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Is the notch locus of Drosophila melanogaster a tandem repeat? Correlation of the genetic map and complementation pattern of selected mutations.

Correlation of the complementation relationships between the Notch locus alleles fa(g), fa(no), Ax(59d) and nd, with their genetic map order, suggests a tandem repetition within the locus of functionally related sites. This observation is discussed in relation to two hypotheses: (1) that the Notch locus contains a tandem repeat of genetic material; and (2) that the tertiary structure of the Notch locus product has a spiral configuration.

Alleles↗

Physical and genetic mapping of the catA region of Pseudomonas aeruginosa.

A prime plasmid has been used as the basis for the construction of a physical and genetic map of a 125 kb segment of the Pseudomonas aeruginosa PAO chromosome. Using pMO1811, a prime plasmid selected for the catA region, a series of Tn5 insertions were obtained which identified two new markers gcu (glycine utilization) and oap (organic acids and alcohols permeability) in the 125 kb region and located them in relation to other known markers of this region. A cosmid bank was constructed from the prime plasmid and an ordered array of cosmid clones for this region identified by restriction endonuclease mapping with EcoRI, HindIII and KpnI, as well as complementation mapping and chromosome walking. By Southern hybridization analyses, it was confirmed that the chromosomal insert carried by pMO1811 was flanked by single, tandemly arranged copies of IS21 and the orientation of the insert on this prime was determined. This cosmid bank provides a resource for the further analysis of this region of the P. aeruginosa genome.

Alcohols↗

Alignment of physical and genetic maps of human 8q23-qter using somatic cell hybrid mapping panel.

We describe a mapping panel for the 8q23-qter region composed of human-hamster hybrid cell lines carrying deletion and translocation derivatives of human chromosome 8. The panel divides this region of the chromosome into nine intervals and has been used to map 40 loci by Southern blot hybridization and PCR. Use of this mapping panel has allowed us to align the terminal portions of two different genetic maps of chromosome 8 with each other and with the physical map of the chromosome.

Animals↗

New tools for the physical and genetic mapping of Lactococcus strains.

Tools for the genetic and physical analysis of the Lactococcus lactis subsp. lactis genome were developed. Plasmid pRC1 does not replicate in Gram+ bacteria; it contains unique ApaI, NotI and SmaI restriction sites and an erythromycin-resistance (ErR) encoding gene, ermAM, functional in L. lactis subsp. lactis. When a chromosomal L. lactis subsp. lactis DNA fragment was cloned into this vector, the resulting plasmid became integrated, after transformation, into the bacterial chromosome by homologous recombination in a Campbell-like manner. The integration lead to the generation of new rare restriction sites near to the host fragment. This procedure allows precise mapping of cloned genes onto the chromosomal restriction map. The mapping of the his operon of L. lactis subsp. lactis provides an illustration. The cloning into pRC1 of an IS element able to transpose into the chromosome of the target cell, gave rise to an integration plasmid able to insert randomly rare restriction sites onto the bacterial chromosome. The L. lactis IS element, ISS1RS, was cloned into pRC1, yielding pRL1. Pulsed-field gel electrophoresis analysis of ErR clones obtained after transformation with pRL1, showed that this plasmid was stably integrated at a number of different sites in the L. lactis subsp. lactis chromosome, via transposition. Plasmids pRC1 and pRL1 can greatly facilitate the construction of the physical and genetic map of the chromosome of lactococcal strains.

Cloning, Molecular↗

Genetic mapping of 21 genes on mouse chromosome 11 reveals disruptions in linkage conservation with human chromosome 5.

We report a high-resolution genetic map of 21 genes on the central region of mouse Chr 11. These genes were mapped by segregation analysis of more than 1650 meioses from three interspecific backcrosses. The order of these genes in mouse was compared to the previously established gene order in human. Eighteen of the 21 genes map to human Chr 5, and 2 of the genes define a proximal border for the region of homology between mouse Chr 11 and human Chr 17. Our results indicate a minimum of four rearrangements within the 10-cM region of synteny homology between mouse Chr 11 and human Chr 5. In addition, the linkage conservation is disrupted by groups of genes that map to mouse Chrs 13 and 18. These data demonstrate that large regions of conserved linkage can contain numerous chromosomal microrearrangements that have occurred since the divergence of mouse and human ancestors. Comparison of the mouse and human maps with data for other species provides an emerging picture of mammalian chromosome evolution.

Animals↗

Alignment of genetic maps and QTLs between inter- and intra-specific sorghum populations.

To increase the value of associated molecular tools and also to begin to explore the degree to which interspecific and intraspecific genetic variation in Sorghum is attributable to corresponding genetic loci, we have aligned genetic maps derived from two sorghum populations that share one common parent (Sorghum bicolor L. Moench accession BTx623) but differ in morphological and evolutionarily distant alternate parents (S. propinquum or S. bicolor accession IS3620C). A total of 106 well-distributed DNA markers provide for map alignment, revealing only six nominal differences in marker order that are readily explained by sampling variation or mapping of paralogous loci. We also report a total of 61 new QTLs detected from 17 traits in these crosses. Among eight corresponding traits (some new, some previously published) that could be directly compared between the two maps, QTLs for two (tiller height and tiller number) were found to correspond in a non-random manner (P<0.05). For several other traits, correspondence of subsets of QTLs narrowly missed statistical significance. In particular, several QTLs for leaf senescence were near loci previously mapped for 'stay-green' that have been implicated by others in drought tolerance. These data provide strong validation for the value of molecular tools developed in the interspecific cross for utilization in cultivated sorghum, and begin to separate QTLs that distinguish among Sorghum species from those that are informative within the cultigen (S. bicolor).

Chromosome Mapping↗

[Genetic mapping of T-DNA integration sites in Xa21 transgenic rice].

The transformation mediated by Agrobacterium has been successfully applied to rice in recent years. In the previous research we have transferred the Xa21 gene into five rice varieties of China, using Agrobacterium-mediated trasformation. In this study, T-DNA flanking sequences of Xa21 transgenic rice lines were obtained by using thermal asymmetric interlaced PCR (TAIL-PCR). The flanking sequences which are actual rice DNA were identified and located on molecular linkage map developed from a ZYQ8/JX17 double haploid (DH) population. A total of 22 T-DNA flanking rice sequences were isolated. Nineteen of them displayed RFLPs between the two parents, ZYQ8 and JX17, and were mapped on the rice chromosomes, 3, 4, 7, 9, 10, 11 and 12, respectively. The genetic mapping of T-DNA integration sites in Xa21 transgenic rice will benefit the study of position effect and stable inheritance of the transgene Xa21.

Base Sequence↗

SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits.

We have previously identified and mapped porcine expressed sequence tags (ESTs) derived from genes that are preferentially expressed in liver. The aim of the present study was to identify single nucleotide polymorphisms (SNPs) in porcine genes encoding enzymes in hepatic metabolic pathways and use the SNPs for mapping. Furthermore, these genes, which are involved in utilization and partitioning of nutrients, were examined for their effects on carcass and meat quality traits by linkage analyses. In total, 100 ESTs were screened for SNPs by single strand conformation polymorphism analyses across a diverse panel of animals with a 36% success rate. Twelve of 36 polymorphic loci segregated in a three-generation Duroc x Berlin Miniature Pig (F2) resource population, the DUMI resource population, and were genetically mapped. Interval mapping of the corresponding chromosomes was performed to verify mapping of the genes within quantitative trait loci (QTL) regions detected in this resource population. QTL with genome-wide significance were detected in the vicinity of GNMT, ESTL147 and HGD. These loci therefore are positional candidate genes.

Animals↗

The use of DNA polymorphisms in genetic mapping.

The introduction of molecular markers has revolutionized genetics. The range of polymorphisms that are available is increasing and the advent of large-scale cDNA and genomic sequencing is a source of an ever-increasing set of available markers. The ease with which any particular marker type can be applied to an experimental system depends, to some extent, on the amount of genomic information available for that system. However, comparative genomics is enabling a wider range of marker technology to be applied to relatively information-poor systems. The types of markers that are available include restriction fragment length polymorphisms, amplified fragment length polymorphisms, ransom amplified polymorphic DNAs, simple sequence repeats, single nucleotide polymorphisms and small insertions/deletions. The types of questions that can be addressed with these molecular markers include the generation of genetic and physical maps for the identification of interesting loci, the development of marker-based gene tags, map-based cloning of agronomically important genes, synteny mapping, marker-assisted selection and quantitative trait analysis. The continued development of technology including new high throughput methods, for example those being applied to single nucleotide polymorphisms, will change the ease with which current questions can be answered as well as enable new analyses that are presently impossible to undertake.

Chromosome Mapping↗

The integration of canine genetic maps with the canine karyotype using specific gene amplification of chromosome-specific DNA.

We have used a rapid approach to place markers that are already represented in current genetic maps onto individual chromosomes in species for which chromosome paints exist. PCR-based techniques are used to look for the presence of individual marker genes within each chromosome-specific DNA pool. The presence of a given marker within a DNA pool allows assignment of the complete radiation hybrid group, or linkage group from which the marker is drawn, to an individual chromosome. We have used this method with a new set of canine chromosome paints (Yang et al., 1999). In this way, we have assigned 39 of 44 published RH or syntenic RH groups to canine chromosomes, together with 33 of 40 canine linkage groups in a recently published map (Neff et al., 1999).

Animals↗

Molecular genetic mapping of the multiple endocrine neoplasia type 1 locus.

Familial multiple endocrine neoplasia type 1 (MEN 1) is an autosomal dominant disorder characterized by the combined occurrence of tumors of the parathyroid glands, the endocrine pancreas, and the pituitary gland. MEN 1 tumors have previously been shown to be associated with the loss of alleles on chromosome 11, and deletion mapping studies together with family linkage studies have localized the MEN 1 gene to 11q13. A detailed genetic map around the MEN 1 locus is required to facilitate further characterization and cloning of the gene (MEN1). We have characterized a panel of seven rodent-human somatic cell hybrids which contain fragments of human chromosome 11 with breakpoints in the pericentromeric region by using eight DNA sequences (D11S149, PGA, PYGM, D11S97, INT2, D11S37, D11S533, and D11S147) to define the region containing MEN1. This will facilitate the rapid localization of additional DNA sequences in this region. In addition, we have used a highly polymorphic repetitive degenerate hexanucleotide sequence, designated D11S533, for segregation studies in one family with MEN 1. These molecular genetic approaches will help to define a precise 1 to 2 centiMorgan map around MEN1.

Chromosome Mapping↗

Genetic mapping of the X-linked dominant mutations striated (Str) and bare patches (Bpa) to a 600-kb region of the mouse X chromosome: implications for mapping human disorders in Xq28.

Striated (Str) and bare patches (Bpa) are X-irradiation-induced, X-linked dominant mouse mutations that are lethal prenatally in hemizygous males. To map the Str mutation, we generated a backcross involving Mus castaneus. Pedigree analysis of 193 affected female and normal male progeny from the cross places Str extremely close to DXMIT1 and favors a gene order of (Cf-9)-Ids-Gabra3-DXS1104h-(Str, DXMIT1)-F8a-DXPas8-DXBay6-DXMIT6 for the loci studied. This region of the mouse X Chromosome (Chr) is syntenic with proximal human Xq28. Based on the mode of inheritance and clinical phenotype, Str may be a homolog of human familial incontinentia pigmenti (IP2). Further refinement of our genetic mapping of bare patches positions that locus between DXS1104h and DXPas8 in the same region as Str, raising the possibility that Bpa and Str may be allelic or are due to mutations in overlapping contiguous genes.

Animals↗

Genetic mapping: chromosomes 6-22.

Using a method that considers physical assignments and the distribution of chiasmata, as well as linkage data, genetic maps are constructed for chromosomes 6, 9, 13, and 16, and unassigned markers are tested for inclusion in these linear maps.

Centromere↗

Physical and genetic map of the Lactococcus lactis subsp. cremoris MG1363 chromosome: comparison with that of Lactococcus lactis subsp. lactis IL 1403 reveals a large genome inversion.

A physical and genetic map of the chromosome of the Lactococcus lactis subsp. cremoris reference strain MG1363 was established. The physical map was constructed for NotI, ApaI, and SmaI enzymes by using a strategy that combines creation of new rare restriction sites by the random-integration vector pRL1 and ordering of restriction fragments by indirect end-labeling experiments. The MG1363 chromosome appeared to be circular and 2,560 kb long. Seventy-seven chromosomal markers were located on the physical map by hybridization experiments. Integration via homologous recombination of pRC1-derived plasmids allowed a more precise location of some lactococcal genes and determination of their orientation on the chromosome. The MG1363 chromosome contains six rRNA operons; five are clustered within 15% of the chromosome and transcribed in the same direction. Comparison of the L. lactis subsp. cremoris MG1363 physical map with those of the two L. lactis subsp. lactis strains IL1403 and DL11 revealed a high degree of restriction polymorphism. At the genetic organization level, despite an overall conservation of gene organization, strain MG1363 presents a large inversion of half of the genome in the region containing the rRNA operons.

Bacteriophages↗

Genetic mapping of reovirus virulence and organ tropism in severe combined immunodeficient mice: organ-specific virulence genes.

We used reovirus reassortant genetics and severe combined immunodeficient (SCID) mice to define viral genes important for organ tropism and virulence in the absence of antigen-specific immunity. Adult SCID mice infected with reovirus serotype 1 strain Lang (T1L) died after 20 +/- 6 days, while infection with serotype 3 strain Dearing (T3D) was lethal after 77 +/- 22 days. One hundred forty-five adult SCID mice were infected with T1L, T3D, and 25 different T1L x T3D reassortant reoviruses, and gene segments associated with the increased virulence of T1L were identified. Gene segments S1, L2, M1, and L1 accounted for > 90% of the genetically determined increase in T1L virulence. Gene segment M1 was independently important for virulence, with S1, L2, and L1 alone or in combination also playing a role. T1L grew to higher titers in multiple organs and caused more severe hepatitis than T3D. Seventy adult SCID mice, T1L, T3D, and 15 T1L x T3D reassortant viruses were used to map genetic determinants of viral titers in the brain, intestines, and liver, as well as the severity of hepatitis. Different sets of gene segments were important for determining viral titers in different organs. Gene segments L1 (encoding a core protein) and L2 (encoding the core spike of the virion) were important in all of the organs analyzed. The M1 gene segment (encoding a core protein), but not the S1 gene segment, was a critical determinant of reovirus titer in the liver and severity of hepatitis. The S1 gene segment (encoding the viral cell attachment protein and a nonstructural protein), but not the M1 gene segment, was a critical determinant of titers in intestines and brains. These studies demonstrate that viral growth in different organs is dependent on different subsets of the genes important for virulence. The virion-associated protein products of the four gene segments (L1, L2, M1, and S1) important for virulence and organ tropism in SCID mice likely form a structural unit, the reovirus vertex. Organs (the brain and intestines versus the liver) differ in properties that determine which virulence genes, and thus which parts of this structural unit, are important.

Animals↗

Genetic mapping of grapevine ( Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight.

Parental and consensus genetic maps of Vitis vinifera L. (2n = 38) were constructed using a F(1) progeny of 139 individuals from a cross between two partially seedless genotypes. The consensus map contained 301 markers [250 amplification fragment length polymorphisms (AFLPs), 44 simple sequence repeats (SSRs), three isozymes, two random amplified polymorphic DNAs (RAPDs), one sequence-characterized amplified region (SCAR), and one phenotypic marker, berry color] mapped onto 20 linkage groups, and covered 1,002 cM. The maternal map consisted of 157 markers covering 767 cM (22 groups). The paternal map consisted of 144 markers covering 816 cM (23 groups). Differences in recombination rates between these maps and another unpublished map are discussed. The major gene for berry color was mapped on both the paternal and consensus maps. Quantitative trait loci (QTLs) for several quantitative subtraits of seedlessness in 3 successive years were searched for, based on parental maps: berry weight, seed number, seed total fresh and dry weights, seed percent dry matter, and seed mean fresh and dry weights. QTLs with large effects (R(2) up to 51%) were detected for all traits and years at the same location on one linkage group, with some evidence for the existence of a second linked major QTL for some of them. For these major QTLs, differences in relative parental effects were observed between traits. Three QTLs with small effects (R(2) from 6% to 11%) were also found on three other linkage groups, for berry weight and seed number in a single year, and for seed dry matter in 2 different years.

Journal Article↗

First restriction and genetic mapping of the genomic DNA of urease-positive thermophilic campylobacters (UPTC), and small restriction fragment sequencing.

A restriction and genetic map of urease-positive thermophilic campylobacter (UPTC) CF89-12 genome DNA is constructed using a pulsed-field gel electrophoresis procedure after digestion with SalI and SmaI and Southern blot hybridisation. Each of the six gene fragments (flaA, glyA, lysS, recA, sodB and ureAB) selected are mapped in only a fragment on the restriction map. Three DNA fragments for rrn operon probes are mapped in multiple regions on the map. When two SmaI-digested neighbouring small fragments hybridised with rrn probes are cloned and sequenced, a total sequence length of 7487 bp is determined. In the sequence, part of the pnp gene (734 bp) bearing a p-independent transcriptional termination region, a cluster of five tRNA genes including the putative promoter region, a hypothetical Cj0171-like 507-bp sequence containing an internal termination codon, and a part of the rrn operon including the putative promoter region (4700 bp) are identified. The 507 bp sequence carried both putative transcriptional promoter sequences, including a ribosome binding site upstream of the ATG start codon and a characteristic G9 structure, and a possible p-independent transcriptional termination region. A hypothetical Cj0170-like 204-bp sequence containing an internal termination codon also occurred, overlapping partly with the Cj0171-like sequence. Based on nucleotide sequence alignment analysis between the UPTC rrn operon examined here and the previously reported one, two different 16S-23S ribosomal DNA (rDNA) internal spacer regions are shown to exist.

Base Sequence↗

[Integration of the genetic map and the physical map of the subterminal region on the longer arm of rice chromosome 6].

The region between RFLP markers G342 and R1167 was the subterminal part of the longer arm on the rice chromosome 6, because Shen et al. (1998) mapped two telomeric repeat associated sequences distal to G342. In order to integrate the genetic map and the physical map of the region, G342 and R1167 were firstly used to screen BAC library. Based on the positive clones detected by the two markers and chromosome walking by using the outer most insert-end of the overlapping clones, a contig containing 16 BAC clones which spanned 500 kb was constructed. All the insert-ends of the BAC clones could be amplified with thermal asymmetric interlaced PCR. Fourteen insert-ends were subcloned. Seven of them were identified as a single or low copy sequences and five were mapped on the expected sites flanking G342 or R1167. The insert fragment isolated from the minimum tile BAC clones of the contig was used to screen a cDNA library and four different positive clones were detected.

Chromosome Mapping↗