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At least 901 records · Page 50Linked to original sources
PubMed2005

A microsatellite-based, gene-rich linkage map for the AA genome of Arachis (Fabaceae).

Cultivated peanut (Arachis hypogaea) is an important crop, widely grown in tropical and subtropical regions of the world. It is highly susceptible to several biotic and abiotic stresses to which wild species are resistant. As a first step towards the introgression of these resistance genes into cultivated peanut, a linkage map based on microsatellite markers was constructed, using an F(2) population obtained from a cross between two diploid wild species with AA genome (A. duranensis and A. stenosperma). A total of 271 new microsatellite markers were developed in the present study from SSR-enriched genomic libraries, expressed sequence tags (ESTs), and by "data-mining" sequences available in GenBank. Of these, 66 were polymorphic for cultivated peanut. The 271 new markers plus another 162 published for peanut were screened against both progenitors and 204 of these (47.1%) were polymorphic, with 170 codominant and 34 dominant markers. The 80 codominant markers segregating 1:2:1 (P<0.05) were initially used to establish the linkage groups. Distorted and dominant markers were subsequently included in the map. The resulting linkage map consists of 11 linkage groups covering 1,230.89 cM of total map distance, with an average distance of 7.24 cM between markers. This is the first microsatellite-based map published for Arachis, and the first map based on sequences that are all currently publicly available. Because most markers used were derived from ESTs and genomic libraries made using methylation-sensitive restriction enzymes, about one-third of the mapped markers are genic. Linkage group ordering is being validated in other mapping populations, with the aim of constructing a transferable reference map for Arachis.

Arachis↗
PubMed1986

Restriction endonuclease map variation in the Adh region in populations of Drosophila melanogaster.

Variation within a 12-kb region of the second chromosome of Drosophila melanogaster which includes the Adh transcriptional unit was studied in 59 isochromosomal lines drawn from two populations. A number of restriction-fragment length polymorphisms due to both restriction-site presence/absence and insertions/deletions were revealed and the proportion of polymorphic nucleotides was estimated as 0.017 in population "Chateau Tahbilk" and 0.025 in population "Groningen." The presence within population Groningen of two complementary haplotypes at a high frequency was noted and its possible origin is discussed. The distribution of insertion/deletion variants within the populations was consistent with an associated deleterious effect and significant clustering of such variants to a 1-kb region approximately 4 kb from the transcriptional unit was also revealed. Analysis of gametic disequilibrium showed that its intensity was not related to the physical distance separating the markers on the chromosome and that strong disequilibria may flank weaker disequilibria. Two alternative interpretations of these data are advanced based upon natural selection and the hitchhiking effect of a favorable mutation. Comparisons of gametic disequilibrium among the four populations now surveyed at this locus were made using model fitting by weighted least squares and several significant contrasts were revealed.

Alcohol Dehydrogenase↗
PubMed1999

Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle.

We previously mapped a quantitative trait locus (QTL) affecting milk production to bovine chromosome 14. To refine the map position of this QTL, we have increased the density of the genetic map of BTA14q11-16 by addition of nine microsatellites and three single nucleotide polymorphisms. Fine-mapping of the QTL was accomplished by a two-tiered approach. In the first phase, we identified seven sires heterozygous "Qq" for the QTL by marker-assisted segregation analysis in a Holstein-Friesian pedigree comprising 1,158 individuals. In a second phase, we genotyped the seven selected sires for the newly developed high-density marker map and searched for a shared haplotype flanking an hypothetical, identical-by-descent QTL allele with large substitution effect. The seven chromosomes increasing milk fat percentage were indeed shown to carry a common chromosome segment with an estimated size of 5 cM predicted to contain the studied QTL. The same haplotype was shown to be associated with increased fat percentage in the general population as well, providing additional support in favor of the location of the QTL within the corresponding interval.

Animals↗
PubMed2026

EPIC: Event Prototyping via Information Constrained graph learning for personalized cancer driver gene prediction.

MOTIVATION: Precision oncology relies on accurately distinguishing patient-specific driver mutations from the vast background of passenger alterations. While graph-based computational methods have emerged as powerful tools for this task, they often struggle to preserve the distinct genomic context of individual mutations within complex biological networks. Consequently, subtle patient-specific driver signals are frequently obscured by dominant topological patterns, critically impeding the identification of individualized oncogenic events essential for personalized cancer therapy. RESULTS: To address this, we propose EPIC, a novel framework for Event Prototyping via Information Constrained Graph Learning. Unlike traditional node-centric approaches, EPIC redefines driver prediction as a metric learning task in an event embedding space. We introduce an information-constrained learning strategy that imposes explicit geometric constraints on feature variance, effectively preventing feature collapse and ensuring that low-frequency driver signals are distinctively preserved. Experiments on large-scale cancer cohorts demonstrate that EPIC significantly outperforms established baselines. Notably, the model prioritizes low-frequency driver variants typically overlooked by population-based methods, mapping them to critical oncogenic mechanisms associated with drug resistance and metastasis. Furthermore, clinical actionability analysis confirms that EPIC substantially expands the patient population eligible for targeted therapies. EPIC provides a robust and context-aware solution for personalized cancer driver discovery, bridging the gap between genomic data and actionable therapeutic insights. AVAILABILITY AND IMPLEMENTATION: The source code and datasets are available at https://github.com/spcho-dev/EPIC.

Humans↗
PubMed2004

The Arabidopsis genome sequence as a tool for genome analysis in Brassicaceae. A comparison of the Arabidopsis and Capsella rubella genomes.

The annotated Arabidopsis genome sequence was exploited as a tool for carrying out comparative analyses of the Arabidopsis and Capsella rubella genomes. Comparison of a set of random, short C. rubella sequences with the corresponding sequences in Arabidopsis revealed that aligned protein-coding exon sequences differ from aligned intron or intergenic sequences in respect to the degree of sequence identity and the frequency of small insertions/deletions. Molecular-mapped markers and expressed sequence tags derived from Arabidopsis were used for genetic mapping in a population derived from an interspecific cross between Capsella grandiflora and C. rubella. The resulting eight Capsella linkage groups were compared to the sequence maps of the five Arabidopsis chromosomes. Fourteen colinear segments spanning approximately 85% of the Arabidopsis chromosome sequence maps and 92% of the Capsella genetic linkage map were detected. Several fusions and fissions of chromosomal segments as well as large inversions account for the observed arrangement of the 14 colinear blocks in the analyzed genomes. In addition, evidence for small-scale deviations from genome colinearity was found. Colinearity between the Arabidopsis and Capsella genomes is more pronounced than has been previously reported for comparisons between Arabidopsis and different Brassica species.

Arabidopsis↗
PubMed2004

Isolates and their potential use in complex gene mapping efforts.

Linkage disequilibrium (LD), detectable with microsatellites in disease alleles over wide genetic intervals in population isolates, has facilitated mapping and positional cloning of numerous disease genes. We, among others, have shown that the LD intervals reach up to 1 Mb in general alleles of young subisolates, and that this feature most probably offers an avenue for the initial locus positioning for complex traits. Development of efficient SNP genotyping and characterization of haploblock structure of the human genome have introduced new prospects to LD-based fine mapping and haplotype-association studies. Encouraging associations have been reported for several complex diseases. Final breakthroughs in mapping of complex disease loci have emerged on large pedigrees in population isolates. Conversely, ignoring genealogical makeup of the study population seems to disclose false negative and false positive associations, directing resources down the drain.

Chromosome Mapping↗
PubMed2002

[QTL analysis of sheath blight resistance in rice (Oryza sativa L.)].

In this study, an indica variety Zhai Ye Qing 8 (ZYQ8) and a japonica variety Jing Xi 17(JX17) and their double haploid (DH) population were used. Sheath blight resistance of the DH population and their parents was investigated using a syringe inoculation method. Quantitative trait loci (QTL) analysis was undertaken based on a constructed molecular linkage map of this population in Hangzhou and Hainandao respectively. A total of four sheath blight resistant QTLs (qSBR-2, qSBR-3, qSBR-7 and qSBR-11) were identified, and located on chromosome 2, 3, 7 and 11, respectively. Resistant alleles of qSBR-2, qSBR-3, and qSBR-7 were derived from the resistant parent ZYQ8, whereas resistant allele of qSBR-11 from susceptible parent JX17. qSBR-2, qSBR-3 and qSBR-7 were detected both in Hangzhou and Hainandao, whereas qSBR-11 was detected only in Hangzhou. Sheath blight response was significantly correlated with culm length and heading date in Hangzhou's test. Among the QTLs for culm length and heading date, only qCL-3 for culm length, was in the same chromosome region of qSBR-3, the other QTLs were not linked to the QTLs for sheath blight resistance.

Chromosome Mapping↗
PubMed2006

Genetic mapping of the gene affecting polyphenol oxidase activity in tetraploid durum wheat.

The quality of durum wheat (Triticum turgidum ssp. durum) is influenced by polyphenol oxidase(PPO) activity and its corresponding substrates. A saturated molecular-marker linkage map was constructed previously by using a set of recombinant inbred (RI) lines, derived from a cross between durum wheat cultivars Jennah Khetifa and Cham 1. Quantitative trait loci (QTL) for PPO activity in seeds were mapped in this population. PPO activity in seeds of the parents and 110 RI lines was measured spectrophotometrically. The PPO activity of Cham 1 was significantly lower than that of Jennah Khetifa. QTL analysis of these data indicated that most of PPO activity was associated with major loci on the long arm of chromosome 2A. The trait was found to be strongly associated with the SSR marker Xgwm312@2A. With this knowledge, marker-assisted selection can be used to select genotypes with lower PPO activity in durum wheat populations.

Breeding↗
PubMed2002

Strong positive selection and habitat-specific amino acid substitution patterns in MHC from an estuarine fish under intense pollution stress.

Population-level studies using the major histocompatibility complex (Mhc) have linked specific alleles with specific diseases, but data requirements are high and the power to detect disease association is low. A novel use of Mhc population surveys involves mapping allelic substitutions onto the inferred structural molecular model to show functional differentiation related to local selective pressures. In the estuarine fish Fundulus heteroclitus, populations experiencing strong differences in antigenic challenges show significant differences in amino acid substitution patterns that are reflected as variation in the structural location of changes between populations. Fish from a population genetically adapted to severe chemical pollution also show novel patterns of DNA substitution at a highly variable Mhc class II B locus including strong signals of positive selection at inferred antigen-binding sites and population-specific signatures of amino acid substitution. Heavily parasitized fish from an extreme PCB-contaminated (U.S. Environmental Protection Agency Superfund) site show enhanced population-specific substitutions in the a-helix portion of the inferred antigen-binding region. In contrast, fish from an unpolluted site show a significantly different pattern focused on the first strand of the B-pleated sheet. Whether Mhc population profile differences represent the direct effects of chemical toxicants or indirect parasite-mediated selection, the result is a composite habitat-specific signature of strong selection and evolution affecting the genetic repertoire of the major histocompatibility complex.

Alleles↗
PubMed1996

The perceptual magnet effect as an emergent property of neural map formation.

The perceptual magnet effect is one of the earliest known language-specific phenomena arising in infant speech development. The effect is characterized by a warping of perceptual space near phonemic category centers. Previous explanations have been formulated within the theoretical framework of cognitive psychology. The model proposed in this paper builds on research from both psychology and neuroscience in working toward a more complete account of the effect. The model embodies two principal hypotheses supported by considerable experimental and theoretical research from the neuroscience literature: (1) sensory experience guides language-specific development of an auditory neural map, and (2) a population vector can predict psychological phenomena based on map cell activities. These hypotheses are realized in a self-organizing neural network model. The magnet effect arises in the model from language-specific nonuniformities in the distribution of map cell firing preferences. Numerical simulations verify that the model captures the known general characteristics of the magnet effect and provides accurate fits to specific psychophysical data.

Auditory Perception↗
PubMed2006

Interaction between Mycobacterium avium subsp. paratuberculosis and environmental protozoa.

BACKGROUND: Interactions between Mycobacterium avium subsp. paratuberculosis (Map) and free-living protozoa in water are likely to occur in nature. The potential impact of ingestion of Map by two naturally occurring Acanthamoeba spp. on this pathogen's survival and chlorine resistance was investigated. RESULTS: Between 4.6 and 9.1% of spiked populations of three Map strains (NCTC 8578, B2 and ATCC 19698), which had been added at a multiplicity of infection of 10:1, were ingested by Acanthamoeba castellanii CCAP 1501/1B and A. polyphaga CCAP 1501/3B during co-culture for 3 h at 25 degrees C. Map cells were observed to be present within the vacuoles of the amoebae by acid-fast staining. During extended co-culture of Map NCTC 8578 at 25 degrees C for 24 d with both A. castellanii and A. polyphaga Map numbers did not change significantly during the first 7 days of incubation, however a 1-1.5 log10 increase in Map numbers was observed between days 7 and 24 within both Acanthamoeba spp. Ingested Map cells were shown to be more resistant to chlorine inactivation than free Map. Exposure to 2 mug/ml chlorine for 30 min resulted in a log10 reduction of 0.94 in ingested Map but a log10 reduction of 1.73 in free Map (p < 0.001). CONCLUSION: This study demonstrated that ingestion of Map by and survival and multiplication of Map within Acanthamoeba spp. is possible, and that Map cells ingested by amoebae are more resistant to inactivation by chlorine than free Map cells. These findings have implications with respect to the efficacy of chlorination applied to Map infected surface waters.

Acanthamoeba↗
PubMed2005

An expressed sequence tag SSR map of tetraploid alfalfa (Medicago sativa L.).

A genetic map constructed from a population segregating for a trait of interest is required for QTL identification. The goal of this study was to construct a molecular map of tetraploid alfalfa (Medicago sativa.) using simple sequence repeat (SSR) markers derived primarily from expressed sequence tags (ESTs) and bacterial artificial chromosome (BAC) inserts of M. truncatula. This map will be used for the identification of drought tolerance QTL in alfalfa. Two first generation backcross populations were constructed from a cross between a water-use efficient, M. sativa subsp. falcata genotype and a low water-use efficient M. sativa subsp. sativa genotype. The two parents and their F(1) were screened with 1,680 primer pairs designed to amplify SSRs, and 605 single dose alleles (SDAs) were amplified. In the F(1), 351 SDAs from 256 loci were mapped to 41 linkage groups. SDAs not inherited by the F(1), but transmitted through the recurrent parents and segregating in the backcross populations, were mapped to 43 linkage groups, and 44 of these loci were incorporated into the composite maps. Homologous linkage groups were joined to form eight composite linkage groups representing the eight chromosomes of M. sativa. The composite maps consist of eight composite linkage groups with 243 SDAs from M. truncatula EST sequences, 38 SDAs from M. truncatula BAC clone sequences, and five SDAs from alfalfa genomic SSRs. The total composite map length is 624 cM, with average marker density per composite linkage group ranging from 1.5 to 4.4 cM, and an overall average density of 2.2 cM. Segregation distortion was 10%, and distorted loci tended to cluster on individual homologues of several linkage groups.

Chromosome Mapping↗
PubMed2007

The quantitative trait gene latexin influences the size of the hematopoietic stem cell population in mice.

We mapped quantitative trait loci that accounted for the variation in hematopoietic stem cell (HSC) numbers between young adult C57BL/6 (B6) and DBA/2 (D2) mice. In reciprocal chromosome 3 congenic mice, introgressed D2 alleles increased HSC numbers owing to enhanced proliferation and self-renewal and reduced apoptosis, whereas B6 alleles had the opposite effects. Using oligonucleotide arrays, real-time PCR and protein blots, we identified latexin (Lxn), a gene whose differential transcription and expression was associated with the allelic differences. Expression was inversely correlated with the number of HSCs; therefore, ectopic expression of Lxn using a retroviral vector decreased stem cell population size. We identified clusters of SNPs upstream of the Lxn transcriptional start site, at least two of which are associated with potential binding sites for transcription factors regulating stem cells. Thus, promoter polymorphisms between the B6 and D2 alleles may affect Lxn gene expression and consequently influence the population size of hematopoietic stem cells.

Animals↗
PubMed2005

A comparative genetic map of the turkey genome.

Genetic markers (microsatellites and SNPs) were used to create and compare maps of the turkey and chicken genomes. A physical map of the chicken genome was built by comparing sequences of turkey markers with the chicken whole-genome sequence by BLAST analysis. A genetic linkage map of the turkey genome (Meleagris gallopavo) was developed by segregation analysis of genetic markers within the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) resource population. This linkage map of the turkey genome includes 314 loci arranged into 29 linkage groups. An additional 40 markers are tentatively placed within linkage groups based on two-point LOD scores and 16 markers remain unlinked. Total map distance contained within linkage groups is 2,011 cM with the longest linkage group (47 loci) measuring 413.3 cM. Average marker interval over the 29 linkage groups was 6.4 cM. All but one turkey linkage group could be aligned with the physical map of the chicken genome. The present genetic map of the turkey provides a comparative framework for future genomic studies.

Animals↗
PubMed2002

[Genetic map of 10 STR loci on chromosome 9].

To understand the genetic polymorphism of 10 STR loci on chromosome 9 and reveal the difference on the linkage maps of different populations, the author used a set of nine tetranucleotide- and one tritranucleotide-repeat STR markers on chromosome 9 chosen from Genome Data Bank. EDTA-blood was collected from unrelated family in Baiyin City, Gansu province. DNA was extracted by Chelex-100 method and amplified by the polymerase chain reaction (PCR). The PCR products were analyzed using PAGE electrophoresis. We calculated the allele frequencies and heterozygosity and PIC of every ten STR loci. Using the data of Chinese Han pedigree, we constructed a genetic map of chromosome 9 making up with 10 STR loci. Then we compared our map with the map in GDB. Our results indicate that there are some differences on the genetic map between Chinese and GDB. That means, it is essential to do some population genetic evaluations before using the data of GDB into Chinese population.

China↗
PubMed1985

Genetic variation in North Amerindian populations: the geography of gene frequencies.

Ten-level synthetic gene frequency maps derived from a principal component analysis of seven polymorphic loci are displayed for a large sample of North Amerindian populations. These maps are useful for assessing population affinities over broad geographical regions and perhaps, as others have argued, for inferring recent migrations. The influence of European admixture is investigated by deleting highly admixed populations and regenerating the maps. In broad outline the resultant geographic patterning, while appearing more homogeneous, preserves many features of the maps that include the highly admixed samples--especially with respect to the Eskimo/non-Eskimo dichotomy. Further, in an effort to evaluate how varying the number of display levels affects patterning as well as interpretation, the maps were replotted at 5 and 20 levels. The 5-level maps are found to accentuate differences between the full data set and the less admixed data set, while the 20-level maps tend to obscure these differences.

Gene Frequency↗
PubMed2004

Detection of a new cerebral malaria susceptibility locus, using CBA mice.

Human cerebral malaria (CM) during acute Plasmodium falciparum infection is a serious neurological complication that leads to coma and death. P. berghei ANKA infection of CBA mice is a useful experimental model of CM. To identify host susceptibility loci, we performed chromosomal mapping in crossbred populations of both CM-susceptible CBA and CM-resistant DBA/2 mice. One significant region for a CM-susceptible locus in CBA mice was mapped to H2 region on Chromosome 17, tentatively designated cmsc. cmsc was mapped to a different chromosomal region from that previously reported in the C57BL/6 mouse model of CM. It is possible that different loci contribute to CM in CBA and C57BL/6 mouse strains. Comparison of the function of CM susceptibility loci between CBA and C57BL/6 mice could have important implications for the study of the complex pathogenesis of CM in humans.

Animals↗
PubMed2002

Mitochondrial DNA restriction map for the Caribbean fruit fly, Anastrepha suspensa, and occurrence of mitochondrial DNA diversity within highly inbred colonies.

A restriction map has been constructed for Anastrepha suspensa mitochondrial DNA. One HaeIII site was found to be polymorphic among individuals in highly inbred colonies and a feral population. Based on mapping information, the polymorphic site was determined to be in the ATPase 6 gene. Primers TK-J-3804 and C3-N-5460 amplified this region. The amplicon was cut by HaeIII in flies of one haplotype and not cut in flies of the other haplotype. From 30 to 43% of the individual flies studied had this additional HaeIlI site. After cloning of the approximately 5200 bp XbaI fragment, the two mitotypes were identified. A 988 base fragment, coding for the entire tRNA-Lys(AAG), tRNA-Asp(GAC), and ATPase 8genes, and a partial ATPase 6gene was sequenced Four silent mutations, including the one at the informative site were located. The HaeIII polymorphism and other sequence differences may prove useful as a diagnostic for identification of the origin of introduced fruit flies.

Animals↗