A mapped set of genetic markers for human chromosome 9

A genetic map of markers for human chromosome 9, spanning a genetic distance of 147 cM in males and 231 cM in females, has been constructed from linkage studies with 19 loci in a large panel of reference families. The markers included four classical systems previously assigned to chromosome 9, and restriction fragment length polymorphisms of two cloned genes, ABL oncogene and argininosuccinase synthetase pseudogene 3 (ASSP3). The remaining 13 marker loci, with an average heterozygosity of 42%, were defined by arbitrary DNA probes newly ascertained from genomic libraries; seven of them were variable number of tandem repeat (VNTR) loci. A subset of 7 of the 19 linked markers is proposed for a primary map that could detect linkage with a genetic defect within the covered region of chromosome 9, provided that at least 45 phase-known meioses were available for study in an affected family.     

A genetic map of human chromosome 17p

A genetic linkage map was constructed with 18 loci from the short arm and pericentric region of chromosome 17 typed on the CEPH reference families. The genetic map includes three markers extracted from the CEPH public database. Nine loci could be ordered using a threshold of odds of at least 1000:1 against alternative orders during the map construction process. With a reduced tolerance of 100:1, a total of 13 loci could be placed on the map spanning a distance of approximately 60 cM in females and 46 cM in males. There were statistically significant differences between the male and the female genetic maps. The order inferred from the genetic data was consistent with the physical localizations of these probes obtained from somatic cell hybrids and tumor deletion studies. This map should be useful for genetic fine mapping of 17p loci.     

A genetic linkage map of 32 loci on human chromosome 10

We have constructed a genetic linkage map of human chromosome 10 based on DNA probes that detect 47 restriction fragment length polymorphisms (RFLPs) at 32 different loci. Segregation data were collected on a set of multigenerational families provided by the Centre d'Etude du Polymorphisme Humain and maps were constructed using recently developed multipoint analysis techniques. The length of the sex-averaged map is 178 cM and the sex-specific map lengths are 131 cM in males and 255 cM in females. Recombination is significantly higher in female meioses. The mean distance between loci is 5.6 cM for the sex-averaged map. The genetic map spans the length of the chromosome as judged by physical localization of probes by in situ hybridization techniques and mapping of the probes on human-hamster hybrid cell lines containing all or part of chromosome 10. The informativeness of two loci near the locus responsible for multiple endocrine neoplasia type 2A (MEN-2A) has been increased by isolation of cosmids that reveal additional RFLPs at these loci.     

Isolation of sequences from Xp22.3 and deletion mapping using sex chromosome rearrangements from human X-Y interchange sex reversals

A repeated DNA element (STIR) interspersed in Xp22.3 and on the Y chromosome has been used as a tag to isolate seven single-copy probes from the human sex chromosomes. The seven probes detect X-specific loci located in Xp22.3. Using a panel of X-chromosomal deletions from X-Y interchange sex reversals (XX males and XY females), these X-specific loci and some additional ones were mapped to four contiguous intervals of Xp22.3, proximal to the pseudoautosomal region and distal to STS. The construction of this deletion map of the terminal part of the human X chromosome can serve as a starting point for a long-range physical map of Xp22.3 and for a more accurate mapping of genetic diseases located in Xp22.3.     

An RFLP-based genetic map of pearl millet (Pennisetum glaucum)

Analysis of a sample of diverse pearl millet genotypes with 200 genomic DNA probes revealed this crop species to be extremely polymorphic. Among these genotypes, 85% of probes detected polymorphism using only two restriction enzymes, with an average pair-wise polymorphism between all of the probe-enzyme combinations of 56%. Two crosses were employed to construct an RFLP-based genetic map. In an intervarietal F₂ population, derived from a single F₁ plant, 181 loci were placed on a linkage map. The total length of this map, which comprised seven linkage groups, was 303 cM and the average map distance between loci was about 2 cM, although a few intervals in excess of 10 cM were present at the ends of a few linkage groups. Very few clones, including those which hybridized to more than one copy, detected more than one locus in the pearl millet genome. The analysis was complicated initially because 83 of the 181 loci mapped to a single linkage group. Analysis of a second cross identified a probable translocation breakpoint in the middle of this large linkage group.     

Highly recombinogenic regions at seed storage protein loci on chromosome 1DS of Aegilops tauschii, the D-genome donor of wheat

A detailed RFLP map was constructed of the distal end of the short arm of chromosome 1D of Aegilops tauschii, the diploid D-genome donor species of hexaploid wheat. Ae. tauschii was used to overcome some of the limitations commonly associated with molecular studies of wheat such as low levels of DNA polymorphism. Detection of multiple loci by most RFLP probes suggests that gene duplication events have occurred throughout this chromosomal region. Large DNA fragments isolated from a BAC library of Ae. tauschii were used to determine the relationship between physical and genetic distance at seed storage protein loci located at the distal end of chromosome 1DS. Highly recombinogenic regions were identified where the ratio of physical to genetic distance was estimated to be <20 kb/cM. These results are discussed in relation to the genome-wide estimate of the relationship between physical and genetic distance.     

A genetic map of rye (Secale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci

Among the cereals, rye (Secale cereale L.) can be grown under extreme climatic and poor soil conditions and, is a major crop in North Europe. In the present paper, we report the development of a genetic linkage map of rye using a pooled F₂ mapping population created from a reciprocal cross of two self-fertile inbred lines. The 183 mapped markers consist 139 RFLPs, 19 isozyme and protein markers, 13 microsatellites, 10 known function sequences and two morphological genes. The markers are randomly distributed on the seven chromosomes with a maximum of 38 on chromosome 5R and a minimum of 19 on chromosome 3R. In addition, 23 gene loci and 25 quantitative trait loci were aligned to chromosome regions. For some of the mapped or aligned genes comparable loci are present in other cereals. The homoeologous relationships of these loci are discussed. The potential of the new map for further genetic studies is outlined. Received: 11 May 2000 / Accepted: 12 July 2000     

A contiguous linkage map of chromosome 13q with 39 distinct loci separated on average by 5.1 centimorgans.

A fine-structure linkage map of chromosome 13q is presented. This map contains 39 continuously linked loci defined by genotypes generated from the CEPH family DNAs with 56 probe and enzyme combinations. An alpha-satellite probe for sequences on chromosome 13 was included, resulting in a complete map of 13q with 39 distinct loci. The map spans 1.715 M in males and 2.099 M in females and the mean genetic distance between adjacent loci is 5.1 cM. Although there was generally a several-fold excess of female recombination in the interstitial portion of 13q, an excess of recombination in males was observed at both ends of this chromosomal arm. This map should be useful for the localization of any additional marker, gene, or disease locus of interest on chromosome 13q.     

A chromosome region-specific mapping strategy reveals gene-rich telomeric ends in wheat

A strategy is described for rapid chromosome region-specific mapping in hexaploid wheat (Triticum aestivum L. em. Thell., 2n=6x=42, AABBDD). The method involves allocation of markers to specific chromosome regions by deletion mapping and ordering of probes by high resolution genetic mapping in Triticum tauschii, the D-genome progenitor species. The strategy is demonstrated using 26 chromosome deletion lines for wheat homoeologous group-6. Twenty-five DNA probes from the T. tauschii genetic linkage map and six wheat homoeologous group-6 specific probes were mapped on the deletion lines. Twenty-four of the 25 probes from 6D of T. tauschii also mapped on wheat homoeologous group-6 chromosomes, and their linear order in wheat is the same as in T. tauschii. A consensus physical map of wheat group-6 was constructed because the linear order and the relative position of the probe loci was the same among the three group-6 chromosomes. Comparison of the consensus physical map with the genetic map demonstrated that most of the recombination occurs in the distal ends of the wheat chromosomes. Most of the loci mapped in the distal regions of the chromosomes. The probes were mostly either PstI genomic clones or cDNA clones indicating that the undermethylated single-copy sequences are concentrated in the distal ends of the wheat chromosomes. Fifteen loci are uniformly distributed in the distal 11% of the group-6 chromosomes. Physically, the region spans only 0.58 m, which in wheat translates to about 40 Mb of DNA. The average distance between the markers is, therefore, less than 2.7 Mb and is in the range of PFGE (pulsed-field gel electrophoresis) resolution. Any gene present in the region can be genetically ordered with respect to the markers since the average recombination frequency in the region is very high (>90 cM genetic distance).     

A genetic linkage map of 96 loci on the short arm of human chromosome 3.

We constructed a genetic map of 96 loci on the short arm of human chromosome 3 (3p) in 59 families provided by the Centre d'Etude du Polymorphisme Humaine (CEPH). Twenty-nine continuously linked loci were placed on the map with likelihood support of at least 1000:1; one locus, D3S213, was placed on the map with likelihood support of 871:1; D3Z1, an alpha satellite centromeric repeat probe, was placed on the map with likelihood support of 159:1; 65 loci were assigned regional locations. The average heterozygosity of the uniquely ordered markers was 49%. The map extends from 3p26, the terminal band of 3p, to the centromere (from D3S211 to D3Z1). Multipoint linkage analysis indicated that the male, female, and sex-averaged maps extend for 102, 147, and 116 cM, respectively. The mean genetic distance between uniquely ordered loci on the sex-averaged map was 4.0 cM. Probe density was greatest for the region of 3p between D3F15S2e and the telomere. The sex-averaged map contained two intervals greater than 10 cM. Seventeen probes were localized by fluorescence in situ hybridization. The loci described in this report will be useful in building an integrated genetic and physical map of this chromosome.     

Five Subunit Genes of the Human Muscle Nicotinic Acetylcholine Receptor Are Mapped to Two Linkage Groups on Chromosomes 2 and 17

RFLPs were detected in the five subunit genes of the human muscle nicotinic acetylcholine receptor (nAChR) using genomic DNA or cDNA probes from the homologous mouse loci. The RFLPs at the alpha-, beta-, gamma-, delta-, and epsilon-subunit gene loci were analyzed for genetic linkage in 16 families (n = 188). Significant evidence was obtained for close linkage of the β- and ε-nAChR genes and much greater genetic distance between the α-nAChR gene and the γ/δ-nAChR gene complex. The linkage analysis program CRI-MAP was used to map the positions of the β- and ε-nAChR genes relative to seven markers on chromosome 17. The results indicate the β- and ε-nAChR genes are separated by about 5 cM and located in the region of chromosome 17p occupied by D17S1, D17S31, TP53, and D17S513. The statistical evidence was confirmed by hybridization of the β- and ε-nAChR probes to a panel of human-hamster somatic cell hybrids. The α-, γ-, and δ-nAChR genes were placed on a map of 13 chromosome 2 markers. The linkage analysis placed the nAChR genes at two sites on chromosome 2q about equidistant from the marker CRYGP1, with the α-nAChR gene about 27 cM proximal and the γ/δ-nAChR gene complex about 31 cM distal to CRYGP1.     

A genetic linkage map of human chromosome 5 with 60 RFLP loci.

A genetic map of human chromosome 5 that contains 60 restriction fragment length polymorphism (RFLP) loci in one linkage group has been constructed. Segregation data using these markers and 40 large multigenerational families supplied by the Centre d'Etude du Polymorphisme Humain have been collected. Linkage analyses were performed with the program package CRI-MAP; using odds greater than 1000:1, 30 RFLP loci could be placed on the map. This genetic map spans 289 cM sex-equal, 353 cM in females, and 244 cM in males. While the relative rate of recombination for female meioses is nearly twice that of males over much of the chromosome, several instances of statistically significant excess male recombination were observed. The order of probes on the genetic map has been confirmed by their physical order as determined by somatic cell hybrid lines containing deletions of normal chromosome 5. There is concordance between the physical positions of markers and their genetic positions. Our most distal probes on the genetic map are cytologically localized to the most distal portions of the chromosome. This suggests that our genetic map spans most of chromosome 5.     

RFLP genetic linkage maps from four F(2.3) populations and a joinmap of Gossypium hirsutum L

An RFLP genetic linkage joinmap was constructed from four different mapping populations of cotton (Gossypium hirsutum L.). Genetic maps from two of the four populations have been previously reported. The third genetic map was constructed from 199 bulk-sampled plots of an F_2.3 (HQ95–6×’MD51ne’) population. The map comprises 83 loci mapped to 24 linkage groups with an average distance between markers of 10.0 centiMorgan (cM), covering 830.1 cM or approximately 18% of the genome. The fourth genetic map was developed from 155 bulk-sampled plots of an F_2.3 (119– 5 sub-okra×’MD51ne’) population. This map comprises 56 loci mapped to 16 linkage groups with an average distance between markers of 9.3 cM, covering 520.4 cM or approximately 11% of the cotton genome. A core of 104 cDNA probes was shared between populations, yielding 111 RFLP loci. The constructed genetic linkage joinmap from the above four populations comprises 284 loci mapped to 47 linkage groups with the average distance between markers of 5.3 cM, covering 1,502.6 cM or approximately 31% of the total recombinational length of the cotton genome. The linkage groups contained from 2 to 54 loci each and ranged in distance from 1.0 to 142.6 cM. The joinmap provided further knowledge of competitive chromosome arrangement, parental relationships, gene order, and increased the potential to map genes for the improvement of the cotton crop. This is the first genetic linkage joinmap assembled in G. hirsutum with a core of RFLP markers assayed on different genetic backgrounds of cotton populations (Acala, Delta, and Texas plain). Research is ongoing for the identification of quantitative trait loci for agronomic, physiological and fiber quality traits on these maps, and the identification of RFLP loci lineage for G. hirsutum from its diploid progenitors (the A and D genomes). Received: 23 February 2001 / Accepted: 8 June 2001     

A polymorphic locus on the long arm of chromosome 20 defined by two probes from a single cosmid

Summary Two probes from the random human cosmid c1-37 detect restriction fragment length polymorphisms in humans. The loci revealed by these probes are in linkage equilibrium and constitute a compound polymorphic locus with a polymorphism information content of 0.54. A somatic cell hybrid panel has been used to map the probes to chromosome 20; in situ hybridization studies confirm this localization and indicate that the locus is on 20q13. This is the first polymorphic locus to be assigned to the long arm of chromosome 20.     

Chromosome-level homeology in paleopolyploid soybean (Glycine max) revealed through integration of genetic and chromosome maps

Soybean has 20 chromosome pairs that are derived from at least two rounds of genomewide duplication or polyploidy events although, cytogenetically, soybean behaves like a diploid and has disomic inheritance for most loci. Genetically anchored genomic clones were used as probes for fluorescence in situ hybridization (FISH) to determine the level of postpolyploid chromosomal rearrangements and to integrate the genetic and physical maps to (1) assign linkage groups to specific chromosomes, (2) assess chromosomal structure, and (3) determine the distribution of recombination along the length of a chromosome. FISH mapping of seven putatively gene-rich BACs from linkage group L (chromosome 19) revealed that most of the genetic map correlates to the highly euchromatic long arm and that there is extensive homeology with another chromosome pair, although colinearity of some loci does appear to be disrupted. Moreover, mapping of BACs containing high-copy sequences revealed sequestration of high-copy repeats to the pericentromeric regions of this chromosome. Taken together, these data present a model of chromosome structure in a highly duplicated but diploidized eukaryote, soybean.     

Comparative RFLP-based genetic maps of barley chromosome 5 (1H) and rye chromosome 1R

Summary A genetic map of barley chromosome 5 (1H) was constructed using DNA markers. Seventeen loci were mapped to 15 locations, and these included the known-function loci (in order from the most distal on the long arm) XAdh (alcohol dehydrogenase), XLec (homologous to wheat germ agglutinin), XHor3 (D-hordein), XPpdk (pyruvate orthophosphate dikinase), centromere, XIcal (chymotrypsin inhibitor), and 6 loci in the B- and C-hordein cluster towards the end of the short arm. The gene order on the barley map agreed closely with that of chromosome 1 of rye. Intervarietal comparisons showed that single-copy cDNA and genomic DNA probes revealed about twice the level of RFLPs found in wheat.     

Localization of the t(2;13) breakpoint of alveolar rhabdomyosarcoma on a physical map of chromosome 2.

A characteristic translocation t(2;13)(q35;q14) has been previously identified in the pediatric soft tissue tumor alveolar rhabdomyosarcoma. We have assembled a panel of lymphoblast, fibroblast, and somatic cell hybrid cell lines with deletions and unbalanced translocations involving chromosome 2 to develop a physical map of the distal 2q region. Twenty-two probes were localized on this physical map by Southern blot analysis of the mapping panel. The position of these probes with respect to the t(2;13) rhabdomyosarcoma breakpoint was then determined by quantitative Southern blot analysis of an alveolar rhabdomyosarcoma cell line with two copies of the derivative chromosome 13 and one copy of the derivative chromosome 2 and by analysis of somatic cell hybrid clones derived from an alveolar rhabdomyosarcoma cell line. We demonstrate that the t(2;13) breakpoint is situated within a map interval delimited by the distal deletion breakpoint in fibroblast line GM09892 and the t(X;2) breakpoint in somatic cell hybrid GM11022. Furthermore, from a comparison of our data with the linkage map of the syntenic region on mouse chromosome 1, we conclude that the t(2;13) breakpoint is most closely flanked by loci INHA and ALPI within this map interval.     

Genetic Analysis of the Fungus, Bremia Lactucae, Using Restriction Fragment Length Polymorphisms

Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.     

Comparison between genetic and physical maps in Zea mays L. of molecular markers linked to resistance against Diatraea spp

In the pachytene stage, chromosomes are maximally extended and can easily be distinguished. Therefore, by applying fluorescence in situ hybridization (FISH) to pachytene chromosomes, it is possible to generate a high-resolution physical map of chromosome 9 in maize. Molecular markers ( umc105a on the short arm of chromosome 9, csu145a on the long arm) were used that flank quantitative trait loci (QTL) for sugarcane borer (SCB) and southwestern corn borer (SWCB) resistance. As reference markers, a centromere-specific probe (CentC) and a knob-specific probe (pZm4-21) were utilized. Two fluorescent dyes with four probes were used to physically position these markers. Signals of repetitive DNA sequences in cosmid probes were suppressed by chromosome in situ suppression (CISS) hybridization. FISH signals were strong and reproducible for all probes. We measured the distances in micrometers for four subchromosomal regions and estimated the corresponding number of base pairs. The physical locations of the markers were compared on mitotic metaphase and pachytene chromosomes to the genetic map of chromosome 9. Genetic analysis positioned the two markers for SCB resistance in a central interval representing approximately 33.7% of the genetic length. However, the physical distance between these probes was determined to encompass about 70% of the physical length of chromosome 9. The two markers were located at distal positions on opposite arms of chromosome 9. Physical maps provide valuable information for gene isolation and understanding recombination.     

A primary genetic map of chromosome 13q.

We have constructed a primary genetic map spanning most of human chromosome 13. A total of 14 polymorphic DNA sequences and one protein polymorphism provided, after construction of haplotypes, seven markers for the long arm of this chromosome. A panel of cell lines from 30 three-generation families with large sibship size served as the sample set. Pairwise cross analysis of the inheritance patterns of the marker loci established that six of the seven loci constituted a single linkage group; the seventh was localized by physical means. Significantly higher recombination rates were found in female than in male meioses in several intervals. The six closely linked loci were arranged, based on the two-point data, in three clusters, and a number of alternate gene orders were excluded by three-point linkage tests. The order and spacing of the individual loci were refined by linkage analyses that considered five loci jointly.