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Inheritance and linkage of allozymes in a Balkan endemic, Pinus peuce Griseb.

This article presents a study of isozyme variation in Pinus peuce Griseb., a Balkan endemic. Among the enzyme systems studied, five were monomorphic and eight were polymorphic in at least one locus. The segregation analysis of the polymorphic loci were consistent with a Mendelian mode of inheritance. No significant deviation from the expected ratio was observed both at the individual and pooled segregation data levels. Segregation patterns were homogeneous across individuals. Two significant linkage groups were found in P. peuce: FEST-2:LAP-2 and 6PG-1:6PG-2, which correspond to the results obtained for other pine species.

Acid Phosphatase↗

HLA antigen distribution and HLA haplotype segregation in Crohn's disease.

A study of the HLA-A, -B, -C, and -DR antigens in patients with Crohn's disease and controls did not reveal a significant strong association with a particular HLA antigens. A segregation analysis of parental HLA haplotypes in nine families with at least two children suffering from Crohn's disease did not show a significant deviation from the expected Mendelian segregation.

Crohn Disease↗

Clinical and genetic aspects in autosomal dominant inherited osteogenesis imperfecta type I.

In 30 fully investigated family pedigrees in which there were at least two generations of people suffering from osteogenesis imperfecta type I (McKusick no. 16620), the data on 144 random offspring could be used for segregation analysis. The major characteristics, blue sclerae, fractures, and hearing loss, were present in every pedigree. Their penetrance was also calculated. Precise definitions were used in the study. The segregation ratio or observed: expected ratio was 70:72. The incidence of blue sclerae was 70:70 (100%), for fractures 61:70 (87%), and for hearing loss 30:70 (43%). There was a very clear relationship between age and the progression of the hearing loss. Dividing the offspring into two groups depending on whether or not male-to-male inheritance was present and performing segregation and penetrance calculation on these data did not produce any indications that there are two genetically distinguishable subtypes of osteogenesis imperfecta type I. In a smaller group of 107 offspring, calculations could be made on several separate generations.

Age Factors↗

Extensions to pedigree analysis I. Likehood calculations for simple and complex pedigrees.

A graph theoretic definition of pedigrees is given and a distinction drawn between simple and complex pedigrees. Algorithms are presented to calculate the likeihood of any kind of pedigree, assuming only segregation at a finite set of loci, nonassortative mating and no environmental correlations; multiple births and consanguineous marriages are explicity allowed for. The formulation given can lead to more powerful genetic counselling, segregation analysis and linkage analysis.

Genetic Linkage↗

Genetics of LDL subclass phenotypes in women twins. Concordance, heritability, and commingling analysis.

Low density lipoprotein (LDL) subclass phenotype B, characterized by a predominance of small LDL as determined by gradient gel electrophoresis, has been associated with increased risk of coronary heart disease and an atherogenic lipoprotein profile. Previous studies employing complex segregation analysis have demonstrated a major, single gene effect on the inheritance of this phenotype in families. Recently, linkage between this phenotype and variation at the LDL receptor locus on chromosome 19 has been reported. However, variation in LDL subclass phenotypes has also been associated with age, gender, diabetes status, beta-blocker medication, and diet. The present study further evaluates the relative importance of genetic and nongenetic influences on LDL subclass phenotypes and on LDL peak particle diameter (as a reflection of the size of the major LDL subclass) in monozygotic and dizygotic women twin pairs. The analysis is based on 203 monozygotic and 145 dizygotic pairs of adult female twins who participated in the second examination of the Kaiser Permanente Women Twins Study. The average age was 51 years at this exam and 90% were white. Concordance analysis revealed that monozygotic cotwins shared LDL subclass phenotypes more frequently than dizygotic cotwins, and this was confirmed using logistic regression analysis after controlling for potential confounding factors. Heritability analyses suggested that approximately one third to one half of the variation in LDL peak particle diameter, a continuous variable reflecting LDL size, could be attributed to genetic influences. Commingling analysis of the frequency distribution of LDL peak particle diameter identified three distinct subgroups of subjects, one of which corresponded to those subjects with LDL subclass phenotype B.(ABSTRACT TRUNCATED AT 250 WORDS)

Female↗

Genome-wide association studies of plant traits and functional analysis of leaf development-related genes in citrus.

Labor-saving and high-light-efficiency tree architecture is a key breeding objective for woody fruit trees like citrus. However, population genetics information on these traits remains limited. In this study, tree architecture, thorn, and leaf traits were evaluated in 353 F2 progeny derived from a cross between Clementine mandarin and precocious trifoliate orange-an early-flowering variety. A random subset of 300 offspring was sequenced for a genome-wide association study (GWAS), which detected 10 216 significantly associated SNPs and defined several major quantitative trait loci (QTLs) for the target traits. Subsequent bulked segregant analysis (BSA) and GWAS on individuals with extreme compound leaf phenotypes mapped the causal gene(s) to a 0.8 Mb region (22.15-22.95 Mb) on chromosome 4. Genetic analysis across multiple hybrid combinations confirmed that the compound leaf trait in trifoliate orange is dominantly inherited and follows Mendelian segregation. Transcriptome profiling of parental leaves at different developmental stages identified a KNOX gene, CiKNAT6, as a candidate. Further validation using CAPS markers and Hi-Tom sequencing demonstrated tight linkage between an InDel polymorphism in CiKNAT6 and leaf shape across diverse citrus species and the F2 population, with co-segregation observed for the compound leaf trait. Due to alternative splicing producing seven splice variants, the CiKNAT6 DNA sequence was selected for genetic transformation experiments. Functional analysis revealed that the Clementine mandarin allele of CiKNAT6 is non-functional owing to an InDel, whereas ectopic expression of the trifoliate orange allele in tobacco and lemon induced leaf curling and reduced leaf size. CRISPR-Cas9 knockout of CiKNAT6 in trifoliate orange resulted in increased leaf area. These findings provide valuable genetic resources and insights for future studies on tree architecture and leaf morphology.

Plant Leaves↗

Familial Mediterranean fever: analysis of inheritance and current linkage data.

Familial Mediterranean fever (FMF) is a genetic disorder characterized by recurrent attacks of fever and inflammation of serosal surfaces. Unlike many mendelian disorders, the mode of transmission has been subject to some controversy as segregation analysis studies have always demonstrated fewer "observed" than "expected" affected individuals. Despite efforts to map the gene causing FMF, no definite linkage has been yet identified. This review analyses the epidemiologic and genetic characteristics in order to evaluate critically the inheritance of the disease and provide a perspective on the current biochemical and molecular genetic studies whose aim is to locate the gene for this disease.

Amyloidosis↗

Genetic analysis of the SA and Na+/K+-ATPase alpha1 genes in the Milan hypertensive rat.

OBJECTIVE: To study whether the SA gene locus (on rat chromosome 1) and the sodium potassium ATPase alpha1 gene locus (on rat chromosome 2) contribute to the elevated blood pressure in the Milan hypertensive rat. DESIGN: Co-segregation analysis using polymorphisms in the SA and Na+/K+-ATPase alpha1 genes in F2 rats from a cross of Milan hypertensive and Milan normotensive rats. Analysis of SA and N+/K+-ATPase alpha1 gene expression in kidneys of 6 and 25 weeks old Milan hypertensive and normotensive rats. METHODS: Genotyping of F2 rat DNA by restriction digestion and Southern blotting and comparison of messenger RNA levels by northern blot analysis. RESULTS: Renal expression of SA was considerably higher in normotensive than it was in hypertensive rats aged 6 and 25 weeks. Despite this difference the SA genotype did not co-segregate with blood pressure, although the Milan hypertensive rat allele did co-segregate with greater body weight (P = 0.0014) for male F2 rats. Expression of Na+/K+-ATPase alpha1 was higher in the kidneys of young hypertensive rats than it was in those of normotensive rats and did not decline with age as occurred in the normotensive rats. However, again the Na+/K+-ATPase alpha1 genotype did not co-segregate with blood pressure. CONCLUSIONS: Despite differences in the patterns of expression of SA and Na+/K+-ATPase alpha1 genes in the kidneys of Milan hypertensive and normotensive rats, we found no evidence of co-segregation of either gene with blood pressure. Our results suggest that either SA is simply acting as marker for a linked gene in other crosses for which co-segregation with blood pressure has been observed, or at least, the level of its renal expression is not the sole determinant of its effect on blood pressure. The failure of the Na+/K+-ATPase alpha1 gene to co-segregate with blood pressure suggests that its greater expression in the kidney of the Milan hypertensive rat is either reactive or controlled by other genetic loci.

Animals↗

Comparative RFLP mapping of an allotetraploid wild rice species (Oryza latifolia) and cultivated rice (O. sativa).

The purpose of this study was to construct a comparative RFLP map of an allotetraploid wild rice species, Oryza latifolia, and to study the relationship between the CCDD genome of O. latifolia and the AA genome of O. sativa. A set of RFLP markers, which had been previously mapped to the AA genome of cultivated rice, were used to construct the comparative map. Fifty-eight F2 progeny, which were derived from a single F1 plant, were used for segregation analysis. The comparative RFLP map contains 149 DNA markers, including 145 genomic DNA markers from cultivated rice, 3 cDNA markers from oat, and one known gene (waxy, from maize). Segregation patterns reflected the allotetraploid ancestry of O. latifolia, and the CC and DD genomes were readily distinguished by most probes tested. There is a high degree of conservation between the CCDD genome of O. latifolia and the AA genome of O. sativa based on our data, but some inversions and translocations were noted.

Biological Evolution↗

Steroid 21-hydroxylase deficiency: mutational spectrum in Denmark, three novel mutations, and in vitro expression analysis.

We have investigated 68 unrelated 21-hydroxylase deficient Danish patients, representing 136 alleles, and determined the mutational spectrum of the CYP21 gene. The most frequent mutations detected were deletion of CYP21 and the splice mutation in intron 2 (I2-splice). Segregation analysis showed evidence of a de novo mutation in each of two patients. Three novel mutations were detected: G64E in exon 1, Q262X in exon 7, and A362V in exon 8. G64E and A362V were introduced in the CYP21 cDNA by in vitro site-directed mutagenesis, and the two corresponding proteins were transiently expressed in COS-7 cells. The activity of 21-hydroxylase was determined using the two hormone substrates 17-hydroxyprogesterone and progesterone. The analysis showed no enzyme activity for any of the substrates, a result that correlates well with the severity of the patients' disease.

Adrenal Hyperplasia, Congenital↗

The 11q;22q translocation: a collaborative study of 20 new cases and analysis of 110 families.

Following a previous collaborative study (Fraccaro et al. 1980), 20 new cases of 11q;22q translocation are described. Twelve families were ascertained through an unbalanced carrier of the translocation and eight cases were ascertained as balanced carriers. A segregation analysis was performed on the 110 families so far published. It was concluded that the 11q;22q translocation is a relatively frequent event, and that all the cases thus far reported might have the same breakpoints at 11q23.3 and 22q11.2. The translocation seems to be independent of environmental factors and it seems to have a low rate of mutation as indicated by the scarcity of de novo cases. The new data confirmed that only one type of unbalanced karyotype (47,XX or XY+der(22)t(11;22)(q23.3;q11.2)) is found among the offspring of the translocation carriers. The minimal overall recurrence risk for an unbalanced translocation was estimated to 2%. There was no difference between the recurrence risks for male and female balanced carriers, while the trend was confirmed of an excess of female balanced carriers among the phenotypically normal offspring of the t(11;22) female carriers.

Abnormalities, Multiple↗

Autosomal dominant gene transmission in a large kindred with Gilles de la Tourette syndrome.

A multiplex kindred ascertained through a single proband with GTS has been systematically investigated with standardised diagnostic instruments for other cases of GTS and related disorders. Complex segregation analysis supported the hypothesis that a single major gene inherited in autosomal dominant fashion but with incomplete penetrance contributed most of the variance in the liability to develop GTS and related disorders. This result is consistent with previous segregation analyses which have employed different methods of ascertainment, and tends to confirm that a proportion of GTS is due to a dominant gene and is suitable for investigation with genetic markers for linkage analysis.

Causality↗

Genetic control of macrophage activation for killing of extracellular targets.

Activated peritoneal macrophages from Corynebacterium parvum-treated mice of most inbred strains, including C57BL/6J (B), are cytotoxic to adherent 1023 sarcoma target cells as well as to larvae of Schistosoma mansoni. Macrophages from A/J (A) strain mice, on the other hand, are defective in this function. Segregation analysis of these two traits was compatible with the hypothesis that effective activation is, in each case, controlled by a single, dominant, autosomal gene. Typing of individual animals of the segregating backcross progeny and of AXB/BXA recombinant inbred strains for the expression of macrophage activation for tumoricidal and schistosomulicidal activity indicates that the genetic control of these two traits is closely linked or identical.

Animals↗

Detection of copy number variations by chromosomal microarray analysis in disorders of sex development of unexplained molecular etiology and association with clinical findings.

PURPOSE: Despite advances in genetic diagnostics, the molecular cause of a significant proportion of DSDs remains unknown. The aim of this study was to identify copy number variations (CNVs) using chromosomal microarray analysis (CMA) technology in DSD patients with previously undetected molecular genetic etiology and to investigate their phenotypic associations with these variations. METHODS: This study included DSD cases without chromosomal abnormalities and without any variants detected by sequence analysis methods, including whole-exome sequencing analysis. We evaluated variant pathogenicity according to the American College of Medical Genetics and Genomics guidelines and recorded the phenotypic findings of the cases. All pathogenic variants were subjected to segregation analysis. RESULTS: Of the 20 patients included in the study, 16 (80%) were classified as 46,XY DSD and 4 (20%) as 46,XX DSD. Initial clinical diagnoses in this 46,XX DSD group included gonadal dysgenesis in two patients (50%) and androgen excess in the remaining two (50%). Among the 46,XY DSD patients, five patients (31.25%) were presumed to be androgen insensitive, nine (56.25%) were diagnosed with defects in androgen biosynthesis, and two (12.5%) had gonadal dysgenesis. CMA detected 38 CNVs in 16 patients (80%), comprising 12 deletions (31.6%) and 26 duplications (68.4%). Three pathogenic CNVs were detected in 3 patients (15%), whereas 27 variants of uncertain significance were identified in 13 patients (65%). CONCLUSION: In selected cases, the diagnostic approach should incorporate CMA to elucidate the molecular etiology of DSD. Furthermore, CMA may prove to be an invaluable tool in the search for new genes responsible for DSD.

Humans↗

Familial thrombocytosis as a recessive, possibly X-linked trait in an Arab family.

Familial thrombocytosis (FT) has previously been described as an autosomal-dominant disorder with manifestations similar to those of sporadic essential thrombocythaemia. We studied an Arab family consisting of four brothers, aged 4-8 years, who had either sustained markedly elevated (> 1000 x 109/l) or moderately elevated (> 500 x 109/l) platelet counts, two healthy sisters and their parents who had normal platelet counts. The four brothers with FT had normal plasma thrombopoietin levels and are currently not presenting with any thrombotic or haemorrhagic complications. Mutation analysis at the thrombopoietin gene (THPO) of the affected family members failed to detect the intron 3 G-->C splice mutation that had been described as causing FT. In addition, segregation analysis using a polymorphic CA marker revealed completely discordant THPO alleles among the affected brothers. We postulate the existence of a new locus for FT whereby the disease is transmitted as a recessive, possibly X-linked trait.

Adult↗

-137 (G/C) IL-18 promoter polymorphism in patients with inflammatory bowel disease.

OBJECTIVE: There is strong evidence that genetic factors contribute to the susceptibility for inflammatory bowel diseases (IBD). Recently, IL-18 promoter polymorphisms were characterized as risk factors for inflammatory diseases such as sepsis, asthma and adult-onset Still's disease. The aim of this study was to determine whether the -137 (G/C) IL-18 promoter polymorphism was associated with IBD susceptibility. MATERIAL AND METHODS: For association analysis, 470 patients with Crohn's disease (CD), 235 unrelated patients with ulcerative colitis (UC) and 347 controls were enrolled. Furthermore, 233 UC and 470 CD trios were included for segregation analysis. Genotyping was performed by application of the TaqMan MGB biallelic discrimination system. RESULTS: When comparing genotype frequencies of CD and UC patients versus controls, no significant difference was found (p=0.089 and p=0.078, respectively). However, the Cochran-Armitage trend test revealed a rising probability for CD and UC with increasing number of G alleles (p=0.030 and 0.028, respectively) for the case-control analysis. On the contrary, the family-based transmission disequilibrium test (TDT) did not show an association of the G allele with CD or UC in 470 CD and 233 UC trios (p=0.53 and p=0.79, respectively). CONCLUSION: The -137 (G/C) IL-18 promoter polymorphism is not a susceptibility factor for IBD in a German cohort.

Adult↗

A common genetic mechanism determines plasma apolipoprotein B levels and dense LDL subfraction distribution in familial combined hyperlipidemia.

Familial combined hyperlipidemia (FCH) is a common lipid disorder characterized by elevations of plasma cholesterol and/or triglyceride in first-degree relatives. A predominance of small, dense LDL particles and elevated apolipoprotein B (apoB) levels is commonly found in members of FCH families. Many studies have investigated the genetic mechanisms determining individuals' lipid levels, in FCH families. Previously, we demonstrated a major gene effect on LDL particle size and codominant Mendelian inheritance involved in determination of apoB levels in a sample of 40 well-defined FCH families. An elevation of apoB levels is associated metabolically with a predominance of small, dense LDL particles in FCH. To establish whether a common gene regulates both traits, we conducted a bivariate genetic analysis to test the hypothesis of a common genetic mechanism. In this study, we found that 66% of the total phenotypic correlation is due to shared genetic components. Further bivariate segregation analysis suggested that both traits share a common major gene plus individual polygenic components. This common major gene explains 37% of the variance of adjusted LDL particle size and 23% of the variance of adjusted apoB levels. Our study suggests that a major gene that has pleiotropic effects on LDL particle size and apoB levels may be the gene underlying FCH in the families we studied.

Apolipoproteins B↗

Heterozygous HESX1 mutations associated with isolated congenital pituitary hypoplasia and septo-optic dysplasia.

We have previously shown that familial septo-optic dysplasia (SOD), a syndromic form of congenital hypopituitarism involving optic nerve hypoplasia and agenesis of midline brain structures, is associated with homozygosity for an inactivating mutation in the homeobox gene HESX1/Hesx1 in man and mouse. However, as most SOD/congenital hypopituitarism occurs sporadically, the possible contribution of HESX1 mutations to the aetiology of these cases is presently unclear. Interestingly, a small proportion of mice heterozygous for the Hesx1 null allele show a milder SOD phenocopy, implying that heterozygous mutations in human HESX1 could underlie some cases of congenital pituitary hypoplasia with or without midline defects. Accordingly, we have now scanned for HESX1 mutations in 228 patients with a broad spectrum of congenital pituitary defects, ranging in severity from isolated growth hormone deficiency to SOD with panhypopituitarism. Three different heterozygous missense mutations were detected in individuals with relatively mild pituitary hypoplasia or SOD, which display incomplete penetrance and variable phenotype amongst heterozygous family members. Gel shift analysis of the HESX1-S170L mutant protein, which is encoded by the C509T mutated allele, indicated that a significant reduction in relative DNA binding activity results from this mutation. Segregation analysis of a haplotype spanning 6.1 cM, which contains the HESX1 locus, indicated that only one HESX1 mutation was present in the families containing the C509T and A541G mutations. These results demonstrate that some sporadic cases of the more common mild forms of pituitary hypoplasia have a genetic basis, resulting from heterozygous mutation of the HESX1 gene.

Alleles↗