single-nucleotide polymorphisms (SNPs) or microsatellite markers? To answer this question we analyzed the simulated data using Duffy's SIB-PAIR program, which can incorporate parental genotypes, and our identity-by-state - identity-by-descent (IBS-IBD) transformation method of affected sib-pair linkage analysis which uses the matrix transformation between IBS and IBD. The advantages of our method are as follows: the assumption of Hardy-Weinberg equilibrium is not necessary; the parental genotype information maybe all unknown; both IBS and its related IBD transformation can be used in the linkage analysis; the determinant of the IBS-IBD transformation matrix provides a quantitative measure of the quality of the marker in linkage analysis. With the originally distributed simulated data, we found that 1) for microsatellite markers there are virtually no differences in types I and II error rates when parental genotypes were or were not used; 2) on average, a microsatellite marker has more power than a SNP marker does in linkage detection; 3) if parental genotype information is used, SNP markers show lower type I error rates than microsatellite markers; and 4) if parental genotypes are not available, SNP markers show considerable variation in type I error rates for different methods.

Chromosome Mapping↗
PubMed2005

Comparing single-nucleotide polymorphism marker-based and microsatellite marker-based linkage analyses.

We compared linkage analysis results for an alcoholism trait, ALDX1 (DSM-III-R and Feigner criteria) using a nonparametric linkage analysis method, which takes into account allele sharing among several affected persons, for both microsatellite and single-nucleotide polymorphism (SNP) markers (Affymetrix and Illumina) in the Collaborative Study on the Genetics of Alcoholism (COGA) dataset provided to participants at the Genetic Analysis Workshop 14 (GAW14). The two sets of linkage results from the dense Affymetrix SNP markers and less densely spaced Illumina SNP markers are very similar. The linkage analysis results from microsatellite and SNP markers are generally similar, but the match is not perfect. Strong linkage peaks were found on chromosome 7 in three sets of linkage analyses using both SNP and microsatellite marker data. We also observed that for SNP markers, using the given genetic map and using the map by converting 1 megabase pair (1 Mb) to 1 centimorgan (cM), did not change the linkage results. We recommend the use of the 1 Mb-to-1 cM converted map in a first round of linkage analysis with SNP markers in which map integration is an issue.

Chromosomes, Human, Pair 7↗