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PubMed1991

Linkage mapping of human polymorphic proteins identified by two-dimensional electrophoresis.

Nineteen polymorphic lymphocyte proteins were previously detected by two-dimensional protein electrophoresis (2DE). In this report, we describe the genetic linkage mapping of six of these polymorphic proteins (PNIA1-PNIA6), the identification by genetic linkage of a seventh (glyoxalase 1 on 6p21), and support for the mapping of an eighth (plastin or LCP1) to near the ESD locus on Chr 13. PNIA1-PNIA6 were assigned, respectively, to 10q26, 16p13.3, 10q, 11p15, 3q, and 19q13. These genetic linkages were achieved by classical linkage analysis of 2DE protein charge polymorphisms to the panel of RFLPs previously typed in nine pedigrees in the Centre D'Etude du Polymorphisme Humain (CEPH) collection.

Blood Proteins↗
PubMed1986

Strategies for studying heterogeneous genetic traits in humans by using a linkage map of restriction fragment length polymorphisms.

Simple single-gene disorders in humans can be genetically mapped by using traditional methods of linkage analysis and increasingly abundant restriction fragment length polymorphisms (RFLPs). Many human diseases and traits, however, can be expected to be genetically heterogeneous (i.e., caused by any one of several genes), and traditional linkage analysis is much less effective in such circumstances. We present two methods, interval mapping and simultaneous search, designed to exploit the full power of a linkage map of the DNA markers. For the simplest situations, only 1/3 as many affected families are needed to map a heterogeneous trait by using these methods. Only 1/5-1/50 as many are needed to detect that genetic heterogeneity is present.

Chromosome Mapping↗
PubMed2005

IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains.

Intermated Recombinant Inbred Lines (IRILs) in plants, or Advanced Recombinant Inbred Strains in animals, are constructed by carrying out generations of intermating between F2 individuals before starting recurrent inbreeding generations by selfing or sib-mating. IRILs are powerful for high-resolution genetic mapping because they have undergone more recombination than usual Recombinant Inbred Lines (RILs). However, there is no mapping software able to generate actual centiMorgan distances from the segregation data obtained with IRILs. IRILmap software converts genetic distances computed with any linkage mapping program designed for RILs, so that IRIL-derived data can be used to get actual centiMorgan distances, directly comparable to F2, backcross or RIL-derived maps.

Algorithms↗
PubMed2006

Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation.

Zinc (Zn) hyperaccumulation seems to be a constitutive species-level trait in Thlaspi caerulescens. When compared under conditions of equal Zn availability, considerable variation in the degree of hyperaccumulation is observed among accessions originating from different soil types. This variation offers an excellent opportunity for further dissection of the genetics of this trait. A T. caerulescens intraspecific cross was made between a plant from a nonmetallicolous accession [Lellingen (LE)], characterized by relatively high Zn accumulation, and a plant from a calamine accession [La Calamine (LC)], characterized by relatively low Zn accumulation. Zinc accumulation in roots and shoots segregated in the F3 population. This population was used to construct an LE/LC amplified fragment length polymorphism (AFLP)-based genetic linkage map and to map quantitative trait loci (QTL) for Zn accumulation. Two QTL were identified for root Zn accumulation, with the trait-enhancing alleles being derived from each of the parents, and explaining 21.7 and 16.6% of the phenotypic variation observed in the mapping population. Future development of more markers, based on Arabidopsis orthologous genes localized in the QTL regions, will allow fine-mapping and map-based cloning of the genes underlying the QTL.

Chromosome Mapping↗
PubMed2003

[A porcine linkage map of microsatellite markers using a commercial population as a reference].

A commercial population created with 19 hybrid boars [Piétrain x (Piétrain x Hampshire)], 52 hybrid sows [Leicoma x (Large White x Landrace)] and their 332 offspring was used to construct a whole genome porcine linkage map. The genetic markers used in this study include 172 microsatellite markers and 3 type- I markers (RYR1, PIT1 and PRKAG3). All microsatellite markers were genotyped using multiplex PCR reactions and visualized on ABI 377 sequencer. Three type I markers were assayed using PCR-RFLP technique. CRIMAP (2.4) analysis revealed a total length of the sex-averaged map for SSC1-SSC18 by 2449.2 cM and the length of SSCX by 143.1 cM. The average interval distance accounts to 16.3 cM. The heterozygosity of the parents at the microsatellite loci averaged 0.70. This map will play an important role in screening of QTL for growth, carcass and meat quality and reproduction in commercial populations.

Animals↗
PubMed1995

High-resolution linkage map in the vicinity of the Lp locus.

Looptail (Lp) is a mutation that profoundly affects neurulation in mouse and is characterized by craniorachischisis, an open neural tube extending from the midbrain to the tail in embryos homozygous for the mutation. Lp maps to the distal portion of mouse chromosome 1, and as part of a positional cloning approach, we have generated a high-resolution linkage map of the Lp chromosomal region. For this, we have carried out extensive segregation analysis in a total of 706 backcross mice informative for Lp and derived from two crosses, (Lp/+ x SJL/J)F1 x SJL/J and (Lp/+ x SWR/J) F1 x SWR/J. In addition, 269 mice from a (Mus spretus x C57BL/6J)F1 x C57BL/6J interspecific backcross were also used to order marker loci and calculate intergene distances for this region. With these mice, a total of 28 DNA markers corresponding to either cloned genes or anonymous markers of the SSLP or SSCP-types were mapped within a 5-cM interval overlapping the Lp region, with the following locus order and interlocus distances (in cM): centromere--D1Mit110/Atp1 beta 1/Cd3 zeta/Cd3 eta/D1Mit145-D1Hun14/D1Mit15- D1Mit111/D1Mit112-D1Mit114-D1Mit148/D1Mit205+ ++/D1Mit36/D1Mit146/D1Mit147/D1Mit270 / D1Hun13-Fcgr2-Mpp-Apoa2/Fcer1 gamma-Lp-D1Mit149/Spna1/Fcer1 alpha-Eph1-Hlix1/D1Mit62. These studies have allowed the delineation of a maximum genetic interval for Lp of 0.5 cM, a size amenable to physical mapping techniques.

Animals↗
PubMed2004

Assignment of fourteen microsatellite markers to the chicken linkage map.

A large mapping population, with 874 F2 individuals, was generated by reciprocally intercrossing 2 chicken lines. A genetic map of 2,426.6 cM comprising 25 linkage groups was established based on 145 microsatellite markers. Chromosome locations were assigned for 14 previously unmapped markers. The marker ADL0132 was previously mapped to chromosome 9; however, here close linkage to the MCW0091 marker on chromosome 4 was found. With this exception, the derived linkage map was in excellent agreement with the chicken consensus map. A comparison with the chicken genome assembly (http://genome.ucsc.edu; February 2004) suggested a few minor errors in the assembly. A PCR-RFLP test was used to genotype a single nucleotide polymorphism in the melanocortin receptor 3 (MC3R) gene in the intercross, and pyrosequencing was used to map the genes for Hemopoetic Cell Kinase (HCK) and Bone Morphogenic Protein 7 (BMP7). The HCK and BMP7 genes on linkage group E32 showed significant linkage to MC3R on the distal end of linkage group E47W24, consequently joining the 2 linkage groups. A comparison between the linkage data in the current study and the physical location of markers as revealed in the chicken genome sequence assembly (February 2004) showed a 3-fold higher recombination rate on microchromosomes than on macrochromosomes.

Animals↗
PubMed2002

On a family-based haplotype pattern mining method for linkage disequilibrium mapping.

Linkage disequilibrium mapping is an important tool in disease gene mapping. Recently, Toivonen et al. [1] introduced a haplotype mining (HPM) method that is applicable to data consisting of unrelated high-risk and normal haplotypes. The HPM method orders haplotypes by their strength of association with trait values, and uses all haplotypes exceeding a given threshold of strength of association to predict the gene location. In this study, we extend the HPM method to pedigree data by measuring the strength of association between a haplotype and quantitative traits of interest using the Quantitative Pedigree Disequilibrium Test proposed by Zhang et al. [2]. This family-based HPM (F-HPM) method can incorporate haplotype information across a set of markers and allow both missing marker data and ambiguous haplotype information. We use a simulation procedure to evaluate the statistical significance of the patterns identified from the F-HPM method. When the F-HPM method is applied to analyze the sequence data from the seven candidate genes in the simulated data sets in the 12th Genetic Analysis Workshop, the association between genes and traits can be detected with high power, and the estimated locations of the trait loci are close to the true sites.

Chromosome Mapping↗
PubMedDate not supplied

Linkage maps for 20 enzyme loci in Aedes triseriatus.

Twenty enzyme loci were mapped on the three linkage groups of Aedes triseriatus using intraspecific and interspecific matings. Large numbers of single-pair forced matings were made among field-collected A. triseriatus. Parents with appropriate isozyme linkage genotypes were identified and the progeny analyzed using standard electrophoretic procedures. Interspecific data were obtained by performing single-pair forced matings between A. triseriatus and either A. hendersoni or A. brelandi and then backcrossing to one of the parental species. Interspecific recombination values were adjusted to compensate for reduced chiasmata (and crossovers) in progeny of interspecific crosses. Four loci--Aat2, Me, Idh 1, and Mpi-- were associated with sex on linkage group (LG)I. The LG I map was about 24% longer than the predicted length of 62 map units. Eleven loci--Gpi, Hk4, Odh, Est2, Pgm, Sod1, Gpd, Had, Aco2, Idh2, and Est5--were assigned to LG II and spanned approximately 60 map units. Five loci--Mdh2, Pgd, Aat1, Gapd, and Fum--were assigned to LG III, but exact positions and distances of loci were not definitely established. The linkage relationships of enzyme loci of A. triseriatus were compared to maps of five other Aedes species in four subgenera. Map differences indicated several major inversions and translocations that separated the subgenera. In addition, several linkage groups appeared to have been conserved during Aedes subgeneric divergence.

Aedes↗
PubMed1988

Genetic linkage map of human chromosome 21.

Two of the most common disorders affecting the human nervous system, Down syndrome and Alzheimer's disease, involve genes residing on human chromosome 21. A genetic linkage map of human chromosome 21 has been constructed using 13 anonymous DNA markers and cDNAs encoding the genes for superoxide dismutase 1 (SOD1) and the precursor of Alzheimer's amyloid beta peptide (APP). Segregation of restriction fragment length polymorphisms (RFLPs) for these genes and DNA markers was traced in a large Venezuelan kindred established as a "reference" pedigree for human linkage analysis. The 15 loci form a single linkage group spanning 81 cM on the long arm of chromosome 21, with a markedly increased frequency of recombination occurring toward the telomere. Consequently, 40% of the genetic length of the long arm corresponds to less than 10% of its cytogenetic length, represented by the terminal half of 21q22.3. Females displayed greater recombination than males throughout the linkage group, with the difference being most striking for markers just below the centromere. Definition of the linkage relationships for these chromosome 21 markers will help refine the map position of the familial Alzheimer's disease gene and facilitate investigation of the role of recombination in nondisjunction associated with Down syndrome.

Chromosome Mapping↗
PubMed1993

A genetic linkage map of Saccharum spontaneum L. 'SES 208'.

The arbitrarily primed polymerase chain reaction was used to detect single-dose polymorphisms that, in turn, were used to generate a linkage map of a polyploid relative of cultivated sugarcane, Saccharum spontaneum 'SES 208' (2n = 64). The mapping population was composed of 88 progeny from a cross between SES 208 and a diploidized haploid derived from SES 208 by anther culture, ADP 85-0068. This cross allowed direct analysis of meiosis in SES 208 and gametic segregation ratios to be observed. One hundred twenty-seven 10-mer oligonucleotide primers of arbitrary sequence were selected from a pool of 420 primers used to screen the mapping parents. Three hundred thirty-six of the 420 primers amplified 4,540 loci or 13.5 loci per primer. The selected 127 primers revealed 2,160 loci of which 279 were present in SES 208 and absent in ADP 85-0068 and easily scored. Two hundred and eight (74.6%) of these 279 polymorphisms were single-dose polymorphisms (i.e., they displayed 1:1 segregation, chi 2 at 98% confidence level). Linkage analysis (theta = 0.25, LOD = 9.0 for two-point analysis, then theta = 0.25, LOD = 6.0 for multipoint analysis) of single-dose polymorphisms placed them into 42 linkage groups containing at least 2 markers. These single-dose markers span 1,500 contiguous centimorgans (cM) with 32 markers remaining unlinked (15.4%). From this 208-marker map we estimated the genome size of SES 208 to be 2,500 cM. The map has a predicted coverage of 85.1% at 30 cM, meaning that any new marker placed has an 85.1% chance of being within 30 cM of an existing marker. Furthermore, we show that SES 208 behaves like an autopolyploid because (i) the ratio of single-dose markers to higher dose markers fit the assumption of auto-octaploidy and (ii) the absence of repulsion phase linkages. This is the first genetic map constructed directly on a polyploid species for which no diploid relatives are known.

Base Sequence↗
PubMed1990

A genetic linkage map of mouse chromosome 10: localization of eighteen molecular markers using a single interspecific backcross.

Interspecific mouse backcross analysis was used to generate a molecular genetic linkage map of mouse chromosome 10. The map locations of the Act-2, Ahi-1, Bcr, Braf, Cdc-2a, Col6a-1, Col6a-2, Cos-1, Esr, Fyn, Gli, Ifg, Igf-1, Myb, Pah, pgcha, Ros-1 and S100b loci were determined. These loci extend over 80% of the genetic length of the chromosome, providing molecular access to many regions of chromosome 10 for the first time. The locations of the genes mapped in this study extend the known regions of synteny between mouse chromosome 10 and human chromosomes 6, 10, 12 and 21, and reveal a novel homology segment between mouse chromosome 10 and human chromosome 22. Several loci may lie close to, or correspond to, known mutations. Preferential transmission of Mus spretus-derived alleles was observed for loci mapping to the central region of mouse chromosome 10.

Animals↗
PubMed2005

Construction of linkage maps in full-sib families of diploid outbreeding species by minimizing the number of recombinations in hidden inheritance vectors.

This article investigates the construction of linkage maps by means of the reconstruction of hidden inheritance vectors. An inheritance vector provides a description of the origin of marker alleles in an individual in terms of a binary code indicating the grandparental origin of the alleles. The practical application that is considered is the full-sib family of a diploid outbreeding species. Essentially, map construction is considered as an optimization problem in which marker data are used as restrictions on hidden inheritance vectors. Simulated annealing, a form of combinatorial optimization, is used to minimize the number of recombinations between adjacent markers. The new algorithm is applied to simulated data as well as to practical data obtained from a cross between two apple cultivars. For the practical data, a detailed procedure for examining the reliability of individual markers and their positions on the map is presented. Extensions of the method for more complicated population structures are discussed.

Algorithms↗
PubMed1992

An interspecific linkage map of mouse chromosome 15 positioned with respect to the centromere.

We have used an interspecific backcross between C57BL/6J and Mus spretus to derive a molecular genetic linkage map of chromosome 15 that includes 25 molecular markers and spans 93% of the estimated length of chromosome 15. Using a second interspecific backcross that was analyzed with a centromere-specific marker, we were also able to position our map with respect to the chromosome 15 centromere. This map provides molecular access to many discrete regions on chromosome 15, thus providing a framework for establishing relationships between cloned DNA markers and known mouse mutations and for identifying homologous genes in mice and humans that may be involved in disease.

Animals↗
PubMed1992

A physical and genetic linkage map of the distal long arm of human chromosome 5.

By in situ hybridization of probes for three cloned genes and eight genetically-linked polymorphic DNA markers, we have prepared a physical map of the distal long arm of chromosome 5. These results, together with the localizations of 11 genes and the genetic linkage map reported previously by us and by other investigators, represent a map that spans 55 cM.

Chromosome Mapping↗
PubMedDate not supplied

Genetics and linkage mapping of Drosophila buzzatii.

Of 51 visible mutants isolated from natural or laboratory populations of Drosophila buzzatii, or X-ray induced, 42 have been assigned to chromosomes, and linkage maps have been constructed. About half of the autosomal mutants map to chromosome 2, with only two on chromosome 3 and none on chromosome 4. For the whole repleta group, chromosome 2 also exhibits much greater inversion variability than other chromosomes, which suggests variation among chromosomes in apparent mutability. The chromosomes of D. buzzatii are homologized to those of D. melanogaster and to the standard chromosomal elements of Drosophila. Sequence comparisons for six X chromosome mutant genes, whose homology is reasonably certain, in 13 Drosophila species confirm linkage group conservation but great variation among species in gene order. The linkage group conservation of single-copy genes stands in contrast to observed transpositions between elements for tandem repeat genes.

Animals↗
PubMed1993

A genetic linkage map of the mouse: current applications and future prospects.

Technological advances have made possible the development of high-resolution genetic linkage maps for the mouse. These maps in turn offer exciting prospects for understanding mammalian genome evolution through comparative mapping, for developing mouse models of human disease, and for identifying the function of all genes in the organism.

Animals↗
PubMed2002

Construction of an RAPD linkage map and localization of QTLs for oleic acid level using recombinant inbreds in mustard (Brassica juncea).

RAPD markers were employed for construction of a linkage map and localization of QTLs for oleic acid level using a set of 94 recombinant inbred lines (RILs) of mustard (Brassica juncea L.) as a mapping population. Only 30% of the 235 random primers used were useful in terms of polymorphism detected and the reproducibility of those patterns. Normal Mendelian segregation was observed for the majority of the 130 markers obtained with 71 informative primers; only 13.1% deviated (P < 0.01) from the expected 1:1 ratio. One-hundred and fourteen markers were assigned to 21 linkage groups (LGs) covering a total length of 790.4 cM with an average distance of 6.93 cM between markers. Two quantitative trait loci (QTL) for oleic acid level were mapped to 14- and 10.6-cM marker intervals on two different LGs. Both loci together explained 32.2% of phenotypic variance. One major QTL explained 28.5% of the trait variance observed in this species.

Breeding↗