Five new linkage groups in the canine linkage map

Nineteen further polymorphic loci were typed on the DogMap reference panel. Five new linkage groups were identified. Additionally, five markers were added to earlier defined linkage groups. Three of the new linkage groups contain markers mapped earlier to specific dog chromosomes by physical mapping. These results make a further contribution to the canine genome map and provides more linkage groups physically assigned to known chromosomes.     

Development and mapping of ten porcine microsatellite markers

Thirty (TG)_n microsatellite clones were isolated from a pig genomic library, sequenced, and tested for their suitability to detect polymorphism on a panel of animals by means of the polymerase chain reaction. Ten of these clones were developed into suitable markers and subsequently segregation of these markers was determined in the five PiGMaP reference pedigrees. A linkage analysis was performed on these 10 microsatellites together with 365 other loci that have been typed on these reference families. Eight of the microsatellites have been mapped to eight different linkage groups that have been previously assigned to different chromosomes (chromosomes 1, 6, 7, 9, 14, 15, 17 and 18). Of the remaining two markers, one is X-linked and the other shows no linkage. The number of alleles detected by these microsatellites, in the reference pedigrees, varied from six to sixteen and the heterozygosity varied from 42 to 85% in the 26 unrelated founder animals of these reference pedigrees.     

Absence of linkage to the ataxia telangiectasia locus in familial breast cancer

Heterozygotes for ataxia-telangiectasia (AT) are known to have an increased risk of breast cancer. The gene (or genes) responsible for almost all cases of AT has been localised to chromosome 11q by genetic linkage analysis. To examine the possibility that AT heterozygosity may account for a substantial proportion of familial breast cancer, we have typed five markers on chromosome 11q in 16 breast cancer families. We have found no evidence for linkage between breast cancer and chromosome 11q markers and conclude that the contribution of AT to familial breast cancer is likely to be minimal.     

Autosomal dominant retinitis pigmentosa: exclusion of a gene from extensive regions of chromosomes 6, 13, 20, and 21

Members of a large pedigree of Irish origin presenting with early onset Type I autosomal dominant retinitis pigmentosa (ADRP) have been typed for polymorphic DNA markers from chromosomes 6, 13, 20, and 21. For each marker close linkage to ADRP has been excluded by pairwise analyses. Using distances fixed from well-established genetic maps of these chromosomes and multipoint analyses with two or three contiguous markers, exclusion of ADRP was extended to the areas between markers, resulting in the exclusion of ADRP from extensive regions of each chromosome, totaling approximately 500 cM or 15% of the genome. The study indicates the large quantity of linkage/exclusion data obtainable using well-spaced highly polymorphic markers.     

Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas

We constructed male and female consensus linkage maps for the Pacific oyster Crassostrea gigas, using a total of 102 microsatellite DNA markers typed in 11-day-old larvae from three families. We identified 11 and 12 linkage groups in the male and female consensus maps, respectively. Alignment of these separate maps, however, suggests 10 linkage groups, which agrees with the haploid chromosome number. The male linkage map comprises 88 loci and spans 616.1 cM, while the female map comprises 86 loci and spans 770.5 cM. The male and the female maps share 74 loci; 2 markers remain unlinked. The estimated coverages for the consensus linkage maps are 79% for the male and 70-75% for the female, on the basis of two estimates of genome length. Ninety-five percent of the genome is expected to lie within 16 and 21 cM of markers on the male and female maps, respectively, while 95% of simulated minimum distances to the male and female maps are within 10.1 and 13.6 cM, respectively. Females have significantly more recombination than males, across 118 pairs of linked markers in common to the parents of the three families. Significant differences in recombination and orders of markers are also evident among same-sex parents of different families as well as sibling parents of opposite sex. These observations suggest that polymorphism for chromosomal rearrangements may exist in natural populations, which could have profound implications for interpreting the evolutionary genetics of the oyster. These are the first linkage maps for a bivalve mollusc that use microsatellite DNA markers, which should enable them to be transferred to other families and to be useful for further genetic analyses such as QTL mapping.     

Genetic markers linked to neuronal ceroid lipofuscinosis in English setter dogs

The neuronal ceroid lipofuscinoses (NCL) are a group of fatal autosomal recessive neurodegenerative diseases occurring in human and some domesticated animal species. A canine form of the disease (CNCL) has been extensively studied in a Norwegian colony of inbred English setters since 1960. A resource family developed for genetic mapping and comprising 170 individuals was typed for 103 genetic markers. Linkage analysis showed three genetic markers to be linked to the disease locus with the closest marker at a distance of about 3 c m . Two other loci were linked with these markers making a linkage group of five genetic markers. The linkage group spanned a distance of 54 c m . Two genes for human forms of the disease, CLN2 and CLN3 , have been identified and mapped to human chromosome 11p15 and 16p12, respectively. The present study did not indicate any linkage between CNCL and the canine CLN3 homologue or to homologues of markers for genes that map close to human CLN2 .     

Strategies for characterizing highly polymorphic markers in human gene mapping.

Before new markers are thoroughly characterized, they are usually screened for high polymorphism on the basis of a small panel of individuals. Four commonly used screening strategies are compared in terms of their power to correctly classify a marker as having heterozygosity of 70% or higher. A small number of typed individuals (10, say) are shown to provide good discrimination power between low- and high-heterozygosity markers when the markers have a small number of alleles. Characterizing markers in more detail requires larger sample sizes (e.g., at least 80-100 individuals) if there is to be a high probability of detecting most or all alleles. For linkage analyses involving highly polymorphic markers, the practice of arbitrarily assuming equal gene frequencies can cause serious trouble. In the presence of untyped individuals, when gene frequencies are unequal but are assumed to be equal in the analysis, recombination-fraction estimates tend to be badly biased, leading to strong false-positive evidence for linkage.     

Centromere-linked microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 of zebrafish (Danio rerio)

A large number of interesting mutations affecting development and organogenesis have been identified through genetic screens in zebrafish. Mapping of these mutations to a chromosomal region can be rapidly accomplished using half-tetrad analysis. However, knowledge of centromere-linked markers on every chromosome is essential to this mapping method. Centromeres on all 25 linkage groups have been mapped on the RAPD zebrafish genetic map. However, species specificity and the lack of codominance make RAPD markers less practical for mapping than microsatellite-based markers. On the microsatellite-based genetic map, centromere-linked markers have been identified for 19 linkage groups. No direct evidence has been published linking microsatellite markers to the centromeres of linkage groups 3, 4, 6, 7, 13, and 20. Therefore, we compared the microsatellite-based genetic map with the RAPD map to identify markers most likely linked to the centromeres of these 6 linkage groups. These candidate markers were tested for potential centromere linkage using four panels of half-tetrad embryos derived by early-pressure treatment of eggs from four different female zebrafish. We have identified microsatellite markers for linkage groups 3, 4, 6, 7, 13, and 20 to within 1.7 cM of their centromeres. These markers will greatly facilitate the rapid mapping of mutations in zebrafish by half-tetrad analysis.     

A microsatellite linkage map of the blacklip abalone, Haliotis rubra

There is considerable scope for genetic improvement of cultured blacklip abalone Haliotis rubra in Australia using molecular marker-assisted, selective-breeding practices. Such improvement is dependent on the availability of primary genetic resources, such as a genetic linkage map. This study presents a first-generation linkage map of H. rubra, containing 122 microsatellite markers typed in a single full-sib family. These loci mapped to 17 and 20 linkage groups for the male and female respectively, and when aligned, the consensus map represented 18 linkage groups. The male linkage map contained 102 markers (one unlinked) covering 621 cM with an average intermarker spacing of 7.3 cM, and the female map contained 98 markers (eight unlinked) covering 766 cM with an average intermarker spacing of 9.8 cM. Analysis of markers informative in both parents showed a significantly higher recombination rate in the female parent, with an average male-to-female recombination ratio of 1:1.45 between linked pairs of markers. This linkage map represents a significant advancement in the genetic resource available for H. rubra and provides a framework for future quantitative trait loci mapping and eventual implementation of marker-assisted selection.     

New markers and map sequences inNeurospora crassa,with a description of mapping by duplication coverage,and of multiple translocation stocks for testing linkage

Thirty previously unmapped markers have been located; 13 are at newly designated loci. Numerous sequences for previously mapped genes have also been determined. A revised map of linkage group I is presented. The order from conventional mapping has been confirmed by testing recessive markers in IL for coverage by duplications. Assignment of new mutants to linkage groups is greatly facilitated by using gene-tagged multiple translocation strains for linkage detection; these “alcoy” tester strains and procedures for using them are described. Recent mapping data of other workers are compiled. Distal markers are now known for all but one of the 14 chromosome arms, but extensive map segments are still devoid of markers.     

Anchoring of canine linkage groups with chromosome-specific markers

A high-resolution genetic map with polymorphic markers spaced frequently throughout the genome is a key resource for identifying genes that control specific traits or diseases. The lack of rigorous selection against genetic disorders has resulted in many breeds of dog suffering from a very high frequency of genetic diseases, which tend to be breed-specific and usually inherited as autosomal recessive or apparently complex genetic traits. Many of these closely resemble human genetic disorders in their clinical and pathologic features and are likely to be caused by mutations in homologous genes. To identify loci important in canine disease genes, as well as traits associated with morphological and behavioral variation, we are developing a genetic map of the canine genome. Here we report on an updated version of the canine linkage map, which includes 341 mapped markers distributed over the X and 37 autosomal linkage groups. The average distance between markers on the map is 9.0 cM, and the linkage groups provide estimated coverage of over 95% of the genome. Fourteen linkage groups contain either gene-associated or anonymous markers localized to cosmids that have been assigned to specific canine chromosomes by FISH. These 14 linkage groups contain 150 microsatellite markers and allow us to assign 40% of the linkage groups to specific canine chromosomes. This new version of the map is of sufficient density and characterization to initiate mapping of traits of interest. Received: 23 February 1999 / Accepted: 28 April 1999     

Sheep Linkage Mapping: Nineteen Linkage Groups Derived from the Analysis of Paternal Half-Sib Families

Nineteen linkage groups containing a total of 52 markers have been identified in the sheep genome after typing large paternal half-sib families. The linkage groups range in size from 2 markers showing no recombination to a group containing 6 markers covering approximately 30 cM of the sheep genome. Thirteen of the groups have been assigned to a sheep chromosome. Three groups contain markers from bovine syntenic groups U2, U7 and U29, and one other group contains a marker that has been mapped only in humans. The remaining three groups are unassigned. This information will provide a useful foundation for a genetic linkage map of sheep.     

Construction of a 5000<Subscript>rad</Subscript> whole-genome radiation hybrid panel in the horse and generation of a comprehensive and comparative map for ECA11

A 5000_rad whole-genome radiation hybrid (RH) panel was created for the horse. The usefulness of the panel for generating physically ordered maps of individual equine chromosomes was tested by typing 24 markers on horse Chromosome 11 (ECA11). The overall retention of markers on this chromosome was 43.6%. Almost complete retention of two of the typed markers—CA062 and AHT44—clearly indicated the location of thymidine kinase gene on the short arm of ECA11. Seven of the typed markers were FISH mapped to align the RH and cytogenetic maps. With the RH-MAPPER approach, a physically ordered map comprising four linkage groups and incorporating all the markers was obtained. The study provides the first comprehensive map for a horse chromosome that integrates all available mapping data and adds new information that spans the entire length of the equine chromosome. The map clearly underlines the resolving power and utility of the panel and emphasizes the need to have uniformly distributed cytogenetic markers for appropriate alignment of RH map with the chromosome. A comparative status of the ECA11 map in relation to the corresponding human/mouse chromosome is presented. Received: 7 June 2001 / Accepted: 4 October 2001     

Incidence and origin of "null" alleles in the (AC)n microsatellite markers.

Twenty-three (AC)n repeat markers from chromosome 16 were typed in the parents of the 40 CEPH (Centre d''Etude du Polymorphisme Humain) families. Where parents were informative, the entire families were then typed. There were seven markers in which null alleles were demonstrated, as recognized by the apparent noninheritance, by a sib, of a parental allele. Four of these markers showed a null allele in a single sibship, while in the other three at least 30% of the CEPH sibships were shown to have a null allele segregating. One null allele was sequenced and shown to be the result of an 8-bp deletion occurring within the priming sequence for PCR amplification of the (AC)n repeats. In gene mapping or in application to diagnosis, the presence of a segregating null allele will not corrupt the linkage data but could result in loss of information. In isolated instances a segregating null allele may be interpreted as nonpaternity. The presence of a null allele may generate misleading data when individuals are haplotyped to determine the presence of linkage disequilibrium with a disease gene.     

A new strategy for estimating recombination fractions between dominant markers from an F2 population

Although most high-density linkage maps have been constructed from codominant markers such as single-nucleotide polymorphisms (SNPs) and microsatellites due to their high linkage information, dominant markers can be expected to be even more significant as proteomic technique becomes widely applicable to generate protein polymorphism data from large samples. However, for dominant markers, two possible linkage phases between a pair of markers complicate the estimation of recombination fractions between markers and consequently the construction of linkage maps. The low linkage information of the repulsion phase and high linkage information of coupling phase have led geneticists to construct two separate but related linkage maps. To circumvent this problem, we proposed a new method for estimating the recombination fraction between markers, which greatly improves the accuracy of estimation through distinction between the coupling phase and the repulsion phase of the linked loci. The results obtained from both real and simulated F2 dominant marker data indicate that the recombination fractions estimated by the new method contain a large amount of linkage information for constructing a complete linkage map. In addition, the new method is also applicable to data with mixed types of markers (dominant and codominant) with unknown linkage phase.     

Human DNA polymorphisms and methods of analysis.

The current predominant method of analyzing base substitution polymorphisms, RFLP analysis, is likely to be gradually supplanted by methods based on PCR because of the improved sensitivity and genotyping rate. The most promising PCR methods for analysis appear to be allele-specific PCR and single-stranded conformational analysis. The single-stranded conformation approach has already been applied to the scanning of cystic fibrosis exons for new mutations. Linkage mapping projects that cover large segments of the human genome will probably rely, in the coming years, primarily on tandem repeat polymorphisms, particularly microsatellite polymorphisms. Microsatellite polymorphisms have at least a fourfold advantage over base substitution RFLPs because they are twice as informative and can be typed at at least twice the rate. The facioscapulohumeral muscular dystrophy gene was recently mapped in just 6 weeks using microsatellite polymorphisms. Because of the informativeness handicap, it will be difficult for base substitution polymorphisms to overtake tandem repeat markers for large-scale linkage mapping. Methods that allow base substitution polymorphisms to be typed at two or three times the rate of microsatellite markers would have to be developed. Most of the other applications of DNA polymorphisms described in the introduction are also increasingly likely to rely on highly informative tandem repeat markers in the future. Methods for analysis will probably be based on PCR. It is easy to envisage, for example, an automated method for large-scale DNA fingerprinting of individuals based upon a standard set of highly informative, dependable microsatellite polymorphisms. Methods for analyzing base substitution polymorphisms will continue to be important for the diagnostic detection of disease-gene alleles.(ABSTRACT TRUNCATED AT 250 WORDS)     

Linkage of the gene for an X-linked mental retardation disorder to a hypervariable (AGAT)n repeat motif within the human hypoxanthine phosphoribosyltransferase (HPRT) locus (Xq26).

We recently reported a new X-linked mental retardation (XLMR) disorder in a four-generation family of Dutch descent. Features included Dandy-Walker malformation, basal ganglia disease, and seizures. Twenty-six family members, including two living affected males and two obligate carriers, were available for study. No evidence of linkage was observed between the disease locus and RFLPs from several X-chromosome regions, including Xp21-p22 (13 markers), proximal Xq (four markers), and Xq28 (three markers). However, a new hypervariable short tandem repeat (STR) within the HPRT gene at Xq26 showed positive linkage to the disease locus, with a maximum lod score of 2.19 at a recombination fraction of 0. A second hypervariable marker in Xq26, the dinucleotide repeat XL90A3 (DXS425), showed a lod score of .84 at a recombination fraction of .11. Both the HPRT and DXS425 markers were typed in 40 CEPH families, and subsequent multipoint linkage analysis showed the following order: Xcen-DXS425-(HPRT,XLMR)-F9-qter. HPRT and these flanking markers are therefore useful for carrier detection and prenatal diagnosis in this family. This study illustrates that hypervariable STRs will be powerful tools for linkage analysis and genetic diagnosis, particularly when relatively small families are involved.     

Single linkage group per chromosome genetic linkage map for the horse, based on two three-generation, full-sibling, crossbred horse reference families

A genetic linkage map of the horse consisting of 742 markers, which comprises a single linkage group for each of the autosomes and the X chromosome, is presented. The map has been generated from two three-generation full-sibling reference families, sired by the same stallion, in which there are 61 individuals in the F2 generation. Each linkage group has been assigned to a chromosome and oriented with reference to markers mapped by fluorescence in situ hybridization. The average interval between markers is 3.7 cM and the linkage groups collectively span 2772 cM. The 742 markers comprise 734 microsatellite and 8 gene-based markers. The utility of the microsatellite markers for comparative mapping has been significantly enhanced by comparing their flanking sequences with the human genome sequence; this enabled conserved segments between human and horse to be identified. The new map provides a valuable resource for genetically mapping traits of interest in the horse.     

An integrated and comparative genetic map of the turkey genome

An integrated genetic linkage map was developed for the turkey (Meleagris gallopavo) that combines the genetic markers from the three previous mapping efforts. The UMN integrated map includes 613 loci arranged into 41 linkage groups. An additional 105 markers are tentatively placed within linkage groups based on two-point LOD scores and 19 markers remain unlinked. A total of 210 previously unmapped markers has been added to the UMN turkey genetic map. Markers from each of the 20 linkage groups identified in the Roslin map and the 22 linkage groups of the Nte map are incorporated into the new integrated map. Overall map distance contained within the 41 linkage groups is 3,365 cM (sex-averaged) with the largest linkage group (94 loci) measuring 533.1 cM. Average marker interval for the map was 7.86 cM. Sequences of markers included in the new map were compared to the chicken genome sequence by 'BLASTN'. Significant similarity scores were obtained for 95.6% of the turkey sequences encompassing an estimated 91% of the chicken genome. A physical map of the chicken genome based on positions of the turkey sequences was built and 36 of the 41 turkey linkage groups were aligned with the physical map, five linkage groups remain unassigned. Given the close similarities between the turkey and chicken genomes, the chicken genome sequence could serve as a scaffold for a genome sequencing effort in the turkey.     

Consensus and comprehensive linkage maps of bovine chromosome 7

The objective of this project was to integrate the currently available linkage maps for bovine chromosome 7 (BTA7) by combining data sets from eight research groups. A total of 54 unique markers were typed in eight pedigrees. Multilocus linkage analysis with CRI-MAP produced a bovine chromosome 7 consensus framework map of 27 loci ordered with odds greater than 1000:1. Furthermore, we present a bovine chromosome 7 comprehensive map integrating 54 loci. The locus order is in general agreement with the recently published linkage maps except for one discrepancy. The order of loci BM9289, BMS713, and ILSTS001 was reversed in the consensus framework map relative to the published USDA-MARC bovine chromosome 7 linkage map.