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PubMed1974

Gene order and co-transduction in the leu-ara-fol-pyrA region of the Salmonella typhimurium linkage map.

The gene order and orientation in the leu-pyrA region of the Salmonella typhimurium linkage map was established by phage P22-mediated transductions. The gene order, in counterclockwise orientation, is leuO-leuA-leuB-leuC-leuD-ara-fol-pyrA. The fol locus is co-transducible with either the ara and leu loci or the pyrA locus, whereas no co-transduction for the ara and pyrA loci can be found.

Arabinose↗
PubMed1990

Detailed genetic linkage map of human chromosome 21: patterns of recombination according to age and sex.

A detailed genetic linkage map of human chromosome 21 will allow the rapid regional assignment of future genes and DNA markers to this autosome. It will also facilitate the precise mapping of the genes responsible for the DS phenotype and the defect causing FAD. This map can also be used to implicate genes involved with specific features of the DS phenotype by permitting the delineation of finite regions of chromosome 21 which are duplicated in patients with partial trisomy 21, and who manifest select symptoms of the DS phenotype. In the case of FAD, most pedigrees are not ideally structured for genetic linkage analysis since affected individuals die relatively soon (6-8 years) after the onset of symptoms. By first establishing the genetic relationships of DNA markers in the vicinity of the FAD defect, multipoint analyses of these markers can then be performed in FAD families. Multipoint analysis carries a greater probability of identifying markers flanking the FAD locus thereby providing landmarks for cloning attempts aimed at isolating and characterizing the FAD gene defect. We have confirmed our initial findings of a dramatically increased rate of recombination at the telomere in both females and males, and significantly higher recombination in females in the pericentromeric region between D21S1/S11 and D21S13/S16. By comparing patterns of recombination in specific regions of chromosome 21 with regard to both parental sex and age, we have identified a statistically significant downward trend in in the frequency of crossovers in the most telomeric portion chromosome 21 with increasing maternal age. A less significant decrease in recombination with increasing maternal age was observed in the sub-centromeric region of the chromosome where recombination in females is overall higher than in males. Future confirmation of these results in combination with investigations aimed at deciphering the role played by recombination in promoting normal segregation during meiosis should help to elucidate the potential relevance of these findings to the etiological basis of nondisjunction.

Chromosome Mapping↗
PubMed2004

A molecular linkage map with associated QTLs from a hulless x covered spring oat population.

In spring-type oat ( Avena sativa L.), quantitative trait loci (QTLs) detected in adapted populations may have the greatest potential for improving germplasm via marker-assisted selection. An F(6) recombinant inbred (RI) population was developed from a cross between two Canadian spring oat varieties: 'Terra', a hulless line, and 'Marion', an elite covered-seeded line. A molecular linkage map was generated using 430 AFLP, RFLP, RAPD, SCAR, and phenotypic markers scored on 101 RI lines. This map was refined by selecting a robust set of 124 framework markers that mapped to 35 linkage groups and contained 35 unlinked loci. One hundred one lines grown in up to 13 field environments in Canada and the United States between 1992 and 1997 were evaluated for 16 agronomic, kernel, and chemical composition traits. QTLs were localized using three detection methods with an experiment-wide error rate of approximately 0.05 for each trait. In total, 34 main-effect QTLs affecting the following traits were identified: heading date, plant height, lodging, visual score, grain yield, kernel weight, milling yield, test weight, thin and plump kernels, groat beta-glucan concentration, oil concentration, and protein. Several of these correspond to QTLs in homologous or homoeologous regions reported in other oat QTL studies. Twenty-four QTL-by-environment interactions and three epistatic interactions were also detected. The locus controlling the covered/hulless character ( N1) affected most of the traits measured in this study. Additive QTL models with N1 as a covariate were superior to models based on separate covered and hulless sub-populations. This approach is recommended for other populations segregating for major genes. Marker-trait associations identified in this study have considerable potential for use in marker-assisted selection strategies to improve traits within spring oat breeding programs.

Agriculture↗
PubMed2005

Construction of 2 intraspecific linkage maps and identification of resistance QTLs for Phytophthora capsici root-rot and foliar-blight diseases of pepper (Capsicum annuum L.).

Two linkage maps of pepper were constructed and used to identify quantitative trait loci (QTLs) conferring resistance to Phytophthora capsici. Inoculations were done with 7 isolates: 3 from Taiwan, 3 from California, and 1 from New Mexico. The first map was constructed from a set of recombinant inbred lines (RILs) of the PSP-11 (susceptible) x PI201234 (resistant) cross; and the second map was from a set of F(2) lines of the Joe E. Parker' (susceptible) x 'Criollo de Morelos 334' (resistant) cross. The RIL map covered 1466.1 cM of the pepper genome, and it consisted of 144 markers -- 91 amplified fragment length polymorphisms (AFLPs), 34 random amplified polymorphic DNA (RAPDs), 15 simple sequence repeats (SSRs), 1 sequence characterized amplified region (SCAR), and 3 morphological markers -- distributed over 17 linkage groups. The morphological markers mapped on this population were erect fruit habit (up), elongated fruit shape (fs(e)), and fasciculate fruit clusters (fa). The F(2) map consisted of 113 markers (51 AFLPs, 45 RAPDs, 14 SSRs, and 3 SCARs) distributed in 16 linkage groups, covering a total of 1089.2 cM of the pepper genome. Resistance to both root rot and foliar blight were evaluated in the RIL population using the 3 Taiwan isolates; the remaining isolates were used for the root-rot test only. Sixteen chromosomal regions of the RIL map contained single QTLs or clusters of resistance QTLs that had an effect on root rot and (or) foliar blight, revealing a complex set of genetics involved in resistance to P. capsici. Five QTLs were detected in the F(2) map that had an effect on resistance to root rot.

Analysis of Variance↗
PubMed1992

A detailed linkage map of subtelomeric murine chromosome 12 region including the situs inversus mutation locus IV.

A mouse model is an invaluable tool to tackle genesis of human congenital diseases that have so far eluded human studies. Homozygote for the i.v. mutation, the murine Si/Col strain presents a left-right lateralization defect of thoracic and abdominal organs and heart defects very similar to human ones. This i.v. mutation has been mapped to the region between the Aat and Igh-C loci, suggesting the presence of an equivalent human gene in the human syntenic 14q3 region. A precise linkage map of the region is, therefore, of great interest since it will contribute to the genetic approach of the i.v. gene. Analysis of 242 back-cross progeny from Mus musculus (MAI) or spretus strains of mice and SI/Col mice has allowed mapping of the i.v. gene to a linkage group of eight markers. It includes four genes: Aat (alpha 1-antitrypsin), Ckb (creatine kinase, brain form), Crip (cysteine-rich intestinal protein), and Igh-C (immunoglobulin heavy chain constant region complex); three murine microsatellites: D12Mit6, D12Mit7, and D12Mit8; and one new marker, D12Mtp1, defined by a minisatellite human probe, pYNZ2. After analysis of the data by the LINKAGE program, the following multilocus map has been constructed: centromere-D12Mit6-6.9 cM-D12Mit7-1.7 cM-D12Mtp1-2.6 cM-Aat-5.0 cM-(Ckb, Igh-C)-0.4 cM-D12Mit8-0.4 cM-Crip-11.2 cM-i.v.-telomere. This map differs from the previous map in placing i.v. locus telomeric to Igh-C. D12Mit6 and D12Mit7 are now precisely mapped centromeric to the locus Aat. In addition, a new locus D12Mtp1 is located between Aat and D12Mit7.

Animals↗
PubMed1999

RAPD-based genetic linkage maps of Tribolium castaneum.

A genetic map of the red flour beetle (Tribolium castaneum) integrating molecular with morphological markers was constructed using a backcross population of 147 siblings. The map defines 10 linkage groups (LGs), presumably corresponding to the 10 chromosomes, and consists of 122 randomly amplified polymorphic DNA (RAPD) markers, six molecular markers representing identified genes, and five morphological markers. The total map length is 570 cM, giving an average marker resolution of 4.3 cM. The average physical distance per genetic distance was estimated at 350 kb/cM. A cluster of loci showing distorted segregation was detected on LG9. The process of converting RAPD markers to sequence-tagged site markers was initiated: 18 RAPD markers were cloned and sequenced, and single-strand conformational polymorphisms were identified for 4 of the 18. The map positions of all 4 coincided with those of the parent RAPD markers.

Alleles↗
PubMed2001

Comparative linkage map development and identification of an autosomal locus for insensitive acetylcholinesterase-mediated insecticide resistance in Culex tritaeniorhynchus.

A comparative linkage map for Culex tritaeniorhynchus was constructed based on restriction fragment length polymorphism markers using cDNAs from Aedes aegypti. Linear orders of marker loci in Cx. tritaeniorhynchus were identical to Culex pipiens wherein chromosomes 2 and 3 reflect whole-arm rearrangements compared to A. aegypti. However, the sex determination locus in Cx. tritaeniorhynchus maps to chromosome 3, in contrast to Cx. pipiens and Ae. aegypti where it is located on chromosome 1. Our results indicate that insensitive acetylcholinesterase (AChE)-mediated organophosphate resistance is controlled by a single major gene (AChE) on chromosome 2, while the AChE structural gene (Ace) is located on chromosome 1. No evidence for a second Ace gene was observed, even under very low stringency hybridization conditions.

Acetylcholinesterase↗
PubMed2002

Linkage mapping of quantitative trait loci in humans: an overview.

In this article, we provide an overview of the different statistical procedures that have been developed for linkage mapping of quantitative trait loci. We outline the model assumptions, the data requirements and the underlying tests for linkage for the different methods.

Chromosome Mapping↗
PubMed2001

Construction of a genetic linkage map in tetraploid species using molecular markers.

This article presents methodology for the construction of a linkage map in an autotetraploid species, using either codominant or dominant molecular markers scored on two parents and their full-sib progeny. The steps of the analysis are as follows: identification of parental genotypes from the parental and offspring phenotypes; testing for independent segregation of markers; partition of markers into linkage groups using cluster analysis; maximum-likelihood estimation of the phase, recombination frequency, and LOD score for all pairs of markers in the same linkage group using the EM algorithm; ordering the markers and estimating distances between them; and reconstructing their linkage phases. The information from different marker configurations about the recombination frequency is examined and found to vary considerably, depending on the number of different alleles, the number of alleles shared by the parents, and the phase of the markers. The methods are applied to a simulated data set and to a small set of SSR and AFLP markers scored in a full-sib population of tetraploid potato.

Algorithms↗
PubMed1993

A genetic linkage map of chromosome 21: a look at meiotic phenomena.

We have developed a genetic linkage map of chromosome 21 using 17 microsatellite marker polymorphisms. The markers span virtually the entire length of 21q, and define a sex-equal map of 56 cM. Extensive error checking has been used to provide an accurate map. All recombination events have been identified, allowing us to place within a small interval any new markers by genotyping only a few critical individuals. The resulting segregation data has been examined for several meiotic phenomena, including sex differences in recombination, age differences in recombination, interference, and segregation distortion.

Alzheimer Disease↗
PubMed2006

Linkage mapping and physical localization of the major histocompatibility complex region of the marsupial Monodelphis domestica.

We used genetic linkage mapping and fluorescence in situ hybridization (FISH) to conduct the first analysis of genic organization and chromosome localization of the major histocompatibility complex (MHC) of a marsupial, the gray, short-tailed opossum Monodelphis domestica. Family based linkage analyses of two M. domestica MHC Class I genes (UA1, UG) and three MHC Class II genes (DAB, DMA, and DMB) revealed that these genes were tightly linked and positioned in the central region of linkage group 3 (LG3). This cluster of MHC genes was physically mapped to the centromeric region of chromosome 2q by FISH using a BAC clone containing the UA1 gene. An interesting finding from the linkage analyses is that sex-specific recombination rates were virtually identical within the MHC region. This stands in stark contrast to the genome-wide situation, wherein males exhibit approximately twice as much recombination as females, and could have evolutionary implications for maintaining equality between males and females in the ability to generate haplotype diversity in this region. These analyses also showed that three non-MHC genes that flank the MHC region on human chromosome 6, myelin oligodendrocyte glycoprotein (MOG), bone morphogenetic protein 6 (BMP6), and prolactin (PRL), are split among two separate linkage groups (chromosomes) in M. domestica. Comparative analysis with eight other vertebrate species suggests strong conservation of the BMP6-PRL synteny among birds and mammals, although the BMP6-PRL-MHC-ME1 synteny is not conserved.

Animals↗
PubMed2000

[Construction of linkage map and mapping resistance gene of Scterotinia scterotiorum in Brassica napus].

Scterotinia scterotiorum (Lib.) de by is a world-wide disease, which seriously decreases the yield and the quality of oil of rapeseed. Mapping resistance genes of S. scterotiorum is of vital effect to breed new elite cultivars resisting the disease. In this paper, we reported that a RAPD linkage map was constructed, including 193 RAPD markers, 19 linkage groups and covering 1,324 cM, by using Mapmaker 3.0. On the basis of map, and resistance genes, Sc1, Sc2 and Sc3, were located in 4th, 8th and 18th linkage groups. Among three QTLs, Sc2 has the characteristics of major gene with explained 29%. The three QTLs together explained about 56% of phenotypic variation.

Brassica↗
PubMed2000

A linkage map of the turnip sawfly Athalia rosae (Hymenoptera: Symphyta) based on random amplified polymorphic DNAs.

A linkage map was constructed for the sawfly, Athalia rosae (Hymenoptera), based on the segregation of random amplified polymorphic DNA (RAPD) markers and a visible mutation, yellow fat body (yfb). Forty haploid male progeny (20 yfb and 20+) from a single diploid female parent (yfb/+) were examined. Sixty-one of the 180 arbitrary primers tested by polymerase chain reaction (PCR) produced one or more RAPD bands. A total of 79 RAPD markers were detected. Of these, seven showed significant deviation from the expected 1:1 ratio, and were therefore excluded from further analysis. The remaining 72 RAPD markers and the marker mutation, yfb, were subjected to linkage analysis. Sixty RAPD markers and the yfb marker were organized into 16 linkage groups, spanning a distance of 517.2 cM. Twelve RAPD markers showed no linkage relationship to any group. Thirteen gel-purified RAPD bands were cloned and sequenced to generate the sequence-tagged sites (STSs). A single locus was represented by two markers, with one of them having a short internal deletion.

Animals↗
PubMed1980

Construction of a genetic linkage map in man using restriction fragment length polymorphisms.

We describe a new basis for the construction of a genetic linkage map of the human genome. The basic principle of the mapping scheme is to develop, by recombinant DNA techniques, random single-copy DNA probes capable of detecting DNA sequence polymorphisms, when hybridized to restriction digests of an individual's DNA. Each of these probes will define a locus. Loci can be expanded or contracted to include more or less polymorphism by further application of recombinant DNA technology. Suitably polymorphic loci can be tested for linkage relationships in human pedigrees by established methods; and loci can be arranged into linkage groups to form a true genetic map of "DNA marker loci." Pedigrees in which inherited traits are known to be segregating can then be analyzed, making possible the mapping of the gene(s) responsible for the trait with respect to the DNA marker loci, without requiring direct access to a specified gene's DNA. For inherited diseases mapped in this way, linked DNA marker loci can be used predictively for genetic counseling.

Chromosome Deletion↗
PubMed1983

Gene in the major cotransduction gap of the Escherichia coli K-12 linkage map required for the expression of chromosomal resistance to tetracycline and other antibiotics.

In Escherichia coli K-12, amplifiable resistance to tetracycline, chloramphenicol, and other unrelated antibiotics was mediated by at least four spatially separated loci. Tetracycline-sensitive mutants were isolated by Tn5 insertional inactivation of an amplified multiply resistant strain. One of these, studied in detail, showed coordinate loss of expression of all other resistance phenotypes. The Tn5 element in this mutant mapped to 34 min on the E. coli K-12 linkage map. We have designated the locus marA (multiple antibiotic resistance). Tetracycline-sensitive mutants containing marA::Tn5 regained all resistance phenotypes at frequencies of 10(-8) to 10(-7) upon precise excision of Tn5. Moreover, a newly described tetracycline efflux system (A. M. George and S. B. Levy, J. Bacteriol. 155:531-540, 1983) was inactivated in tetracycline-sensitive mutants, but recovered in tetracycline-resistant revertants. In merodiploids, F-prime marA+ expressed partial or complete dominance over corresponding mutant chromosomal alleles. Dominance tests also established that a previously amplified host and a mutant marA allele were preconditions for the expression of phenotypic resistances.

Anti-Bacterial Agents↗
PubMed1993

A genetic linkage map of the chromosome 4 short arm.

We have generated an 18-interval contiguous genetic linkage map of human chromosome 4 spanning the entire short arm and proximal long arm. Fifty-seven polymorphisms, representing 42 loci, were analyzed in the Venezuelan reference pedigree. The markers included seven genes (ADRA2C, ALB, GABRB1, GC, HOX7, IDUA, QDPR), one pseudogene (RAF1P1), and 34 anonymous DNA loci. Four loci were represented by microsatellite polymorphisms and one (GC) was expressed as a protein polymorphism. The remainder were genotyped based on restriction fragment length polymorphism. The sex-averaged map covered 123 cM. Significant differences in sex-specific rates of recombination were observed only in the pericentromeric and proximal long arm regions, but these contributed to different overall map lengths of 115 cM in males and 138 cM in females. This map provides 19 reference points along chromosome 4 that will be particularly useful in anchoring and seeding physical mapping studies and in aiding in disease studies.

Base Sequence↗
PubMed1991

A multipoint linkage map of the distal short arm of the human X chromosome.

The distal portion of the short arm of the human X chromosome (Xp) exhibits many unique and interesting features. Distal Xp contains the pseudoautosomal region, a number of disease loci, and several cell-surface markers. Several genes in this area have also been observed to escape X-chromosomal inactivation. The characterization of new polymorphic loci in this region has permitted the construction of a refined multipoint linkage map extending 15 cM from the Xp telomere. This interval is known to contain the loci for the diseases X-linked ichthyosis, chondrodysplasia punctata, and Kallmann syndrome, as well as the cell-surface markers Xg and 12E7. This region also contains the junction between the pseudoautosomal region and strictly X-linked sequences. The locus MIC2 has been demonstrated by linkage analysis to be indistinguishable from the pseudoautosomal junction. The steroid sulfatase locus has been mapped to an interval adjacent to the DXS278 locus and 6 cM from the pseudoautosomal junction. The polymorphic locus (STS) DXS278 was shown to be informative in all families studied, and linkage analysis reveals that the locus represents a low-copy repeat with at least one copy distal to the STS gene. The generation of a multipoint linkage map of distal Xp will be useful in the genetic dissection of many of the unique features of this region.

Alleles↗
PubMed1995

A 37-marker PCR-based genetic linkage map of human chromosome 9: observations on mutations and positive interference.

Refinement of an "index" marker genetic linkage map of human chromosome 9 using the CEPH reference pedigrees has been achieved through the addition of 11 markers to the previous map of 26 markers. Five of the 11 markers added to the map are new markers of the GATA repeat type, 1 is a complex repeat, and the remaining 5 as well as the original 26 markers are all GT/CA repeats. Twelve definite and five probable mutations were detected in this analysis and were more common for the GATA repeats than the GT/CA repeats. Strong evidence for positive interference was seen over the length of the chromosome, but there were significantly more double recombination events in the pericentromeric region than elsewhere, suggesting that interference is less strong in that region.

Base Sequence↗