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Mutational analysis of the RNX gene in congenital central hypoventilation syndrome.

Congenital central hypoventilation syndrome (CCHS) is a rare syndrome characterized by failure of autonomic respiratory control, often presenting with other dysfunctions of the autonomic nervous system. Segregation analysis suggested a complex model of inheritance with a major locus involved. Disruption of the Rnx gene, a member of the Hox11 family of homeobox genes, in embryonic stem cells produced mice showing a phenotype similar to CCHS. Based on this observation, we have carried out mutation screening of the RNX gene in a set of 13 patients affected with CCHS, 2 of whom showing association with Hirschsprung disease. Single-strand conformational polymorphism analysis and direct sequencing of the whole coding portion of the RNX gene and of 1,311 bp of 5' flanking region were performed. No sequence variant was identified, with the exception of a private nucleotide change at position -874 bp from the ATG codon in two siblings affected with isolated CCHS. A functional test, performed by using the luciferase gene reporter system, has not shown any significant difference in the activity of the promoter region carrying this latter nucleotide change with respect to the wild-type allele. We conclude that RNX, and presumably its expression, are not altered in our index cases of CCHS.

Animals↗

Linkage analysis of infantile pyloric stenosis and markers from chromosome 9q11-q33: no evidence for a major gene in this candidate region.

A genetic component in the aetiology of infantile pyloric stenosis (PS) is well established. Segregation analysis is compatible with a multifactorial sex modified threshold model of inheritance but a major gene of low penetrance has not been excluded. PS has been reported to occur in 57% (four of seven) of cases with duplication of chromosome 9q11-q33. Twenty families with PS were studied using genetic markers at loci D9S55, D9S111, D9S15, D9S12, D9S56, D9S59, and ASS from this region of chromosome 9. Pairwise lod scores of -2 were obtained with all these markers at recombination fractions greater or equal to 0.04 under both autosomal dominant and autosomal recessive models of inheritance. This provides evidence against the existence of a major locus predisposing to PS within chromosome 9q11-q33.

Chromosomes, Human, Pair 9↗

Restriction fragment length polymorphism analysis in ankylosing spondylitis.

We utilized the technique of restriction fragment length polymorphism (RFLP) analysis in order to examine class I major histocompatibility complex genes in 52 Alabama ankylosing spondylitis patients and 107 local control subjects. A 9.2-kilobase PvuII RFLP was identified using the class I-specific B7 cDNA probe pDP001 that was closely associated with ankylosing spondylitis, most specifically with peripheral joint (including shoulder and hip) involvement. This fragment is associated with human leukocyte antigen A3 and A9 alleles, and segregation analysis in 11 multiplex families showed the RFLP to frequently segregate independently of B27 haplotypes. Two more recent studies have not confirmed the association of the 9.2-kilobase PvuII RFLP with ankylosing spondylitis per se, believed to be due to clinical and possibly genetic differences between the patient groups studied. These data strongly suggest at least one other major histocompatibility complex class I gene to be operative in predisposition to or modification of ankylosing spondylitis.

Deoxyribonucleases, Type II Site-Specific↗

Isolation of a full-length mitotic cyclin cDNA clone CycIIIMs from Medicago sativa: chromosomal mapping and expression.

Cyclins in association with the protein kinase p34cdc2 and related cyclin-dependent protein kinases (cdks) are key regulatory elements in controlling the cell division cycle. Here, we describe the identification and characterization of a full-length cDNA clone of alfalfa mitotic cyclin, termed CycIIIMs. Computer analysis of known plant cyclin gene sequences revealed that this cyclin belongs to the same structural group as the other known partial alfalfa cyclin sequences. Genetic segregation analysis based on DNA-DNA hybridization data showed that the CycIIIMs gene(s) locates in a single chromosomal region on linkage group 5 of the alfalfa genetic map between RFLP markers UO89A and CG13. The assignment of this cyclin to the mitotic cyclin class was based on its cDNA-derived sequence and its differential expression during G2/M cell cycle phase transition of a partially synchronized alfalfa cell culture. Sequence analysis indicated common motifs with both the A- and B-types of mitotic cyclins similarly to the newly described B3-type of animal cyclins.

Amino Acid Sequence↗

Partial silencing of the NEC1 gene results in early opening of anthers in Petunia hybrida.

The NEC1 gene, previously isolated from Petunia hybrida, is expressed at high levels in nectaries, and in a very localized fashion in stamens, particularly in the anther stomium cells and the upper part of the filament. To elucidate the function of the NEC1 gene, co-suppression was employed for down-regulation of NEC1 expression, and transposon insertion mutagenesis was used to knock out the NEC1 function. Among the transgenic plants and plants carrying dTph1 inserted in the NEC1 gene, an "early open anther" phenotype was observed. In this mutant phenotype, the anthers already open in young flower buds (1.8 cm) that still contain immature pollen, resulting in poor pollen quality and impaired pollen release. The results obtained indicate that NEC1 might be involved in the development of stomium cells, which are ruptured during the normal process of anther dehiscence to release mature pollen. Southern analysis revealed the presence of a highly homologous NEC1-like gene, named NEC2, in the P. hybrida genome. The presence of NEC2 was confirmed by segregation analysis and sequencing of genomic clones. The implications of these results and possible reasons why no visually obvious phenotype in nectaries could be produced by co-suppression or transposon insertion mutagenesis are discussed.

Alleles↗

Organization of the canine gene encoding the E isoform of retinal guanylate cyclase (cGC-E) and exclusion of its involvement in the inherited retinal dystrophy of the Swedish Briard and Briard-beagle dogs.

Intracellular cyclic GMP concentration is known to change in response to a wide variety of agents, including hormones, neurotransmitters or light. In vertebrate photoreceptors, different membrane-bound guanylate cyclase isoforms are responsible for cGMP synthesis and thus directly involved in termination of light signalling via the phototransduction cascade and recovery of the dark state. We have characterized a 4.7 kb long cDNA for the canine retinal guanylate cyclase isoform E (cGC-E) predicting a polypeptide of 1109 amino acids. The genomic structure and the complete sequence of the canine GC-E gene, which consists of 20 exons and spans about 14.5 kb, has also been determined. Northern blot analysis showed that GC-E was expressed in the canine retina as a 4.7 and 6.1 kb large transcript. RT-PCR analysis also detected low expression in cerebrum (occipital lobe). We performed a sequence analysis of the cGC-E gene in animals of a Swedish Briard and Briard-Beagle dog kinship in which an inherited retinal dystrophy is segregating. Several intragenic DNA polymorphisms were identified and used for segregation analysis which excluded cGC-E as a candidate gene for this type of canine retinal dystrophy.

Amino Acid Sequence↗

DNA profiling of cattle using micro- and minisatellite core probes.

We have evaluated 15 different micro- and minisatellite core probes for use in identity and paternity testing in cattle, based on Southern blot hybridization analysis. The core probes were tested in animals of different breeds and by analysis of seven two-generation pedigrees. Of the 15 core probes tested, seven were able to detect on average seven variant bands per individual animal. Segregation analysis showed that on average two out of 36 variant bands scored per core probe were genetically linked while two out of 12 variant bands correspond to the same allelic pair. The results obtained demonstrate the effectiveness of multilocus core probes for determining identity and paternity in cattle.

Animals↗

[Genetic mapping of resistant gene to southern corn rust and the tagging analysis on different genetic background].

Southern corn rust (SCR) is a destructive disease in maize. The inbred line Qi319 is highly resistant to southern corn rust. SSR technique was employed to preliminary mapping of the resistance gene. Bulked segregant analysis revealed that two primers, phi 118 and phi 041, amplified polymorphic bands. SSR analysis on populations indicated the two primers were linked to the rust resistance gene, which was mapped on the short arm of chromosome 10. In addition, comparative analysis of the amplification bands among different populations revealed that the amplification products with the same primer in different populations were dissimilar. This result indicates that the genetic background may affect results of gene mapping and tagging. So, it is important to select suitable population to performing molecular marker analysis and gene mapping.

Basidiomycota↗

Rapid identification of Arabidopsis insertion mutants by non-radioactive detection of T-DNA tagged genes.

To assist in the analysis of plant gene functions we have generated a new Arabidopsis insertion mutant collection of 90 000 lines that carry the T-DNA of Agrobacterium gene fusion vector pPCV6NFHyg. Segregation analysis indicates that the average frequency of insertion sites is 1.29 per line, predicting about 116 100 independent tagged loci in the collection. The average T-DNA copy number estimated by Southern DNA hybridization is 2.4, as over 50% of the insertion loci contain tandem T-DNA copies. The collection is pooled in two arrays providing 40 PCR templates, each containing DNA from either 4000 or 5000 individual plants. A rapid and sensitive PCR technique using high-quality template DNA accelerates the identification of T-DNA tagged genes without DNA hybridization. The PCR screening is performed by agarose gel electrophoresis followed by isolation and direct sequencing of DNA fragments of amplified T-DNA insert junctions. To estimate the mutation recovery rate, 39 700 lines have been screened for T-DNA tags in 154 genes yielding 87 confirmed mutations in 73 target genes. Screening the whole collection with both T-DNA border primers requires 170 PCR reactions that are expected to detect a mutation in a gene with at least twofold redundancy and an estimated probability of 77%. Using this technique, an M2 family segregating a characterized gene mutation can be identified within 4 weeks.

Algorithms↗

Genetic and environmental influences on IL-6 and TNF-alpha plasma levels in apparently healthy general population.

Dysregulation of cytokines synthesis is thought to play a role in the development of a number of age-related conditions, such as rheumatoid arthritis, osteoporosis, atherosclerosis, and others, but observational studies have led to contradictory results. We investigated potential familial influences on the plasma levels of IL-6 and TNF-alpha in 91 nuclear and more complex pedigrees of Caucasian ethnic origin (N=401 individuals). The maximum likelihood based variance decomposition analysis showed significant positive correlation between circulating IL-6 and age in both genders. The magnitude of these correlations in our sample ranged from 0.22 in females to 0.28 in males (P<0.001). Significant association between TNF-alpha and IL-6 (r=0.28, r=0.43; P<0.001; respectively for men and women) was also observed. Likelihood ratio test clearly revealed that additive genetic effect for TNF-alpha was highly significant (P<0.001), and accounted over 80% of its variation, adjusted for IL-6 levels and age. In contrast, heritability estimate for IL-6 adjusted for age and TNF-alpha, revealed small contribution of genetic factors (24.1 +/- 10.2%). The bivariate variance component analysis demonstrated that significant relationship between IL-6 and TNF-alpha was due to shared environment only (r(E)=0.760 +/- 0.140). As evinced from our complex segregation analysis the nature of the genetic determinant of each of these two cytokines is quite complex and it is probably oligogenic.

Adult↗

The Clinical Lipid Research Clinic Family Study: familial determinants of plasma uric acid.

Commingling analysis of plasma uric acid levels in a random sample of 160 nuclear families supports the hypothesis that there is a mixture of three distributions. Assuming one, two, and three components in the underlying distribution, we obtained the corresponding p-values (for power transformation) as 0.059, 1.040, and 1.643, respectively. Path analysis with p = 0.059, 1.040, and 1.643 respectively. Path analysis with p = 0.059 gives genetic (h2) and cultural (c2) heritabilities as 0.256 and 0.199, without much support for intergenerational differences, assortative mating, or maternal effects. Complex segregation analysis with p = 0.059 supports multifactorial inheritance, consistent with the findings of Gulbrandsen et al. (1979) and Morton (1979) in other populations. This study also fails to support a major locus hypothesis, contrary to earlier reports.

Adolescent↗

Evidence for a new major gene influencing meat quality in pigs.

The present investigation primarily deals with the inheritance of a pigmeat quality trait, the Napole technological yield (RTN), a measure of cooked weight to fresh weight. This trait as well as lean percentage at 100 kg liveweight and fattening length from 20 to 100 kg liveweight were recorded on 3459 offspring from 67 sires and 433 dams, and 3052 offspring from 64 sires and 405 dams in Penshire (P66) and Pen Ar Lan (P77) composite lines respectively. The hypothesis of a major 2-allele locus contributing to RTN was tested by use of a segregation analysis method. Highly significant likelihood ratios (mixed vs. polygenic transmission models) lead us to conclude that a major gene RN- exerting an unfavourable effect on RTN is segregating in both lines. Maximum likelihood estimates of the parameters under the hypothesis of mixed (monogenic + polygenic) inheritance show that the difference between the means of the 2 homozygotes amounts to about 3 phenotypic standard deviations of the trait, whereas the complete dominance of RN- cannot be rejected. The frequency of RN- is about 0.6 in both lines. These results are discussed in connection with the previously reported 'Hampshire effect' on pigmeat quality, as the Hampshire breed is a common component of the foundation stock of the 2 composite lines under study.

Adipose Tissue↗

Mode of inheritance in mood disorder families according to fluvoxamine response.

Mood disorders are known to cluster within families, but the mode of transmission remains largely unknown. The purpose of our analysis was to determine whether selection of a sample that was homogeneous in its response to an antidepressant provided stronger evidence for a single major locus. Complex segregation analysis was applied to a sample of 171 Italian families of bipolar and unipolar probands that were responsive to the antidepressant fluvoxamine. We used regressive logistic analyses to determine the best fit from among environmental, arbitrary Mendelian, dominant, recessive and additive models. For the 171 affective families with probands that were responsive to the antidepressant fluvoxamine, a Mendelian model of inheritance was rejected. When considering 68 families of bipolar probands, the best fit was obtained for a Mendelian dominant model of transmission. The identification of a Mendelian mode of transmission in bipolar subjects who were selected according to their response to fluvoxamine supports the use of a pharmacological criterion as a tool for identifying true genetic disorders.

Adult↗

A xanthomatosis-susceptibility gene may exist in a Syrian family with familial hypercholesterolemia.

Familial hypercholesterolemia (FH) is an autosomal-dominant inherited disorder characterized by high serum low-density lipoprotein (LDL)-cholesterol concentrations, xanthoma formation, and premature atherosclerosis. Homozygous individuals die of vascular disease as children or young adults; heterozygous persons are at high risk for premature cardiovascular death. Mutations in the LDL-receptor gene are responsible for FH. We studied 49 members of a consanguineous Syrian kindred containing 6 homozygous individuals from the same pedigree. Half of the homozygotes had giant xanthomas, while half did not, even though their LDL-cholesterol concentrations were elevated to similar degrees (> 14 mmol/l). Heterozygous FH individuals from this family were also clearly distinguishable with respect to xanthoma size. We performed DNA analysis and were successful in identifying a hitherto not described mutation in this family's LDL receptor. DNA sequence analysis of the LDL-receptor gene revealed a T to C substitution at nucleotide 1,999 in codon 646 of exon 14. We next conducted a segregation analysis, which suggests that a susceptibility gene may explain the formation of giant xanthomas in this family. We raise the hypothesis that the appearance of giant xanthomas in this FH family is controlled by a second gene acting in an autosomal-dominant or recessive fashion. Elucidation of this 'xanthoma' gene may shed additional light on LDL-cholesterol deposition.

Adolescent↗

Orofaciodigital syndrome, type I: a phenotypic and genetic analysis.

An additional family with the orofaciodigital syndrome. Type I, is presented. On the basis of previously published pedigrees, as well as the present case, data are presented that conclusively support an X-linked dominant mode of inheritance. Segregation analysis demonstrated that not only is there lethality in the male but there is significant lethality in the female due to lyonization. In addition, a review of the familial cases will demonstrate a large degree of intra- and interfamilial variation.

Abnormalities, Multiple↗

Identification of a major gene and RAPD markers for yellow seed coat colour in Brassica napus.

The development of yellow-seeded Brassica napus for improving the canola-meal quality characteristics of lower fibre content and higher protein content has been restricted because no yellow-seeded forms of B. napus exist, and their conventional development requires interspecific introgression of yellow seed coat colour genes from related species. A doubled-haploid (DH) population derived from the F1 generation of the cross 'Apollo' (black-seeded) x YN90-1016 (yellow-seeded) B. napus was analysed via bulked segregant analysis to identify molecular markers associated with the yellow-seed trait in B. napus for future implementation in marker-assisted breeding. A single major gene (pigment 1) flanked by eight RAPD markers was identified co-segregating with the yellow seed coat colour trait in the population. This gene explained over 72% of the phenotypic variation in seed coat colour. Further analysis of the yellow-seeded portion of this DH population revealed two additional genes favouring 'Apollo' alleles, explaining 11 and 8.5%, respectively, of the yellow seed coat colour variation. The data suggested that there is a dominant, epistatic interaction between the pigment I locus and the two additional genes. The potential of the markers to be implemented in plant breeding for the yellow-seed trait in B. napus is discussed.

Brassica napus↗

Testicular teratocarcinogenesis in mice--a review.

Spontaneous testicular germ cell tumours in humans and mice are remarkable for their diverse composition. These tumours are usually composed of an extraordinary variety of cell and tissue types including muscle, skin, bone, cartilage, and neuroepithelia. Their diverse composition reflects their origin from totipotent primordial germ cells at about Day 12 of fetal development. Although much is known about the development of these tumours, remarkably little is known about the genetics of the mammalian primordial germ cell lineage or about the genes that control susceptibility to spontaneous testicular germ cell tumours in humans or mice. Conventional genetic analysis of susceptible 129/Sv mice is difficult because of the large number of susceptibility genes and their low penetrance. We are taking advantage of the Ter mutation to simplify the genetic analysis. Various evidence suggests that Ter is neither necessary nor sufficient for tumourigenesis. Instead, Ter acts as a modifier, dramatically increasing tumour incidence from approximately 1% in +/+ males, to approximately 17% in Ter/+ males and approximately 94% in Ter/Ter males. Segregation analysis suggests that Ter increases tumour incidence by requiring some, but perhaps not all, of the 129/Sv-derived susceptibility genes. With standard crosses that segregate for the Ter mutation, identification not only of Ter but also of these 129/Sv-derived susceptibility genes should be possible. In this paper, we review the genetics and development of germ cell tumours in 129/Sv mice, summarize the status of Ter mapping, and provide evidence that different genetic pathways lead to unilateral and bilateral tumours.

Animals↗

Combined segregation and linkage analysis for IDDM and HLA-DR under several ascertainment assumptions.

Combined segregation and linkage analysis of the Genetic Analysis Workshop 5 (GAW5) data suggests a complex basis for susceptibility to insulin-dependent diabetes mellitus (IDDM). One susceptibility gene, linked to the HLA-DR region, is additive on the liability scale (d = .49 +/- .15, t = 2.9 +/- .6) with a gene frequency q = .30 +/- .03. A second locus, with a gene frequency of q = .07 +/- .02, which is recessive and unlinked to HLA, is also suggested by the analysis. The ascertainment correction used has little effect on the results, presumably because most of the information comes from the cosegregation of HLA alleles and disease status. The results are consistent with a direct involvement of the HLA-DR region in susceptibility, but are not a proof of it.

Computer Simulation↗