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PubMed1996

Genetic mapping and embryonic expression of a novel, maternally transcribed gene Mem3.

To study the molecular function of genes expressed during preimplantation development, we isolated a novel maternal transcript SSEC (Stage Specific Embryonic cDNA)-26 from a partial subtraction library of mouse unfertilized eggs and preimplantation embryos. The SSEC-26 transcript is abundant in the unfertilized egg and also actively transcribed from the newly formed zygotic genome. On the basis of its expression in eggs and embryos, this new mouse gene is named Mem (maternal-embryonic) 3. The genomic locus of Mem3 has been mapped to Chromosome (Chr) 8 near the D8Mit78 marker and the glutaryl CoA dehydrogenase (Gcdh) locus. The deduced amino acid sequence of MEM3 resembles that of the yeast VPS (Vacuolar Protein Sorting) 35 in two separate domains. A cDNA sequence of the potential human homolog of Mem3 has been assembled with partial clones from the EST database and assigned to human Chr 16.

Amino Acid Sequence↗
PubMed1985

Physical and genetic map of a Rhizobium meliloti nodulation gene region and nucleotide sequence of nodC.

Infection of alfalfa by the soil bacterium Rhizobium meliloti proceeds by deformation of root hairs and bacterial invasion of host tissue by way of an infection thread. We studied an 8.7-kilobase (kb) segment of the R. meliloti megaplasmid, which contains genes required for infection. Site-directed Tn5 mutagenesis was used to examine this fragment for nodulation genes. A total of 81 R. meliloti strains with mapped Tn5 insertions in the 8.7-kb fragment were evaluated for nodulation phenotype on alfalfa plants; 39 of the insertions defined a 3.5-kb segment containing nodulation functions. Of these 39 mutants, 37 were completely nodulation deficient (Nod-), and 2 at the extreme nif-distal end were leaky Nod-. Complementation analysis was performed by inoculating plants with strains carrying a genomic Tn5 at one location and a plasmid-borne Tn5 at another location in the 3.5-kb nodulation segment. Mutations near the right border of the fragment behaved as two distinct complementation groups. The segment in which these mutations are located was analyzed by DNA sequencing. Several open reading frames were found in this region, but the one most likely to function is 1,206 bases long, reading from left to right (nif distal to proximal) and spanning both mutation groups. The genetic behavior of this segment may be due either to the gene product having two functional domains or to a recombinational hot spot between the apparent complementation groups.

Amino Acid Sequence↗
PubMed1999

North Carolina macular dystrophy (MCDR1) locus: a fine resolution genetic map and haplotype analysis.

PURPOSE: We previously reported linkage of North Carolina macular dystrophy in a single isolated family to a broad region on chromosome 6q16. In order to refine the localization of the MCDR1 gene (North Carolina macular dystrophy), additional families with this disease and new markers were studied. METHODS: We ascertained 10 families with the North Carolina macular dystrophy phenotype (MCDR1). These families were of various ethnic and geographic origins such as Caucasian, Mayan Indian, African-American, French, British, German, and American of European decent. Two hundred thirty-two individuals in these families underwent comprehensive ophthalmic examinations and blood was collected for genotyping. One hundred seventeen were found to be affected. Linkage simulation studies were performed. Two-point linkage, haplotype analysis, and multipoint linkage was performed using VITESSE and FASTLINK. HOMOG was used to test for genetic heterogeneity. RESULTS: The clinical features were consistent with the diagnosis of North Carolina macular dystrophy in all families. Multipoint linkage analysis indicates that the MCDR1 gene is in the interval between D6D249 and D6S1671 with a maximum LOD score of 41.52. There was no evidence of genetic heterogeneity among the families studied. Families 765, 768, 772, 1193, and 1292 shared the same chromosomal haplotype in this region. CONCLUSIONS: This is the largest single data set of families with the MCDR1 phenotype. The single large family from North Carolina continues to be informative for the closest flanking markers and alone supports the minimal candidate region as suggested by previous studies. There remains no evidence of genetic heterogeneity in this disease. Most of the American families appear to have descended from the same ancestral mutation. The remaining families could each represent independent origins of the mutation in the MCDR1 gene.

Adolescent↗
PubMed1999

High-throughput genetic mapping in Arabidopsis thaliana.

To facilitate rapid determination of the chromosomal location of novel mutations, we have improved current approaches to gene mapping using microsatellite length polymorphisms. The high-throughput linkage analysis method described here allows a novel gene to be tested for linkage against the whole genome of a multicellular eukaryote, Arabidopsis thaliana, in a single polyacrylamide gel. The procedure is based on the simultaneous co-amplification of 21 microsatellites in a single tube, using a multiplex PCR mix containing 21 primer pairs, each including one oligonucleotide labeled with one of three fluorescent dyes that have different emission wavelengths. The amplification products, which range in number from 21 to 42, depending on the genotype of the individual being tested, are electrophoresed in a single lane on a polyacrylamide gel. The use of an automated fragment analyzer makes it possible to perform linkage analysis on a one gel-one gene basis using DNA samples from 19 F2 individuals obtained from an outcross involving a mutant and a wild-type that is genetically polymorphic with respect to the ecotype in which the mutant was generated. Discrimination of the amplification products is facilitated not only by labeling with different fluorochromes, but also by prior testing of different sequences for the ability to prime the amplification of each microsatellite, in order to ensure that multiplex PCR yields compatible amplification products of non-overlapping size. The method is particularly useful in large-scale mutagenesis projects, as well as for routine mapping of single mutants, since it reveals the map position of a gene less than 24 h after the F2 individuals to be analyzed have become available. The concepts employed here can easily be extended to other biological systems.

Arabidopsis↗
PubMed2026

Identification of Novel Sources and Genetic Mapping for Bacterial Leaf Streak Resistance in a Geographically Diverse Panel of Wheat.

Bacterial leaf streak (BLS), caused by Xanthomonas translucens pv. undulosa (Xtu), has recently emerged as a significant threat to wheat production in the Northern Great Plains region of the United States. Deploying resistant cultivars is an economical and practical method of controlling BLS. To identify novel sources of BLS resistance, we screened a set of 355 bread wheat landraces and cultivars representing global diversity for their response to BLS. A wide distribution of seedling responses against BLS was observed, with most genotypes displaying a moderately to highly susceptible response. Notably, we identified 5 resistant and 33 moderately resistant responses. A high-resolution genome-wide association study using 302,524 high-quality single-nucleotide polymorphisms (SNPs) identified 10 significant marker-trait associations (MTAs) on chromosomes 1A, 1D, 3B, 4A, and 5A corresponding to unique genomic regions associated with BLS resistance. Compared with previous studies, four of these genomic regions are likely novel. Of these, MTA 'scaffold15531_2782724' associated with q5A.1 was highly significant (-log10P = 9.39) and exhibited the highest SNP effect (0.35). An association on chromosome 3B validated a previously identified 3B quantitative trait locus (QTL) mapped at approximately 6 Mbp in the hard red spring wheat cultivar 'Boost', and the high-resolution mapping from our study further refined the interval for this QTL. Furthermore, the narrow haplotype blocks reported in this study could be valuable for fine mapping of important regions. The novel resistant sources, along with identified genomic loci and corresponding SNP markers from this study, would be helpful for wheat-breeding programs to enhance BLS resistance.[Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

BLS↗
PubMed1989

Identification and genetic mapping of the structural gene for an essential Escherichia coli membrane protein.

Attempts to isolate conditionally lethal recB and recC mutations of Escherichia coli K-12 by P1 localized mutagenesis led to the identification of the structural gene for an essential membrane protein. Located on a 1.5-kilobase-pair DNA fragment which physically mapped immediately 5' to the thyA gene, the product of the umpA (unidentified membrane protein) gene is a 25,000 Mr membrane-associated polypeptide. These results provide an explanation for why several research groups have been unable to obtain chromosomal deletions of the entire thyA gene. A possible interaction between the umpA and thyA genes is also discussed.

Escherichia coli↗
PubMed1984

The use of transposon Tn5 mutagenesis in the rapid generation of correlated physical and genetic maps of DNA segments cloned into multicopy plasmids--a review.

The properties of transposon Tn5 that render it useful for in vivo mutagenesis of cloned DNA sequences are reviewed. Transposition frequency, insertional specificity, polarity and stability of Tn5 insertion mutations are among the topics discussed. Examples are cited from the published literature which illustrate the applications of Tn5 mutagenesis to the analysis of cloned prokaryotic and eukaryotic genes. A methods section is included which outlines precisely how to carry out transposon Tn5 mutagenesis analysis of cloned DNA segments.

Bacteriophage lambda↗
PubMed1983

Genetic mapping in the major histocompatibility complex by restriction enzyme site polymorphisms: most mouse class I genes map to the Tla complex.

From a genomic library constructed from sperm DNA of the inbred BALB/c mouse, we previously isolated 54 cosmid clones that contain 36 class I genes and can be divided by restriction map analyses into 13 gene clusters. We have isolated single- and low-copy DNA probes from each of these clusters to visualize restriction enzyme site polymorphisms in the DNAs from various congeneic and recombinant congeneic mice. These polymorphisms permit us to map each of the 13 cosmid clusters to a precise location in the major histocompatibility complex of the mouse. Thirty-one of 36 class I genes map into the Tla complex of the major histocompatibility complex whereas the remaining 5 genes map to the H-2 complex. Thus, all 36 class I genes are located in the major histocompatibility complex. Analysis of the number of restriction enzyme fragments visualized by the single- and low-copy DNA probes suggests that the class I genes in different inbred strains of mice probably undergo gene duplications and deletions, presumably by homologous but unequal crossing-over.

Animals↗
PubMed1994

Construction of genetic maps for some Eurasian coniferous species using allozyme genes.

In an analysis of allozyme genes in three pine and one spruce species distributed in Eurasia, 45 of 87 loci were mapped. Four linkage groups in Pinus sylvestris and Picea abies, three in Pinus pallasiana, and two in Pinus pumila were determined. The order and the locations of homologous genes in the linkage groups in the different species were similar. The data suggest that during the separate development of the Pinus and Picea genera that has lasted for millions of years, there was not any large inversion, translocation, or other significant chromosomal change, at least in the gene blocks analyzed.

Commonwealth of Independent States↗
PubMed1980

Genetic mapping of bovine mitochondrial DNA from a single animal.

Using a physical map of bovine mitochondrial DNA derived from the liver of a single Holstein cow, we have determined the location of the genes specifying the large and small ribosomal RNAs by hybridization analysis and electron microscopic observations of R-loop forms. Also, the position of the origin of DNA replication (D-loop) has been located by electron microscopy. Additionally, the direction of D-loop expansion and the polarity of the large and small ribosomal RNA genes were determined.

Animals↗
PubMed1984

Genetic mapping, cloning and physiological aspects of the glucose kinase gene of Streptomyces coelicolor.

Glucose kinase in Streptomyces coelicolor has a molecular weight of about 110,000. In crude extracts, the enzyme exhibited apparent Km values of 0.20 mM for ATP, 0.27 mM for glucose, and 2.2 mM for the glucose analogue 2-deoxyglucose. Mutations (glk) to 2-deoxyglucose-resistance, which greatly reduce glucose kinase activity and result in relief of glucose repression of utilisation of various carbon sources, were mapped between proA and hisA in the S. coelicolor linkage map. Glucose kinase activity, 2-deoxyglucose-sensitivity, glucose utilisation and glucose repression, were all restored to glk mutants by a 3.5 kb DNA fragment cloned from S. coelicolor into a phage vector (phi C31 KC515), and by larger (10-30 kb) fragments cloned into a low copy number plasmid vector (pIJ916). The glk gene was further localised to a 2.9 kb BclI fragment of the cloned DNA by sub-cloning. Part or all of this fragment was present in each of five primary plasmid clones tested.

Cloning, Molecular↗
PubMed2003

Genetic mapping of QTLs affecting productivity and plant architecture in a full-sib cross from non-inbred parents in Cassava (Manihot esculenta Crantz).

An attempt was made to identify quantitative trait loci (QTLs) for several productivity and plant architecture traits in a full-sib progeny of 144 individuals from two non-inbred parents in cassava. A molecular linkage map of this cross constructed previously with over 250 markers was the source of molecular markers. The progeny were grown under field conditions at two locations (Palmira and Quilichao) in Colombia and evaluated in 2 years (1998 and 1999) for architecture and productivity traits. Architecture traits evaluated were plant height (PH), branching height (BH), branching levels (BL), branching index (BI), stem portion with leaves (SPL) and leaf area index (LAI). Productivity traits were those related to total dry matter production and distribution, namely fresh root yield (FRY), fresh shoot yield (FSY), harvest index (HI) and the number of storage roots (NR). Phenotypic evaluation of the traits in this population revealed continuous variation for all traits. Broad-sense heritability estimates, ranged from 36% (for NR) to 94% (for BH). Several significant phenotypic correlations were observed between architecture and productivity traits. Primary QTLs, using the single-QTL model, and secondary QTLs, by a primary QTL interaction model, were detected by interval mapping. A total of 30 primary QTLs and 84 secondary QTLs were detected. We identified 35% of detected QTLs in two or more trials, the other QTLs were environment-specific. These results underscore the significant genotype x environment interactions found for most of the traits. Several genomic segments affecting multiple traits were identified and were in agreement with correlation among traits. All QTLs identified for FRY were found associated with either component traits of productivity or architecture traits. This study suggests that QTLs for plant architecture can be used to improve productivity. However an exhaustive search and analysis of QTLs controlling architecture is required before marker-assisted selection (MAS) for increasing productivity can be initiated.

Crosses, Genetic↗
PubMed1993

Molecular analysis and genetic mapping of the rhodopsin gene in families with autosomal dominant retinitis pigmentosa.

Eighty-eight patients/families with autosomal dominant retinitis pigmentosa (RP) were screened for rhodopsin mutations. Direct sequencing revealed 13 different mutations in a total of 14 (i.e., 16%) unrelated patients. Five of these mutations (T4K, Q28H, R135G, F220C, and C222R) have not been reported so far. In addition, multipoint linkage analysis was performed on two large families with autosomal dominant RP due to rhodopsin mutations by using five DNA probes from 3q21-q24. No tight linkage was found between the rhodopsin locus (RHO) and D3S47 (theta max = 0.08). By six-point analysis, RHO was localized in the region between D3S21 and D3S47, with a maximum lod score of 13.447 directly at D3S20.

Australia↗
PubMed2005

Genetic mapping of the cold-adapted phenotype of B/Ann Arbor/1/66, the master donor virus for live attenuated influenza vaccines (FluMist).

Cold adapted (ca) B/Ann Arbor/1/66 is the master donor virus for the influenza B (MDV-B) vaccine component of the live attenuated influenza vaccine (FluMist). The six internal genes contributed by MDV-B confer the characteristic cold-adapted (ca), temperature-sensitive (ts) and attenuated (att) phenotypes to the vaccine strains. Previously, it has been determined that the PA and NP segments of MDV-B control the ts phenotype while the att phenotype requires the M segment in addition to PA and NP. Here, we show that the PA, NP and PB2 segments are responsible for the ca phenotype of MDV-B when examined in chicken cell lines. Five loci in three RNA segments, R630 in PB2, M431 in PA and A114, H410 and T509 in NP, are sufficient to allow efficient virus growth at 25 degrees C. Substitution of these five amino acids with wt (wild type) residues completely reverted the MDV-B ca phenotype. Conversely, introduction of these five ca amino acids into B/Yamanashi/166/98 imparted the ca phenotype to this heterologous wt virus. In addition, we also found that the MDV-B M1 gene affected virus replication in chicken cells at 33 and 37 degrees C. Recombinant viruses containing the two MDV-B M1 residues (Q159, V183) replicated less efficiently than those containing wt M1 residues (H159, M183) at 33 and 37 degrees C, implicating the role of the MDV-B M segment to the att phenotype. The complexity of the multigenic signatures controlling the ca, ts and att phenotypes of MDV-B provides the molecular basis for the observed genetic stability of the FluMist vaccines.

Adaptation, Physiological↗
PubMed1978

Genetic map of the bacteriocinogenic plasmid CLO DF13 derived by insertion of the transposon Tn901.

An ampicillin transposon Tn901 was used as a "mutagen" to isolate insertion mutants of the bacteriocinogenic plasmid Clo DF13. By combining the obtained heteroduplex and restriction maps of the Clo DF13::Tn901 plasmids (van Emboden et al., 1977b) with their polypeptide pattern in minicells, we were able to map five genes on the Clo DF13 genome. These five genes designated A (cloacin gene), B, C, D, and G cover 55% of the coding capacity of Clo DF13 DNA. Since integration of Tn901 within these five genes did not result in a loss of the Clo DF13::Tn901 plasmids involved, it is suggested that these genes do not play an essential role in the maintenance of these plasmid insertion mutants. In addition, the described methods allowed us to indicate the initiation site of cloacin synthesis and to propose the counter-clockwise direction of transcription of the cloacin gene. The Tn901 DNA directed the synthesis of at least three polypeptides one of which is shown to be a TEM-1 beta-lactamase.

Ampicillin↗
PubMed1995

Genetic mapping of the cleidocranial dysplasia (CCD) locus on chromosome band 6p21 to include a microdeletion.

Cleidocranial dysplasia (CCD) is a generalized skeletal dysplasia with autosomal dominant inheritance. Recently, the CCD disease locus was localized to 23 [Mundlos et al., 1995] and 17 cM regions [Feldman et al., 1995], of chromosome band 6p21 by linkage studies of seven affected families. Of note, the 23 cM region contained a microdeletion detected in one family at D6S459, an interval that was excluded in the 17 cM overlapping region. Here, linkage of CCD to 6p21 was independently confirmed with a maximal two-point LOD score of Z = 5.12 with marker D6S452 at theta = 0.00. Recombinant events in two affected individuals defined a CCD region of 7 cM from D6S465 to D6S282, which overlapped with the CCD region containing the microdeletion but did not overlap with the 17 cM critical region from D6S282 to D6S291. These results suggest the refined localization of the CCD region to 6 cM spanning markers D6S438 to D6S282, thereby reviving the possibility that the CCD gene lies within the microdeletion at D6S459.

Chromosomes, Human, Pair 6↗
PubMed1996

Genetic mapping indicates that VP4 is the rotavirus cell attachment protein in vitro and in vivo.

To identify the rotavirus protein which mediates attachment to cells in culture, viral reassortants between the simian rotavirus strain RRV and the murine strains EHP and EW or between the simian strain SA-11 and the human strain DS-1 were isolated. These parental strains differ in the requirement for sialic acid to bind and infect cells in culture. Infectivity and binding assays with the parental and reassortant rotaviruses indicate that gene 4 encodes the rotavirus protein which mediates attachment to cells in culture for both sialic acid-dependent and -independent strains. Using ligated intestinal segments of newborn mice and reassortants obtained between the murine strain EW and RRV, we developed an in vivo infectivity assay. In this system, the infectivity of EW was not affected by prior treatment of the enterocytes with neuraminidase, while neuraminidase treatment reduced the infectivity of a reassortant carrying gene 4 from RRV on an EW background more than 80% relative to the controls. Thus, VP4 appears to function as the cell attachment protein in vivo as well as in vitro.

Animals↗
PubMed1978

Genetic mapping of tyramine oxidase and arylsulfatase genes and their regulation in intergeneric hybrids of enteric bacteria.

The genes for arylsulfatase (atsA) and tyramine oxidase (tynA) have been mapped in Klebsiella aerogenes by P1 transduction. They are linked to gdhD and trp in the order atsA-tynA-gdhD-trp-pyrF. Complementation analysis using F' episomes from Escherichia coli suggested an analogous location of these genes in E. coli, although arylsulfatase activity was not detected in E. coli. P1 phage and F' episomes were used to create intergeneric hybrid strains of enteric bacteria by transfer of the ats and tyn genes between K. aerogenes, E. coli, and Salmonella typhimurium. Intergeneric transduction of the tynK gene from K. aerogenes to an E. coli restrictionless strain was one to two orders less frequent than that of the leuK gene. The tyramine oxidase of E. coli and S. typhimurium in regulatory activity resemble very closely the enzyme of K. aerogenes. The atsE gene from E. coli was expressed, and latent arylsulfatase protein was formed in K. aerogenes and S typhimurium. The results of tyramine oxidase and arylsulfatase synthesis in intergeneric hybrids of enteric bacteria suggest that the system for regulation of enzyme synthesis is conserved more than the structure or function of enzyme protein during evolution.

Arylsulfatases↗