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At least 1,279 records · Page 71Linked to original sources
PubMed2003

Frontonasal dysplasia in 3H1 Br/Br mice.

The adult Brachyrrhine (3H1 Br/+) mouse displays severe midfacial retrognathia, with a "pugnose" external appearance, but information concerning craniofacial morphology of the homozygote (3H1 Br/Br) mutant is lacking. This study characterized craniofacial phenotype and genotypic features of the homozygous condition. Segregation analysis was performed by phenotypic scoring of offspring from 3H1 Br/+ reciprocal matings. Whole-mount staining was undertaken to determine the presence or absence of cranial base structures in newborn and adult mice, while features of cranial base chondrification were examined using light microscopy and type II collagen immunohistochemistry. Karyotype analysis was performed to determine whether gross chromosomal aberrations were present. Finally, microsatellite mapping analysis was undertaken to provide further resolution of the Br locus. Results showed that Br was inherited as an autosomal semidominant feature. 3H1 Br/Br mice consistently lacked a presphenoid (with its lateral projections, including a preoptic root, postoptic root, and lesser wing). Karyotyping did not reveal major gross aberrations; however, microsatellite analysis localized Br to distal mouse chromosome 17 in the vicinity of D17Mit155. These results indicated that 3H1 Br/Br mice show characteristic features of frontonasal dysplasia, including median facial clefting and bifid cranium, as well sphenoidal malformations. Furthermore, this mutant should serve as a useful model for examining mechanisms of frontonasal dysplasia.

Animals↗
PubMed2001

A linkage analysis of sex determination in Bombus terrestris (L.) (Hymenoptera: Apidae).

We constructed a linkage map of Bombus terrestris (Hymenoptera, Apidae) phase unknown. The map contains 79 markers (six microsatellite and 73 RAPD markers) in 21 linkage groups and spans over 953.1 cM. The minimal recombinational size of the B. terrestris genome was estimated to be 1073 cM. Using flow cytometry, the physical size of the haploid genome of B. terrestris was calculated to be 274 Mb. This is the second linkage map for a social insect species. Bombus terrestris has on average five times less recombinational events per kb than the honey bee Apis mellifera. Male haploidy, chromosome size, and eusociality can now be excluded as reasons for the high recombination frequency of Apis mellifera. Finally, the sex determination locus of B. terrestris was placed on the map using bulked segregant analysis.

Animals↗
PubMed2002

Morphological, cytological and BSA-based testing on limited segregation population AFLPs.

Cytoplasmic male sterility (cms) in rye (Secale cereale L.), especially cytoplasma PAMPA, is used commercially in hybrid breeding programmes. The development of molecular markers that are tightly linked to the numerous genes coding for pollen fertility is expected to have great impact in the field. Morphological and cytological analyses of plants from a three-way cross C394: [(S67P/94 x S38/94) x CHD296] indicated the presence of at least several genes acting at different stages of pollen grain development, and proved the concurrence of both approaches in plant classification. The AFLP technique combined with the Bulk Segregant Analysis (BSA) were applied to identify DNA fragments linked to the genes of interest. All the 256 possible primer pair combinations based on the MseI and EcoRI restriction sites generated distinct band patterns allowing the identification of 31143 DNA fragments, visualised using the isotopic method. On average, any given primer combination generated 122 fragments. Among 1111 and 431 potential genetic markers respectively identified in the restorer form and the maternal lines, 775 and 295 were present in the F2 population. These numbers were then reduced to 109 and 51. The identified DNA fragments were tested on a limited segregating population, C394-F2, in order to eliminate false signals and to select markers for a future marker-assisted selection programme. Twenty-five markers were selected. Four of these markers were not identified via the BSA approach, indicating that if a highly polymorphic component is used for a cross, or a polygenic trait is studied, then the use of a limited population may be required.

Breeding↗
PubMed1997

Genetic analysis of adult-onset cataract in a city-based ophthalmic hospital.

Adult-onset cataract (AOC) is a major ocular health problem and is the number one cause of blindness in the world. It is interesting to note that if the development of cataract is delayed by 10 years, the number of cataract surgeries needed would decrease by 45%. To prevent or delay cataract, the molecular pathological mechanisms underlying the lens change have to be understood, and this requires that the genes involved in such mechanisms should be identified. Hence, in this study we aim to identify AOC families which show a clear mendelian inheritance pattern, as only these families would be ideal for mapping the genes responsible. Over a period of 8 months, from September 1995-April 1996, 17 families with two or more affected members were identified. Segregation analysis showed autosomal dominant inheritance in multiple affected families. We propose to map the genes responsible for cataract in these families by linkage analysis and mutational screening of candidate genes.

Adult↗
PubMed2005

Inheritance of total serum IgE in the isolated Tangier Island population from Virginia: complexities associated with genealogical depth of pedigrees in segregation analyses.

OBJECTIVES: This study was aimed at performing a segregation analysis of total serum immunoglobulin E (tIgE) in an isolated population using maximal genealogical information permitted by current software and computer capacities, while assessing the reliability of the best-fitting model of inheritance for tIgE through simulations. METHODS: All current Tangier Island, VA, residents (n = 664) belonged to one large extended pedigree (n = 3,501) spanning 13 generations, with an average inbreeding coefficient of 0.009. Phenotype data were obtained on 453 (68.2%) of the residents using a population-based recruitment scheme. Due to computational limitations resulting from the extremely complex pedigree structure, analysis on only two pedigree reconstructions was feasible: a reduced pedigree retaining all phenotyped individuals and their parents as 57 distinct families, and 922 nuclear families. RESULTS: Familial correlations and heritability calculations reveal a significant genetic component to tIgE in these data (heritability = 26%). The most parsimonious model to explain tIgE distribution indicated by the reduced pedigree structure was a two-distribution Mendelian model. However, larger and non-genetic models could not be rejected. Simulations over 200 replicates performed to evaluate the reliability of this model, indicated that using restricted genealogical information had minimal impact on results of segregation analyses performed here.

Adolescent↗
PubMed1981

Idiotypic analysis of anti-GAT antibodies. IX. Genetic mapping of the Gte idiotypic marker within the Igh-V locus.

The gene controlling the expression of the murine Gte idiotype marker was mapped within the Igh-V gene complex. This idiotypic marker was identified in B6, C.B-20 and A/J and C.AL-20 anti-GAT antisera, but either was not detectable or was present in very low quantities in the anti-GAT antisera obtained from BALB/c, BAB-14, SM/J, NZW, and NZB mice. The data are consistent with the interpretation that the latter 5 strains do not process Igh-Gte genes and the Igh haplotypes of these strains represent examples of crossing over within the Igh complex. Furthermore, the expression of the Gte idiotype(s) is not influenced by the Lyt-3 linked genes that control the kappa light chain polymorphism. Segregation analysis with 52 recombinant inbred strains confirmed the close linkage of Igh-Gte idiotype with Igh-1b locus. The recombination frequency between these loci was calculated to be 1 +/- 0.7 percent. Furthermore, by using B X D recombinant inbred strains, the Igh-Gte gene was mapped within the Igh-V region gene closely linked to the Igh-Np, Igh-Nbp, and Igh-BgI genes.

Animals↗
PubMed1999

Lung cancer risk in families of nonsmoking probands: heterogeneity by age at diagnosis.

In an earlier investigation, we did not detect a major genetic component to lung cancer in families of nonsmoking lung cancer probands. However, heterogeneity with respect to familial aggregation, based on probands' age at diagnosis, was evident. We reanalyzed our previously collected data of 257 families, stratified by age at diagnosis of the probands, using complex segregation analysis. We specifically tested the effects of a Mendelian diallelic gene, history of tobacco use, and history of selected chronic lung diseases in families with a proband diagnosed at the age of 60 years or older and in families with a younger proband (i.e. , under 60 years of age). Cases were identified from the Metropolitan Detroit Cancer Surveillance System. Information on lung cancer occurrence, smoking history, and chronic respiratory diseases in first-degree relatives was obtained for 210 older probands and for 47 younger probands. In older probands' families, no evidence of a major genetic effect was detected. A history of emphysema and tobacco-smoke exposure were found to be significant risk factors. In younger probands' families, a Mendelian codominant model with significant modifying effects of smoking and chronic bronchitis best explained the observed data. Our results suggest the presence of a high-risk gene contributing to early-onset lung cancer in a population where the probands are nonsmokers.

Adult↗
PubMedDate not supplied

Genetic analysis of hemostasis and thrombosis using vascular occlusion.

The zebrafish is an excellent model for mammalian hemostasis and thrombosis since it possesses coagulation factors, thrombocyte receptors and responds to anti-coagulant and anti-platelet drugs commonly used in clinical treatment. In this study, exposure of larvae to FeCl(3) or laser irradiation produced a vessel injury that caused a visible vascular occlusion as a result of thrombus formation. Using the time to vascular occlusion as an assay, two screening strategies were tested for their utility in identifying novel genes involved in thrombosis. Morpholino knockdown studies of zebrafish factor VII showed a prolongation of the time to occlusion of the vessel whereas knockdown of the recently discovered factor VIIi resulted in a shortening of the time. Genetic screening of a population of zebrafish identified mutants that showed a prolongation of the time to occlusion. Bulk segregant analysis showed linkage of one mutant to a locus, victoria, on linkage group 7. Thus, the vascular occlusion assay developed in this report measures in vivo thrombus formation and is a powerful tool for identifying novel genes involved in thrombosis.

Animals↗
PubMed1985

Homozygous typing cell-defined HLA-Dw specificities correlate better than serologically defined HLA-DR specificities with restriction elements for influenza virus-specific proliferative human T lymphocyte clones.

Human T lymphocyte clones with specific proliferative response to influenza A virus were derived by limiting dilution from peripheral blood lymphocytes (PBL) after in vitro stimulation with autologous irradiated, virus-infected PBL. Four OKT3+4+8- T lymphocyte clones (TLC) that showed HLA-restricted antigen-specific proliferative responses were used for a detailed analysis of the restriction elements for antigen presentation. None of the clones showed alloreactivity and all required the presence on the antigen-presenting cell of HLA class II antigens of one or other haplotype of the donor. Restriction elements for two clones were correlated with Dw1 rather than DR1, and for two others with Dw6 rather than DRw6. These latter clones showed differential recognition of HLA-Dw6 subtypes as defined tentatively by homozygous typing cells, without relationship to putative serological "splits" of DRw6. One of the Dw6-restricted clones was specific for a Dw6.1 (now Dw18) "subtype," confirmed by family segregation analysis, the other for a broad Dw6 (Dw18 and Dw19) specificity. Studies with a panel of monoclonal antibodies against monomorphic determinants of HLA class II antigens revealed heterogeneous patterns of blocking activity, distinguishing between clones of different restriction specificity. Inhibition patterns were partly as predictable from the known activity of the monoclonal antibody in alloantigeneic PLT systems. These results provide evidence that certain structures that function as restriction elements for antigen presentation also carry alloantigeneic determinants.

Antibodies, Monoclonal↗
PubMed1996

Simple sequence repeats for germplasm analysis and mapping in maize.

Simple sequence repeats (SSRs) are a relatively new class of DNA markers consisting of short runs of tandemly repeated sequence motifs evenly distributed throughout eukaryotic genomes. Owing to the high rate of variation in the number of repeat units, the polymorphism level shown by SSRs is high. Furthermore, they are easy to analyze by means of the polymerase chain reaction, using flanking unique sequence primers. In order to establish the utility of SSR markers for genetic mapping and for the analysis of corn germplasm, corn genomic libraries were constructed and screened for clones containing dinucleotide and trinucleotide repeats. One hundred and fifty clones were isolated and 34 of them were used in this study to analyze 15 (AG)n repeats, 15 (AC)n repeats, and 4 trinucleotide repeats. Twelve corn inbred lines, representing 87% of the RFLP alleles present in a collection of public corn cultivars, were used to assess the information content of the SSR markers. The expected heterozygosity of each SSR marker was compared with the expected heterozygosity of 100 different RFLP markers. The stability of SSRs was also tested through segregation analysis on an existing mapping population.

Alleles↗
PubMed2006

Allele frequency misspecification: effect on power and Type I error of model-dependent linkage analysis of quantitative traits under random ascertainment.

BACKGROUND: Studies of model-based linkage analysis show that trait or marker model misspecification leads to decreasing power or increasing Type I error rate. An increase in Type I error rate is seen when marker related parameters (e.g., allele frequencies) are misspecified and ascertainment is through the trait, but lod-score methods are expected to be robust when ascertainment is random (as is often the case in linkage studies of quantitative traits). In previous studies, the power of lod-score linkage analysis using the "correct" generating model for the trait was found to increase when the marker allele frequencies were misspecified and parental data were missing. An investigation of Type I error rates, conducted in the absence of parental genotype data and with misspecification of marker allele frequencies, showed that an inflation in Type I error rate was the cause of at least part of this apparent increased power. To investigate whether the observed inflation in Type I error rate in model-based LOD score linkage was due to sampling variation, the trait model was estimated from each sample using REGCHUNT, an automated segregation analysis program used to fit models by maximum likelihood using many different sets of initial parameter estimates. RESULTS: The Type I error rates observed using the trait models generated by REGCHUNT were usually closer to the nominal levels than those obtained when assuming the generating trait model. CONCLUSION: This suggests that the observed inflation of Type I error upon misspecification of marker allele frequencies is at least partially due to sampling variation. Thus, with missing parental genotype data, lod-score linkage is not as robust to misspecification of marker allele frequencies as has been commonly thought.

Alleles↗
PubMed2002

Inheritance of pancreatic acinar atrophy in German Shepherd Dogs.

OBJECTIVE: To assess the heritability of pancreatic acinar atrophy (PAA) in German Shepherd Dogs (GSDs) in the United States. ANIMALS: 135 GSDs belonging to 2 multigenerational pedigrees. PROCEDURE: Two multigenerational pedigrees of GSDs with family members with PAA were identified. The clinical history of each GSD enrolled in the study was recorded, and serum samples for canine trypsin-like immunoreactivity (cTLI) analysis were collected from 102 dogs. Dogs with a serum cTLI concentration < or = 2.0 microg/L were considered to have exocrine pancreatic insufficiency (EPI) and were assumed to have PAA. RESULTS: Pedigree I consisted of 59 dogs and pedigree II of 76 dogs. Serum cTLI concentrations were measured in 48 dogs from pedigree I and 54 dogs from pedigree II. A total of 19 dogs (14.1%) were determined to have EPI, 9 in pedigree I (15.3%) and 10 in pedigree II (13.6%). Of the 19 dogs with EPI, 8 were male and 11 were female. CONCLUSIONS AND CLINICAL RELEVANCE: Evaluation of data by complex segregation analysis is strongly suggestive of an autosomal recessive mode of inheritance for EPI in GSDs in the United States.

Animals↗
PubMed2000

Development of PCR-based markers linked to the fertility restorer gene for the polima cytoplasmic male sterility in rapeseed (Brassica napus L.).

Bulked segregant analysis was used to identify RAPD markers linked to the Rfp of pol cms in rapeseed (Brassica napus L.) from the fertile and sterile DNA bulks. DNA bands amplified from 1040 random 10-mer primers were screened. Two polymorphic bands S1019(720) and S1036(810) were found linked to the Rfp locus at the same side with a map distance of 5.8 cM and 12.3 cM respectively. These polymorphic fragments were cloned and sequenced. Nucleotide sequence information was used to design 20-24-mer oligo nucleotide primers for PCR amplification. The SCAR markers that generated from the long primers showed the same pattern of segregation as the original RAPD markers in the backcross population. The SCAR markers would facilitate selection on the Pol CMS restorer lines in rapeseed.

Brassica↗
PubMed2005

Identification of SCAR markers linked to Rca 2 anthracnose resistance gene and their assessment in strawberry germ plasm.

Bulked segregant analysis combined with AFLPs was used to identify molecular markers linked to the Rca 2 gene conferring resistance to Colletotrichum acutatum pathogenicity group 2 which causes anthracnose in the octoploid strawberry Fragaria x ananassa. DNA bulks originating from a cross between the resistant cultivar 'Capitola' and the susceptible cultivar 'Pajaro' were screened with 110 EcoRI/M se IAFLP combinations. Four AFLP markers were found linked in coupling phase to Rca 2 with recombination percentages between 0% and 17.7%. Among the four markers linked to the resistance gene, two were converted into SCAR markers (STS-Rca 2417 and STS-Rca 2240) and screened in a large segregating population including 179 genotypes. The Rca 2 resistance gene was estimated to be 0.6 cM from STS-Rca 2417 and 2.8 cM from STS-Rca 2240. The presence/absence of the two SCAR markers was further studied in 43 cultivars of F. x ananassa, including 14 susceptible, 28 resistant, and one intermediate genotype. Results showed that 81.4% and 62.8% of the resistant/susceptible genotypes were correctly predicted by using STS-Rca 2417 and STS-Rca 2240, respectively. The 14 susceptible genotypes showed no amplification for either SCARs. These developed SCARs constitute new tools for indirect selection criteria of anthracnose resistance genotypes in strawberry breeding programs.

Base Sequence↗
PubMed1989

Co-segregation of HLA and rheumatoid arthritis in multicase families.

Inheritance of parental HLA haplotypes was examined in the offspring of 95 multicase rheumatoid arthritis (RA) families. Overall, in these families there was no evidence of preferential transmission of one parental haplotype, although this might have been expected given the loading of these families with RA cases. However, there was a difference in inheritance when the affected and non-affected offspring were compared. A co-segregation analysis showed that the inheritance of parental HLA haplotypes was different between the affected and the unaffected offspring. Unlike a previous report, no difference was demonstrated in this study between the offspring of affected and non-affected parents. Similarly, the affected offspring of HLA DR4 heterozygote parents were more likely to inherit HLA DR4 than the non-affected offspring. It is concluded first that linkage studies of RA using the affected sib-pair method are not invalidated, which would have been the case in the presence of preferential transmission of HLA to all offspring. Secondly, HLA and specifically HLA-DR4 does co-segregate with RA, and, finally, parental RA status, independent of DR4, has little influence in explaining the genetic susceptibility to RA.

Arthritis, Rheumatoid↗
PubMed2002

Identification of RAPD markers and their use for molecular mapping in pea (Pisum sativum L.).

The RAPD method (Random Amplified Polymorphic DNA) was used for identifying and mapping new molecular markers in pea. RAPD analysis of various cultivars and lines of pea was carried out using 10-mer random primers. The presence of multiple polymorphism between cultivars and lines was revealed; at least one fragment for any given primer was present in the DNA of one form of pea and absent in the DNA of another line or cultivar. To detect molecular markers linked to the genes of chi-15, xa-18 and also to the 12 morphological markers of the L-1238 line, the F2 populations (Chi-15 ? L-1238), (Vio ? L-1238), (Xa-18 ? L-1238), (L-111 ? Chi-15) and (L-84 ? Xa-18) were studied via bulked segregant analysis. DNA molecular analysis of F1 hybrids revealed the presence of parental polymorphic fragments in all of the populations. The study of the F2 plants showed that the obtained fragments are inherited as Mendelian factors. 13 RAPD-markers linked to genes of A/a (flower color), I/i (seed color), Gp/gp (pod color), R/r (seed form), S/s (seeds linkage), and also to genes of Chi-15/chi-15 (leaf color) and Xa-18/xa-18 (leaf color) were discovered. The study of individual plant DNA from the F2 populations allowed us to determine the genetic distances between genes and the RAPD markers linked to them.

Base Sequence↗
PubMed2024

A novel start-loss mutation of the SLC29A3 gene in a consanguineous family with H syndrome: clinical characteristics, in silico analysis and literature review.

BACKGROUND: The SLC29A3 gene, which encodes a nucleoside transporter protein, is primarily located in intracellular membranes. The mutations in this gene can give rise to various clinical manifestations, including H syndrome, dysosteosclerosis, Faisalabad histiocytosis, and pigmented hypertrichosis with insulin-dependent diabetes. The aim of this study is to present two Iranian patients with H syndrome and to describe a novel start-loss mutation in SLC29A3 gene. METHODS: In this study, we employed whole-exome sequencing (WES) as a method to identify genetic variations that contribute to the development of H syndrome in a 16-year-old girl and her 8-year-old brother. These siblings were part of an Iranian family with consanguineous parents. To confirmed the pathogenicity of the identified variant, we utilized in-silico tools and cross-referenced various databases to confirm its novelty. Additionally, we conducted a co-segregation study and verified the presence of the variant in the parents of the affected patients through Sanger sequencing. RESULTS: In our study, we identified a novel start-loss mutation (c.2T&#x2009;>&#x2009;A, p.Met1Lys) in the SLC29A3 gene, which was found in both of two patients. Co-segregation analysis using Sanger sequencing confirmed that this variant was inherited from the parents. To evaluate the potential pathogenicity and novelty of this mutation, we consulted various databases. Additionally, we employed bioinformatics tools to predict the three-dimensional structure of the mutant SLC29A3 protein. These analyses were conducted with the aim of providing valuable insights into the functional implications of the identified mutation on the structure and function of the SLC29A3 protein. CONCLUSION: Our study contributes to the expanding body of evidence supporting the association between mutations in the SLC29A3 gene and H syndrome. The molecular analysis of diseases related to SLC29A3 is crucial in understanding the range of variability and raising awareness of H syndrome, with the ultimate goal of facilitating early diagnosis and appropriate treatment. The discovery of this novel biallelic variant in the probands further underscores the significance of utilizing genetic testing approaches, such as WES, as dependable diagnostic tools for individuals with this particular condition.

Humans↗
PubMed2004

Screening of a RAPD marker tightly linked to Co gene in apple and the SCAR marker conversion.

A DNA marker linked to the columnar gene (Co) in apple (Malus domestica) was explored based on the population of 105 progenies of 'Spur Fuji' x 'Telamon' by bulk segregant analysis (BSA) and Random Amplified Polymorphic DNA (RAPD) technique. A total of 300 random primers were screened and a RAPD marker (S1142(682)) closely linked to Co gene (2.86 cM) was identified and then sequenced. Four specific PCR primers (two forward primers and two reverse primers) were designed,and the products of SCAR-PCR indicated that all the four pairs of primers could amplify polymorphic bands between columnar and non-columnar traits, so any of them could serve as the specific SCAR primers. One pair of these specific primers was chosen to amplify each individual in the population, and the result showed that the co-segregation pattern of this SCAR marker and Co gene was the same as that of the RAPD marker. Furthermore, it was found that the nucleotide sequence of the RAPD marker fragment contained an open reading frame (ORF) that could encode 68 deduced amino acid residues at the position of +45 - +251.

Amino Acid Sequence↗