Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic mapping”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMed1995

Advanced intercross lines, an experimental population for fine genetic mapping.

An advanced intercrossed line (AIL) is an experimental population that can provide more accurate estimates of quantitative trait loci (QTL) map location than conventional mapping populations. An AIL is produced by randomly and sequentially intercrossing a population that initially originated from a cross between two inbred lines or some variant thereof. This provides increasing probability of recombination between any two loci. Consequently, the genetic length of the entire genome is stretched, providing increased mapping resolution. In this way, for example, with the same population size and QTL effect, a 95% confidence interval of QTL map location of 20 cM in the F2 is reduced fivefold after eight additional random mating generations (F10). Simulation results showed that to obtain the anticipated reduction in the confidence interval, breeding population size of the AIL in all generations should comprise an effective number of > or = 100 individuals. It is proposed that AILs derived from crosses between known inbred lines may be a useful resource for fine genetic mapping.

Animals↗
PubMed1995

Genetic mapping of the determinants of plaque morphology of coxsackievirus B4.

The genetic determinants of plaque size of two variants of coxsackie-virus B4, CB4-P and CB4-V, were identified using a panel of recombinant, chimeric viruses. When grown in monkey kidney cells, CB4-V yielded large plaques with an average size of 1.0 cm while CB4-P yielded small plaques with an average size of 0.4 cm. Two genetic domains, the 5' untranslated region and the VP4 gene sequence, independently influenced plaque size. Recombinant viruses containing the CB4-P genetic background with point mutations in either the VP1 or VP2 coding sequences had small plaque phenotypes. However, two additional chimerics containing the CB4-P genetic background with either a point mutation in the VP4 sequence or four substitutions in the 5' untranslated region, had large plaque phenotypes. Plaque size correlated with growth kinetics under single-step conditions. Large-plaque variants replicated to higher titers than small-plaque variants. Comparison of the growth kinetics of the recombinant viruses revealed some differences in viral replication. These data suggest that both the 5' untranslated region and arg-16 of VP4 influence viral replication but at different stages of the replication cycle.

Animals↗
PubMed1995

Genetic mapping of the dentinogenesis imperfecta type II locus.

Dentinogenesis imperfecta type II (DGI-II) is an autosomal dominant disorder of dentin formation, which has previously been mapped to chromosome 4q12-21. In the current study, six novel short tandem-repeat polymorphisms (STRPs) have been isolated, five of which show significant evidence of linkage to DGI-II. To determine the order of the STRPs and define the genetic distance between them, nine loci (including polymorphisms for two known genes) were mapped through the CEPH reference pedigrees. The resulting genetic map encompasses 16.3 cM on the sex-averaged map. To combine this map with a physical map of the region, all of the STRPs were mapped through a somatic cell hybrid panel. The most likely location for the DGI-II locus within the fixed marker map is in the D4S2691-D4S2692 interval of 6.6 cM. The presence of a marker that shows no recombination with the DGI-II phenotype between the flanking markers provides an important anchor point for the creation of physical continuity across the DGI-II candidate region.

Base Sequence↗
PubMed1992

Close linkage between bovine prolactin and BoLA-DRB3 genes: genetic mapping in cattle by single sperm typing.

The major histocompatibility complex and prolactin (PRL) genes are syntenic in humans and cattle but the genetic distance between these loci has not been determined for either species. In this study, the sperm typing technique was used to measure the recombination frequency between the bovine lymphocyte antigen (BoLA)-DRB3 and PRL loci. A total of 300 sperm were typed from one doubly heterozygous bull for segregation of DRB3 and PRL alleles. Sperm typing was performed using the polymerase chain reaction (PCR) and restriction enzyme cleavage of the PCR products, followed by resolution of the restriction fragments in polyacrylamide gels. Digestion with the restriction endonuclease RsaI allowed the unambiguous discrimination of alleles for both loci. The maximum likelihood estimation of the recombination fraction theta = 0.04, with a 95% confidence interval of 0.01 to 0.07. Close linkage between PRL and DRB3 has important implications for marker-assisted selection in animal breeding since PRL has been shown to be closely linked to a locus that affects milk yield, and BoLA loci influence susceptibility to a number of infectious diseases. Our results demonstrate the general applicability of the sperm typing procedure for gene mapping in species other than humans and provide an example of how parallel efforts to map the genomes of agriculturally important species of animals can have a positive impact on the development of a primary human linkage map.

Alleles↗
PubMed1991

Physical and genetic mapping of a novel chromosome 19 ERCC1 marker showing close linkage with myotonic dystrophy.

Recent genetic linkage analyses have mapped the myotonic dystrophy locus to the region of 19q13.2-13.3 lying distal to the gene for creatine kinase subunit M (CKM). The human excision repair gene ERCC1 has also been mapped to this region of chromosome 19. A novel polymorphic DNA marker, pEO.8, has been isolated from a chromosome 19 ERCC1-containing cosmid that maps to a 300-kb NotI fragment encompassing both CKM and ERCC1. Genetic linkage analysis reveals close linkage between pEO.8 and myotonic dystrophy (DM) (zmax = 19.3, theta max = 0.01). Analysis of two key recombinant events suggests a mapping of DM distal to pEO.8 and CKM.

Blotting, Southern↗
PubMed1998

Physical and genetic mapping of the human X chromosome centromere: repression of recombination.

Classical genetic studies in Drosophila and yeast have shown that chromosome centromeres have a cis-acting ability to repress meiotic exchange in adjacent DNA. To determine whether a similar phenomenon exists at human centromeres, we measured the rate of meiotic recombination across the centromere of the human X chromosome. We have constructed a long-range physical map of centromeric alpha-satellite DNA (DXZ1) by pulsed-field gel analysis, as well as detailed meiotic maps of the pericentromeric region of the X chromosome in the CEPH family panel. By comparing these two maps, we determined that, in the proximal region of the X chromosome, a genetic distance of 0.57 cM exists between markers that span the centromere and are separated by at least the average 3600 kb physical distance mapped across the DXZ1 array. Therefore, the rate of meiotic exchange across the X chromosome centromere is <1 cM/6300 kb (and perhaps as low as 1 cM/17,000 kb on the basis of other physical mapping data), at least eightfold lower than the average rate of female recombination on the X chromosome and one of the lowest rates of exchange yet observed in the human genome.

Centromere↗
PubMed2001

Multipoint genetic mapping with trisomy data.

Trisomy is the most common genetic abnormality in humans and is the leading cause of mental retardation. Although molecular studies that use a large number of highly polymorphic markers have been undertaken to understand the recombination patterns for chromosome abnormalities, there is a lack of multilocus approaches to incorporating crossover interference in the analysis of human trisomy data. In the present article, we develop two statistical methods that simultaneously use all genetic information in trisomy data. The first approach relies on a general relationship between multilocus trisomy probabilities and multilocus ordered-tetrad probabilities. Under the assumption that no more than one chiasma exists in each marker interval, we describe how to use the expectation-maximization algorithm to examine the probability distribution of the recombination events underlying meioses that lead to trisomy. One limitation of the first approach is that the amount of computation increases exponentially with the number of markers. The second approach models the crossover process as a chi(2) model. We describe how to use hidden Markov models to evaluate multilocus trisomy probabilities. Our methods are applicable when both parents are available or when only the nondisjoining parent is available. For both methods, genetic distances among a set of markers can be estimated and the pattern of overall chiasma distribution can be inspected for differences in recombination between meioses exhibiting trisomy and normal meioses. We illustrate the proposed approaches through their application to a set of trisomy 21 data.

Algorithms↗
PubMed2006

Identification and genetic mapping of highly polymorphic microsatellite loci from an EST database of the septoria tritici blotch pathogen Mycosphaerella graminicola.

A database of 30,137 EST sequences from Mycosphaerella graminicola, the septoria tritici blotch fungus of wheat, was scanned with a custom software pipeline for di- and trinucleotide units repeated tandemly six or more times. The bioinformatics analysis identified 109 putative SSR loci, and for 99 of them, flanking primers were developed successfully and tested for amplification and polymorphism by PCR on five field isolates of diverse origin, including the parents of the standard M. graminicola mapping population. Seventy-seven of the 99 primer pairs generated an easily scored banding pattern and 51 were polymorphic, with up to four alleles per locus, among the isolates tested. Among these 51 loci, 23 were polymorphic between the parents of the mapping population. Twenty-one of these as well as two previously published microsatellite loci were positioned on the existing genetic linkage map of M. graminicola on 13 of the 24 linkage groups. Most (66%) of the primer pairs also amplified bands in the closely related barley pathogen Septoria passerinii, but only six were polymorphic among four isolates tested. A subset of the primer pairs also revealed polymorphisms when tested with DNA from the related banana black leaf streak (Black Sigatoka) pathogen, M. fijiensis. The EST database provided an excellent source of new, highly polymorphic microsatellite markers that can be multiplexed for high-throughput genetic analyses of M. graminicola and related species.

Alleles↗
PubMed2003

Physical and genetic mapping of the rainbow trout major histocompatibility regions: evidence for duplication of the class I region.

One of the most unexpected discoveries in MHC genetics came from studies dealing with the teleost MHC. Initially discovered in zebrafish, the MHC class I and II regions of all bony fish are not linked. Previous segregation analysis in trout suggested that the class I and II regions reside on completely different chromosomes. To learn more about MHC genomics in trout, we have isolated BAC clones harboring class Ia and Ib loci, a single BAC clone containing an MH class II gene ( DAB), as well as BAC clones containing the ABCB2 gene. Upon PCR and sequence confirmation, BAC clones were labeled and used as probes for in situ hybridization on rainbow trout metaphase chromosomes for determination of the physical locations of the trout MH regions. Finally, SNPs, RFLPs, and microsatellites found within the BAC clones allowed for these regions to be assigned to specific linkage groups on the OSU x Hotcreek (HC) and OSU x Arlee (ARL) genetic linkage maps. Our data demonstrate that the trout MH regions are located on at least four different chromosomes and the corresponding linkage groups, while also providing direct evidence for the partial duplication of the MH class I region in trout.

Animals↗
PubMed1996

A genetic map of quantitative trait loci for body weight in the mouse.

The genetic basis of body weight in the mouse was investigated by measuring frequency changes of microsatellite marker alleles in lines divergently selected for body weight from a base population of a cross between two inbred strains. In several regions of the genome, sharp peaks of frequency change at linked markers were detected, which suggested the presence of single genes of moderate effect, although in several other regions, significant frequency changes occurred over large portions of chromosomes. A method based on maximum likelihood was used to infer effects and map positions of quantitative trait loci (QTLs) based on genotype frequencies at one or more marker loci. Eleven QTLs with effects in the range 0.17-0.28 phenotypic standard deviations were detected; but under an additive model, these did not fully account for the observed selection response. Tests for the presence of more than one QTL in regions where there were large changes of marker allele frequency were mostly inconclusive.

Alleles↗
PubMed1994

Physical and genetic map of 5q31: use of fluorescence in situ hybridization data to identify errors in the CEPH database. Centre d'Etude de Polymorphisme Humain.

Chromosome 5, band q31, contains the genes responsible for a number of interesting genetic and malignant diseases, as well as many cloned genes. To prepare a high-resolution map of this region, eight anonymous DNA markers were mapped by combining genetic data derived from linkage analysis, with physical data obtained using two-color fluorescent in situ hybridization (FISH). Probe order was determined by FISH on metaphase cells, supplemented with interphase analysis, while genetic distance and likely order were determined by multipoint linkage analysis using genotype data from Centre d'Etude de Polymorphisme Humain (CEPH) pedigrees. Discrepancies between the genetic and physical maps suggested that there was a high rate of genotyping errors in the CEPH data for these markers, and prompted a statistical analysis to identify these errors. By assuming a known physical order (as determined by FISH) it was possible to identify markers which had the greatest degree of error. The average typing error was estimated at 1.8%, but several markers had much higher error rates; a 14% error rate was predicted for one locus, which was subsequently confirmed by retyping. The analysis led to the preparation of a revised map spanning 24.5 cM of 5q31. This study illustrates the power of FISH to determine physical order over a wide genomic distance, and demonstrates how order can be used as an adjunct to linkage analysis, particularly in the identification of genotyping errors.

Chromosome Mapping↗
PubMed2002

An integrated physical and genetic map of the rice genome.

Rice was chosen as a model organism for genome sequencing because of its economic importance, small genome size, and syntenic relationship with other cereal species. We have constructed a bacterial artificial chromosome fingerprint-based physical map of the rice genome to facilitate the whole-genome sequencing of rice. Most of the rice genome ( approximately 90.6%) was anchored genetically by overgo hybridization, DNA gel blot hybridization, and in silico anchoring. Genome sequencing data also were integrated into the rice physical map. Comparison of the genetic and physical maps reveals that recombination is suppressed severely in centromeric regions as well as on the short arms of chromosomes 4 and 10. This integrated high-resolution physical map of the rice genome will greatly facilitate whole-genome sequencing by helping to identify a minimum tiling path of clones to sequence. Furthermore, the physical map will aid map-based cloning of agronomically important genes and will provide an important tool for the comparative analysis of grass genomes.

Chromosomes, Artificial, Bacterial↗
PubMed1998

Dominant optic atrophy: exclusion and fine genetic mapping of the candidate gene, HRY.

Autosomal dominant optic atrophy (OPA1) maps to Chromosome (Chr) 3q28, and the disease interval has been refined to within 1.4 cM, flanked by the markers D3S3669 and D3S3562. HRY, the human homolog of the Drosophila segmentation gene, hairy, maps by in situ hybridization to the chromosomal region 3q28-q29. We screened for mutations in HRY in 36 patients from 18 pedigrees with dominant optic atrophy and a group of normal control individuals. Heteroduplex mutation analysis and direct sequencing of all four coding exons and one upstream putative untranslated exon were performed. No disease-associated sequence alterations were identified. A polymorphism in the untranslated region of exon 2 was found, with four alleles. PCR amplification of this part of exon 2 in four of the pedigrees affected by autosomal dominant optic atrophy mapping to chromosome 3q, followed by haplotype analysis, showed recombination between HRY and OPA1 in one pedigree. This allows us to genetically position HRY in relation to known microsatellite markers in the region, placing HRY telomeric to marker D3S3562 and centromeric to D3S1305. This is outside the published critical disease interval for dominant optic atrophy. We have, therefore, excluded HRY as the gene for dominant optic atrophy by sequence analysis, mapped it genetically, and identified a polymorphism in our population.

Animals↗
PubMed1998

Integrated YAC/STS physical and genetic map of 22.5 Mb of human Xq24-q26 at 56-kb inter-STS resolution.

A yeast artificial chromosome sequence-tagged site-based (YAC/STS) physical map of 22.5 Mb of the Xq24-q26 cytogenetic band region of the human X chromosome has been assembled. DNA coverage includes 857 large-insert clones formatted with 405 STSs to provide ninefold depth of DNA. At five points, no bridging clones have been recovered from 20 X-chromosome equivalents of human DNA in YACs or bacterial clones, but the placement of 25 ("CA")n polymorphic markers permits the ordering of contigs by comparison with the genetic linkage map and radiation hybrid data. The map localizes the X3000 translocation breakpoint and six genes (ANT2, NDUFA1, LAMP2, OCRL, IGSF1, and HDGF) at better than 100-kb resolution. The relatively gene-poor nature of the region is consistent with relatively low uniform 34-42% GC content in STSs across nearly all of the region.

Chromosome Breakage↗
PubMed2004

Molecular genetic mapping of Gby, a new greenbug resistance gene in bread wheat.

The greenbug, Schizaphis graminum (Rhodani),is one of the major insect pests of wheat worldwide and it is important to develop a basic understanding of the chromosomal locations of known and new greenbug resistance genes. Gby is a new greenbug resistance gene in the wheat line 'Sando's selection 4040'. A mapping population used in this study was derived from a cross of Sando's 4040 and PI220127, a greenbug susceptible wheat land race from Afghanistan. A progeny test indicated that Gby is inherited as a single semi-dominant gene. A genetic linkage map consisting of Gby, Xgwm322 (a wheat microsatellite marker), XksuD2 (an STS marker) and 18 restriction fragment length polymorphism (RFLP) loci was constructed. We used DNA from Chinese Spring 7A deletion lines to show that the gwm332 and ksuD2 amplified fragments mapped in this study are located on along arm of chromosome 7A. This suggests that Gby is located on wheat chromosome 7A. Gby was mapped to the area in the middle of the 'island' of putative defense response genes that are represented by RFLP markers(Xpsr l9, XZnfp, Xbcd98 and Prl b) previously mapped to the distal part of the short arm of wheat chromosome group 7. This region of chromosome 7A is characterized by a high recombination rate and a high physical density of markers which makes Gby a very good candidate for map-based cloning. The selection accuracy when theRFLP markers Xbcd98, Xpsrll9 or XZnfp and Prlb flanking Gby are used together to tag Gby is 99.78%,suggesting that they can be successfully used in marker assisted selection.

Afghanistan↗
PubMed1978

Genetic mapping of the chromosome of Rhizobium trifolii.

Cultures of the wild strain and auxotrophic mutants of Rhizobium trifolii T37 synchronized by means of phenylethanol have been mutagenized with nitrosoguanidine. Fifteen genetic markers were characterized in respect of their order and the time of replication based on the peaks of mutations of the genes. The time of R. trifolii chromosome replication was estimated using inhibitors of the initiation of DNA replication: rifampicin, chloramphenicol and phenylethanol. The replicative map of R. trifolii chromosome has been constructed. Taking into account the replicative map, linkages of the genes, and the bidirectional model of the Rhizobium chromosome replication, a circular genetic map of the chromosome of R. trifolii T37 was elaborated.

Chloramphenicol↗
PubMed1994

Genetic mapping of the FACC gene and linkage analysis in Fanconi anaemia families.

Fanconi anaemia is an autosomal recessive disorder associated with increased chromosome breakage and progressive bone marrow failure. The gene for complementation group C (FACC) has been cloned and mapped to chromosome 9q22.3, but neither its genetic location nor the proportion of patients belonging to group C is known. We have used a polymorphism within the FACC gene to localise it within a 5 cM interval on chromosome 9q, bounded by D9S196/D9S197 and D9S176. The genes for Gorlin's syndrome and multiple self-healing squamous epitheliomata have also been mapped to this interval. Linkage analysis with the three highly informative microsatellite polymorphisms flanking FACC in 36 Fanconi anaemia families showed that only 8% of families were linked to this locus. This indicates that the genes for the other Fanconi anaemia complementation groups must map to one or more different chromosomal locations. The markers also allowed rapid exclusion of 56% of the families in our panel from complementation group C, thus substantially reducing the number of patients who need to be screened for FACC mutations.

Chromosome Mapping↗