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PubMed2006

Genetic analysis and fine mapping of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene bph19(t).

Genetic analysis and fine mapping of a resistance gene against brown planthopper (BPH) biotype 2 in rice was performed using two F(2) populations derived from two crosses between a resistant indica cultivar (cv.), AS20-1, and two susceptible japonica cvs., Aichi Asahi and Lijiangxintuanheigu. Insect resistance was evaluated using F(1) plants and the two F(2) populations. The results showed that a single recessive gene, tentatively designated as bph19(t), conditioned the resistance in AS20-1. A linkage analysis, mainly employing microsatellite markers, was carried out in the two F(2) populations through bulked segregant analysis and recessive class analysis (RCA), in combination with bioinformatics analysis (BIA). The resistance gene locus bph19(t) was finely mapped to a region of about 1.0 cM on the short arm of chromosome 3, flanked by markers RM6308 and RM3134, where one known marker RM1022, and four new markers, b1, b2, b3 and b4, developed in the present study were co-segregating with the locus. To physically map this locus, the bph19(t)-linked markers were landed on bacterial artificial chromosome or P1 artificial chromosome clones of the reference cv., Nipponbare, released by the International Rice Genome Sequencing Project. Sequence information of these clones was used to construct a physical map of the bph19(t) locus, in silico, by BIA. The bph19(t) locus was physically defined to an interval of about 60 kb. The detailed genetic and physical maps of the bph19(t) locus will facilitate marker-assisted gene pyramiding and cloning.

Animals↗
PubMed1995

The influence of response bias on segregation and linkage analysis.

Response bias in epidemiologic studies can occur if affected individuals are more (or less) likely to participate in a survey than their unaffected counterparts. To examine the effect of response bias in the context of a family study, we conducted segregation and linkage analysis in all 1,000 individuals in the Problem 2 data set, and in two different 65% samples: one sample consisting of 648 randomly selected individuals, and the other sample nonrandomly constructed so that individuals with high levels of Q1 were oversampled. In this simulation the ability to detect major genes for Q1-Q4 in segregation analysis and to link these putative major genes to genetic markers in linkage analysis was not markedly different between the 65% random and the 65% enriched samples.

Alleles↗
PubMed2003

18q-syndrome: brain MRI shows poor differentiation of gray and white matter on T2-weighted images.

PURPOSE: To study brain MRI findings in patients with 18q- syndrome and to correlate these findings with the results of the molecular breakpoint analysis. MATERIALS AND METHODS: Brain MR images of 17 patients with 18q- syndrome were evaluated. Segregation analysis was performed with 15 microsatellite markers to determine the deletion breakpoints and whether the deletion included the myelin basic protein (MBP) gene. RESULTS: One patient had an interstitial deletion of 18q which spared the MBP gene. He was the only one with normal brain MRI. All 16 patients with deletions including the MBP gene had abnormal white matter in MRI. The main finding was poor differentiation of gray and white matter on T2-weighted images due to increased white matter signal intensity. In addition, measured signal intensity of the white matter was significantly increased in patients compared with controls. CONCLUSIONS: Poor differentiation of gray and white matter on T2-weighted images is the most typical MRI finding of the 18q- syndrome. These results support the postulation that abnormal myelination in 18q- syndrome is due to haploinsufficiency at or near the MBP locus.

Abnormalities, Multiple↗
PubMed1991

DNA variants with telomere probe enable genetic mapping of ends of mouse chromosomes.

Dde I-digested DNA fragments from 11 inbred mouse strains were separated by electrophoresis, blotted and probed with a labeled oligomer, TELO, containing five repeats of the consensus mammalian telomere sequence, TTAGGG. Each strain produced a unique set of hybridizing fragments. Segregation analysis of TELO-hybridizing fragments from the BXD RI strains indicated that each fragment segregated as expected for a single gene. One fragment from strain DBA/2J was genetically linked to locus Xmv-9, previously mapped near the distal end of the map of chromosome (Chr) 4 and three fragments to Cck, near the distal end of Chr 9, suggesting that these fragments are telomeric and represent the ends of the chromosome maps. Confirmation of these map positions was obtained from a backcross. Fragments associated with the short arm of the Y Chr were found in DNA from strains C57BL/6J and DBA/2J. TELO-hybridizing fragments from DBA/2J were digested by the exonuclease Bal 31, under conditions in which fragments hybridizing to a cDNA probe for the metallothionein locus, located at the middle of mouse Chr 8, remained intact. Thus both biochemical and genetic tests indicate that several TELO-hybridizing fragments from Dde I-digested DNA are at the ends of chromosomes and probably derive from mouse telomeres. Using this approach should allow the mapping of genes relative to the ends of other mouse chromosomes.

Animals↗
PubMed2004

Characterization of the common wheat (Triticum aestivum L.) mutation line producing three pistils in a floret.

In a normal wheat (Triticum ssp.L.) spike, one floret carries only one pistil that will further develop into one grain after fertilization. The cultivated common wheat (T. aestivum L.) mutation line Three Pistils (TP) carried three pistils in a floret. Although one or two of the pistils died out before seed set in some florets, there were exist many florets that set three seeds. Normally, it was observed that there were one to three seeds in different florets of the same spike. Therefore, this mutation trait could raise considerably the number of grains per spike. The weight of 100 grains in three seeds set florets was lower than that of in one seed set florets. But three seeds set florets were significantly to surpass the one seed set florets in grain(s) weight per floret. Based on these results, the three pistils trait was suggested to be an interesting germplasm resource. Localisation of the gene controlling the three pistils trait was carried out by the method of crossing TP with the Chinese Spring disomic substitutions. F2 population segregation analysis revealed that only the 5B F2 population did not show homogeneity to control population. chi2-test analysis indicated that 5B F2 population, and only this population, was deviated from the Mendelian segregation ratio (3:1). As a conclusion, the gene for three pistils trait was located on chromosome 5B. According to the Recommended rules for gene symbolization in wheat, the name of the dominant gene for three pistils trait in the line TP was suggested as Pis1.

Genes, Plant↗
PubMed1995

Molecular analysis and predictive testing in retinoblastoma.

Predictive testing using molecular analysis is an integral part of contemporary retinoblastoma management. We have made extensive use of segregation analysis for risk assessment in both familial and sporadic disease. Investigation of loss of heterozygosity in tumor samples proved to be invaluable for the identification of linkage phase. In many families, however, accurate carrier risk assessment depends on direct identification of the causative R B I mutation. Consequently, we have developed methods for rapid mutation screening. Using these techniques, mutation analysis can now be offered to an increasing number of individuals.

DNA Mutational Analysis↗
PubMed1989

Meiotic chromosome segregation in human t(11;22)(q23;q11) carriers: a theoretical consideration.

The t(11;22)(q23;q11) translocation is the most frequently encountered familial reciprocal translocation in humans. In the majority of reported cases ascertainment has been through the birth of a child with the chromosomal constitution 47,XX,+der(22) or 47,XY,+der(22), i.e., tertiary trisomy. Previous segregation analysis of familial cases showed a number of interesting features. Thus, euploid unbalanced genotypes resulting from adjacent segregation are absent in the progeny, and only tertiary trisomic offspring are recovered. To explain this unusual progeny output we present here a model for the meiotic behavior of this translocation in the carriers based on an analysis of cytogenetic data of progeny of carriers. This model predicts the formation of a chain trivalent with chromosome order 11-der(11)-22 during prophase I and its predominant alternate orientation at metaphase I.

Chromosomes, Human, Pair 11↗
PubMed2006

Backcross and partial advanced intercross analysis of nonobese diabetic gene-mediated effects on collagen-induced arthritis reveals an interactive effect by two major loci.

Genetic segregation analysis between NOD and C57BL strains have been used to identify loci associated with autoimmune disease. Only two loci (Cia2 and Cia9) had earlier been found to control development of arthritis, whereas none of the previously identified diabetes loci was of significance for arthritis. We have now made a high-powered analysis of a backcross of NOD genes on to the B10.Q strain for association with collagen-induced arthritis. We could confirm relevance of both Cia2 and Cia9 as well as the interaction between them, but we did not identify any other significant arthritis loci. Immune cellular subtyping revealed that Cia2 was also associated with the number of blood macrophages. Congenic strains of the Cia2 and Cia9 loci on the B10.Q background were made and used to establish a partial advanced intercross (PAI). Testing the PAI mice for development of collagen-induced arthritis confirmed the loci and the interactions and also indicated that at least two genes contribute to the Cia9 locus. Furthermore, it clearly showed that Cia2 is dominant protective but that the protection is not complete. Because these results may indicate that the Cia2 effect on arthritis is not only due to the deficiency of the complement C5, we analyzed complement functions in the Cia2 congenics as well as the PAI mice. These data show that not only arthritis but also C5-dependent complement activity is dominantly suppressed, confirming that C5 is one of the major genes explaining the Cia2 effect.

Animals↗
PubMed2000

Inheritance of the waist-to-hip ratio in the National Heart, Lung, and Blood Institute Family Heart Study.

OBJECTIVE: Considering that waist-to-hip ratio (WHR) is a simple anthropometric measure of obesity and is a better predictor of coronary heart disease than body mass index (BMI), the genetic underpinnings of WHR are of interest. The inheritance pattern of WHR, before and after adjustment for BMI (WHR-BMI), was investigated in 2713 individuals from 1038 nuclear families in the National Heart, Lung, and Blood Institute Family Heart Study (NHLBI-FHS). RESEARCH METHODS AND PROCEDURES: Waist and hip measurements were taken twice, and the means of the measurements were used to calculate the WHR. Adjustments for age were carried out separately by sex, using stepwise multiple regression procedures for WHR and WHR-BMI phenotypes. Segregation analysis was applied using the unified model as implemented in the computer program POINTER. RESULTS: For age-adjusted WHR, the segregation results suggested an additive major gene that accounts for 35% of the phenotypic variance, and approximately 30% of the sample are homozygous for the "high" genotype. The results for age- and BMI-adjusted WHR were also compatible with a major gene; however, the multifactorial model provided the most parsimonious fit to the data. DISCUSSION: Although the genetic mechanisms for several obesity traits have been studied, tests of Mendelian segregation on this simple anthropometric measure (WHR) have not been reported previously. This study provides evidence for the presence of a major gene for age-adjusted WHR, suggesting that it is an appropriate trait for further genetic analysis, especially because it has strong predictive value and probably relates biologically to cardiovascular risk.

Body Constitution↗
PubMed2002

Inheritance of resistance to covered smut in barley and development of a tightly linked SCAR marker.

Inheritance of resistance to covered smut in the barley line Q21861 was studied using a doubled-haploid population produced by crossing Q21861 with the line SM89010. Based on 3 years of screening in the field and two seasons in the greenhouse, segregation for resistance/susceptibility fits a one-gene ratio, indicating a single major gene for resistance in Q21861. Of 440 random 10-mer primers tested using bulked segregant analysis, one primer (OPJ10) resulted in a reproducible polymorphic band. RAPD marker OPJ10(450) co-segregated in repulsion with the covered smut resistance. This marker was converted to a sequence-characterized amplified region (SCAR) marker linked in coupling (5.5 cM) with the covered smut resistant gene in Q21861. The SCAR marker was amplified in the line TR640 which is also resistant to covered smut, but not in the other resistant lines. The SCAR marker will be useful for marker-assisted selection for covered smut in barley breeding programs.

Journal Article↗
PubMed2000

A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1.

Resistance to submergence stress is an important breeding objective in areas where rice cultivars are subjected to complete inundation for a week or more. The present study was conducted to develop a high-resolution map of the region surrounding the submergence tolerance gene Sub1 in rice, which derives from the Indian cultivar FR13A. Submergence screening of 8-day-old plants of F3 families kept for 14 days submerged in 60 cm of water allowed an accurate classification of Sub1 phenotypes. Bulked segregant analysis was used to identify AFLP markers linked to Sub1. A population of 2950 F2 plants segregating for Sub1 was screened with two RFLP markers flanking the Sub1 locus, 2.4 and 4.9 cM away. Submergence tolerance was measured in the recombinant plants, and AFLP markers closely linked to Sub1 were mapped. Two AFLP markers cosegregated with Sub1 in this large population, and other markers were localized within 0.2 cM of Sub1. The high-resolution map should serve as the basis for map-based cloning of this important locus, as it will permit the identification of BAC clones spanning the region.

Chromosome Mapping↗
PubMed2000

Alterations in CER6, a gene identical to CUT1, differentially affect long-chain lipid content on the surface of pollen and stems.

Very long chain lipids contribute to the hydrophobic cuticle on the surface of all land plants and are an essential component of the extracellular pollen coat in the Brassicaceae. Mutations in Arabidopsis CER genes eliminate very long chain lipids from the cuticle surface and, in some cases, from the pollen coat. In Arabidopsis, the loss of pollen coat lipids can disrupt interactions with the stigma, inhibiting pollen hydration and causing sterility. We have positionally cloned CER6 and demonstrate that a wild-type copy complements the cer6-2 defect. In addition, we have identified a fertile, intragenic suppressor, cer6-2R, that partially restores pollen coat lipids but does not rescue the stem wax defect, suggesting an intriguing difference in the requirements for CER6 activity on stems and the pollen coat. Importantly, analysis of this suppressor demonstrates that low amounts of very long chain lipids are sufficient for pollen hydration and germination. The predicted CER6 amino acid sequence resembles that of fatty acid-condensing enzymes, consistent with its role in the production of epicuticular and pollen coat lipids >28 carbons long. DNA sequence analysis revealed the nature of the cer6-1, cer6-2, and cer6-2R mutations, and segregation analysis showed that CER6 is identical to CUT1, a cDNA previously mapped to a different chromosome arm. Instead, we have determined that a new gene, CER60, with a high degree of nucleotide and amino acid similarity to CER6, resides at the original CUT1 locus.

Acyltransferases↗
PubMed1996

Identification of RAPD markers for common root rot and spot blotch (Cochliobolus sativus) resistance in barley.

The identification of RAPD markers associated with genes for resistance to Cochliobolus sativus in barley would increase the efficiency of gene manipulation by reducing the number of lines that must be evaluated from a resistant by susceptible cross and by allowing selection during the off season. Two barley crosses consisting of resistant and susceptible parent genotypes ('Virden' x 'Ellice' and Fr926-77 x 'Deuce', both 2 row x 6 row crosses) and more than 140 homozygous progeny lines were rated for their reactions in field nurseries to common root rot and in a controlled environment for spot blotch. Putative RAPD markers were identified using bulked segregant analysis followed by individual progeny line analyses. Polymorphisms associated with disease reaction were detected between bulked segregant samples as differences in the band intensity of DNA fragments. The bulked segregant samples were screened against 186 RAPD primers (decamers) using the polymerase chain reaction. For the cross Fr926-77 x 'Deuce', one RAPD marker was obtained that did not segregate as expected but was associated with both diseases. For the cross 'Virden' x 'Ellice', a single RAPD marker was obtained that did not have the expected segregation ratio but was associated with spot blotch reaction. One RAPD marker linked to 2-rowed and 6-rowed spike locus was obtained in each cross, and both the marker and row type were associated with common root rot and spot blotch reactions. For the cross 'Virden' x 'Ellice', a linkage group consisting of three RAPD markers was associated with common root rot and spot blotch reaction. The genes associated with these markers condition significant levels of resistance to C. sativus and may be used to increase the speed and precision of resistance gene manipulation in barley germplasm.

Ascomycota↗
PubMed2006

A type I and type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms.

BACKGROUND: The development of large genomic resources has become a prerequisite to elucidate the wide-scale evolution of genomes and the molecular basis of complex traits. Linkage maps represent a first level of integration and utilization of such resources and the primary framework for molecular analyses of quantitative traits. Previously published linkage maps have already outlined the main peculiarities of the rainbow trout meiosis and a correspondance between linkage groups and chromosome arms has been recently established using fluorescent in situ hybridization. The number of chromosome arms which were covered by these maps remained unknown. RESULTS: We report an updated linkage map based on segregation analysis of more than nine hundred microsatellite markers in two doubled haploid gynogenetic lines. These markers segregated into 31 linkage groups spanning an approximate total map length of 2750 cM. Centromeres were mapped for all the linkage groups using meiogenetic lines. For each of the 31 linkage groups, the meta or acrocentric structure infered from centromere mapping was identical with those recently found with fluorescent in situ hybridization results. The present map is therefore assumed to cover the 52 chromosome arms which constitute the rainbow trout karyotype. Our data confirm the occurrence of a high interference level in this species. Homeologous regions were identified in eleven linkage groups, reflecting the tetraploid nature of the salmonid genome. The data supported the assumption that gene orders are conserved between duplicated groups and that each group is located on a single chromosome arm. Overall, a high congruence with already published rainbow trout linkage maps was found for both gene syntenies and orders. CONCLUSION: This new map is likely to cover the whole set of chromosome arms and should provide a useful framework to integrate existing or forthcoming rainbow trout linkage maps and other genomic resources. Since very large numbers of EST containing microsatellite sequences are available in databases, it becomes feasible to construct high-density linkage maps localizing known genes. This will facilitate comparative mapping and, eventually, identification of candidate genes in QTL studies.

Animals↗
PubMed1987

Decay-accelerating factor. Genetic polymorphism and linkage to the RCA (regulator of complement activation) gene cluster in humans.

We have investigated the genetic relationships between the human decay-accelerating factor (DAF) and a group of complement components including the C3b/C4b receptor (CR1), C4-binding protein (C4bp), and factor H (H), to which DAF is structurally and functionally related. CR1, C4bp, and H were previously demonstrated to be encoded by a cluster of closely linked genes, which we have designated regulator of complement activation (RCA). Southern blot analysis of genomic DNA using a DAF cDNA probe unraveled the existence of restriction fragment length polymorphism (RFLP) for both Bam HI and Hind III restriction endonucleases. Segregation analysis of these polymorphic fragments in families informative for the segregation of alleles at the CR1, C4BP, and H loci (RCA-haplotypes), demonstrated that, in humans, the gene encoding DAF is located within the RCA gene cluster. No recombinants between DAF and C4BP/CR1 were encountered in 32 informative meioses. In addition, in two individuals showing recombination between the CR1/C4BP and H loci, DAF segregated with the CR1/C4BP segment. Thus, the DAF gene maps closer to the CR1/C4BP loci than to the H gene, from which it can be separated by genetic recombination.

CD55 Antigens↗
PubMedDate not supplied

Uniparental disomy in cartilage-hair hypoplasia.

Cartilage-hair hypoplasia (CHH) is an autosomal recessive disorder that presents with pleiotropic manifestations including impaired skeletal growth and cellular immunity. It is most prevalent among two founder populations, the Old Order Amish in the USA and the Finns. The gene has been localized to 9p13 by linkage analysis and linkage disequilibrium mapping. A statistically significant deficiency of affected members resulting in a lower than expected segregation ratio has been reported in the Amish, but was not found in a previous study in Finnish CHH families. Reduced penetrance was the mechanism suggested in the Amish, but could not be verified by haplotype analyses performed after the assignment of the CHH gene. Here we have carried out segregation analysis of 101 Finnish CHH families, but again, evidence of a significant deficiency of affected members was not found. Nevertheless, among 54 uniplex families, 2 patients with CHH and uniparental disomy (UPD) for chromosome 9 were discovered. UPD might contribute to low segregation ratios by increasing the number of families with only 1 affected individual. These observations show that UPD may occur in an unexpectedly high number of the patients and should be taken into account in the genetic counselling and prenatal diagnostics of CHH families.

Abnormalities, Multiple↗
PubMed2000

Estimation of penetrance from twin data.

A simple method for estimating the gene frequency p and the penetrance value K from data on polymorphic monogenic characteristics on monozygotic twin pairs is presented. In spite of the method here presented having limited value because the results it yields cannot be evaluated on their own, the estimates of p and K it provides can be indirectly tested by comparing them to the ones obtained in familial aggregates through classical segregation analysis or by using the latter to calculate the expected proportions of dominant-dominant, dominant-recessive and recessive-recessive monozygotic twin pairs. When the method is applied to data on tongue-rolling ability published in the literature, a good agreement is observed between twin and familial estimates, thus indicating that the method is reliable and that it can be used as an ancillary way of corroborating or otherwise evidence of monogenic autosomal dominant mechanism inferred from the analysis of familial data.

Chromosome Segregation↗
PubMed1985

Tissue-specific expression of the newly acquired ecotropic Emv-18 provirus in Fv-2 congenic mice.

Expression of endogenous retroviral sequences in Fv-2 congenic mouse strains was examined by Northern blot analysis. Endogenous ecotropic virus transcripts were observed in total spleen RNA of B6.S (Fv-2ss) mice. Endogenous ecotropic transcripts were not detected in spleen RNA of C57BL/6, the Fv-2rr congenic partner of B6.S, nor in spleens of the C57BL/10 (Fv-2rr) and B10.C (Fv-2ss) congenic strains. Mendelian segregation analysis revealed that only backcross mice segregating the newly acquired Fv-2-linked endogenous ecotropic provirus had endogenous ecotropic transcripts in spleen RNA. Examination of different tissues of B6.S mice showed that Emv-18 transcription was highest in spleen and bone marrow, tissues in which Fv-2 has been shown to function. These results support the conclusion that chromosomal location is an important factor controlling Emv-18 expression in B6.S mice. We also report the presence in the spleen of a novel xenotropic virus transcript detectable only in B6.S mice.

Animals↗