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1

Allelic association between marker loci  

PubMed Central

Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker × oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

Lonjou, C.; Collins, A.; Morton, N. E.

1999-01-01

2

Pooled Genotyping of Microsatellite Markers in Parent-Offspring Trios  

PubMed Central

We studied the extent to which genotyping of simple sequence repeat polymorphisms (SSRs) in pooled DNA samples can be used to predict differences in allele frequencies between parents and their affected offspring. We also developed a simple method of correction for the effects of stutter and differential amplification on the analysis of SSRs in pooled DNA samples based on widely available software. We genotyped individually eight polymorphic microsatellite markers in 110 parent–offspring trios affected with bipolar affective disorder (BP). Analysis of pooled DNA samples predicted very accurately the differences in individual allele frequency distributions between children and their parents. The mean error was <1% (range 0%–3.2%) when marker-specific corrections for stutter and differential amplification were performed. We show that if an individual allele is significantly preferentially transmitted from parents to affected offspring, the difference in the frequency of that allele would be sufficiently large to be detected with pooling in most situations. We propose recommendations for disequilibrium mapping with pooling in which both case-control samples and trios are used in an initial screen and markers are genotyped individually only if they satisfy very relaxed criteria for statistical significance. The use of case-control samples should reduce the false-negative rate as the differences in allele frequencies between cases and controls are twice as high in the presence of the same genetic effect. The use of trios will confirm or reject any suggested differences, thus reducing the false-positive rate that can be created by hidden population stratification.

Kirov, George; Williams, Nigel; Sham, Pak; Craddock, Nick; Owen, Michael J.

2000-01-01

3

Incidence and origin of [open quotes]Null[close quotes] alleles in the (AC)n microsatellite markers  

SciTech Connect

Twenty-three (AC)n repeat markers from chromosome 16 were typed in the parents of the 40 CEPH (Centre d'Etude du Polymorphisme Humain) families. Where parents were informative, the entire families were then typed. There were seven markers in which null alleles were demonstrated, as recognized by the apparent noninheritance, by a sib, of a parental allele. Four of these markers showed a null allele in a single sibship, while in the other three at least 30% of the CEPH sibships were shown to have a null allele segregating. One null allele was sequenced and shown to be the result of an 8-bp deletion occurring within the priming sequence for PCR amplification of the (AC)n repeats. In gene mapping or in application to diagnosis, the presence of a segregating null allele will not corrupt the linkage data but could result in loss of information. In isolated instances a segregating null allele may be interpreted as nonpaternity. The presence of a null allele may generate misleading data when individuals are haplotyped to determine the presence of linkage disequilibrium with a disease gene. 10 refs., 2 figs., 1 tab.

Callen, D.F.,; Thompson, A.D.; Shen, Y.; Phillips, H.A.; Richards, R.I.; Mulley, J.C.; Sutherland, G.R. (Women's and Children's Hospital, North Adelaide (Australia))

1993-05-01

4

Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines.  

PubMed Central

This article reports the marker-assisted introgression of favorable alleles at three quantitative trait loci (QTL) for earliness and grain yield among maize elite lines. The QTL were originally detected in 1992 by means of ANOVA in a population of 96 recombinant inbred lines (RILs). Introgression started from a selected RIL, which was crossed three times to one of the original parents and then self-fertilized, leading to BC(3)S(1) progenies. Markers were used to assist both foreground and background selection at each generation. At the end of the program, the effect of introgression was assessed phenotypically in agronomic trials, and QTL detection was performed by composite interval mapping among BC(3)S(1) progenies. The marker-assisted introgression proved successful at the genotypic level, as analyzed by precision graphical genotypes, although no emphasis was put on the reduction of linkage drag around QTL. Also, QTL positions were generally sustained in the introgression background. For earliness, the magnitude and sign of the QTL effects were in good agreement with those expected from initial RIL analyses. Conversely, for yield, important discrepancies were observed in the magnitude and sign of the QTL effects observed after introgression, when compared to those expected from initial RIL analyses. These discrepancies are probably due to important genotype-by-environment interactions.

Bouchez, Agnes; Hospital, Frederic; Causse, Mathilde; Gallais, Andre; Charcosset, Alain

2002-01-01

5

Allele-specific parental imprinting of dzr1, a posttranscriptional regulator of zein accumulation.  

PubMed Central

Parental imprinting describes the phenomenon of unequivalent gene function based on transmission from the female or male parent. We have discovered parental imprinting of an allele of the dzr1 locus that posttranscriptionally regulates the accumulation of 10-kDa zein in the maize endosperm. The imprinted allele of MO17 inbred origin, dzr1 + MO17, conditions low accumulation of the 10-kDa zein and is dominant when transmitted through the female but recessive when transmitted through the male. Analyzing endosperms with equal parental contributions of dzr1 + MO17 ruled out the possibility that the unequivalent phenotype of dzr1 + MO17 was due to parental dosage imbalance in the triploid endosperm. Second-generation studies show that the dominant or recessive phenotype of dzr1 + MO17 is determined at every generation based on immediate parental origin with no grandparental effect. Images

Chaudhuri, S; Messing, J

1994-01-01

6

Allelic Associations between 100 DNA Markers and High versus Low IQ.  

ERIC Educational Resources Information Center

For DNA markers in or near genes of neurological relevance, allelic frequencies were compared for groups of high- and low-IQ children (total sample of 86). This study adds 40 markers to the 60 already studied. Only one showed a significant association with IQ in original and replication samples. (SLD)

Plomin, Robert; And Others

1995-01-01

7

Models of frequency-dependent selection with mutation from parental alleles.  

PubMed

Frequency-dependent selection (FDS) remains a common heuristic explanation for the maintenance of genetic variation in natural populations. The pairwise-interaction model (PIM) is a well-studied general model of frequency-dependent selection, which assumes that a genotype's fitness is a function of within-population intergenotypic interactions. Previous theoretical work indicated that this type of model is able to sustain large numbers of alleles at a single locus when it incorporates recurrent mutation. These studies, however, have ignored the impact of the distribution of fitness effects of new mutations on the dynamics and end results of polymorphism construction. We suggest that a natural way to model mutation would be to assume mutant fitness is related to the fitness of the parental allele, i.e., the existing allele from which the mutant arose. Here we examine the numbers and distributions of fitnesses and alleles produced by construction under the PIM with mutation from parental alleles and the impacts on such measures due to different methods of generating mutant fitnesses. We find that, in comparison with previous results, generating mutants from existing alleles lowers the average number of alleles likely to be observed in a system subject to FDS, but produces polymorphisms that are highly stable and have realistic allele-frequency distributions. PMID:23852384

Trotter, Meredith V; Spencer, Hamish G

2013-09-01

8

Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers  

PubMed Central

Background and Aims The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships. Methods Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed. Key Results and Conclusions We determine the closest diploid progenitors of the triploid ‘Cavendish’ and ‘Gros Michel’ subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. ‘Cavendish’, ‘Plantain’ and ‘Mutika-Lujugira’), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.

Hippolyte, I.; Jenny, C.; Gardes, L.; Bakry, F.; Rivallan, R.; Pomies, V.; Cubry, P.; Tomekpe, K.; Risterucci, A. M.; Roux, N.; Rouard, M.; Arnaud, E.; Kolesnikova-Allen, M.; Perrier, X.

2012-01-01

9

Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool  

Microsoft Academic Search

In the ideal case, molecular markers used for marker-assisted selection are allele-specific even if the alleles differ only by a few nucleotide polymorphisms within the coding sequence of target genes. Such ‘perfect’ markers are completely correlated with the trait of interest. In hexaploid wheat (Triticum aestivum L.) the Pm3 locus encodes seven alleles (Pm3a–Pm3g) conferring resistance to different races of

L. Tommasini; N. Yahiaoui; P. Srichumpa; B. Keller

2006-01-01

10

New FACTOR IX linked marker alleles in African Haemophilia B patients.  

PubMed

Three markers, one restriction length polymorphism (RFLP) (MseI) and two microsatellite markers (Intron 1 and 3'UTR), linked to the FACTOR IX gene, were assessed for the purpose of genetic testing for Haemophilia B families in South Africa. This was carried out using seven Haemophilia B families and fifty random control samples. We observed five new alleles for the Intron 1 marker within the black control and patient sample groups, and informativity in 89% (8/9) of all carrier females for at least one of the three markers observed. These markers are useful for carrier detection and prenatal diagnosis of Haemophilia B in the great majority of South African black and white families. PMID:17880456

Mitchell, C; Mitchell, C L; Krause, A

2007-09-01

11

Understanding allele shift using SSR markers in pedigree, modified bulk, and SSD breeding methods in rice  

Microsoft Academic Search

needs to be maintained or increased in the selected progenies and the favorite genes from the donor parents should be increased. Comparative studies on different breeding methods using DNA markers are not well established. In this study, three breeding procedures—pedigree, SSD, and modified bulk—were used to advance the materials derived from a cross between divergent rice parents Moroberekan and IR20

A. Kanbar; N Pirany; A Al-Ouda; HE Shashidhar

2009-01-01

12

Allele-specific nuclear positioning of the monoallelically expressed astrocyte marker GFAP  

PubMed Central

Chromosomes and genes are nonrandomly arranged within the mammalian cell nucleus. However, the functional significance of nuclear positioning in gene expression is unclear. Here we directly probed the relationship between nuclear positioning and gene activity by comparing the location of the active and inactive copies of a monoallelically expressed gene in single cell nuclei. We demonstrate that the astrocyte-specific marker GFAP (glial fibrillary acidic protein) is monoallelically expressed in cortical astrocytes. Selection of the active allele occurs in a stochastic manner and is generally maintained through cell division. Taking advantage of the monoallelic expression of GFAP, we show that the functionally distinct alleles occupy differential radial positions within the cell nucleus and differentially associate with intranuclear compartments. In addition, coordinately regulated astrocyte-specific genes on distinct chromosomes spatially associate in their inactive state and dissociate upon activation. These results provide direct evidence for function-related differential positioning of individual gene alleles within the interphase nucleus.

Takizawa, Takumi; Gudla, Prabhakar R.; Guo, Liying; Lockett, Stephan; Misteli, Tom

2008-01-01

13

High-Resolution Analysis of Parent-of-Origin Allelic Expression in the Arabidopsis Endosperm  

PubMed Central

Genomic imprinting is an epigenetic phenomenon leading to parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, genomic imprinting has mainly been observed in the endosperm, an ephemeral triploid tissue derived after fertilization of the diploid central cell with a haploid sperm cell. In an effort to identify novel imprinted genes in Arabidopsis thaliana, we generated deep sequencing RNA profiles of F1 hybrid seeds derived after reciprocal crosses of Arabidopsis Col-0 and Bur-0 accessions. Using polymorphic sites to quantify allele-specific expression levels, we could identify more than 60 genes with potential parent-of-origin specific expression. By analyzing the distribution of DNA methylation and epigenetic marks established by Polycomb group (PcG) proteins using publicly available datasets, we suggest that for maternally expressed genes (MEGs) repression of the paternally inherited alleles largely depends on DNA methylation or PcG-mediated repression, whereas repression of the maternal alleles of paternally expressed genes (PEGs) predominantly depends on PcG proteins. While maternal alleles of MEGs are also targeted by PcG proteins, such targeting does not cause complete repression. Candidate MEGs and PEGs are enriched for cis-proximal transposons, suggesting that transposons might be a driving force for the evolution of imprinted genes in Arabidopsis. In addition, we find that MEGs and PEGs are significantly faster evolving when compared to other genes in the genome. In contrast to the predominant location of mammalian imprinted genes in clusters, cluster formation was only detected for few MEGs and PEGs, suggesting that clustering is not a major requirement for imprinted gene regulation in Arabidopsis.

Roszak, Pawel; Beisel, Christian; Donoghue, Mark T. A.; Spillane, Charles; Nordborg, Magnus; Rehmsmeier, Marc; Kohler, Claudia

2011-01-01

14

Genetic Diversity Analysis of Sugarcane Parents in Chinese Breeding Programmes Using gSSR Markers  

PubMed Central

Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use.

You, Qian; Xu, Liping; Zheng, Yifeng; Que, Youxiong

2013-01-01

15

An estimation of the minimum number of SSR alleles needed to reveal genetic relationships in wheat varieties. I. Information from large-scale planted varieties and cornerstone breeding parents in Chinese wheat improvement and production.  

PubMed

The genetic relationships of 43 wheat varieties were analyzed with SSR markers. The materials employed included 14 cornerstone breeding parents used before 1980 and another 29 other large-scale planted varieties currently in use in China. A total of 501 different alleles were amplified, including 166 alleles of the A genome, 174 of the B genome and 161 of the D genome. Data obtained were used to estimate genetic similarity using the DICE coefficient, and dendrograms were constructed using the UPGMA method. The dendrogram with 501 alleles successfully differentiated all the cornerstone breeding parents and the large-scale planted varieties, and the dendogram tree was basically consistent with the pedigrees of these varieties. The correlation coefficient between the genetic distance matrix of 501 alleles and that of 450 was 0.99. Correlation coefficients among random samples of alleles suggested that 350 to 400 alleles were needed to detect genetic relationships among common wheat varieties. Correlation coefficients of a genetic similarity matrix based on 580, and those of 501 and 400, random alleles were 0.96 and 0.94, respectively. However, there were marked differences between the matrix based on the 501 alleles and those based on markers located on the A-, B- or D-genome independently. The correlation coefficients between the genetic distance matrix of 501 alleles and alleles within A, B or D genomes were 0.77, 0.76 and 0.67. The estimation of genetic similarity should be based on data from all genomes rather than any one genome. PMID:12582878

Zhang, X Y; Li, C W; Wang, L F; Wang, H M; You, G X; Dong, Y S

2002-12-01

16

A genome-wide study of allelic imbalance in human testicular germ cell tumors using microsatellite markers  

Microsoft Academic Search

Testicular germ cell tumors (TGCT) arise by multistep carcinogenesis pathways involving selective losses and gains of chromosome material. To locate cancer genes underlying this selection, we performed a genome-wide study of allelic imbalance (AI) in 32 tumors, using 710 microsatellite markers. The highest prevalence of AI was found at 12p, in line with previous studies finding consistent gain of the

Jon Thor Bergthorsson; Bjarni Agnar Agnarsson; Tomas Gudbjartsson; Kjartan Magnusson; Asgeir Thoroddsen; Birgir Palsson; Johannes Bjornsson; Kari Stefansson; Jeffrey Gulcher; Gudmundur Vikar Einarsson; Laufey Thora Amundadottir; Rosa Bjork Barkardottir

2006-01-01

17

Surfactant protein gene A, B, and D marker alleles in chronic obstructive pulmonary disease of a Mexican population  

Microsoft Academic Search

Surfactant protein gene A, B, and D marker alleles in chronic obstructive pulmonary disease of a Mexican population. X. Guo, H-M. Lin, Z. Lin, M. Montano, R. Sansores, G. Wang, S. DiAngelo, A. Pardo, M. Selman, J. Floros. #ERS Journals Ltd 2001. ABSTRACT: Chronic obstructive pulmonary disease (COPD) is characterized by chronic inflammation. It is most likely the result of

X. Guo; H. M. Lin; Z. Lin; M. Montaño; R. Sansores; G. Wang; S. Diangelo; A. Pardoz; M. Selman; J. Floros

2001-01-01

18

Allele frequencies of 15 STR loci of three main ethnic populations in Singapore using an in-house marker panel  

Microsoft Academic Search

Allele frequency data for 15 Short Tandem Repeat (STR) loci was studied for the three main ethnic groups residing in Singapore, namely Chinese, Malay and Indian. An in-house STR marker panel was employed, consisting all 13 tetranucleaotide STR listed in CODIS (Combined DNA Index System, USA) and two pentanucleaotide STR, Penta D and Penta E. This represents a comprehensive report

R. Y. Y Yong; L. T Aw; E. P. H Yap

2004-01-01

19

SNPs and real-time quantitative PCR method for constitutional allelic copy number determination, the VPREB1 marker case  

PubMed Central

Background 22q11.2 microdeletion is responsible for the DiGeorge Syndrome, characterized by heart defects, psychiatric disorders, endocrine and immune alterations and a 1 in 4000 live birth prevalence. Real-time quantitative PCR (qPCR) approaches for allelic copy number determination have recently been investigated in 22q11.2 microdeletions detection. The qPCR method was performed for 22q11.2 microdeletions detection as a first-level screening approach in a genetically unknown series of patients with congenital heart defects. A technical issue related to the VPREB1 qPCR marker was pointed out. Methods A set of 100 unrelated Italian patients with congenital heart defects were tested for 22q11.2 microdeletions by a qPCR method using six different markers. Fluorescence In Situ Hybridization technique (FISH) was used for confirmation. Results qPCR identified six patients harbouring the 22q11.2 microdeletion, confirmed by FISH. The VPREB1 gene marker presented with a pattern consistent with hemideletion in one 3 Mb deleted patient, suggestive for a long distal deletion, and in additional five non-deleted patients. The long distal 22q11.2 deletion was not confirmed by Comparative Genomic Hybridization. Indeed, the VPREB1 gene marker generated false positive results in association with the rs1320 G/A SNP, a polymorphism localized within the VPREB1 marker reverse primer sequence. Patients heterozygous for rs1320 SNP, showed a qPCR profile consistent with the presence of a hemideletion. Conclusions Though the qPCR technique showed advantages as a screening approach in terms of cost and time, the VPREB1 marker case revealed that single nucleotide polymorphisms can interfere with qPCR data generating erroneous allelic copy number interpretations.

2011-01-01

20

Marker-Assisted Selection for Recognizing Wheat Mutant Genotypes Carrying HMW Glutenin Alleles Related to Baking Quality  

PubMed Central

Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker's results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism).

Zamani, Mohammad Javad; Bihamta, Mohammad Reza; Naserian Khiabani, Behnam; Tahernezhad, Zahra; Hallajian, Mohammad Taher; Shamsi, Marzieh Varasteh

2014-01-01

21

Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining  

PubMed Central

Background Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection.

2014-01-01

22

Methylation of novel markers of fragile X alleles is inversely correlated with FMRP expression and FMR1 activation ratio  

PubMed Central

The fragile X syndrome (FXS) is caused by silencing of the fragile X mental retardation gene (FMR1) and the absence of its product, fragile X mental retardation protein (FMRP), resulting from CpG island methylation associated with large CGG repeat expansions (more than 200) termed full mutation (FM). We have identified a number of novel epigenetic markers for FXS using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), naming the most informative fragile X-related epigenetic element 1 (FREE1) and 2 (FREE2). Methylation of both regions was correlated with that of the FMR1 CpG island detected using Southern blot (FREE1 R = 0.97; P < 0.00001, n = 23 and FREE2 R = 0.93; P < 0.00001, n = 23) and negatively correlated with lymphocyte expression of FMRP (FREE1 R = ?0.62; P = 0.01, n = 15 and FREE2 R = ?0.55; P = 0.03, n = 15) in blood of partially methylated ‘high functioning’ FM males. In blood of FM carrier females, methylation of both markers was inversely correlated with the FMR1 activation ratio (FREE1 R = ?0.93; P < 0.0001, n = 12 and FREE2 R = ?0.95; P < 0.0001, n = 9). In a sample set of 49 controls, 18 grey zone (GZ 40–54 repeats), 22 premutation (PM 55–170 repeats) and 22 (affected) FXS subjects, the FREE1 methylation pattern was consistent between blood and chorionic villi as a marker of methylated FM alleles and could be used to differentiate FXS males and females from controls, as well as from carriers of GZ/PM alleles, but not between GZ and PM alleles and controls. Considering its high-throughput and specificity for pathogenic FM alleles, low cost and minimal DNA requirements, FREE MALDI-TOF MS offers a unique tool in FXS diagnostics and newborn population screening.

Godler, David Eugeny; Tassone, Flora; Loesch, Danuta Zuzanna; Taylor, Annette Kimball; Gehling, Freya; Hagerman, Randi Jenssen; Burgess, Trent; Ganesamoorthy, Devika; Hennerich, Debbie; Gordon, Lavinia; Evans, Andrew; Choo, K.H.; Slater, Howard Robert

2010-01-01

23

Allelic deletion in pituitary adenomas reflects aggressive biological activity and has potential value as a prognostic marker.  

PubMed

Tumors of the pituitary gland are usually benign adenomas and account for 10% of all intracranial neoplasms. Five pituitary tumors have previously been reported to harbor multiple allelic deletions. Of these, three displayed particularly aggressive biological behavior, whereas there were no clinical details provided for the others. This study was designed to test the hypothesis that genetic deletions are a marker of invasive behavior and to identify the loci most commonly involved. Accordingly, we studied two cohorts of pituitary tumors, classified radiologically as invasive or noninvasive, for loss of heterozygosity (LOH). There is a significantly higher frequency of LOH in invasive tumors (10.8% of all loci examined) compared to noninvasive tumors (2.4%; P < 0.001). Of the 11 loci investigated, 75% of the allelic deletions identified in invasive tumors were found at 4 loci: 11q13, 13q12-14, 10q, and 1p. Twenty of 47 invasive tumors had evidence of at least 1 allelic deletion, whereas 14 of 20 had more than 1. Of the 6 tumors with only 1 deletion, 5 involved the 11q13 locus, suggesting that this is an early change in the transition from noninvasive to invasive adenoma. Comparison of invasive and noninvasive tumors demonstrates a significantly higher frequency of deletions affecting 11q13 (P < 0.001), 13q12-14 (P < 0.05), and 10q26 (P < 0.05) in invasive tumors. In addition, allelic deletion correlates with increasingly invasive behavior (modified Hardy classification), as 73% of grade 4 tumors compared to 33% of grade 3 and 9.5% of grade 1 and 2 tumors demonstrated LOH at any locus. Furthermore, in some tumors we identified a breakpoint between markers intragenic and extragenic to the retinoblastoma gene (Rb1) on chromosome 13q, suggesting that tumor suppressor genes other than or in addition to Rb1 may be involved in pituitary tumorigenesis. This was further supported by the presence of Rb protein in two of four tumors where the genetic loss extended to include the intragenic marker D13S153. Early identification of tumors with likely invasive potential by means of genetic analysis (LOH) may provide useful information on potential tumor behavior and aid tumor management in a manner that is not possible using routine histological methods. A large prospective study is required in patients without radiological evidence of invasion to assess the value of LOH in predicting outcome and for planning treatment. PMID:9062489

Bates, A S; Farrell, W E; Bicknell, E J; McNicol, A M; Talbot, A J; Broome, J C; Perrett, C W; Thakker, R V; Clayton, R N

1997-03-01

24

Microsatellite markers to identify specific alleles in DNA extracted from monovarietal virgin olive oils  

Microsoft Academic Search

The suitability of DNA present in olive oil for PCR analysis has been reported by several authors. However, low concentration,\\u000a degradation, and the possible presence of additional alleles due to paternal contribution in oils extracted from entire drupes,\\u000a should be taken into consideration when comparing the amplification profiles of leaves with the corresponding oils for varietal\\u000a traceability purposes. The aim

Vittorio Alba; Wilma Sabetta; Antonio Blanco; Antonella Pasqualone; Cinzia Montemurro

2009-01-01

25

Global analysis of Plasmodium falciparum Na(+)/H(+) exchanger (pfnhe-1) allele polymorphism and its usefulness as a marker of in vitro resistance to quinine.  

PubMed

The aim of this study was to provide a comprehensive analysis of the worldwide genetic polymorphism of ms4760 alleles of the pfnhe-1 gene and to discuss their usefulness as molecular marker of quinine resistance (QNR). A new numbering of ms4760 allele, classification grouping ms4760 alleles according to the number of DNNND and DDNHNDNHNND repeat motifs in blocks II and V was also proposed. A total of 1508 ms4760 sequences from isolates, culture-adapted parasites or reference strains from various geographical regions were retrieved from GenBank (last update on 15th June 2012) or from publications and were used for genetic analyses. The association of different alleles of pfnhe-1 with resistance to quinoline antimalarial drugs showed marked geographic disparities. The validity and reliability of candidate polymorphisms in pfnhe-1 gene as molecular markers of QNR appeared restricted to endemic areas from South Asia or possibly East African countries and needs to be confirmed. PMID:24533289

Ménard, Didier; Andriantsoanirina, Valérie; Khim, Nimol; Ratsimbasoa, Arsène; Witkowski, Benoit; Benedet, Christophe; Canier, Lydie; Mercereau-Puijalon, Odile; Durand, Rémy

2013-12-01

26

Identical marker alleles in Podolic cattle ( Bos taurus) and Indian zebu ( Bos indicus)  

Microsoft Academic Search

In the context of biochemical marker research and in order to add new information on native breeds, the present work focuses on a local Southern Italy cattle, namely Italian Podolic. We provide the complete structural characterisation of ?-lactalbumins and ?-globin chains isolated from Podolic cattle (Bos taurus). Given the unavailability of the complete sequence for ?-lactalbumin A of taurine cattle

E Pieragostini; A Scaloni; R Rullo; A Di Luccia

2000-01-01

27

RFLP markers to identify the alleles on the Mla locus conferring powdery mildew resistance in barley  

Microsoft Academic Search

To identify the mildew resistance locus Mla in barley with molecular markers, closely linked genomic RFLP clones were selected with the help of near-isogenic lines having the ‘Pallas’ and ‘Siri’ background. Out of 22 polymorphic clones 3 were located around the Mla locus on chromosome 5 with a distance of 5.1 + 2.9 cM (MWG 1H068), 4.2±1.7 cM (MWG 1H060)

C. Schiiller; G. Backes; G. Fischbeck; A. Jahoor

1992-01-01

28

Identical marker alleles in Podolic cattle (Bos taurus) and Indian zebu (Bos indicus).  

PubMed

In the context of biochemical marker research and in order to add new information on native breeds, the present work focuses on a local Southern Italy cattle, namely Italian Podolic. We provide the complete structural characterisation of alpha-lactalbumins and beta-globin chains isolated from Podolic cattle (Bos taurus). Given the unavailability of the complete sequence for alpha-lactalbumin A of taurine cattle in the literature, we intended to check its structure in order to ascertain the absence of any possible silent mutation. Screening the Podolic cattle, we found a new beta-globin variant not detectable by conventional methods. The presence of such a new variant might be helpful in the study of the Podolic population genetic structure and for a better knowledge of the gene pool per se, and in comparison with the other breeds. Structural analyses showed that the new beta-globin Podolic variant exhibited the same sequence as beta-globin Azebu. The alpha-lactalbumin A was the same as that isolated from zebu cattle (Bos indicus). The results are discussed in relation to the possible involvement of the two markers in the debate on the origin of the Podolic breed. PMID:11126744

Pieragostini, E; Scaloni, A; Rullo, R; Di Luccia, A

2000-09-01

29

Allelic database and divergence among Psidium accessions by using microsatellite markers.  

PubMed

This study aimed to investigate the genetic variability among guava accessions and wild Psidium species of the Embrapa Semiárido germplasm collection by using microsatellite loci to guide genetic resources and breeding programs, emphasizing crosses between guava and other Psidium species. DNA was extracted using the 2X CTAB method, and polymerase chain reaction products were analyzed on 6% denatured polyacrylamide gels stained with silver nitrate. The unweighted pair-group method using arithmetic average dendrogram generated from the distance matrix of the Jaccard coefficient for 183 alleles of 13 microsatellite loci was used for visualization of genetic similarity. The number of base pairs was estimated using inverse mobility method based on the regression of known-size products. Analysis of molecular variance was performed using total decomposition between and within guava accessions. The accessions showed similarity from 0.75 to 1.00, with the dendrogram presenting cophenetic value of 0.85. Five groups were observed: the first included guava accessions; the second, P. guineense accessions; the third, one accession of P. friedrichsthalianum; and the last 2 groups, P. cattleianum. The genetic similarity among P. guineense and some guava accessions were above 80%, suggesting greater possibility to obtain interspecies hybrids between these 2 species. The genetic variability between the accessions was considered to be high (?ST = 0.238), indicating that guava genetic variability is not uniformly distributed among the 9 Brazilian states from where the accession were obtained. Obtaining a greater number of accessions by Brazilian states is recommended in order to have greater diversity among the species. PMID:24391028

da Costa, S R; Santos, C A F

2013-01-01

30

Segregation analysis and RFLP mapping of the R1 and R3 alleles conferring race-specific resistance to Phytophthora infestans in progeny of dihaploid potato parents.  

PubMed

Phytophthora infestans (Mont.) de Bary is the most important fungal pathogen of the potato (Solanum tuberosum). The introduction of major genes for resistance from the wild species S. demissum into potato cultivars is the earliest example of breeding for resistance using wild germplasm in this crop. Eleven resistance alleles (R genes) are known, differing in the recognition of corresponding avirulence alleles of the fungus. The number of R loci, their positions on the genetic map and the allelic relationships between different R variants are not known, except that the R1 locus has been mapped to potato chromosome V. The objective of this work was the further genetic analysis of different R alleles in potato. Tetraploid potato cultivars carrying R alleles were reduced to the diploid level by inducing haploid parthenogenetic development of 2n female gametes. Of the 157 isolated primary dihaploids, 7 set seeds and carried the resistance alleles R1, R3 and R10 either individually or in combinations. Independent segregation of the dominant R1 and R3 alleles was demonstrated in two F1 populations of crosses among a dihaploid clone carrying R1 plus R3 and susceptible pollinators. Distorted segregation in favour of susceptibility was found for the R3 allele in 15 of 18 F1 populations analysed, whereas the R1 allele segregated with a 1:1 ratio as expected in five F1 populations. The mode of inheritance of the R10 allele could not be deduced as only very few F1 hybrids bearing R10 were obtained. Linkage analysis in two F1 populations between R1, R3 and RFLP markers of known position on the potato RFLP maps confirmed the position of the R1 locus on chromosome V and localized the second locus, R3, to a distal position on chromosome XI. PMID:7908718

el-Kharbotly, A; Leonards-Schippers, C; Huigen, D J; Jacobsen, E; Pereira, A; Stiekema, W J; Salamini, F; Gebhardt, C

1994-03-01

31

DXS10011: studies on structure, allele distribution in three populations and genetic linkage to further q-telomeric chromosome X markers.  

PubMed

The hypervariable tetranucleotide STR polymorphism DXS10011 is a powerful marker for forensic purposes. Investigation of this STR led to an allele nomenclature which is in consensus with the ISFG recommendations. DXS10011 is located at Xq28 and genetically closely linked to DXS7423 and DXS8377 but is unlinked to HPRTB and more distant X-chromosomal STRs. DXS10011 is a very complex marker exhibiting some structural variants within alleles of identical length. Two types of repeat structure (regular and inter-alleles) are known and described as types A and B. Two SNPs which are in strong linkage disequilibrium to the different sequence types were found in the repeat flanking region. The type A sequence consists of a long stretch of uninterrupted homogenous repeats which is highly susceptible to slippage mutation during male meiosis. PMID:15248074

Hering, Sandra; Brundirs, Nicola; Kuhlisch, Eberhard; Edelmann, Jeanett; Plate, Ines; Benecke, Mark; Van, Pham Hung; Michael, Matthias; Szibor, Reinhard

2004-12-01

32

HLA Class II Alleles Susceptibility Markers of Type 1 Diabetes Fail to Specify Phenotypes of Ketosis-Prone Diabetes in Adult Tunisian Patients  

PubMed Central

We aimed to characterize the different subgroups of ketosis-prone diabetes (KPD) in a sample of Tunisian patients using the A? scheme based on the presence or absence of ?-cell autoantibodies (A+ or A?) and ?-cell functional reserve (?+ or ??) and we investigated whether HLA class II alleles could contribute to distinct KPD phenotypes. We enrolled 43 adult patients with a first episode of ketosis. For all patients we evaluated clinical parameters, ?-cell autoimmunity, ?-cell function and HLA class II alleles. Frequency distribution of the 4 subgroups was 23.3% A+??, 23.3% A???, 11.6% A+?+ and 41.9% A??+. Patients from the group A+?? were significantly younger than those from the group A??? (P = .002). HLA susceptibility markers were significantly more frequent in patients with autoantibodies (P = .003). These patients also had resistance alleles but they were more frequent in A+?+ than A+?? patients (P = .04). Insulin requirement was not associated to the presence or the absence of HLA susceptibility markers. HLA class II alleles associated with susceptibility to autoimmune diabetes have not allowed us to further define Tunisian KPD groups. However, high prevalence of HLA resistance alleles in our patients may reflect a particular genetic background of Tunisian KPD population.

Laadhar, Lilia; Harzallah, Fatma; Zitouni, Mondher; Kallel-Sellami, Maryam; Fekih, Moncef; Kaabachi, Naziha; Slimane, Hadia; Makni, Sondes

2011-01-01

33

Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents.  

PubMed

Hexaploid tritordeum (H(ch)H(ch)AABB; 2n?=?42) results from the cross between Hordeum chilense (H(ch)H(ch); 2n?=?14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n?=?28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70 % of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop. PMID:24733248

Cabo, Sandra; Ferreira, Luciana; Carvalho, Ana; Martins-Lopes, Paula; Martín, António; Lima-Brito, José Eduardo

2014-08-01

34

Parenting  

MedlinePLUS

... parents, people are always ready to offer advice. Parenting tips, parents' survival guides, dos, don'ts, shoulds ... right" way to be a good parent. Good parenting includes Keeping your child safe Showing affection and ...

35

A genome-wide study of allelic imbalance in human testicular germ cell tumors using microsatellite markers.  

PubMed

Testicular germ cell tumors (TGCT) arise by multistep carcinogenesis pathways involving selective losses and gains of chromosome material. To locate cancer genes underlying this selection, we performed a genome-wide study of allelic imbalance (AI) in 32 tumors, using 710 microsatellite markers. The highest prevalence of AI was found at 12p, in line with previous studies finding consistent gain of the region in TGCTs. High frequency of AI was also observed at chromosome arms 4p, 9q, 10p, 11q, 11p, 13q, 16q, 18p, and 22q. Within 39 candidate regions identified by mapping of smallest regions of overlap (SROs), the highest frequency of AI was at 12p11.21 approximately p11.22 (62%), 12p12.1 approximately p13.1 (53%), 12p13.1 approximately p13.2 (53%), 11q14.1 approximately q14.2 (53%), 11p13 approximately p14.3 (47%), 9q21.13 approximately q21.32 (47%), and 4p15.1 approximately p15.2 (44%). Two genes known to be involved in cancer reside in these regions, ETV6 at 12p13.2 (TEL oncogene) and WT1 at 11p13. We also found a significant association (P = 0.02) between AI at 10q21.1 approximately q22.2 and higher clinical stage. This study contributes to the ongoing search for genes involved in transformation of germ cells and provides a useful reference point to previous studies using cytogenetic techniques to map chromosome changes in TGCTs. PMID:16364756

Bergthorsson, Jon Thor; Agnarsson, Bjarni Agnar; Gudbjartsson, Tomas; Magnusson, Kjartan; Thoroddsen, Asgeir; Palsson, Birgir; Bjornsson, Johannes; Stefansson, Kari; Gulcher, Jeffrey; Einarsson, Gudmundur Vikar; Amundadottir, Laufey Thora; Barkardottir, Rosa Bjork

2006-01-01

36

Chromosome Instability and Oxidative Stress Markers in Patients with Ataxia Telangiectasia and Their Parents  

PubMed Central

Ataxia telangiectasia (AT) is a rare neurodegenerative disorder, inherited in an autosomal recessive manner. Total blood samples were collected from 20 patients with AT, 13 parents of patients, and 17 healthy volunteers. This study aimed at evaluating the frequency of chromosomal breaks in spontaneous cultures, induced by bleomycin and ionizing radiation, and further evaluated the rates of oxidative stress in AT patients and in their parents, compared to a control group. Three cell cultures were performed to each individual: the first culture did not receive induction to chromosomal instability, the second was exposed to bleomycin, and the last culture was exposed to ionizing radiation. To evaluate the rates of oxidative stress, the markers superoxide dismutase (SOD), catalase (CAT), and thiobarbituric acid (TBARS) were utilized. Significant differences were observed between the three kinds of culture treatments (spontaneous, bleomycin, and radiation induced) and the breaks and chromosomal aberrations in the different groups. The oxidative stress showed no significant differences between the markers. This study showed that techniques of chromosomal instability after the induction of ionizing radiation and bleomycin are efficient in the identification of syndrome patients, with the ionizing radiation being the most effective.

Bitelo Ludwig, Luciane; Valiati, Victor Hugo; Palazzo, Roberta Passos; Jardim, Laura Bannach; da Rosa, Darlan Pase; Bona, Silvia; Rodrigues, Graziela; Marroni, Norma Possa; Pra, Daniel; Maluf, Sharbel Weidner

2013-01-01

37

Marker-assisted selection of high molecular weight glutenin alleles related to bread-making quality in Iranian common wheat (Triticum aestivum L.).  

PubMed

Bread-making quality in hexaploid wheats is a complex trait. It has been shown that the amount and composition of protein can influence dough rheological properties. The high-molecular-weight (HMW) glutenins are encoded by a complex locus, Glu-1, on the long arm of group-1 homoeologus chromosome of the A, B and D genomes. In this work we used PCR-based DNA markers as a substitution tool to distinguish wheat bread-making quality. We detected PCR-based DNA markers for coding sequence of Glu-A1x, Glu-B1x and Glu-D1x to be 2300 bp, 2400 bp and 2500 bp respectively. DNA markers related to coding sequence of Glu-A1y, Glu-B1y and Glu-D1y were; 1800 bp, 2100 bp and 1950 bp, however, the repetitive region of their coding sequence were shown to be about 1300 bp, 1500 bp and 1600 bp. The results demonstrate that the size variation was due to different lengths of the central repetitive domain. Good or poor bread-making quality in wheat is associated with two allelic pairs of Glu-D1, designated 1Dx5-1Dy10 and 1Dx2-1Dy12. The 1Bx7 allele has moderate-to-good quality score. The specific DNA markers, of 450 bp, 576 bp, 612 bp and 2400 bp respectively were characterized for 1Dx5, 1Dy10, 1Dy12 and 1Bx7 alleles. These markers are very important in screening of wheat for bread-making quality. PMID:22942089

Izadi-Darbandi, Ali; Yazdi-Samadi, Bahman

2012-08-01

38

Distribution of mating-type alleles and M13 PCR markers in the black leaf spot fungus Mycosphaerella fijiensis of bananas in Brazil.  

PubMed

The fungus Mycosphaerella fijiensis is the causative agent of black sigatoka, which is one of the most destructive diseases of banana plants. Infection with this pathogen results in underdeveloped fruit, with no commercial value. We analyzed the distribution of the M. fijiensis mating-type system and its genetic variability using M13 phage DNA markers. We found a 1:1 distribution of mating-type alleles, indicating MAT1-1 and MAT1-2 idiomorphs. A polymorphism analysis using three different primers for M13 markers showed that only the M13 minisatellite primers generated polymorphic products. We then utilized this polymorphism to characterize 40 isolates from various Brazilian states. The largest genetic distances were found between isolates from the same location and between isolates from different parts of the country. Therefore, there was no correlation between the genetic similarity and the geographic origin of the isolates. The M13 marker was used to generate genetic fingerprints for five isolates; these fingerprints were compared with the band profiles obtained from inter-simple sequence repeat (UBC861) and inter-retrotransposon amplified polymorphism analyses. We found that the M13 marker was more effective than the other two markers for differentiating these isolates. PMID:23420369

Queiroz, C B; Miranda, E C; Hanada, R E; Sousa, N R; Gasparotto, L; Soares, M A; Silva, G F

2013-01-01

39

Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers  

PubMed Central

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding.

Roorkiwal, Manish; Nayak, Spurthi N.; Thudi, Mahendar; Upadhyaya, Hari D.; Brunel, Dominique; Mournet, Pierre; This, Dominique; Sharma, Prakash C.; Varshney, Rajeev K.

2014-01-01

40

Allele diversity for abiotic stress responsive candidate genes in chickpea reference set using gene based SNP markers.  

PubMed

Chickpea is an important food legume crop for the semi-arid regions, however, its productivity is adversely affected by various biotic and abiotic stresses. Identification of candidate genes associated with abiotic stress response will help breeding efforts aiming to enhance its productivity. With this objective, 10 abiotic stress responsive candidate genes were selected on the basis of prior knowledge of this complex trait. These 10 genes were subjected to allele specific sequencing across a chickpea reference set comprising 300 genotypes including 211 genotypes of chickpea mini core collection. A total of 1.3 Mbp sequence data were generated. Multiple sequence alignment (MSA) revealed 79 SNPs and 41 indels in nine genes while the CAP2 gene was found to be conserved across all the genotypes. Among 10 candidate genes, the maximum number of SNPs (34) was observed in abscisic acid stress and ripening (ASR) gene including 22 transitions, 11 transversions and one tri-allelic SNP. Nucleotide diversity varied from 0.0004 to 0.0029 while polymorphism information content (PIC) values ranged from 0.01 (AKIN gene) to 0.43 (CAP2 promoter). Haplotype analysis revealed that alleles were represented by more than two haplotype blocks, except alleles of the CAP2 and sucrose synthase (SuSy) gene, where only one haplotype was identified. These genes can be used for association analysis and if validated, may be useful for enhancing abiotic stress, including drought tolerance, through molecular breeding. PMID:24926299

Roorkiwal, Manish; Nayak, Spurthi N; Thudi, Mahendar; Upadhyaya, Hari D; Brunel, Dominique; Mournet, Pierre; This, Dominique; Sharma, Prakash C; Varshney, Rajeev K

2014-01-01

41

Sibs with atopy and asthma share marker alleles at 11q13, but not at 7q31 or 14q32  

SciTech Connect

We studied allele sharing in 26 sib-pairs affected with atopy and asthma, recruited through a pediatric pulmonology department. Inclusion criteria were a positive score (2 symptoms or more) on a modified Dutch version of the MRC/ECCS questionnaire on respiratory symptoms and positive IgE tests (specific IgE 0.35 PRU/ml or more; total serum IgE for children under 10 years as described by Kjellmann et al., 1976; for older children 100 U/ml or over). Twenty-six sibpairs fulfilled these criteria. The microsatellites and polymorphic markers used in the analysis were 17bTA (an intragenic marker in the cystic fibrosis gene on 7q31); D11S534, D11S527, D11S97, PYGM, D11S480, Fc{epsilon}RI (all on 11q13, ordered from telomere to centromere) and D14S51 (a CA repeat close to the {alpha}-1-antitrypsin gene). We observed no sharing with the markers on 7q31 and 14q32, but significant sharing with markers on chromosome 11q13, especially D11S97, PYGM and D11S480. Sharing patterns were consistent with the existence of a dominant gene involved in the pathogenesis of atopic asthma on chromosome 11.

Kate, L.P. ten; Collee, J.M. [Free Univ., Amsterdam (Netherlands); Vries, H.G. de [Univ. of Groningen (Netherlands)] [and others

1994-09-01

42

Detection and Molecular Characterization of Two FAD3 Genes Controlling Linolenic Acid Content and Development of Allele-Specific Markers in Yellow Mustard (Sinapis alba)  

PubMed Central

Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, and low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 and Y1035 with low (3.8%), medium (12.3%) and high (20.8%) linolenic acid (C18?3) content, respectively, in this species. Inheritance studies detected two fatty acid desaturase 3 (FAD3) gene loci controlling the variation of C18?3 content. QTL mapping revealed that the two FAD3 gene loci responsible for 73.0% and 23.4% of the total variation and were located on the linkage groups Sal02 and Sal10, respectively. The FAD3 gene on Sal02 was referred to as SalFAD3.LA1 and that on Sal10 as SalFAD3.LA2. The dominant and recessive alleles were designated as LA1 and la1 for SalFAD3.LA1, and LA2 and la2 for SalFAD3.LA2. Cloning and alignment of the coding and genomic DNA sequences revealed that the SalFAD3.LA1 and SalFAD3.LA2 genes each contained 8 exons and 7 introns. LA1 had a coding DNA sequence (CDS) of 1143 bp encoding a polypeptide of 380 amino acids, whereas la1 was a loss-of-function allele due to an insertion of 584 bp in exon 3. Both LA2 and la2 had a CDS of 1152 bp encoding a polypeptide of 383 amino acids. Allele-specific markers for LA1, la1, LA2 and la2 co-segregated with the C18?3 content in the F2 populations and will be useful for improving fatty acid composition through marker assisted selection in yellow mustard breeding.

Tian, Entang; Zeng, Fangqin; MacKay, Kimberly; Roslinsky, Vicky; Cheng, Bifang

2014-01-01

43

Dissemination of the highly expressed Bx7 glutenin subunit (Glu-B1al allele) in wheat as revealed by novel PCR markers and RP-HPLC.  

PubMed

Increased expression of the high molecular weight glutenin subunit (HMW-GS) Bx7 is associated with improved dough strength of wheat (Triticum aestivum L.) flour. Several cultivars and landraces of widely different genetic backgrounds from around the world have now been found to contain this so-called 'over-expressing' allelic form of the Bx7 subunit encoded by Glu-B1al. Using three methods of identification, SDS-PAGE, RP-HPLC and PCR marker analysis, as well as pedigree information, we have traced the distribution and source of this allele from a Uruguayan landrace, Americano 44D, in the mid-nineteenth century. Results are supported by knowledge of the movement of wheat lines with migrants. All cultivars possessing the Glu-B1al allele can be identified by the following attributes: (1) the elution of the By sub-unit peak before the Dx sub-unit peak by RP-HPLC, (2) high expression levels of Bx7 (>39% Mol% Bx), (3) a 43 bp insertion in the matrix-attachment region (MAR) upstream of the gene promoter relative to Bx7 and an 18 bp nucleotide duplication in the coding region of the gene. Evidence is presented indicating that these 18 and 43 bp sequence insertions are not causal for the high expression levels of Bx7 as they were also found to be present in a small number of hexaploid species, including Chinese Spring, and species expressing Glu-B1ak and Glu-B1a alleles. In addition, these sequence inserts were found in different isolates of the tetraploid wheat, T. turgidum, indicating that these insertion/deletion events occurred prior to hexaploidization. PMID:15340686

Butow, B J; Gale, K R; Ikea, J; Juhász, A; Bedö, Z; Tamás, L; Gianibelli, M C

2004-11-01

44

Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelihood methods  

Microsoft Academic Search

1691 F-2 progeny of a cross between Lycopersicon esculentum and L pimpinellifolium grown under field conditions were scored for 18 quantitative traits of economic interest and 10 segregating genetic markers. Each parental strain was homozygous for one allele of each marker. Four of the markers were electrophoretic, and six were morphological. Three pairs of the genetic markers were linked. An

J I Weller

1987-01-01

45

Identification of FAD2 and FAD3 genes in Brassica napus genome and development of allele-specific markers for high oleic and low linolenic acid contents.  

PubMed

Modification of oleic acid (C18:1) and linolenic acid (C18:3) contents in seeds is one of the major goals for quality breeding after removal of erucic acid in oilseed rape (Brassica napus). The fatty acid desaturase genes FAD2 and FAD3 have been shown as the major genes for the control of C18:1 and C18:3 contents. However, the genome structure and locus distributions of the two gene families in amphidiploid B. napus are still not completely understood to date. In the present study, all copies of FAD2 and FAD3 genes in the A- and C-genome of B. napus and its two diploid progenitor species, Brassica rapa and Brassica oleracea, were identified through bioinformatic analysis and extensive molecular cloning. Two FAD2 genes exist in B. rapa and B. oleracea, and four copies of FAD2 genes exist in B. napus. Three and six copies of FAD3 genes were identified in diploid species and amphidiploid species, respectively. The genetic control of high C18:1 and low C18:3 contents in a double haploid population was investigated through mapping of the quantitative trait loci (QTL) for the traits and the molecular cloning of the underlying genes. One major QTL of BnaA.FAD2.a located on A5 chromosome was responsible for the high C18:1 content. A deleted mutation in the BnaA.FAD2.a locus was uncovered, which represented a previously unidentified allele for the high oleic variation in B. napus species. Two major QTLs on A4 and C4 chromosomes were found to be responsible for the low C18:3 content in the DH population as well as in SW Hickory. Furthermore, several single base pair changes in BnaA.FAD3.b and BnaC.FAD3.b were identified to cause the phenotype of low C18:3 content. Based on the results of genetic mapping and identified sequences, allele-specific markers were developed for FAD2 and FAD3 genes. Particularly, single-nucleotide amplified polymorphisms markers for FAD3 alleles were demonstrated to be a reliable type of SNP markers for unambiguous identification of genotypes with different content of C18:3 in amphidiploid B. napus. PMID:22534790

Yang, Qingyong; Fan, Chuchuan; Guo, Zhenhua; Qin, Jie; Wu, Jianzhong; Li, Qingyuan; Fu, Tingdong; Zhou, Yongming

2012-08-01

46

Mapping of the loci controlling oleic and linolenic acid contents and development of fad2 and fad3 allele-specific markers in canola (Brassica napus L.).  

PubMed

The quality of canola oil is determined by its constituent fatty acids such as oleic acid (C18:1), linoleic acid (C18:2) and linolenic acid (C18:3). Most canola cultivars normally produce oil with about 55-65% oleic acid and 8-12% linolenic acid. High concentrations of linolenic acid lead to oil instability and off-type flavor, while high levels of oleic acid increase oxidative stability and nutritional value of oil. Therefore, development of canola cultivars with increased oleic acid and reduced linolenic acid is highly desirable for canola oil quality. In this study, we have mapped one locus that has a major effect and one locus that has a minor effect for high oleic acid and two loci that have major effects for low linolenic acid in a doubled haploid population. The major locus for high C18:1 was proven to be the fatty acid desaturase-2 (fad2) gene and it is located on the linkage group N5; the minor locus is located on N1. One major QTL for C18:3 is the fatty acid desaturase-3 gene of the genome C (fad3c) and it is located on N14. The second major QTL resides on N4 and is the fad3a gene of the A genome. We have sequenced genomic clones of the fad2 and fad3c genes amplified from an EMS-induced mutant and a wild-type canola cultivar. A comparison of the mutant and wild-type allele sequences of the fad2 and fad3c genes revealed single nucleotide mutations in each of the genes. Detailed sequence analyses suggested mechanisms by which both the mutations can cause altered fatty acid content. Based on the sequence differences between the mutant and wild-type alleles, two single nucleotide polymorphism (SNP) markers, corresponding to the fad2 and fad3c gene mutations, were developed. These markers will be highly useful for direct selection of desirable fad2 and fad3c alleles during marker-assisted trait introgression and breeding of canola with high oleic and low linolenic acid. PMID:16767448

Hu, Xueyi; Sullivan-Gilbert, Mandy; Gupta, Manju; Thompson, Steven A

2006-08-01

47

Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern  

USGS Publications Warehouse

The influence of study design on the ability to detect the effects of landscape pattern on gene flow is one of the most pressing methodological gaps in landscape genetic research. To investigate the effect of study design on landscape genetics inference, we used a spatially-explicit, individual-based program to simulate gene flow in a spatially continuous population inhabiting a landscape with gradual spatial changes in resistance to movement. We simulated a wide range of combinations of number of loci, number of alleles per locus and number of individuals sampled from the population. We assessed how these three aspects of study design influenced the statistical power to successfully identify the generating process among competing hypotheses of isolation-by-distance, isolation-by-barrier, and isolation-by-landscape resistance using a causal modelling approach with partial Mantel tests. We modelled the statistical power to identify the generating process as a response surface for equilibrium and non-equilibrium conditions after introduction of isolation-by-landscape resistance. All three variables (loci, alleles and sampled individuals) affect the power of causal modelling, but to different degrees. Stronger partial Mantel r correlations between landscape distances and genetic distances were found when more loci were used and when loci were more variable, which makes comparisons of effect size between studies difficult. Number of individuals did not affect the accuracy through mean equilibrium partial Mantel r, but larger samples decreased the uncertainty (increasing the precision) of equilibrium partial Mantel r estimates. We conclude that amplifying more (and more variable) loci is likely to increase the power of landscape genetic inferences more than increasing number of individuals. ?? 2011 Blackwell Publishing Ltd.

Landguth, E. L.; Fedy, B. C.; Oyler-Mccance, S. J.; Garey, A. L.; Emel, S. L.; Mumma, M.; Wagner, H. H.; Fortin, M. -J.; Cushman, S. A.

2012-01-01

48

HLA-B*5801 allele as a genetic marker for severe cutaneous adverse reactions caused by allopurinol  

Microsoft Academic Search

Allopurinol, a commonly prescribed medication for gout and hyperuricemia, is a frequent cause of severe cutaneous adverse reactions (SCAR), which include the drug hypersensitivity syndrome, Stevens-Johnson syndrome, and toxic epidermal necrolysis. The adverse events are unpredictable and carry significant morbidity and mortality. To identify genetic markers for allopurinol-SCAR, we carried out a case-control association study. We enrolled 51 patients with

Shuen-Iu Hung; Wen-Hung Chung; Lieh-Bang Liou; Chen-Chung Chu; Marie Lin; Hsien-Ping Huang; Yen-Ling Lin; Joung-Liang Lan; Li-Cheng Yang; Hong-Shang Hong; Ming-Jing Chen; Ping-Chin Lai; Mai-Szu Wu; Chia-Yu Chu; Kuo-Hsien Wang; Chien-Hsiun Chen; Cathy S. J. Fann; Jer-Yuarn Wu; Yuan-Tsong Chen

2005-01-01

49

Psychosocial and Biological Markers of Daily Lives of Midlife Parents of Children with Disabilities*  

PubMed Central

Using daily telephone interviews, 82 midlife parents (mean age = 57.4) of children with disabilities (mean age = 29.9) were compared with a closely matched sample of unaffected parents (n = 82) to elucidate the daily experience of nonnormative parenting. In addition, salivary cortisol samples were obtained to examine whether parents of children with disabilities had dysregulated diurnal rhythms and the extent to which the amount of time spent with children was associated with divergent patterns of cortisol expression. We found that parents of children with disabilities had similar patterns of daily time use and similar likelihood of positive daily events as the comparison group, but they had elevated levels of stress, negative affect, and physical symptoms, all reported on a daily basis. In addition, their diurnal rhythm of cortisol expression differed significantly from the comparison group, a pattern that was strongest for parents of children with disabilities on days when they spent more time with their children.

Seltzer, Marsha Mailick; Almeida, David M.; Greenberg, Jan S.; Savla, Jyoti; Stawski, Robert S.; Hong, Jinkuk; Taylor, Julie Lounds

2009-01-01

50

Developing KDML105 Backcross Introgression Lines Using Marker-Assisted Selection for QTLs Associated with Drought Tolerance in Rice  

Microsoft Academic Search

Marker-assisted selection (MAS) has been employed to improve the efficiency and speed up breeding programs, specifically in selection. A major use of MAS is in assisting backcrossing of genes\\/QTLs to elite cultivars. Markers aid in the selection of target alleles and in the assessment of a recipient's parent genome. Introgression and selection of QTLs using molecular markers in foreground selection

Jonaliza L. Siangliw; Boonrat Jongdee; Grienggrai Pantuwan; Theerayut Toojinda

2007-01-01

51

Parenting.  

ERIC Educational Resources Information Center

The newsletter of the California Association for the Gifted includes the following brief articles on parenting: "Your Challenge, Their Lives" (Barry Ziff); "Courage to Be Who I Am, Unafraid" (Elizabeth Meckstroth); "Attribution: A Key to Encouraging More Responsible Behavior in the Gifted" (Saundra Sparling); "A Parent's Perspective" (Carolyn…

Ziff, Barry, Ed.; Hostettler, Karen, Ed.

1989-01-01

52

Standardization and conversion of marker polymorphism measures.  

PubMed

Large scale gene mapping efforts in domestic animals have generated and mapped a large number of genetic markers that are useful for mapping quantitative trait and disease loci and for DNA diagnostic purposes such as parentage testing. Marker polymorphism is an important criterion for selecting genetic markers in planning experiment for mapping quantitative trait loci or for DNA diagnostic purposes. Current formulations of marker polymorphism measures are functions of marker allele frequencies. In this study, two measures of marker polymorphism that are available from gene mapping studies and do not require allele frequencies were proposed and analyzed: the observed polymorphic information content (PIC) and the observed family information content (FIC). The observed FIC was more stable than the observed PIC because the observed FIC is unaffected by the variation in the frequency of heterozygous parents. However, both FIC and PIC are dependent on the gene mapping design. The effective number of alleles is recommended as a tool to standardize marker polymorphism measures so that polymorphism of different markers can be compared on an equal basis, and to obtain a new polymorphism measure (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize FIC, PIC and exclusion probabilities is illustrated using genetic markers in a published linkage map. PMID:10654428

Da, Y; VanRaden, P M; Ron, M; Beever, J E; Paszek, A A; Song, J; Wiggans, G R; Ma, R; Weller, J I; Lewin, H A

1999-01-01

53

Genetic Variation at Selected SNPs in the Leptin Gene and Association of Alleles with Markers of Kidney Disease in a Xhosa Population of South Africa  

PubMed Central

Background Chronic kidney disease (CKD) is a significant public health problem that leads to end-stage renal disease (ESRD) with as many as 2 million people predicted to need therapy worldwide by 2010. Obesity is a risk factor for CKD and leptin, the obesity hormone, correlates with body fat mass and markers of renal function. A number of clinical and experimental studies have suggested a link between serum leptin and kidney disease. We hypothesised that variants in the leptin gene (LEP) may be associated with markers of CKD in indigenous black Africans. Methodology/Principal Findings Black South Africans of Xhosa (distinct cultural Bantu-speaking population) descent were recruited for the study and four common polymorphisms of the LEP (rs7799039, rs791620, rs2167270 and STS-U43653 [ENSSNP5824596]) were analysed for genotype and haplotype association with urine albumin-to-creatinine ratio (UACR), estimated glomerular filtration rate (eGFR), Serum creatinine (Scr) and serum leptin level. In one of the four single nucleotide polymorphisms (SNPs) we examined, an association with the renal phenotypes was observed. Hypertensive subjects with the T allele (CT genotype) of the ENSSNP5824596 SNP had a significantly higher eGFR (p?=?0.0141), and significantly lower Scr (p?=?0.0137). This was confirmed by haplotype analysis. Also, the haplotype GAAC had a modest effect on urine albumin-to-creatinine ratio in normotensive subjects (p?=?0.0482). Conclusions/Significance These results suggest that genetic variations of the LEP may be associated with phenotypes that are markers of CKD in black Africans.

Okpechi, Ikechi G.; Rayner, Brian L.; van der Merwe, Lize; Mayosi, Bongani M.; Adeyemo, Adebowale; Tiffin, Nicki; Ramesar, Rajkumar

2010-01-01

54

Markers  

ERIC Educational Resources Information Center

Dry erase whiteboards come with toxic dry erase markers and toxic cleaning products. Dry erase markers labeled "nontoxic" are not free of toxic chemicals and can cause health problems. Children are especially vulnerable to environmental health hazards; moreover, schools commonly have problems with indoor air pollution, as they are more densely…

Healthy Schools Network, Inc., 2011

2011-01-01

55

Bi-parentally inherited species-specific markers identify hybridization between rainbow trout and cutthroat trout subspecies  

USGS Publications Warehouse

Eight polymerase chain reaction primer sets amplifying bi-parentally inherited species-specific markers were developed that differentiate between rainbow trout (Oncorhynchus mykiss) and various cutthroat trout (O. clarki) subspecies. The primers were tested within known F1 and first generation hybrid backcrosses and were shown to amplify codominantly within hybrids. Heterozygous individuals also amplified a slower migrating band that was a heteroduplex, caused by the annealing of polymerase chain reaction products from both species. These primer sets have numerous advantages for native cutthroat trout conservation including statistical genetic analyses of known crosses and simple hybrid identification.

Ostberg, C. O.; Rodriguez, R. J.

2004-01-01

56

Nonword Repetition - A Clinical Marker for Specific Language Impairment in Swedish Associated with Parents' Language-Related Problems  

PubMed Central

First, we explore the performance of nonword repetition (NWR) in children with specific language impairment (SLI) and typically developing children (TD) in order to investigate the accuracy of NWR as a clinical marker for SLI in Swedish-speaking school-age children. Second, we examine the relationship between NWR, family aggregation, and parental level of education in children with SLI. A sample of 61 children with SLI, and 86 children with TD, aged 8–12 years, were administered an NWR test. Family aggregation, measured as the prevalence of language and/or literacy problems (LLP) in parents of the children with SLI, was based on family history interviews. The sensitivity and specificity of nonword repetition was analyzed in a binary logistic regression, cut-off values were established with ROC curves, and positive and negative likelihood ratios reported. Results from the present study show that NWR distinguishes well between Swedish-speaking school-children with and without SLI. We found 90.2% sensitivity and 97.7% specificity at a cut-off level of ?2 standard deviations for binary scoring of nonwords. Differences between the SLI and TD groups showed large effect sizes for the two scoring measures binary (d?=?2.11) and percent correct consonants (PCC) (d?=?1.79). The children with SLI were split into two subgroups: those with no parents affected with LLP (n?=?12), and those with one or both parents affected (n?=?49). The subgroup consisting of affected parents had a significantly lower score on NWR binary (p?=?.037), and there was a great difference between the subgroups (d?=?0.7). When compared to the TD group, the difference from the subgroup with affected parents was almost one standard deviation larger (d?=?2.47) than the difference from the TD to the subgroup consisting of non-affected parents (d?=?1.57). Our study calls for further exploration of the complex interaction between family aggregation, language input, and phenotypes of SLI.

Kalnak, Nelli; Peyrard-Janvid, Myriam; Forssberg, Hans; Sahlen, Birgitta

2014-01-01

57

Clinic-Referred Mothers' Autobiographical Narratives as Markers of Their Parenting Styles  

ERIC Educational Resources Information Center

Forty clinic-referred mothers completed questionnaires describing their children's problems and the mothers' parenting styles. In addition, each mother told three stories about their personal experiences in child care and one story about being cared for in their families of origin. Each story was transcribed and rated for coherence on six…

Rowinski, Katherine S.; Wahler, Robert G.

2010-01-01

58

Allele coding in genomic evaluation  

PubMed Central

Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general, two approaches have been used. One approach estimates the marker effects first and then, genomic breeding values are obtained by summing marker effects. In the second approach, genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele, one for the heterozygote, and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered, and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding, provided that the model has a fixed general mean. For the equivalent models, the same results hold, even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient matrix depend on the allele coding because different allele coding methods imply different models. Finally, allele coding affects the mixing of Markov chain Monte Carlo algorithms, with the centered coding being the best. Conclusions Different allele coding methods lead to the same inference in the marker-based and equivalent models when a fixed general mean is included in the model. However, reliabilities of genomic breeding values are affected by the allele coding method used. The centered coding has some numerical advantages when Markov chain Monte Carlo methods are used.

2011-01-01

59

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions  

PubMed Central

DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential for many interactions between cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation was established in the parental germlines or post-fertilization in the embryo is not a determinant in CTCF or cohesin binding. These findings link CTCF and cohesin with the control regions of a subset of imprinted genes, supporting the notion that imprinting control is mechanistically diverse.

Prickett, Adam R.; Barkas, Nikolaos; McCole, Ruth B.; Hughes, Siobhan; Amante, Samuele M.; Schulz, Reiner; Oakey, Rebecca J.

2013-01-01

60

Frequent allelic losses of 9p21 markers and low incidence of mutations at p16(CDKN2) gene in non-Hodgkin lymphomas of B-cell lineage  

Microsoft Academic Search

We present an allelotype analysis of 35 cases of non-Hodgkin lymphomas and normal pairs using four microsatellite markers that flank the region occupied by the CDKN2 gene locus at 9p21. Frequent allelic losses (LOH) were detected in B-cell lineage NHLs, including Burkitt lymphoma (33.3% of total, if we only consider high grade tumors). In five of these tumors LOH did

José Fernández-Piqueras; Javier Santos; Ignacio Pérez de Castro; Bárbara Meléndez; Beatríz Martínez; Mercedes Robledo; Carmen Rivas; Javier Benítez

1997-01-01

61

Comparison of the observed with the simulated distributions of the parental genome contribution in two marker-assisted backcross programs in rice  

Microsoft Academic Search

Computer simulations are useful tools to optimize marker-assisted breeding programs. The objective of our study was to investigate\\u000a the closeness of computer simulations of the recurrent parent genome recovery with experimental data obtained in two marker-assisted\\u000a backcrossing programs in rice (Orzya sativa L.). We simulated the breeding programs as they were practically carried out. In the simulations we estimated the

Vanessa Prigge; Hans Peter Maurer; David J. Mackill; Albrecht E. Melchinger; Matthias Frisch

2008-01-01

62

Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid  

Microsoft Academic Search

Pusa RH10, the widely cultivated superfine grain aromatic rice hybrid, and its parental lines Pusa6B and PRR78 are susceptible\\u000a to bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae. Pusa1460, a Basmati rice variety, was utilized as the donor for introgressing BB resistance genes xa13 and Xa21 into Pusa6B and PRR78 using a marker-assisted backcross breeding program. The markers

S. H. Basavaraj; Vikas K. Singh; Ashok K. Singh; Ashutosh Singh; Anita Singh; Deepti Anand; Sheel Yadav; Ranjith K. Ellur; Devinder Singh; S. Gopala Krishnan; M. Nagarajan; T. Mohapatra; K. V. Prabhu

2010-01-01

63

Regression models for allele sharing: analysis of accumulating data in affected sib pair studies.  

PubMed

Advances in human genome mapping have led to the identification of large numbers of genetic markers that allow systematic searches for multiple disease susceptibility genes for complex traits. A common design involves the recruitment of families with at least two children affected with the disease of interest. The objective is to find chromosomal regions that harbour susceptibility genes for the disease. The affected children, their parents if available, and sometimes other, unaffected, siblings are genotyped using sets of microsatellite DNA markers representing chromosomal sites distributed across the genome. Each marker can occur in several different variants known as alleles, and a pair of alleles constitutes the marker genotype. Each child randomly inherits one of their mother's two alleles and one of their father's two alleles. If a marker is close to a disease susceptibility gene, then affected siblings are expected to have more sharing of the same maternal and/or paternal marker alleles. Statistical methods are used to estimate the distribution of allele sharing in each affected sib pair (ASP) using the set of markers typed across each chromosome, and to test for the presence of excess sharing in the families as a group at each point across the genome. Regression models that allow the allele sharing proportions to depend on characteristics of the family such as diagnostic subtype or ethnic background have been developed to address the heterogeneity that is characteristic of complex disease, but these have not yet been widely applied. In this paper, we apply regression modelling to investigate variation associated with family-level covariates and with the order in which families are recruited and genotyped. We also discuss how some of the concepts of group sequential analysis apply to accumulating data from genome scans of complex disease. PMID:11813229

Bull, Shelley B; Greenwood, Celia M T; Mirea, Lucia; Morgan, Kenneth

2002-02-15

64

Combined linkage and association analyses of the 124-bp allele of marker D2S2944 with anxiety, depression, neuroticism and major depression.  

PubMed

A central issue in psychiatric genetics is whether positive findings replicate. Zubenko et al. (2002b, Mol. Psychiatry 7:460-467) reported an association of the 124-bp allele of D2S2944 with recurrent early-onset major depression for females. We tested for association of this allele to continuous measures of anxiety, depression and neuroticism in a Dutch sample of 347 males and 448 females, and to DSM-IV major depression in a subsample of 210 males and 295 females. The association of the 124-bp allele to depression in females was not replicated, but there were significant associations (not significant after correction for multiple testing) with anxiety and anxious depression in males. However, the association occurred in the absence of evidence for linkage in this region on chromosome 2. PMID:16378170

Beem, A Leo; Geus, Eco J C de; Hottenga, Jouke-Jan; Sullivan, Patrick F; Willemsen, Gonneke; Slagboom, P Eline; Boomsma, Dorret I

2006-01-01

65

Allelic Variants of TNF Superfamily Genes Serve as Markers of Disease Severity in Patients with Chronic Obstructive Pulmonary Disease and Bronchiectatic Disease  

Microsoft Academic Search

The distribution of allelic variants of genes of theTNFsuperfamily (TNFA andLTA) was studied in 172 patients with chronic obstructive pulmonary disease (COPD), bronchiectatic disease (n = 22), and in healthy individuals (n = 169). Analysis of the TNFA gene locus –308G ? A revealed no differences between the examined groups. Analysis of the LTA gene polymorphic locus +252A ? G

D. G. Yanbaeva; G. F. Korytina; T. V. Viktorova

2004-01-01

66

Molecular validation of multiple allele inheritance for dominant genic male sterility gene in Brassica napus L.  

PubMed

Dominant genic male sterility (DGMS) has been playing an increasingly important role, not only as a tool for assisting in recurrent selection but also as an alternative approach for efficient production of hybrids. Previous studies indicate that fertility restoration of DGMS is the action of another unlinked dominant gene. Recently, through classical genetic analysis with various test populations we have verified that in a DGMS line 609AB the trait is inherited in a multiple allelic pattern. In this study, we applied molecular marker technology to provide further validation of the results. Eight amplified fragment length polymorphism (AFLP) markers tightly linked to the male sterility allele (Ms) were identified in a BC1 population from a cross between 609A (a sterile plant in 609AB) and a temporary maintainer GS2467 as recurrent parent. Four out of the eight markers reproduced the same polymorphism in a larger BC(1) population generated with microspore-derived doubled haploid (DH) parents (S148 and S467). The two nearest AFLP markers SA12MG14 and P05MG15, flanking the Ms locus at respective distances of 0.3 centiMorgan (cM) and 1.6 cM, were converted into sequence characterized amplified region (SCAR) markers designated SC6 and SC9. Based on the sequence difference of the marker P05MG15 between S148 and a DH restorer line S103, we further developed a SCAR marker SC9f that is specific to the restorer allele (Mf). The map distance between SC9f and Mf was consistent with that between SC9 and Ms allele. Therefore, successful conversion of the marker tightly linked to Ms into a marker tightly linked to Mf suggested that the restoration for DGMS in 609AB is controlled by an allele at the Ms locus or a tightly linked gene (regarded as an allele in practical application). The Ms and Mf-specific markers developed here will facilitate the breeding for new elite homozygous sterile lines and allow further research on map-based cloning of the Ms gene. PMID:16783591

Song, Lai-Qiang; Fu, Ting-Dong; Tu, Jin-Xing; Ma, Cao-Zhi; Yang, Guang-Sheng

2006-06-01

67

IDDM2 - VNTR -encoded Susceptibility to Type 1 Diabetes: Dominant Protection and Parental Transmission of Alleles of the Insulin Gene-linked Minisatellite Locus  

Microsoft Academic Search

IDDM2-encoded predisposition to type 1 diabetes has recently been mapped to the minisatellite or variable number of tandem repeat (VNTR) locus upstream of the insulin and insulin-like growth factor II genes on human chromosome 11p15.5. In a UK case-control study (n=228 sporadic diabetics;n=441 healthy controls), we show here that the genotype homozygous for VNTR class I alleles is predisposing to

Simon T. Bennett; Amanda J. Wilson; Francesco Cucca; Jørn Nerup; Flemming Pociot; Patricia A. McKinney; Anthony H. Barnett; Stephen C. Bain; John A. Todd

1996-01-01

68

Genetic linkage of IgA deficiency to the major histocompatibility complex: evidence for allele segregation distortion, parent-of-origin penetrance differences, and the role of anti-IgA antibodies in disease predisposition.  

PubMed Central

Immunoglobulin A (IgA) deficiency (IgAD) is characterized by a defect of terminal lymphocyte differentiation, leading to a lack of IgA in serum and mucosal secretions. Familial clustering, variable population prevalence in different ethnic groups, and a predominant inheritance pattern suggest a strong genetic predisposition to IgAD. The genetic susceptibility to IgAD is shared with a less prevalent, but more profound, defect called "common variable immunodeficiency" (CVID). Here we show an increased allele sharing at 6p21 in affected members of 83 multiplex IgAD/CVID pedigrees and demonstrate, using transmission/diseqilibrium tests, family-based associations indicating the presence of a predisposing locus, designated "IGAD1," in the proximal part of the major histocompatibility complex (MHC). The recurrence risk of IgAD was found to depend on the sex of parents transmitting the defect: affected mothers were more likely to produce offspring with IgAD than were affected fathers. Carrier mothers but not carrier fathers transmitted IGAD1 alleles more frequently to the affected offspring than would be expected under random segregation. The differential parent-of-origin penetrance is proposed to reflect a maternal effect mediated by the production of anti-IgA antibodies tentatively linked to IGAD1. This is supported by higher frequency of anti-IgA-positive females transmitting the disorder to children, in comparison with female IgAD nontransmitters, and by linkage data in the former group. Such pathogenic mechanisms may be shared by other MHC-linked complex traits associated with the production of specific autoantibodies, parental effects, and a particular MHC haplotype.

Vorechovsky, I; Webster, A D; Plebani, A; Hammarstrom, L

1999-01-01

69

Allelic variation of polyphenol oxidase (PPO) genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat  

Microsoft Academic Search

Polyphenol oxidase (PPO) activity is highly related to the undesirable browning of wheat-based end products, especially Asian\\u000a noodles. Characterization of PPO genes and the development of their functional markers are of great importance for marker-assisted\\u000a selection in wheat breeding. In the present study, complete genomic DNA sequences of two PPO genes, one each located on chromosomes\\u000a 2A and 2D and

X. Y. He; Z. H. He; L. P. Zhang; D. J. Sun; C. F. Morris; E. P. Fuerst; X. C. Xia

2007-01-01

70

[Distribution of genetic markers in offsprings of irradiated individuals].  

PubMed

For the estimation of radiation exposure on genetic processes in Mayak PA population we studied the distribution of a number of genetic markers in offsprings of Mayak PA workers depending on radiation (preconceptive and antenatal chronic exteral gamma-radiation) and non-radiation (age-sex characteristics of children and age characteristics of parents to the moment of conception) factors. Relatively unfavorable changes in distribution of genotypes and genes of haptoglobin genetic system in offsprings, whose parents (one or both) were exposed to external gamma-radiation in preconceptive cumulative dose of more than 200 cGy were detected. The most obvious reason of such changes may consist in directed gametic selection (Hp2 allele versus Hp1 allele) which turns out in abnormalities of segregation of Hp2-1 heterozygote that have both alleles. Effect of antenatal exposure on distribution of studied genetic markers in offspring of exposed population in studied dose range were not found. Homotypic changes in distribution of ABO bood groups and alleles in offspring of exposed and unexposed individuals depending on age characteristics of parents (middle age and age differences of both parents) for the moment of conception were also detected. PMID:19004327

Tel'nov, V I

2008-01-01

71

Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis.  

PubMed

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1-0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies. PMID:10964223

Gerber, S; Mariette, S; Streiff, R; Bodénès, C; Kremer, A

2000-08-01

72

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

PubMed Central

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.

Mandal, Diptasri M; Sorant, Alexa JM; Atwood, Larry D; Wilson, Alexander F; Bailey-Wilson, Joan E

2006-01-01

73

OptiMAS: a decision support tool to conduct marker-assisted selection programs.  

PubMed

Ongoing major advances in plant genotyping and phenotyping lead to a better understanding of genetic architecture of agronomical traits. In this context, it is important to develop decision support tools to help breeders in implementing marker-assisted selection (MAS) projects to assemble new allele combinations. Algorithms have been developed within an interactive graphical interface to (a) trace parental QTL alleles throughout selection generations, (b) propose strategies to select the best plants based on estimated molecular scores, and (c) efficiently intermate them depending on the expected value of their progenies. By investigating multi-allelic context and diverse pedigree structure, OptiMAS enables to assemble favorable alleles issued from diverse parents and further accelerate genetic gain. PMID:24816663

Valente, Fabio; Gauthier, Franck; Bardol, Nicolas; Blanc, Guylaine; Joets, Johann; Charcosset, Alain; Moreau, Laurence

2014-01-01

74

SNaPshot Assay in Quantitative Detection of Allelic Nondisjunction in Down Syndrome  

PubMed Central

Aim: We wished to identify markers associated with allelic nondisjunction in nuclear families with Down syndrome (DS) offspring. Since the GRIK1 and GARS-AIRS-GART genes, mapping to chromosome 21q22.1, may be informative in this regard, we genotyped four single-nucleotide polymorphisms [30952599(A/G) rs363484; 30924733(A/G) rs363506; 34901423(A/G) rs2834235; 34877070(A/G) rs7283354] present in these genes using the SNaPshot™ assay protocol. Results: We have reported 30952599(A/G)-rs363484 to be monomorphic in our sample population. Genotyping revealed 35/65 families to be informative for 34877070(A/G)-rs7283354 (GARS-AIRS-GART), whereas only 25/65 and 11/65 are informative for 34901423(A/G)-rs2834235 (GARS-AIRS-GART) and 30924733(A/G)-rs363506 (GRIK1) polymorphisms, respectively. The parent- and stage-of-origin of nondisjunction could be traced in 48/65 families using at least one polymorphic marker. A single trio provided internal validation for assignment of the parent- and stage-of-origin of nondisjunction whereby the nondisjoining alleles were independently identified as G-rs363506, G-rs2834235, and G-rs7283354, respectively. An enhanced ratio of meiosis-I to meiosis-II errors during maternal or paternal meioses accounts for allelic nondisjunction. Conclusions The SNaPshot assay is quantitative and permits multiplexing for detection of allelic nondisjunction. Inclusion of additional informative chromosome 21-specific markers may aid rapid aneuploidy detection, screening, and prenatal counseling of parents at risk of having babies with DS.

Ghosh, Debarati; Gochhait, Sailesh; Banerjee, Disha; Chatterjee, Anindita; Sinha, Swagata

2012-01-01

75

A restriction fragment of the C2 gene is a unique marker for C2 deficiency and the uncommon C2 allele C2*B (a marker for type 1 diabetes).  

PubMed Central

There are three common C2 protein alleles in caucasians, C2*C, C2*B, and C2*Q0, with allele frequencies of 0.96, 0.03, and 0.01, as well as Sst I RFLP variants of 2.75, 2.7, 2.65, 2.55, and 2.4 kb, with frequencies of 0.017, 0.533, 0.358, 0.017, and 0.075. Thus, C2*C is informatively split by the RFLP. Of 94 nonrandomly ascertained caucasian complotypes, 77 contained C2*C, four contained C2*Q0, and 13 had C2*B. None of the C2*C-containing complotypes carried the 2.75 kb Sst I fragment and all of the complotypes with C2*B or C2*Q0 carried it. All of the C2*Q0 alleles were associated with C4A*4, C4B*2 in the complotype S042 as previously reported. C2*B was usually (9/13) in the complotype SB42, occasionally (1/13 each) in SB45, SB41, SB(4,3)0, and SB31. Thus, the association of the C2 2.75-kb fragment was with C2*B and C2*Q0, not with C4A*4, C4B*2, or even C4A*4 alone. The complotype SC42 was associated with the 2.65-kb Sst I fragment in four of five instances and in a single example with the 2.7-kb fragment. C2*B and C2*Q0 possibly had a common evolutionary ancestor complotype which carried the 2.75-kb Sst I fragment, and BF*S, C4A*4, and C4B*2. C2*B (particularly as the haplotype HLA-Bw62, SB42, DR4) is associated with type 1 diabetes but C2*Q0 is protective.

Simon, S; Awdeh, Z; Campbell, R D; Ronco, P; Brink, S J; Eisenbarth, G S; Yunis, E J; Alper, C A

1991-01-01

76

Nuclear and cytoplasmic genome components of Solanum tuberosum + S. chacoense somatic hybrids and three SSR alleles related to bacterial wilt resistance.  

PubMed

The somatic hybrids were derived previously from protoplast fusion between Solanum tuberosum and S. chacoense to gain the bacterial wilt resistance from the wild species. The genome components analysis in the present research was to clarify the nuclear and cytoplasmic composition of the hybrids, to explore the molecular markers associated with the resistance, and provide information for better use of these hybrids in potato breeding. One hundred and eight nuclear SSR markers and five cytoplasmic specific primers polymorphic between the fusion parents were used to detect the genome components of 44 somatic hybrids. The bacterial wilt resistance was assessed thrice by inoculating the in vitro plants with a bacterial suspension of race 1. The disease index, relative disease index, and resistance level were assigned to each hybrid, which were further analyzed in relation to the molecular markers for elucidating the potential genetic base of the resistance. All of the 317 parental unique nuclear SSR alleles appeared in the somatic hybrids with some variations in the number of bands detected. Nearly 80 % of the hybrids randomly showed the chloroplast pattern of one parent, and most of the hybrids exhibited a fused mitochondrial DNA pattern. One hundred and nine specific SSR alleles of S. chacoense were analyzed for their relationship with the disease index of the hybrids, and three alleles were identified to be significantly associated with the resistance. Selection for the resistant SSR alleles of S. chacoense may increase the possibility of producing resistant pedigrees. PMID:23580089

Chen, Lin; Guo, Xianpu; Xie, Conghua; He, Li; Cai, Xingkui; Tian, Lingli; Song, Botao; Liu, Jun

2013-07-01

77

Complete sequence of HLA-B27 cDNA identified through the characterization of structural markers unique to the HLA-A, -B, and -C allelic series  

SciTech Connect

Antigen HLA-B27 is a high-risk genetic factor with respect to a group of rheumatoid disorders, especially ankylosing spondylitis. A cDNA library was constructed from an autozygous B-cell line expressing HLA-B27, HLA-Cw1, and the previously cloned HLA-A2 antigen. Clones detected with an HLA probe were isolated and sorted into homology groups by differential hybridization and restriction maps. Nucleotide sequencing allowed the unambiguous assignment of cDNAs to HLA-A, -B, and -C loci. The HLA-B27 mRNA has the structure features and the codon variability typical of an HLA class I transcript but it specifies two uncommon amino acid replacements: a cysteine in position 67 and a serine in position 131. The latter substitution may have functional consequences, because it occurs in a conserved region and at a position invariably occupied by a species-specific arginine in humans and lysine in mice. The availability of the complete sequence of HLA-B27 and of the partial sequence of HLA-Cw1 allows the recognition of locus-specific sequence markers, particularly, but not exclusively, in the transmembrane and cytoplasmic domains.

Szoets, H.; Reithmueller, G.; Weiss, E.; Meo, T.

1986-03-01

78

Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism.  

PubMed

Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits. PMID:23975245

Bardol, N; Ventelon, M; Mangin, B; Jasson, S; Loywick, V; Couton, F; Derue, C; Blanchard, P; Charcosset, A; Moreau, Laurence

2013-11-01

79

Tests and estimates of allelic association in complex inheritance  

PubMed Central

Family-based procedures such as the transmission disequilibrium test (TDT) were motivated by concern that sample-based methods to map disease genes by allelic association are not robust to population stratification, migration, and admixture. Other factors to consider in designing a study of allelic association are specification of gene action in a weakly parametric model, efficiency, diagnostic reliability for hypernormal individuals, interest in linkage and imprinting, and sibship composition. Family-based samples lend themselves to the TDT despite its inefficiency compared with cases and unrelated normal controls. The TDT has an efficiency of 1/2 for parent-offspring pairs and 2/3 for father-mother-child trios. Against cases and hypernormal controls, the efficiency is only 1/6 on the null hypothesis. Although dependent on marker gene frequency and other factors, efficiency for hypernormal controls is always greater than for random controls. Efficiency of the TDT is increased in multiplex families and by inclusion of normal sibs, approaching a case-control design with normal but not hypernormal controls. Isolated cases favor unrelated controls, and only in exceptional populations would avoidance of stratification justify a family-based design to map disease genes by allelic association.

Morton, N. E.; Collins, A.

1998-01-01

80

Genomic prediction of hybrid performance in maize with models incorporating dominance and population specific marker effects.  

PubMed

Identifying high performing hybrids is an essential part of every maize breeding program. Genomic prediction of maize hybrid performance allows to identify promising hybrids, when they themselves or other hybrids produced from their parents were not tested in field trials. Using simulations, we investigated the effects of marker density (10, 1, 0.3 marker per mega base pair, Mbp(-1)), convergent or divergent parental populations, number of parents tested in other combinations (2, 1, 0), genetic model (including population-specific and/or dominance marker effects or not), and estimation method (GBLUP or BayesB) on the prediction accuracy. We based our simulations on marker genotypes of Central European flint and dent inbred lines from an ongoing maize breeding program. To simulate convergent or divergent parent populations, we generated phenotypes by assigning QTL to markers with similar or very different allele frequencies in both pools, respectively. Prediction accuracies increased with marker density and number of parents tested and were higher under divergent compared with convergent parental populations. Modeling marker effects as population-specific slightly improved prediction accuracy under lower marker densities (1 and 0.3 Mbp(-1)). This indicated that modeling marker effects as population-specific will be most beneficial under low linkage disequilibrium. Incorporating dominance effects improved prediction accuracies considerably for convergent parent populations, where dominance results in major contributions of SCA effects to the genetic variance among inter-population hybrids. While the general trends regarding the effects of the aforementioned influence factors on prediction accuracy were similar for GBLUP and BayesB, the latter method produced significantly higher accuracies for models incorporating dominance. PMID:22733443

Technow, Frank; Riedelsheimer, Christian; Schrag, Tobias A; Melchinger, Albrecht E

2012-10-01

81

Mining the human phenome using allelic scores that index biological intermediates.  

PubMed

It is common practice in genome-wide association studies (GWAS) to focus on the relationship between disease risk and genetic variants one marker at a time. When relevant genes are identified it is often possible to implicate biological intermediates and pathways likely to be involved in disease aetiology. However, single genetic variants typically explain small amounts of disease risk. Our idea is to construct allelic scores that explain greater proportions of the variance in biological intermediates, and subsequently use these scores to data mine GWAS. To investigate the approach's properties, we indexed three biological intermediates where the results of large GWAS meta-analyses were available: body mass index, C-reactive protein and low density lipoprotein levels. We generated allelic scores in the Avon Longitudinal Study of Parents and Children, and in publicly available data from the first Wellcome Trust Case Control Consortium. We compared the explanatory ability of allelic scores in terms of their capacity to proxy for the intermediate of interest, and the extent to which they associated with disease. We found that allelic scores derived from known variants and allelic scores derived from hundreds of thousands of genetic markers explained significant portions of the variance in biological intermediates of interest, and many of these scores showed expected correlations with disease. Genome-wide allelic scores however tended to lack specificity suggesting that they should be used with caution and perhaps only to proxy biological intermediates for which there are no known individual variants. Power calculations confirm the feasibility of extending our strategy to the analysis of tens of thousands of molecular phenotypes in large genome-wide meta-analyses. We conclude that our method represents a simple way in which potentially tens of thousands of molecular phenotypes could be screened for causal relationships with disease without having to expensively measure these variables in individual disease collections. PMID:24204319

Evans, David M; Brion, Marie Jo A; Paternoster, Lavinia; Kemp, John P; McMahon, George; Munafò, Marcus; Whitfield, John B; Medland, Sarah E; Montgomery, Grant W; Timpson, Nicholas J; St Pourcain, Beate; Lawlor, Debbie A; Martin, Nicholas G; Dehghan, Abbas; Hirschhorn, Joel; Davey Smith, George

2013-10-01

82

Characterization of the Soybean Genome Using EST-derived Microsatellite Markers  

PubMed Central

Abstract We generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9%) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar ‘Misuzudaizu’ and the Chinese line ‘Moshidou Gong 503’, were examined using 10% polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

Hisano, Hiroshi; Sato, Shusei; Isobe, Sachiko; Sasamoto, Shigemi; Wada, Tsuyuko; Matsuno, Ai; Fujishiro, Tsunakazu; Yamada, Manabu; Nakayama, Shinobu; Nakamura, Yasukazu; Watanabe, Satoshi; Harada, Kyuya; Tabata, Satoshi

2007-01-01

83

Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds  

PubMed Central

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ?1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

McClure, Matthew C.; Sonstegard, Tad S.; Wiggans, George R.; Van Eenennaam, Alison L.; Weber, Kristina L.; Penedo, Cecilia T.; Berry, Donagh P.; Flynn, John; Garcia, Jose F.; Carmo, Adriana S.; Regitano, Luciana C. A.; Albuquerque, Milla; Silva, Marcos V. G. B.; Machado, Marco A.; Coffey, Mike; Moore, Kirsty; Boscher, Marie-Yvonne; Genestout, Lucie; Mazza, Raffaele; Taylor, Jeremy F.; Schnabel, Robert D.; Simpson, Barry; Marques, Elisa; McEwan, John C.; Cromie, Andrew; Coutinho, Luiz L.; Kuehn, Larry A.; Keele, John W.; Piper, Emily K.; Cook, Jim; Williams, Robert; Van Tassell, Curtis P.

2013-01-01

84

High-Density Linkage Maps and Sex-Linked Markers for the Black Tiger Shrimp (Penaeus monodon)  

PubMed Central

We report on the construction of sex-specific high-density linkage maps and identification of sex-linked markers for the black tiger shrimp (Penaeus monodon). Overall, we identified 44 male and 43 female linkage groups (2n = 88) from the analysis of 2306 AFLP markers segregating in three full-sib families, covering 2378 and 2362 cM, respectively. Twenty-one putatively homologous linkage groups, including the sex-linkage groups, were identified between the female and male linkage maps. Six sex-linked AFLP marker alleles were inherited from female parents in the three families, suggesting that the P. monodon adopts a WZ–ZZ sex-determining system. Two sex-linked AFLP markers, one of which we converted into an allele-specific assay, confirmed their association with sex in a panel of 52 genetically unrelated animals.

Staelens, Jan; Rombaut, Debbie; Vercauteren, Ilse; Argue, Brad; Benzie, John; Vuylsteke, Marnik

2008-01-01

85

Identification of AFLP markers linked to a resistance gene against pine needle gall midge in Japanese black pine.  

PubMed

Bulked segregant and AFLP analyses of two mapping populations (R17 x S6 and R17 x S1) were used to identify markers linked to Rpgm, the only known gene responsible for resistance to pine needle gall midge in Pinus thunbergii Parl. Rpgm was found to be bracketed by ACCC/CCTTT(190) on one side at a distance of 6.6 cM and ACGT/CCCGC(250) at 15.3 cM on the other side. The segregation of these markers was analyzed in two other families in order to determine their phase and transferability. One of the two additional resistant parents carried ACCC/CCTTT(190) in the homozygous state while the marker was in coupling (plus marker allele linked with an R allele) in a resistant parent, R17. The marker ACGT/CCCGC(250) was in a repulsion phase in R17 and was not detected in the other two resistant pine trees. Out of four AFLP markers identified, only ACGT/CCAAT(290) was transferable in all resistant trees tested, although its phase was opposite for different trees. These results indicate that in applying those markers to select resistant trees, the phase state of the markers in each resistant tree with respect to Rpgm needs to be considered. PMID:15067405

Hayashi, E; Kondo, T; Terada, K; Kuramoto, N; Kawasaki, S

2004-04-01

86

A study of GluK1 kainate receptor polymorphisms in Down syndrome reveals allelic non-disjunction at 1173(C/T).  

PubMed

Mechanisms underlying Down syndrome (DS)-related mental retardation (MR) remain poorly understood. In trisomic offspring, non-disjunction may result in the reduction to homozygosity of a susceptibility allele inherited from a heterozygous parent. Accordingly, we sought evidence for allelic non-disjunction in the GluK1 gene that encodes the critical kainite-binding glutamate receptor subunit-5, maps to chromosome 21q22.1 in the DS critical region and is expressed in brain regions responsible for learning and memory. Three polymorphisms of GluK1 [522(A/C) rs363538; 1173(C/T) rs363430 and 2705(T/C) rs363504] were genotyped in 86 DS patient families by means of PCR-coupled RFLP assays and evaluated with respect to allele frequency, heterozygosity, linkage disequilibrium, stage and parental origin of allelic non-disjunction. We report that the distribution of allele frequencies is in Hardy-Weinberg equilibrium. Moderate heterozygosity (0.339) and a major allele frequency of 0.78 render the 1173(C/T) marker informative. Pair-wise comparisons reveal that 522(A/C)-1173(C/T) [chi;{2} = 31.2, df = 1, p = 0.0001; D' = 0.42] and 1173(C/T)-2705(T/C) [chi;{2} = 18.3, df = 1, p = 0.0001; D' = 0.34] are in significant linkage disequilibrium of weak magnitude. The estimated ratio of meiosis-I to meiosis-II errors arising from allelic non-disjunction of 1173(C/T) is 4:1 in maternal cases and 2:1 in paternal cases. Studies including additional markers and patient samples are warranted to further substantiate present findings. PMID:19893199

Ghosh, Debarati; Sinha, Swagata; Chatterjee, Anindita; Nandagopal, Krishnadas

2009-01-01

87

Methods for detection of parent-of-origin effects in genetic studies of case-parents triads.  

PubMed Central

When affected probands and their biological parents are genotyped at a candidate gene or a marker, the resulting case-parents-triad data enable powerful tests for linkage in the presence of association. When linkage disequilibrium has been detected in such a study, the investigator may wish to look further for possible parent-of-origin effects. If, for example, the transmission/disequilibrium test restricted to fathers is statistically significant, whereas that restricted to mothers is not, the investigator might interpret this as evidence for nonexpression of the maternally derived disease gene-that is, imprinting. This report reviews existing methods for detection of parent-of-origin effects, showing that each can be invalid under certain scenarios. Two new methods are proposed, based on application of likelihood-based inference after stratification on both the parental mating type and the inherited number of copies of the allele under study. If there are no maternal genetic effects expressed prenatally during gestation, the parental-asymmetry test is powerful and provides valid estimation of a parent-of-origin parameter. For diseases for which there could be maternal effects on risk, the parent-of-origin likelihood-ratio test provides a robust alternative. Simulations based on an admixed population demonstrate good operating characteristics for these procedures, under diverse scenarios.

Weinberg, C R

1999-01-01

88

Haras rare alleles in breast cancer susceptibility  

Microsoft Academic Search

Over the last several years, evidence has accumulated to support the idea that rare Ha-ras polymorphisms are associated with inherited susceptibility to certain human cancers. A recent epidemiologic study conducted at our institution found a significant association specifically with breast cancer, although the mechanism underlying this relationship remains unclear. We have proposed that rare Ha-ras alleles are markers of a

Kathleen Conway; Sharon Edmiston; Daniel B. Fried; Barbara S. Hulka; Peter A. Garrett; Edison T. Liu

1995-01-01

89

Model-Free Analysis and Permutation Tests for Allelic Associations  

Microsoft Academic Search

In this short report, we address some practical problems in performing likelihood-based allelic association analysis of case-control data. Model-free statistics are proposed and their properties assessed by simulation, and procedures based on permutation tests are described for marker-marker as well as marker-disease associations. A memory-efficient algorithm is developed which enables several highly polymorphic markers to be analysed.

Jing Hua Zhao; David Curtis; Pak Chung Sham

2000-01-01

90

Parental Antagonism, Relatedness Asymmetries, and Genomic Imprinting  

Microsoft Academic Search

The theory of inclusive fitness can be modified to consider separate coefficients of relatedness for an individual's maternal and paternal alleles. A gene is said to have parentally antagonistic effects if it has an inclusive fitness benefit when maternally derived, but an inclusive fitness cost when paternally derived (or vice versa). Parental antagonism favours the evolution of alleles that are

David Haig

1997-01-01

91

Resistance gene-analog polymorphism markers co-segregating with the YR5 gene for resistance to wheat stripe rust.  

PubMed

The Yr5 gene confers resistance to all races of the stripe rust pathogen ( Puccinia striiformis f. sp. tritici) of wheat in the United States. To develop molecular markers for Yr5, a BC(7):F(3) population was developed by backcrossing the Yr5 donor ' Triticum spelta album' (TSA) with the recurrent parent 'Avocet Susceptible' (AVS). Seedlings of the Yr5 near-isogenic lines (AVS/6* Yr5), AVS, TSA, and the BC(7):F(3) lines were tested with North American races of P. striiformis f. sp. tritici under controlled greenhouse conditions. The single gene was confirmed by a 1:2:1 segregation ratio for homozygous-resistant, heterozygous and homozygous-susceptible BC(7):F(3) lines. Genomic DNA was extracted from the parents (the Yr5 near-isogenic line and AVS) and 202 BC(7):F(3) lines. The resistance gene-analog polymorphism (RGAP) technique was used to identify molecular markers. The parents and the homozygous-resistant and homozygous-susceptible BC(7):F(3) bulks were used to identify putative RGAP markers for Yr5. Association of the markers with Yr5 was determined using segregation analysis with DNA from the individual BC(7):F(3) lines. Of 16 RGAP markers confirmed by segregation analysis with 109 BC(7):F(3) lines, and nine of the markers confirmed with an additional 93 BC(7):F(3) lines, three markers co-segregated with the resistance allele and three markers co-segregated with the susceptibility allele at the Yr5 locus. The other four markers were tightly linked to the locus. Analysis of a set of Chinese Spring nulli-tetrasomic lines with three markers that co-segregated with, or were linked to, the susceptibility allele confirmed that the Yr5 locus is on chromosome 2B. Of five RGAP markers that were cloned and sequenced, markers Xwgp-17 and Xwgp-18 that co-segregated with the Yr5 locus were co-dominant and had 98% homology with each other in both DNA and translated amino-acid sequences. The two markers had 97% homology with a resistance gene-like sequence from Aegilops ventricosa and had significant homology with many known plant resistance genes, resistance gene analogs and expressed sequence tags (ESTs) from wheat and other plant species. The markers Xwgp-17 and Xwgp-18 also had significant homology with the NB-ARC domain that is in several genes for plant resistance to diseases, nematode cell death and human apoptotic signaling. These markers should be useful to clone Yr5 and combine Yr5 with other genes for durable and superior resistance for the control of stripe rust. PMID:12595992

Yan, G P; Chen, X M; Line, R F; Wellings, C R

2003-02-01

92

Power of association and linkage tests when the disease alleles are unobserved.  

PubMed Central

Genomewide association studies have been advocated as a promising alternative to genomewide linkage scans for detection of small-effect genes in complex diseases. Comparisons of power and sample size between the two strategies have shown considerable advantages for the association studies. These comparisons assume that the set of markers includes the exact disease-related polymorphism. A concern, however, is that the power of an association study decreases when this is not the case, because of discrepant allele frequencies and less-than-maximum disequilibrium between the disease-related polymorphism and its nearest marker. Here, we quantify this concern by comparing the sample sizes needed by the two strategies when the markers exclude the disease-related polymorphism. For affected sib pairs and their parents, we found that incomplete disequilibrium and differing allele frequencies can have substantial negative impact on the power of association studies, resulting, in some circumstances, in little gain and even in loss of power, compared with linkage analysis. We provide some guidelines for choosing between strategies, for the detection of genes for complex diseases.

Tu, I P; Whittemore, A S

1999-01-01

93

Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program  

Microsoft Academic Search

One hundred and ninety three parental lines obtained from 26 countries for an international rice molecular breeding program were evaluated using 101 well-distributed simple sequence repeat (SSR) markers. An overall genetic diversity of 0.68 and an average of 6.3 alleles per locus were revealed, indicating a high level of genetic variation in these lines. Cluster analysis of the 193 accessions

S. B. Yu; W. J. Xu; C. H. M. Vijayakumar; J. Ali; B. Y. Fu; J. L. Xu; Y. Z. Jiang; R. Marghirang; J. Domingo; C. Aquino; S. S. Virmani; Z. K. Li

2003-01-01

94

The optimal measure of allelic association  

PubMed Central

Allelic association between pairs of loci is derived in terms of the association probability ? as a function of recombination ?, effective population size N, linear systematic pressure v, and time t, predicting both ?rt, the decrease of association from founders and ?ct, the increase by genetic drift, with ?t = ?rt + ?ct. These results conform to the Malecot equation, with time replaced by distance on the genetic map, or on the physical map if recombination in the region is uniform. Earlier evidence suggested that ? is less sensitive to variations in marker allele frequencies than alternative metrics for which there is no probability theory. This robustness is confirmed for six alternatives in eight samples. In none of these 48 tests was the residual variance as small as for ?. Overall, efficiency was less than 80% for all alternatives, and less than 30% for two of them. Efficiency of alternatives did not increase when information was estimated simultaneously. The swept radius within which substantial values of ? are conserved lies between 385 and 893 kb, but deviation of parameters between measures is enormously significant. The large effort now being devoted to allelic association has little value unless the ? metric with the strongest theoretical basis and least sensitivity to marker allele frequencies is used for mapping of marker association and localization of disease loci.

Morton, N. E.; Zhang, W.; Taillon-Miller, P.; Ennis, S.; Kwok, P.-Y.; Collins, A.

2001-01-01

95

The optimal measure of allelic association.  

PubMed

Allelic association between pairs of loci is derived in terms of the association probability rho as a function of recombination theta, effective population size N, linear systematic pressure v, and time t, predicting both rho(rt), the decrease of association from founders and rho(ct), the increase by genetic drift, with rho(t) = rho(rt) + rho(ct). These results conform to the Malecot equation, with time replaced by distance on the genetic map, or on the physical map if recombination in the region is uniform. Earlier evidence suggested that rho is less sensitive to variations in marker allele frequencies than alternative metrics for which there is no probability theory. This robustness is confirmed for six alternatives in eight samples. In none of these 48 tests was the residual variance as small as for rho. Overall, efficiency was less than 80% for all alternatives, and less than 30% for two of them. Efficiency of alternatives did not increase when information was estimated simultaneously. The swept radius within which substantial values of rho are conserved lies between 385 and 893 kb, but deviation of parameters between measures is enormously significant. The large effort now being devoted to allelic association has little value unless the rho metric with the strongest theoretical basis and least sensitivity to marker allele frequencies is used for mapping of marker association and localization of disease loci. PMID:11309498

Morton, N E; Zhang, W; Taillon-Miller, P; Ennis, S; Kwok, P Y; Collins, A

2001-04-24

96

Patterns of inheritance with RAPD molecular markers reveal novel types of polymorphism in the honey bee.  

PubMed

The polymerase chain reaction (PCR) was used to generate random amplified polymorphic DNA (RAPD) from honey bee DNA samples in order to follow the patterns of inheritance of RAPD markers in a haplodiploid insect. The genomic DNA samples from two parental bees, a haploid drone and a diploid queen, were screened for polymorphism with 68 different tennucleotide primers of random sequence. Parents were scored for the presence or absence of individual bands. An average of 6.3 bands and 1.3 polymorphisms for presence/absence were observed per primer between the parents. Thirteen of these primers were used to determine the inheritance of RAPD marker alleles in the resulting progeny and in haploid drones from a daughter queen. Four types of polymorphisms were observed. Polymorphisms for band presence/absence as well as for band brightness were inherited as dominant markers, meeting Mendelian expectations in haploid and diploid progeny. Polymorphisms for fragment-length were also observed. These segregated in a near 1?1 ratio in drone progeny. The last type of polymorphism was manifested as a diploid-specific band. Mixing of amplification products after PCR showed that the diploid-specific band was the result of heteroduplex formation from the DNA of alternate alleles in heterozygotes. In two of the four cases of heteroduplex formation, the alternative alleles were manifested as small fragment-length polymorphisms, resulting in co-dominant markers. This is the first demonstration that a proportion of RAPD markers are not inherited in a dominant fashion. PMID:24197223

Hunt, G J; Page, R E

1992-10-01

97

Assignment of SNP allelic configuration in polyploids using competitive allele-specific PCR: application to citrus triploid progeny  

PubMed Central

Background Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. Scope This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Conclusions Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [? angle = tan?1 (y/x) and y? = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis.

Cuenca, Jose; Aleza, Pablo; Navarro, Luis; Ollitrault, Patrick

2013-01-01

98

Characterization of nine novel microsatellite markers from Brandt's vole (Lasiopodomys brandtii).  

PubMed

Highly polymorphic microsatellite markers are the most powerful tools to infer kinship relations. In this study, a library enriched for (AC)(n) (AG)(n) and (AGAT)(n) was constructed for screening microsatellite markers in Brandt's vole (Lasiopodomys brandtii), and nine novel polymorphic microsatellite markers were developed and characterized. The number of alleles ranged from 4 to 11 per locus and the mean polymorphism information content was 0.7535. The observed and the expected heterozygosity values averaged 0.760 (0.554-0.908) and 0.7914 (0.718-0.845), respectively. Average nonexclusion probability for one candidate parent varied from 0.485 to 0.716. These nine novel markers are highly polymorphic and powerful enough for our future kinship analysis. PMID:21564873

Yue, Ling-Fen; Wang, D A-Wei; Huang, Bao-Huan; Liu, Xiao-Hui

2009-07-01

99

Allelic association in the FRAX region.  

PubMed

The sex chromosomes enable direct determination of haplotypes, and the analysis of 8 microsatellite markers from the FRAX region on Xq27-q28 contributes 7219 independent haplotypes from our study in Wessex. Allelic association increases with frequency of alleles, and is less for trinucleotide than dinucleotide repeats. The estimate of epsilon, the exponential decline of association with distance in kb, is 0.0023. The swept radius 1/epsilon estimates the distance at which disequilibrium falls to e(-1) approximately .37 of its initial value. The current study estimates the swept radius of association to be 433 kb, which is surprisingly close to estimates for SNPs, and suggests that a marker density of 1/100 kb should be powerful in regions such as FRAX. An explanation for these results is offered, and some speculations made about what will be found when SNPs are subjected to an equally intensive study in multiple regions. PMID:11281215

Ennis, S; Collins, A; Murray, A; Macpherson, J N; Morton, N E

2000-11-01

100

Resistance gene deployment strategies in cereal hybrids using marker-assisted selection: Gene pyramiding, three-way hybrids, and synthetic parent populations  

Microsoft Academic Search

Marker-assisted selection (MAS) for resistance genes (R-genes), identified using molecular markers and quantitative trait\\u000a loci (QTL) analysis, is now possible in many crops. MAS can be used to pyramid several R-genes into a single host genotype.\\u000a However, this may not provide durable genetic resistance because the pathogen is exposed to a full homozygous pyramid during\\u000a hybrid seed production and to

J. R. Witcombe; C. T. Hash

2000-01-01

101

EST and EST-SSR marker resources for Iris  

PubMed Central

Background Limited DNA sequence and DNA marker resources have been developed for Iris (Iridaceae), a monocot genus of 200–300 species in the Asparagales, several of which are horticulturally important. We mined an I. brevicaulis-I. fulva EST database for simple sequence repeats (SSRs) and developed ortholog-specific EST-SSR markers for genetic mapping and other genotyping applications in Iris. Here, we describe the abundance and other characteristics of SSRs identified in the transcript assembly (EST database) and the cross-species utility and polymorphisms of I. brevicaulis-I. fulva EST-SSR markers among wild collected ecotypes and horticulturally important cultivars. Results Collectively, 6,530 ESTs were produced from normalized leaf and root cDNA libraries of I. brevicaulis (IB72) and I. fulva (IF174), and assembled into 4,917 unigenes (1,066 contigs and 3,851 singletons). We identified 1,447 SSRs in 1,162 unigenes and developed 526 EST-SSR markers, each tracing a different unigene. Three-fourths of the EST-SSR markers (399/526) amplified alleles from IB72 and IF174 and 84% (335/399) were polymorphic between IB25 and IF174, the parents of I. brevicaulis × I. fulva mapping populations. Forty EST-SSR markers were screened for polymorphisms among 39 ecotypes or cultivars of seven species – 100% amplified alleles from wild collected ecotypes of Louisiana Iris (I.brevicaulis, I.fulva, I. nelsonii, and I. hexagona), whereas 42–52% amplified alleles from cultivars of three horticulturally important species (I. pseudacorus, I. germanica, and I. sibirica). Ecotypes and cultivars were genetically diverse – the number of alleles/locus ranged from two to 18 and mean heterozygosity was 0.76. Conclusion Nearly 400 ortholog-specific EST-SSR markers were developed for comparative genetic mapping and other genotyping applications in Iris, were highly polymorphic among ecotypes and cultivars, and have broad utility for genotyping applications within the genus.

Tang, Shunxue; Okashah, Rebecca A; Cordonnier-Pratt, Marie-Michele; Pratt, Lee H; Ed Johnson, Virgil; Taylor, Christopher A; Arnold, Michael L; Knapp, Steven J

2009-01-01

102

A genetic linkage map for hazelnut (Corylus avellana L.) based on RAPD and SSR markers.  

PubMed

A linkage map for European hazelnut (Corylus avellana L.) was constructed using random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers and the 2-way pseudotestcross approach. A full-sib population of 144 seedlings from the cross OSU 252.146 x OSU 414.062 was used. RAPD markers in testcross configuration, segregating 1:1, were used to construct separate maps for each parent. Fifty additional RAPD loci were assigned to linkage groups as accessory markers whose exact location could not be determined. Markers in intercross configuration, segregating 3:1, were used to pair groups in one parent with their homologues in the other. Eleven groups were identified for each parent, corresponding to the haploid chromosome number of hazelnut (n = x = 11). Thirty of the 31 SSR loci were able to be assigned to a linkage group. The maternal map included 249 RAPD and 20 SSR markers and spanned a distance of 661 cM. The paternal map included 271 RAPD and 28 SSR markers and spanned a distance of 812 cM. The maps are quite dense, with an average of 2.6 cM between adjacent markers. The S-locus, which controls pollen-stigma incompatibility, was placed on chromosome 5S where 6 markers linked within a distance of 10 cM were identified. A locus for resistance to eastern filbert blight, caused by Anisogramma anomala, was placed on chromosome 6R for which two additional markers tightly linked to the dominant allele were identified and sequenced. These maps will serve as a starting point for future studies of the hazelnut genome, including map-based cloning of important genes. The inclusion of SSR loci on the map will make it useful in other populations. PMID:16498462

Mehlenbacher, Shawn A; Brown, Rebecca N; Nouhra, Eduardo R; Gökirmak, Tufan; Bassil, Nahla V; Kubisiak, Thomas L

2006-02-01

103

The Maintenance of Single-Locus Polymorphism. IV. Models with Mutation from Existing Alleles  

PubMed Central

The ability of viability selection to maintain allelic polymorphism is investigated using a constructionist approach. In extensions to the models we have previously proposed, a population is bombarded with a series of mutations whose fitnesses in conjunction with other alleles are functions of the corresponding fitnesses with a particular allele, the parent allele, already in the population. Allele frequencies are iterated simultaneously, thus allowing alleles to be driven to extinction by selection. Such models allow very high levels of polymorphism to evolve: up to 38 alleles in one case. Alleles that are lethal as homozygotes can evolve to surprisingly high frequencies. The joint evolution of allele frequencies and viabilities highlights the necessity to consider more than the current morphology of a population. Comparisons are made with the neutral theory of evolution and it is suggested that failure to reject neutrality using the Ewens-Watterson test cannot be regarded as evidence for the neutral theory.

Spencer, H. G.; Marks, R. W.

1992-01-01

104

Quality characteristics and field performance of selectable marker-free transgenic rice with antisense Wx gene and improved quality derived from the elite parents of hybrid indica rice  

Microsoft Academic Search

In rice grains, high amylose content (AC) is correlated with poor grain quality, particularly in indica hybrid rice. To obtain indica hybrid rice with improved cooking and eating qualities, we introduced the antisense Waxy (Wx) gene into 2 elite parental lines of indica hybrid rice by using co-transformation methods. Subsequently, we selected several elite homozygous transgenic lines that did not

Heng-Xiu Yu; Qiao-Quan Liu; Li Xu; Mei-Fang Lu; Xiao-Jun Yang; Zhi-Yun Gong; Xiu-Lin Cai; Yuan-San Zhang; Chang-Quan Zhang; Zong-Yang Wang; Ming-Hong Gu

2009-01-01

105

No evidence for allelic association between bipolar disorder and monoamine oxidase A gene polymorphisms.  

PubMed

We have tested the hypothesis that DNA markers in the MAOA gene show allelic association with bipolar affective disorder. Eighty-four unrelated Caucasian patients with DSM III-R bipolar disorder and 84 Caucasian controls were typed for three markers in MAOA: a dinucleotide repeat in intron 2, a VNTR in intron 1, and an Fnu4HI RFLP in exon 8. No evidence for allelic association was observed between any of the markers and bipolar disorder. PMID:7485269

Craddock, N; Daniels, J; Roberts, E; Rees, M; McGuffin, P; Owen, M J

1995-08-14

106

No evidence for allelic association between bipolar disorder and monoamine oxidase A gene polymorphisms  

SciTech Connect

We have tested the hypothesis that DNA markers in the MAOA gene show allelic association with bipolar affective disorder. Eighty-four unrelated Caucasian patients with DSM III-R bipolar disorder and 84 Caucasian controls were typed for three markers in MAOA: a dinucleotide repeat in intron 2, a VNTR in intron 1, and an Fnu4HI RFLP in exon 8. No evidence for allelic association was observed between any of the markers and bipolar disorder. 9 refs., 1 tab.

Craddock, N.; Daniels, J.; Roberts, E. [Univ. of Wales, College of Medicine, Cardiff (United Kingdom)] [and others

1995-08-14

107

Sexual and parental antagonism shape genomic architecture.  

PubMed

Populations with two sexes are vulnerable to a pair of genetic conflicts: sexual antagonism that can arise when alleles have opposing fitness effects on females and males; and parental antagonism that arises when alleles have opposing fitness effects when maternally and paternally inherited. This paper extends previous theoretical work that found stable linkage disequilibrium (LD) between sexually antagonistic loci. We find that LD is also generated between parentally antagonistic loci, and between sexually and parentally antagonistic loci, without any requirement of epistasis. We contend that the LD in these models arises from the admixture of gene pools subject to different selective histories. We also find that polymorphism maintained by parental antagonism at one locus expands the opportunity for polymorphism at a linked locus experiencing parental or sexual antagonism. Taken together, our results predict the chromosomal clustering of loci that segregate for sexually and parentally antagonistic alleles. Thus, genetic conflict may play a role in the evolution of genomic architecture. PMID:24026821

Patten, Manus M; Ubeda, Francisco; Haig, David

2013-11-01

108

Evidence for linkage of bipolar disorder to chromosome 18 with a parent-of-origin effect  

SciTech Connect

A susceptibility gene on chromosome18 and a parent-of-origin effect have been suggested for bipolar affective disorder (BPAD). We have studied 28 nuclear families selected for apparent unilineal transmission of the BPAD phenotype, by using 31 polymorphic markers spanning chromosome 18. Evidence for linkage was tested with affected-sib-pair and LOD score methods under two definitions of the affected phenotype. The affected-sib-pair analyses indicated excess allele sharing for markers on 18p within the region reported previously. The greatest sharing was at D18S37: 64% in bipolar and recurrent unipolar (RUP) sib pairs (P = .0006). In addition, excess sharing of the paternally, but not maternally, transmitted alleles was observed at three markers on 18q: at D18S41, 51 bipolar and RUP sib pairs were concordant for paternally transmitted alleles, and 21 pairs were discordant (P = .0004). The evidence for linkage to loci on both 18p and 18q was strongest in the 11 paternal pedigrees, i.e., those in which the father or one of the father`s sibs is affected. In these pedigrees, the greatest allele sharing (81%; P = .00002) and the highest LOD score (3.51; {theta} = 0.0) were observed at D18S41. Our results provide further support for linkage of BPAD to chromosome 18 and the first molecular evidence for a parent-of-origin effect operating in this disorder. The number of loci involved, and their precise location, require further study. 49 refs., 2 figs., 5 tabs.

Stine, O.C.; Xu, Jianfeng; McMahon, F.J. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)] [and others

1995-12-01

109

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis  

PubMed Central

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene’s expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.

West, Marilyn A.L.; van Leeuwen, Hans; Kozik, Alexander; Kliebenstein, Daniel J.; Doerge, R.W.; St. Clair, Dina A.; Michelmore, Richard W.

2006-01-01

110

SNP marker diversity in common bean (Phaseolus vulgaris L.).  

PubMed

Single nucleotide polymorphism (SNP) markers have become a genetic technology of choice because of their automation and high precision of allele calls. In this study, our goal was to develop 94 SNPs and test them across well-chosen common bean (Phaseolus vulgaris L.) germplasm. We validated and accessed SNP diversity at 84 gene-based and 10 non-genic loci using KASPar technology in a panel of 70 genotypes that have been used as parents of mapping populations and have been previously evaluated for SSRs. SNPs exhibited high levels of genetic diversity, an excess of middle frequency polymorphism, and a within-genepool mismatch distribution as expected for populations affected by sudden demographic expansions after domestication bottlenecks. This set of markers was useful for distinguishing Andean and Mesoamerican genotypes but less useful for distinguishing within each gene pool. In summary, slightly greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool but polymorphism rate between genotypes was consistent with genepool and race identity. Our survey results represent a baseline for the choice of SNP markers for future applications because gene-associated SNPs could themselves be causative SNPs for traits. Finally, we discuss that the ideal genetic marker combination with which to carry out diversity, mapping and association studies in common bean should consider a mix of both SNP and SSR markers. PMID:21785951

Cortés, Andrés J; Chavarro, Martha C; Blair, Matthew W

2011-09-01

111

Assessment of Parent-of-Origin Effects in Linkage Analysis of Quantitative Traits  

PubMed Central

Methods are presented for incorporation of parent-of-origin effects into linkage analysis of quantitative traits. The estimated proportion of marker alleles shared identical by descent is first partitioned into a component derived from the mother and a component derived from the father. These parent-specific estimates of allele sharing are used in variance-components or Haseman-Elston methods of linkage analysis so that the effect of the quantitative-trait locus carried on the maternally derived chromosome is potentially different from the effect of the locus on the paternally derived chromosome. Statistics for linkage between trait and marker loci derived from either or both parents are then calculated, as are statistics for testing whether the effect of the maternally derived locus is equal to that of the paternally derived locus. Analyses of data simulated for 956 siblings from 263 nuclear families who had participated in a linkage study revealed that type I error rates for these statistics were generally similar to nominal values. Power to detect an imprinted locus was substantially increased when analyzed with a model allowing for parent-of-origin effects, compared with analyses that assumed equal effects; for example, for an imprinted locus accounting for 30% of the phenotypic variance, the expected LOD score was 4.5 when parent-of-origin effects were incorporated into the analysis, compared with 3.1 when these effects were ignored. The ability to include parent-of-origin effects within linkage analysis of quantitative traits will facilitate genetic dissection of complex traits.

Hanson, Robert L.; Kobes, Sayuko; Lindsay, Robert S.; Knowler, William C.

2001-01-01

112

Prediction of liability to orofacial clefting using genetic and craniofacial data from parents.  

PubMed Central

BACKGROUND: Cleft lip with or without cleft palate (CL(P)) and isolated cleft palate (CP) are separate clinical entities and for both polygenic multifactorial aetiology has been proposed. Parents of children with orofacial clefting have been shown to have distinctive differences in their facial shape when compared to matched controls. OBJECTIVE: To test the hypothesis that genetic and morphometric factors predispose to orofacial clefting and that these markers differ for CL(P) and CP. Methods-Polymorphisms at the transforming growth factor alpha (TGFalpha) locus in 83 parents of children with nonsyndromic orofacial clefts were analysed, and their craniofacial morphology was assessed using lateral cephalometry. RESULTS: Parents of children with CL(P) and CP showed an increased frequency of the TGFalpha/TaqI C2 allele (RR=4.10, p=0.009) relative to the comparison group. Also the TGFalpha/BamHI A1 allele was more prevalent in the CP parents. MULTIVARIATE STATISTICAL ANALYSIS: Using stepwise logistic regression analysis the TGFalpha/TaqI C2 polymorphism provides the best model for liability to orofacial clefting. To determine the type of clefting a model involving interaction between the parental TGFalpha/BamHI and TGFalpha/RsaI genotypes showed the best fit. Using genotype only to predict the clefting defect in the children according to parental genotype, 68.3% could be correctly classified. By adding information on craniofacial measurements in the parents, 76% of CP and 94% of CL(P) parents could be correctly classified. CONCLUSIONS: This study provides a model for prediction of liability to orofacial clefting. These findings suggest that different molecular aberrations at the TGFalpha locus may modify the risk for CP and CL(P). Images

Mossey, P A; Arngrimsson, R; McColl, J; Vintiner, G M; Connor, J M

1998-01-01

113

Parent-of-origin dependent gene-specific knock down in mouse embryos  

SciTech Connect

In mice hemizygous for the Oct4-GFP transgene, the F1 embryos show parent-of-origin dependent expression of the marker gene. F1 embryos with a maternally derived OG2 allele (OG2{sup mat}/-) express GFP in the oocyte and during preimplantation development until the blastocyst stage indicating a maternal and embryonic expression pattern. F1-embryos with a paternally inherited OG2 allele (OG2{sup pat}/-) express GFP from the 4- to 8-cell stage onwards showing only embryonic expression. This allows to study allele specific knock down of GFP expression. RNA interference (RNAi) was highly efficient in embryos with the paternally inherited GFP allele, whereas embryos with the maternally inherited GFP allele showed a delayed and less stringent suppression, indicating that the initial levels of the target transcript and the half life of the protein affect RNAi efficacy. RT-PCR analysis revealed only minimum of GFP mRNA. These results have implications for studies of gene silencing in mammalian embryos.

Iqbal, Khursheed [Department of Biotechnology, Institute for Animal Breeding, Mariensee, 31535 Neustadt (Germany); Kues, Wilfried A. [Department of Biotechnology, Institute for Animal Breeding, Mariensee, 31535 Neustadt (Germany); Niemann, Heiner [Department of Biotechnology, Institute for Animal Breeding, Mariensee, 31535 Neustadt (Germany)]. E-mail: niemann@tzv.fal.de

2007-07-06

114

Trans allele methylation and paramutation-like effects in mice  

PubMed Central

In mammals, imprinted genes have parent-of-origin–specific patterns of DNA methylation that cause allele-specific expression. At Rasgrf1 (encoding RAS protein-specific guanine nucleotide-releasing factor 1), a repeated DNA element is needed to establish methylation and expression of the active paternal allele1. At Igf2r (encoding insulin-like growth factor 2 receptor), a sequence called region 2 is needed for methylation of the active maternal allele2,3. Here we show that replacing the Rasgrf1 repeats on the paternal allele with region 2 allows both methylation and expression of the paternal copy of Rasgrf1, indicating that sequences that control methylation can function ectopically. Paternal transmission of the mutated allele also induced methylation and expression in trans of the normally unmethylated and silent wild-type maternal allele. Once activated, the wild-type maternal Rasgrf1 allele maintained its activated state in the next generation independently of the paternal allele. These results recapitulate in mice several features in common with paramutation described in plants4.

Herman, Herry; Lu, Michael; Anggraini, Melly; Sikora, Aimee; Chang, Yanjie; Yoon, Bong June; Soloway, Paul D

2009-01-01

115

RNA-Seq Identifies SNP Markers for Growth Traits in Rainbow Trout  

PubMed Central

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of heterozygosity. A subset of SNPs (n?=?54) were validated and evaluated for association with growth traits in 778 individuals of a three-generation parent/offspring panel representing 40 families. Twenty-two SNP markers and one mitochondrial haplotype were significantly associated with growth traits. Polymorphism of 48 of the markers was confirmed in other commercially important aquaculture stocks. Many markers were clustered into genes of metabolic energy production pathways and are suitable candidates for genetic selection. The study demonstrates that RNA-Seq at low sequence coverage of divergent populations is a fast and effective means of identifying SNPs, with allelic imbalances between phenotypes. This technique is suitable for marker development in non-model species lacking complete and well-annotated genome reference sequences.

Salem, Mohamed; Vallejo, Roger L.; Leeds, Timothy D.; Palti, Yniv; Liu, Sixin; Sabbagh, Annas; Rexroad, Caird E.; Yao, Jianbo

2012-01-01

116

Parent University.  

ERIC Educational Resources Information Center

A description of the Parent University program of the San Rafael (California) City Schools is presented. The Parent University is described as a 1-day event in which parents are offered a variety of seminars and workshops on topics in education and parenting. Materials included in this document are: (1) an overview of the second annual Parent

Howlett, Hoyt S.

117

Cystic fibrosis allele frequency, sex ratio anomalies and fertility: a new theory for the dissemination of mutant alleles  

Microsoft Academic Search

The observation that mothers of cystic fibrosis patients come from sibships that are larger than those of the fathers is explained by a decrease in sex ratio with increasing size of parental sibships. This feature also provides the basis for a new theory for the dissemination of the major mutant allele, deduced to have arisen 2700–5000 years ago, in accordance

Dorian J. Pritchard

1991-01-01

118

Prognostic Value of Allelic Imbalance in Prostate Biopsy.  

National Technical Information Service (NTIS)

Purpose: The novel Concept that is being tested in this project is that allelic imbalance (Al) in tissue obtained at prostate biopsy can serve as a sensitive and independent marker for staging and predicting disease recurrence in prostate cancer. Scope: T...

J. K. Griffith

2006-01-01

119

Prognostic Value of Allelic Imbalance in Prostate Biopsy.  

National Technical Information Service (NTIS)

The novel concept that is being tested in this project is that allelic imbalance (AI) in tissue obtained at prostate biopsy can serve as a sensitive and independent marker for staging and predicting disease recurrence in prostate cancer. The two aims of t...

J. K. Griffith

2005-01-01

120

Homoeologous GSL-ELONG gene replacement for manipulation of aliphatic glucosinolates in Brassica rapa L. by marker assisted selection  

PubMed Central

Aliphatic glucosinolates are the predominant sulfur-rich plant secondary metabolites in economically important Brassica crops. Glucosinolates and their hydrolysis products are involved in plant–microbe, plant–insect, plant–animal, and plant–human interactions. It is, therefore, important to manipulate glucosinolate profiles and contents in Brassica species. In this study, aliphatic glucosinolates were genetically manipulated through homoeologous recombination in backcross lines followed by marker assisted selection in B. rapa. A resynthesized B. napus line, from a cross between B. rapa and B. oleracea, was backcrossed with Chinese cabbage doubled haploid line, RI16. Marker assisted selection for non-functional gene was performed in each backcross generations. Advanced backcross progenies (BC3F2) were developed to identify homoeologous gene replacement and/or introgression. Reduction in 5C aliphatic glucosinolates (gluconapoleiferin, glucoalyssin, and glucobrassicanapin) was observed in BC3F2 progenies of the recurrent parent that carried the GSL-ELONG- gene. The GSL-ELONG- positive backcross progenies were also screened by the A-genome and BraGSL-ELONG gene specific marker, which linked with 5C aliphatic glucosinolates. The A-genome specific marker was absent in the plants of advanced backcross progenies which showed reduction in 5C aliphatic glucosinolates. The results suggest that the functional allele had been replaced by the non-functional GSL-ELONG- allele from B. oleracea. Some advanced backcross progenies (BC3F2) positive for the GSL-ELONG- allele and the A-genome specific SCAR marker BraMAM1-1 did not show reduction in 5C aliphatic glucosinolates, suggesting that GSL-ELONG- allele is recessive. Replacement of the functional locus in the A-genome by non-functional counterpart in the C-genome reduced the content of 5C aliphatic glucosinolates in B. rapa seeds with 20 ?mol/g.

Hirani, Arvind H.; Zelmer, Carla D.; McVetty, Peter B. E.; Daayf, Fouad; Li, Genyi

2013-01-01

121

DNA profiling of pineapple cultivars in Japan discriminated by SSR markers  

PubMed Central

We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of ‘N67-10’ and ‘Hawaiian Smooth Cayenne’. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders’ rights.

Shoda, Moriyuki; Urasaki, Naoya; Sakiyama, Sumisu; Terakami, Shingo; Hosaka, Fumiko; Shigeta, Narumi; Nishitani, Chikako; Yamamoto, Toshiya

2012-01-01

122

Parent Soup  

NSDL National Science Digital Library

Parent Soup is an online community for parents. It dubs itself the "neighborhood's favorite kitchen table" where parents can exchange views in discussion groups or talk with one another in the chat room. The concept of a virtual community can be seen in the Parents' Pick area where parents share their opinions on books, baby products, toys, computers, web sites and movies. Parent Soup members can find other Parent Soupers who share their interests, hobbies and concerns through personal profiles posted on "cyberfridges." The site also features a parenting library with information in sixteen major topics and a Baby Name Finder with information on more than 5,000 names.

123

Fluorescent-labeled microsatellite panels useful for detecting allelic diversity in cultivated rice ( Oryza sativa L.)  

Microsoft Academic Search

Four multiplex panels of fluorescent-labeled rice microsatellite markers were designed to survey allelic diversity at a total of 27 simple sequence repeat loci. Automated fragment detection, size calling and binning were used to identify the microsatellite alleles. The panels were tested on 72 accessions representing the diversity of ecotypes and isozyme groups in cultivated rice (Oryza sativa L.). Genetic diversity

Matthew W. Blair; Veena Hedetale; Susan R. McCouch

2002-01-01

124

Linkage mapping in apomictic and sexual Kentucky bluegrass ( Poa pratensis L.) genotypes using a two way pseudo-testcross strategy based on AFLP and SAMPL markers.  

PubMed

The high versatility of the mode of reproduction and the retention of a pollen recognition system are the factors responsible for the extreme complexity of the genome in Poa pratensis L. Two genetic maps, one of an apomictic and one of a sexual genotype, were constructed using a two-way pseudo-testcross strategy and multiplex PCR-based molecular markers (AFLP and SAMPL). Due to the high ploidy level and the uncertainty of chromosome pairing-behavior at meiosis, only parent-specific single-dose markers (SDMs) that segregated 1:1 in an F(1) mapping population (161 out of 299 SAMPLs, and 70 out of 275 AFLPs) were used for linkage analysis. A total of 41 paternal (33 SAMPLs and 8 AFLPs) and 47 maternal (33 SAMPLs and 14 AFLPs) SDMs, tested to be linked in coupling phase, were mapped to 7+7 linkage groups covering 367 and 338.4 cM, respectively. The comparison between the two marker systems revealed that SAMPL markers were statistically more efficient than AFLP ones in detecting parent-specific SDMs (75% vs 32.4%). There were no significant differences in the percentages of distorted marker alleles detected by the two marker systems (27.8% of SAMPLs vs 21.3% of AFLPs). The pairwise comparison of co-segregational groups for linkage detection between marker loci suggested that at least some of the P. pratensis chromosomes pair preferentially at meiosis-I. PMID:12582697

Porceddu, A.; Albertini, E.; Barcaccia, G.; Falistocco, E.; Falcinelli, M.

2002-02-01

125

Undetected Genotyping Errors Cause Apparent Overtransmission of Common Alleles in the Transmission/Disequilibrium Test  

PubMed Central

The transmission/disequilibrium test (TDT), a family-based test of linkage and association, is a popular and intuitive statistical test for studies of complex inheritance, as it is nonparametric and robust to population stratification. We carried out a literature search and located 79 significant TDT-derived associations between a microsatellite marker allele and a disease. Among these, there were 31 (39%) in which the most common allele was found to exhibit distorted transmission to affected offspring, implying that the allele may be associated with either susceptibility to or protection from a disease. In 27 of these 31 studies (87%), the most common allele appeared to be overtransmitted to affected offspring (a risk factor), and, in the remaining 4 studies, the most common allele appeared to be undertransmitted (a protective factor). In a second literature search, we identified 92 case-control studies in which a microsatellite marker allele was found to have significantly different frequencies in case and control groups. Of these, there were 37 instances (40%) in which the most common allele was involved. In 12 of these 37 studies (32%), the most common allele was enriched in cases relative to controls (a risk factor), and, in the remaining 25 studies, the most common allele was enriched in controls (a protective factor). Thus, the most common allele appears to be a risk factor when identified through the TDT, and it appears to be protective when identified through case-control analysis. To understand this phenomenon, we incorporated an error model into the calculation of the TDT statistic. We show that undetected genotyping error can cause apparent transmission distortion at markers with alleles of unequal frequency. We demonstrate that this distortion is in the direction of overtransmission for common alleles. Therefore, we conclude that undetected genotyping errors may be contributing to an inflated false-positive rate among reported TDT-derived associations and that genotyping fidelity must be increased.

Mitchell, Adele A.; Cutler, David J.; Chakravarti, Aravinda

2003-01-01

126

An evaluation of sequence tagged microsatellite site markers for genetic analysis within Citrus and related species.  

PubMed

Microsatellites, also called sequence tagged microsatellite sites (STMSs), have become important markers for genome analysis but are currently little studied in plants. To assess the value of STMSs for analysis within the Citrus plant species, two example STMSs were isolated from an intergeneric cross between rangpur lime (Citrus x limonia Osbeck) and trifoliate orange (Poncirus trifoliata (L.) Raf.). Unique flanking primers were constructed for polymerase chain reaction amplification both within the test cross and across a broad range of citrus and related species. Both loci showed length variation between test cross parents with alleles segregating in a Mendelian fashion to progeny. Amplification across species showed the STMS flanking primers to be conserved in every genome tested. The traits of polymorphism, inheritance, and conservation across species mean that STMS markers are ideal for genome mapping within Citrus, which contains high levels of genetic variability. PMID:7774802

Kijas, J M; Fowler, J C; Thomas, M R

1995-04-01

127

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping  

PubMed Central

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5? untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication.

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S.; Tripathi, Shailesh; Upadhyaya, Hari D.; Gowda, C.L.L.; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K.; Parida, Swarup K.

2013-01-01

128

Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping.  

PubMed

We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5' untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication. PMID:23633531

Kujur, Alice; Bajaj, Deepak; Saxena, Maneesha S; Tripathi, Shailesh; Upadhyaya, Hari D; Gowda, C L L; Singh, Sube; Jain, Mukesh; Tyagi, Akhilesh K; Parida, Swarup K

2013-08-01

129

Sequence determination of an allelic ladder for the STR polymorphism at the CD4 locus and application of the ladder in testing an Austrian Caucasian population sample  

Microsoft Academic Search

The short tandem repeat (STR) polymorphism at the CD4 locus, designated HUMCD4. was examined by PCR, native polyacrylamide electrophoresis and subsequent silver staining using an allelic ladder of eight distinguishable alleles occurring in an Austrian Caucasian population sample as a standard size marker. The ladder was produced by pooling equal concentrations of eluted, separately amplified and sequenced alleles, which were

Barbara Glock; Dieter W. M. Schwartz; Elisabeth M. Schwartz-Jungl; Wolfgang R. Mayr

1996-01-01

130

Parenting Multiples  

MedlinePLUS

... to take care of your babies. Back Continue Parenting Issues With Multiples It can be impossible to ... on it's apparent that their relationship is special. Parenting multiples has its challenges, but the rewards are ...

131

Teen Parents  

MedlinePLUS

... Teen > Dating & Sex > Teen Parents Ages & Stages Listen Teen Parents Article Body A girl who has decided ... prenatal vitamins and iron is so important. Preparing Teens For Parenthood Fears about the future are common ...

132

Molecular mapping of stripe rust resistance gene YrCH42 in Chinese wheat cultivar Chuanmai 42 and its allelism with Yr24 and Yr26.  

PubMed

Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is one of the most devastating diseases in common wheat (Triticum aestivum L.) worldwide. The objectives of this study were to map a stripe rust resistance gene in Chinese wheat cultivar Chuanmai 42 using molecular markers and to investigate its allelism with Yr24 and Yr26. A total of 787 F2 plants and 186 F3 lines derived from a cross between resistant cultivar Chuanmai 42 and susceptible line Taichung 29 were used for resistance gene tagging. Also 197 F2 plants from the cross Chuanmai 42xYr24/3*Avocet S and 726 F2 plants from Chuanmai 42xYr26/3*Avocet S were employed for allelic test of the resistance genes. In all, 819 pairs of wheat SSR primers were used to test the two parents, as well as resistant and susceptible bulks. Subsequently, nine polymorphic markers were employed for genotyping the F2 and F3 populations. Results indicated that the stripe rust resistance in Chuanmai 42 was conferred by a single dominant gene, temporarily designated YrCH42, located close to the centromere of chromosome 1B and flanked by nine SSR markers Xwmc626, Xgwm273, Xgwm11, Xgwm18, Xbarc137, Xbarc187, Xgwm498, Xbarc240 and Xwmc216. The resistance gene was closely linked to Xgwm498 and Xbarc187 with genetic distances of 1.6 and 2.3 cM, respectively. The seedling tests with 26 PST isolates and allelic tests indicated that YrCH42, Yr24 and Yr26 are likely to be the same gene. PMID:16525837

Li, G Q; Li, Z F; Yang, W Y; Zhang, Y; He, Z H; Xu, S C; Singh, R P; Qu, Y Y; Xia, X C

2006-05-01

133

Parenting Matters  

ERIC Educational Resources Information Center

Parenting is a subject about which people typically hold strong opinions, but about which too little solid information or considered reflection exists. And clearly critical questions about parenting abound. Moreover, the family generally, and parenting specifically, are today in a greater state of flux, question, and re-definition than perhaps…

Bornstein, Marc H.

2005-01-01

134

Valuing Parents.  

ERIC Educational Resources Information Center

This theme issue on the role of parents in the education of their gifted children contains two feature articles. "'Pushy and Domineering': A Stigma Placed on Parents of Gifted Children," by Lynn C. Cole and Roxana M. DellaVecchia, examines how parents are perceived as "pushy and domineering" when they strongly advocate for appropriate education…

Silverman, Linda Kreger, Ed.

1993-01-01

135

Conditional Allele Mouse Planner (CAMP): software to facilitate the planning and design of breeding strategies involving mice with conditional alleles  

Microsoft Academic Search

Transgenic and conditional knockout mouse models play an important role in biomedical research and their use has grown exponentially\\u000a in the last 5–10 years. Generating conditional knockouts often requires breeding multiple alleles onto the background of a\\u000a single mouse or group of mice. Breeding these mice depends on parental genotype, litter size, transmission frequency, and\\u000a the number of breeding rounds. Therefore,

Jason D. Hoffert; Trairak Pisitkun; R. Lance Miller

136

Allelic imbalance and biochemical outcome after radical prostatectomy  

Microsoft Academic Search

Objective:To compare the incidence of allelic imbalance (AI) in men with rapid disease progression with those who remained disease free after radical prostatectomy, with the aim of identifying genetic markers to predict prognosis and guide further treatment.Patients and methods:Tumour and normal DNA were extracted from two matched groups of 31 men with extracapsular node-negative (pT3N0) prostate cancer who had undergone

S R J Bott; J R W Masters; M C Parkinson; R S Kirby; M Feneley; J Hooper; M Williamson; SRJ Bott

2006-01-01

137

Human leptin locus (LEP) alleles and BMI in Samoans  

Microsoft Academic Search

Objectives: Because of their location in known candidate gene regions for obesity the associations between six microsatellite markers (D2S2170, D2S144, D2S1268, D2S1788, D2S1348 and a tetranucleotide repeat in the 3? UTR of the LEP locus) and body mass index (BMI) were studied in adult Samoans.Design: The study was designed to detect differences in the proportion of alleles at the six

ST McGarvey; W Forrest; G Sun; D Smelser; J Tufa; S Viali; R Deka

2002-01-01

138

Correlation between the individual heterozygosity of parents and their offspring  

Microsoft Academic Search

Specific formulations are derived for the correlation between the heterozygosity of a randomly mating parent and its offspring for a diallelic locus, and for the correlation when multiple loci are considered. The expected correlation is maximal, approaching r=0.50, when allelic frequencies are highly asymmetric, and it is zero when the allelic frequencies are equal to 0.50. Parent-offspring correlations, up to

J. B. Mitton; W S F Schuster; E G Cothran; J C De Fries

1993-01-01

139

Allele-Dependent Barley Grain ?-Amylase Activity1  

PubMed Central

The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high ?-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and ?-amy1 gene characterization to demonstrate that the high ?-amylase trait in the backcross line is co-inherited with the ?-amy1 gene from the H. spontaneum parent. We have analyzed the ?-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct ?-amy1 alleles. Two of these ?-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain ?-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated ?-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of ?-amylase activity in barley grain is proposed.

Erkkila, Maria J.; Leah, Robert; Ahokas, Hannu; Cameron-Mills, Verena

1998-01-01

140

Balancer-Cre transgenic mouse germ cells direct the incomplete resolution of a tri-loxP-targeted Cyp1a1 allele, producing a conditional knockout allele.  

PubMed

To generate conditional alleles, genes are commonly engineered to contain recognition sites for bacteriophage recombinases, such as Cre recombinase. When such motifs (lox sites) flank essential gene sequences, and provided that Cre recombinase is expressed, Cre recombinase will excise the flanked sequence-creating a conditional knockout allele. Targeted conditional alleles contain a minimum of three lox sites. It would be desirable to have Cre recombinase perform partial resolution (i.e., recombination some of the time between only the two lox sites flanking the marker gene). Here we report use of the commercially available Balancer2-Cre transgenic mouse line to carry out this function from a tri-loxP-site-containing cytochrome p450 1A1 (Cyp1a1) targeted allele. Such incomplete resolution of this complex locus occurred progressively with age in germ cells of male mice; the conditional Cyp1a1 gene was recovered in offspring from mice containing the targeted Cyp1a1 allele and the Cre recombinase transgene. Removal of the marker gene resulted in a conditional Cyp1a1 allele whose expression was indistinguishable from that of the wild-type allele. PMID:14637164

Uno, Shigeyuki; Wang, Bin; Shertzer, Howard G; Nebert, Daniel W; Dalton, Timothy P

2003-12-12

141

CAPs markers to assist selection for low vicine and convicine contents in faba bean (Vicia faba L.).  

PubMed

The antinutritional factors (ANFs) present in Vicia spp. seeds are a major constraint to the wider utilization of these crops as grain legumes. In the case of faba bean (Vicia faba L.), a breeding priority is the absence vicine and convicine (v-c); responsible for favism in humans and for the reduced animal performance or low egg production in laying hens. The discovery of a spontaneous mutant allele named vc-, which induces a 10-20 fold reduction of v-c contents, may facilitate the process. However, the high cost and difficulty of the chemical detection of v-c seriously restricts the advances in breeding-selection. To identify random amplified polymorphic DNA (RAPD) markers linked to this gene, we have analysed an F(2 )population derived from a cross between a line with high v-c content (Vf6) and the vc- genotype (line 1268). Quantification of v-c was done by spectrophotometry on the parents and the F(2 )population (n = 136). By using bulked segregant analysis (BSA), two RAPD markers linked in coupling and repulsion phase to the allele vc- were identified and further converted into sequence characterized amplified regions (SCARs). Amplification of SCARS was more consistent, although the initial polymorphism between pools was lost. To recover the polymorphisms several approaches were explored. Restriction digestion with HhaI (for SCAR SCH01(620)) and RsaI (for SCAR SCAB12(850)) revealed clear differences between the parental lines. The simultaneous use of the two cleavage amplified polymorphism (CAP) markers will allow the correct fingerprinting of faba bean plants and can be efficiently used in breeding selection to track the introgression of the vc- allele to develop cultivars with low v-c content and improved nutritional value. PMID:17013617

Gutierrez, N; Avila, C M; Duc, G; Marget, P; Suso, M J; Moreno, M T; Torres, A M

2006-12-01

142

Two mutated HEXA alleles in a Druze patient with late-infantile Tay-Sachs disease.  

PubMed

Two affected HEXA alleles were found in an Israeli Druze Tay-Sachs child born to first-cousin parents. His paternal allele contained two adjacent changes in exon 5: delta496C, which resulted in a frameshift and premature termination codon 96 nucleotides downstream, and 498C-->G, a silent mutation. The maternal allele had a 835T-->C transition in exon 8 (S279P). Phosphoimaging quantitation of the parents' RNAs showed that the steady-state levels of mRNAs of the mutant exons 5 and 8 were 5% and 50%, respectively, of normal levels. The exon 5 mutated allele with the premature translation termination resulted in severe deficiency of Hex A. Transient expression of the exon 8 mutated alpha-chain cDNA in COS-1 cells resulted in deficiency of enzymatic activity. The child exhibited a late-infantile-type disease. PMID:9401008

Drucker, L; Hemli, J A; Navon, R

1997-01-01

143

Genetic diversity and relatedness of sweet cherry (prunus avium L.) cultivars based on single nucleotide polymorphic markers.  

PubMed

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3' untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3' UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, "Stella" was separated from "Compact Stella." This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3' UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry. PMID:22737155

Fernandez I Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font I Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

144

Genetic Diversity and Relatedness of Sweet Cherry (Prunus Avium L.) Cultivars Based on Single Nucleotide Polymorphic Markers  

PubMed Central

Most previous studies on genetic fingerprinting and cultivar relatedness in sweet cherry were based on isoenzyme, RAPD, and simple sequence repeat (SSR) markers. This study was carried out to assess the utility of single nucleotide polymorphism (SNP) markers generated from 3? untranslated regions (UTR) for genetic fingerprinting in sweet cherry. A total of 114 sweet cherry germplasm representing advanced selections, commercial cultivars, and old cultivars imported from different parts of the world were screened with seven SSR markers developed from other Prunus species and with 40 SNPs obtained from 3? UTR sequences of Rainier and Bing sweet cherry cultivars. Both types of marker study had 99 accessions in common. The SSR data was used to validate the SNP results. Results showed that the average number of alleles per locus, mean observed heterozygosity, expected heterozygosity, and polymorphic information content values were higher in SSRs than in SNPs although both set of markers were similar in their grouping of the sweet cherry accessions as shown in the dendrogram. SNPs were able to distinguish sport mutants from their wild type germplasm. For example, “Stella” was separated from “Compact Stella.” This demonstrates the greater power of SNPs for discriminating mutants from their original parents than SSRs. In addition, SNP markers confirmed parentage and also determined relationships of the accessions in a manner consistent with their pedigree relationships. We would recommend the use of 3? UTR SNPs for genetic fingerprinting, parentage verification, gene mapping, and study of genetic diversity in sweet cherry.

Fernandez i Marti, Angel; Athanson, Blessing; Koepke, Tyson; Font i Forcada, Carolina; Dhingra, Amit; Oraguzie, Nnadozie

2012-01-01

145

[Parenting styles].  

PubMed

Parental educational styles constitute one of the key elements of family socialization. The aim of the present essay is to present the results of a research project carried out in the Principality of Asturias (Spain) among 2,965 families with children of infant and primary-school age (5-8 years old). This research attempts to analyse, among other aspects, parental behaviour tendencies in child upbringing. The analysis of the results obtained allows us to: 1) identify the most common attitudinal and behavioural tendencies of parents in the upbringing of their children; 2) determine how many people have a well defined parental style, and delimit their socio-educational characteristics. Lastly, we consider the need to change some parental behaviour patterns and stress the importance of family education programmes, with the aim of promoting appropriate parenting models and modifying or improving current practices. PMID:18206067

Torío López, Susana; Peña Calvo, José Vicente; Inda Caro, Mercedes

2008-02-01

146

Genetic diversity studies of Kherigarh cattle based on microsatellite markers  

Microsoft Academic Search

We report a genetic diversity study of Kherigarh cattle, a utility draught-purpose breed of India, currently declining at\\u000a a startling rate, by use of microsatellite markers recommended by the Food and Agriculture Organization. Microsatellite genotypes\\u000a were derived, and allelic and genotypic frequencies, heterozygosities and gene diversity were estimated. A total of 131 alleles\\u000a were distinguished by the 21 microsatellite markers

A. K. Pandey; Rekha Sharma; Yatender Singh; B. B. Prakash; S. P. S. Ahlawat

2006-01-01

147

Evidence for a genetic association between alleles of monoamine oxidase A gene and bipolar affective disorder  

SciTech Connect

We present evidence of a genetic association between bipolar disorder and alleles at 3 monoamine oxidase A (MAOA) markers, but not with alleles of a monoamine oxidase B (MAOB) polymorphism. The 3 MAOA markers, including one associated with low MAOA activity, show strong allelic association with each other but surprisingly not with MAOB. Our results are significantly only for females, though the number of males in our sample is too small to draw any definite conclusions. Our data is consistent with recent reports of reduced MAOA activity in patients with abnormal behavioral phenotypes. The strength of the association is weak, but significant, which suggests that alleles at the MAOA locus contribute to susceptibility to bipolar disorder rather than being a major determinant. 58 refs., 1 fig., 3 tabs.

Lim, L.C.C.; Sham, P.; Castle, D. [Institute of Psychiatry, London (United Kingdom)] [and others

1995-08-14

148

Valuing Parents  

ERIC Educational Resources Information Center

Recently, a young faculty member commented that e-mail and inexpensive long distance rates were hampering her first-year students' development by making it too easy for them to stay in touch with their parents. Similarly, Judith Shapiro, president of Barnard College, argued in her August 22, 2002, New York Times op-ed piece, "Keeping Parents Off…

Gerdes, Eugenia Proctor

2004-01-01

149

Variations and transmission of QTL alleles for yield and fiber qualities in upland cotton cultivars developed in China.  

PubMed

Cotton is the world's leading cash crop, and genetic improvement of fiber yield and quality is the primary objective of cotton breeding program. In this study, we used various approaches to identify QTLs related to fiber yield and quality. Firstly, we constructed a four-way cross (4WC) mapping population with four base core cultivars, Stoneville 2B, Foster 6, Deltapine 15 and Zhongmiansuo No.7 (CRI 7), as parents in Chinese cotton breeding history and identified 83 QTLs for 11 agronomic and fiber quality traits. Secondly, association mapping of agronomical and fiber quality traits was based on 121 simple sequence repeat (SSR) markers using a general linear model (GLM). For this, 81 Gossypium hirsutum L. accessions including the four core parents and their derived cultivars were grown in seven diverse environments. Using these approaches, we successfully identified 180 QTLs significantly associated with agronomic and fiber quality traits. Among them were 66 QTLs that were identified via linkage disequilibrium (LD) and 4WC family-based linkage (FBL) mapping and by previously published family-based linkage (FBL) mapping in modern Chinese cotton cultivars. Twenty eight and 44 consistent QTLs were identified by 4WC and LD mapping, and by FBL and LD mapping methods, respectively. Furthermore, transmission and variation of QTL-alleles mapped by LD association in the three breeding periods revealed that some could be detected in almost all Chinese cotton cultivars, suggesting their stable transmission and some identified only in the four base cultivars and not in the modern cultivars, suggesting they were missed in conventional breeding. These results will be useful to conduct genomics-assisted breeding effectively using these existing and novel QTL alleles to improve yield and fiber qualities in cotton. PMID:23468939

Zhang, Tianzhen; Qian, Neng; Zhu, Xiefei; Chen, Hong; Wang, Sen; Mei, Hongxian; Zhang, Yuanming

2013-01-01

150

Examining markers in 8q24 to explain differences in evidence for association with cleft lip with/without cleft palate between Asians and Europeans  

PubMed Central

In a recent genome wide association study (GWAS) from an international consortium, evidence of linkage and association in chr8q24 was much stronger among non-syndromic cleft lip/palate (CL/P) case-parent trios of European ancestry than among trios of Asian ancestry. We examined marker information content and haplotype diversity across 13 recruitment sites (from Europe, USA and Asia) separately, and conducted principal components analysis (PCA) on parents. As expected, PCA revealed large genetic distances between Europeans and Asians, and a north-south cline from Korea to Singapore in Asia, with Filipino parents forming a somewhat distinct Southeast Asian cluster. Hierarchical clustering of SNP heterozygosity revealed two major clades consistent with PCA results. All genotyped SNPs giving p<10?6 in the allelic TDT showed higher heterozygosity in Europeans than Asians. On average, European ancestry parents had higher haplotype diversity than Asians. Imputing additional variants across chr8q24 increased the strength of statistical evidence among Europeans and also revealed a significant signal among Asians (although it did not reach genome-wide significance). Tests for SNP-population interaction were negative, indicating the lack of strong signal for 8q24 in families of Asian ancestry was not due to any distinct genetic effect, but could simply reflect low power due to lower allele frequencies in Asians.

Murray, Tanda; Taub, Margaret A.; Ruczinski, Ingo; Scott, Alan F.; Hetmanski, Jacqueline B.; Schwender, Holger; Patel, Poorav; Zhang, Tian Xiao; Munger, Ronald G.; Wilcox, Allen J.; Ye, Xiaoqian; Wang, Hong; Wu, Tao; Wu-Chou, Yah Huei; Shi, Bing; Jee, Sun Ha; Chong, Samuel; Yeow, Vincent; Murray, Jeffrey C.; Marazita, Mary L.; Beaty, Terri H.

2013-01-01

151

Allelic Variation in Paralogs of GDP-l-Galactose Phosphorylase Is a Major Determinant of Vitamin C Concentrations in Apple Fruit1[C][W][OA  

PubMed Central

To identify the genetic factors underlying the regulation of fruit vitamin C (l-ascorbic acid [AsA]) concentrations, quantitative trait loci (QTL) studies were carried out in an F1 progeny derived from a cross between the apple (Malus × domestica) cultivars Telamon and Braeburn over three years. QTL were identified for AsA, glutathione, total antioxidant activity in both flesh and skin tissues, and various quality traits, including flesh browning. Four regions on chromosomes 10, 11, 16, and 17 contained stable fruit AsA-QTL clusters. Mapping of AsA metabolic genes identified colocations between orthologs of GDP-l-galactose phosphorylase (GGP), dehydroascorbate reductase (DHAR), and nucleobase-ascorbate transporter within these QTL clusters. Of particular interest are the three paralogs of MdGGP, which all colocated within AsA-QTL clusters. Allelic variants of MdGGP1 and MdGGP3 derived from the cultivar Braeburn parent were also consistently associated with higher fruit total AsA concentrations both within the mapping population (up to 10-fold) and across a range of commercial apple germplasm (up to 6-fold). Striking differences in the expression of the cv Braeburn MdGGP1 allele between fruit from high- and low-AsA genotypes clearly indicate a key role for MdGGP1 in the regulation of fruit AsA concentrations, and this MdGGP allele-specific single-nucleotide polymorphism marker represents an excellent candidate for directed breeding for enhanced fruit AsA concentrations. Interestingly, colocations were also found between MdDHAR3-3 and a stable QTL for browning in the cv Telamon parent, highlighting links between the redox status of the AsA pool and susceptibility to flesh browning.

Mellidou, Ifigeneia; Chagne, David; Laing, William A.; Keulemans, Johan; Davey, Mark W.

2012-01-01

152

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.  

PubMed

A mapping population was created to detect quantitative trait loci (QTL) for resistance to stem rust caused by Puccinia graminis subsp. graminicola in Lolium perenne. A susceptible and a resistant plant were crossed to produce a pseudo-testcross population of 193 F(1) individuals. Markers were produced by the restriction-site associated DNA (RAD) process, which uses massively parallel and multiplexed sequencing of reduced-representation libraries. Additional simple sequence repeat (SSR) and sequence-tagged site (STS) markers were combined with the RAD markers to produce maps for the female (738 cM) and male (721 cM) parents. Stem rust phenotypes (number of pustules per plant) were determined in replicated greenhouse trials by inoculation with a field-collected, genetically heterogeneous population of urediniospores. The F(1) progeny displayed continuous distribution of phenotypes and transgressive segregation. We detected three resistance QTL. The most prominent QTL (qLpPg1) is located near 41 cM on linkage group (LG) 7 with a 2-LOD interval of 8 cM, and accounts for 30-38% of the stem rust phenotypic variance. QTL were detected also on LG1 (qLpPg2) and LG6 (qLpPg3), each accounting for approximately 10% of phenotypic variance. Alleles of loci closely linked to these QTL originated from the resistant parent for qLpPg1 and from both parents for qLpPg2 and qLpPg3. Observed quantitative nature of the resistance may be due to partial-resistance effects against all pathogen genotypes, or qualitative effects completely preventing infection by only some genotypes in the genetically mixed inoculum. RAD markers facilitated rapid construction of new genetic maps in this outcrossing species and will enable development of sequence-based markers linked to stem rust resistance in L. perenne. PMID:21344184

Pfender, W F; Saha, M C; Johnson, E A; Slabaugh, M B

2011-05-01

153

Genetic diversity and geographical differentiation of Iranian landrace, cultivars, and exotic chickpea lines as revealed by morphological and microsatellite markers.  

PubMed

Assessment of the extent of genetic variability within chickpea is fundamental for chickpea breeding and conservation of genetic resources and is particularly useful as a general guide in the choice of parents for breeding hybrids. To establish genetic diversity among 60 accessions of chickpea comprising landraces, internationally developed improved lines, and cultivars, genetic distances were evaluated using 14 simple sequence repeat markers. These markers showed a high level of polymorphism; a total of 59 different alleles were detected, with a mean of 4.2 alleles per locus. The polymorphic information content (PIC) value ranged from 0.31 to 0.89. All the markers, with the exception of TAA170, TA110, GA34, and Ts35, were considered to be informative (PIC?>?0.5), indicating their potential usefulness for cultivar identification. Based on the UNJ clustering method, all accessions were clustered in five groups, which indicated the probable origin and region similarity of Iranian landraces over the other cultivars. It also represents a wide diversity among available germplasm. The result has firmly established that introduction of genetic materials from exotic sources has broadened the genetic base of the national chickpea breeding program. As further implications of the findings, this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs. PMID:24757326

Ghaffari, Parvin; Talebi, Reza; Keshavarzi, Fatemeh

2014-04-01

154

Development of PCR-based markers for thermosensitive genetic male sterility gene tms3(t) in rice (Oryza sativa L.).  

PubMed

Development of simple and reliable PCR-based markers is an important component of marker-aided selection (MAS) activities for agronomically important genes in rice breeding. In order to develop PCR-based markers for a rice thermosensitive genetic male sterility gene tms3(t), located on chromosome 6, the nucleotide sequences of four linked RAPD markers OPF18(2600), OPAC3(640), OPB19(750) and OPM7(550) were used to design and synthesize several pairs of specific primers for PCR amplification of the genomic DNA of both the parents IR32364TGMS (sterile) and IR68 (fertile), involved in mapping this gene. For the RAPD marker OPF 18(2600), two pairs of specific primer pair combination from different positions of the sequence resulted in generation of two codominant STS (Sequence Tagged Sites) markers. In case of markers OPAC3(640), OPB19(750) and OPAA7(550) the first two could generate dominant polymorphism, while the last one could not be successful in PCR amplification. Both the codominant STSs with primer combinations F18F/F18RM and F18FM/F18RM were found to be tightly linked to the tms3(t) gene with a genetic distance of 2.7 cM. The sizes of the different alleles in case of F18F/F18RM, F18FM/F18RM combinations were 2300 bp, 1050 bp, and 1900 bp, 1000 bp respectively. The efficiency of marker-assisted selection for this trait was estimated as 84.6%. Polymorphism survey of 12 elite rice lines, indicated that these PCR-based markers for tms3(t) can now be used in selecting TGMS plants at seeding stage in the segregating populations in environment independent of controlled temperature regime. PMID:10680295

Lang, N T; Subudhi, P K; Virmani, S S; Brar, D S; Khush, G S; Li, Z; Huang, N

1999-01-01

155

Microevolution of S-allele frequencies in wild cherry populations: respective impacts of negative frequency dependent selection and genetic drift.  

PubMed

Negative frequency dependent selection (NFDS) is supposed to be the main force controlling allele evolution at the gametophytic self-incompatibility locus (S-locus) in strictly outcrossing species. Genetic drift also influences S-allele evolution. In perennial sessile organisms, evolution of allelic frequencies over two generations is mainly shaped by individual fecundities and spatial processes. Using wild cherry populations between two successive generations, we tested whether S-alleles evolved following NFDS qualitative and quantitative predictions. We showed that allelic variation was negatively correlated with parental allelic frequency as expected under NFDS. However, NFDS predictions in finite population failed to predict more than half S-allele quantitative evolution. We developed a spatially explicit mating model that included the S-locus. We studied the effects of self-incompatibility and local drift within populations due to pollen dispersal in spatially distributed individuals, and variation in male fecundity on male mating success and allelic frequency evolution. Male mating success was negatively related to male allelic frequency as expected under NFDS. Spatial genetic structure combined with self-incompatibility resulted in higher effective pollen dispersal. Limited pollen dispersal in structured distributions of individuals and genotypes and unequal pollen production significantly contributed to S-allele frequency evolution by creating local drift effects strong enough to counteract the NFDS effect on some alleles. PMID:22276543

Stoeckel, Solenn; Klein, Etienne K; Oddou-Muratorio, Sylvie; Musch, Brigitte; Mariette, Stéphanie

2012-02-01

156

DRD2 and DRD4 in relation to regular alcohol and cannabis use among adolescents: Does parenting modify the impact of genetic vulnerability? The TRAILS study  

PubMed Central

Aims The aims of the present study were to determine the direct effect of DRD2 and DRD4, as well as their interaction with parenting (i.e. rejection, overprotection and emotional warmth), on the development of regular alcohol and cannabis use in 1192 Dutch adolescents from the general population. Methods Information was obtained by self-report questionnaires. Perceived rejection, overprotection and emotional warmth were assessed at age 10–12. Regular alcohol and cannabis use were determined at age 15–18 and defined as the consumption of alcohol on 10 or more occasions in the past four weeks, and the use of cannabis on 4 or more occasions in the past four weeks. Models were adjusted for age, sex, parental alcohol or cannabis use, and externalizing behavior. Results Carrying the A1 allele of the DRD2 TaqIA polymorphism, or the 7 repeat DRD4, was not directly related to regular alcohol or cannabis use. In addition, adolescent carriers of these genetic risk markers were not more susceptible to the influence of less optimal parenting. Main effects for parenting indicated that overprotection increased the risk of regular alcohol use, whereas the risk of cannabis use was enhanced by parental rejection and buffered by emotional warmth. Conclusions Our findings do not support an association between DRD2/DRD4 and regular alcohol and cannabis use in adolescents. Given the substance-specific influences of rejection, overprotection and emotional warmth, these parenting factors might be promising candidates for prevention work.

Creemers, H.E.; Harakeh, Z.; Dick, D.M.; Meyers, J.; Vollebergh, W.A.M.; Ormel, J.; Verhulst, F.C.; Huizink, A.C.

2014-01-01

157

Deviations from Hardy-Weinberg Equilibrium in Parental and Unaffected Sibling Genotype Data  

PubMed Central

Background Genotyping error can increase both type I and II errors. In order to elucidate potential genotyping errors, data quality control often includes testing genotype data for deviations from Hardy-Weinberg Equilibrium (HWE). Methods The Hardy-Weinberg Disequilibrium (HWD) coefficient and the ability to reject the null hypothesis of HWE were calculated analytically for genotype data from parents and unaffected siblings of affected probands. Results Genotype data from parents and unaffected siblings display deviations from HWE when functional or markers in LD with functional locus are tested. For the parental genotype data all deviations from HWE are negative, indicating an excess of heterozygous genotypes with the strongest deviations from HWE observed for the multiplicative model. In contrast, for affected proband genotype data, there is no deviation from HWE under the multiplicative model and the deviations from HWE for the recessive model are positive. For the unaffected sibling data, patterns of deviation from HWE are similar to those observed in the proband data with the exception of the multiplicative model where the HWD coefficient although close to 0 can be either positive or negative depending on the allele frequency. Conclusion Deviations from HWE in parental and unaffected sibling genotype data could be due to an association with the functional locus. However these deviations for genotypic relative risk ?2.0 are not large and therefore the power to detect them is usually low. Testing for deviations from HWE in parental and unaffected sibling genotype data is still beneficial for quality control even though functional loci, in parental and unaffected sibling genotype data, can produce an association signal.

Li, Bingshan; Leal, Suzanne M.

2009-01-01

158

Parenting perceptions and behaviors of preschool parents  

Microsoft Academic Search

Perceptions and behaviors of parents of young preschoolers is a subject that has not been extensively researched. Many studies have explored global parenting styles and child developmental outcomes, rather than the way parents conceptualize their roles. Further, most research considers parenting typical children. However, parenting special needs children is challenging. When children with special needs are young, parents are faced

Shoshana Sperling

2003-01-01

159

Invasive Allele Spread under Preemptive Competition  

NASA Astrophysics Data System (ADS)

We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

Yasi, J. A.; Korniss, G.; Caraco, T.

160

Parenting Your Adopted Teenager  

MedlinePLUS

... Care Stay Connected Home » Parenting Your Adopted Teenager Parenting Your Adopted Teenager Email Print (PDF 325 KB) ... For expectant parents considering adoption and birth parents Parenting after adoption Postplacement casework Search & reunion Adoption Month ...

161

Parent role characteristics: Parents' perceptions of their parent role  

Microsoft Academic Search

Research has widely examined the various beliefs, attitudes, and perceptions held by parents. However, few have formally examined parents' perceptions of their role or the characteristics that encompass this role, even though many have argued that the job of parent is most difficult. This study utilized the Parent Role Questionnaire (PRQ), developed by Mowder in 1990, to examine how parents

Rose Anne Turiano

2001-01-01

162

Estimating African American Admixture Proportions by Use of Population-Specific Alleles  

Microsoft Academic Search

Summary We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine au- tosomal DNA markers. These markers either are pop- ulation-specific or show frequency differences 145% be- tween the parental populations and are thus

Esteban J. Parra; Amy Marcini; Joshua Akey; Jeremy Martinson; Mark A. Batzer; Richard Cooper; Terrence Forrester; David B. Allison; Ranjan Deka; Robert E. Ferrell; Mark D. Shriver

1998-01-01

163

Transgene- and locus-dependent imprinting reveals allele-specific chromosome conformations  

PubMed Central

When positioned into the integrin ?-6 gene, an Hoxd9lacZ reporter transgene displayed parental imprinting in mouse embryos. While the expression from the paternal allele was comparable with patterns seen for the same transgene when present at the neighboring HoxD locus, almost no signal was scored at this integration site when the transgene was inherited from the mother, although the Itga6 locus itself is not imprinted. The transgene exhibited maternal allele-specific DNA hypermethylation acquired during oogenesis, and its expression silencing was reversible on passage through the male germ line. Histone modifications also corresponded to profiles described at known imprinted loci. Chromosome conformation analyses revealed distinct chromatin microarchitectures, with a more compact structure characterizing the maternally inherited repressed allele. Such genetic analyses of well-characterized transgene insertions associated with a de novo-induced parental imprint may help us understand the molecular determinants of imprinting.

Lonfat, Nicolas; Montavon, Thomas; Jebb, David; Tschopp, Patrick; Nguyen Huynh, Thi Hanh; Zakany, Jozsef; Duboule, Denis

2013-01-01

164

Estimation of quantitative trait locus allele frequency via a modified granddaughter design.  

PubMed Central

A method is described on the basis of a modification of the granddaughter design to obtain estimates of quantitative trait loci (QTL) allele frequencies in dairy cattle populations and to determine QTL genotypes for both homozygous and heterozygous grandsires. The method is based on determining the QTL allele passed from grandsires to their maternal granddaughters using haplotypes consisting of several closely linked genetic markers. This method was applied to simulated data of 10 grandsire families, each with 500 granddaughters, and a QTL with a substitution effect of 0.4 phenotypic standard deviations and to actual data for a previously analyzed QTL in the center of chromosome 6, with substitution effect of 1 phenotypic standard deviation on protein percentage. In the simulated data the standard error for the estimated QTL substitution effect with four closely linked multiallelic markers was only 7% greater than the expected standard error with completely correct identification of QTL allele origin. The method estimated the population QTL allelic frequency as 0.64 +/- 0.07, compared to the simulated value of 0.7. In the actual data, the frequency of the allele that increases protein percentage was estimated as 0.63 +/- 0.06. In both data sets the hypothesis of equal allelic frequencies was rejected at P < 0.05.

Weller, Joel Ira; Weller, Hayim; Kliger, David; Ron, Micha

2002-01-01

165

A powerful likelihood method for the analysis of linkage disequilibrium between trait loci and one or more polymorphic marker loci  

Microsoft Academic Search

Historically, most methods for detecting linkage disequilibrium were designed for use with diallelic marker loci, for which the analysis is straightforward. With the advent of polymorphic markers with many alleles, the normal approach to their analysis has been either to extend the methodology for two-allele systems (leading to an increase in df and to a corresponding loss of power) or

Jd Terwilliger

1995-01-01

166

Equivalence of single- and multilocus markers: power to detect linkage with composite markers derived from biallelic loci.  

PubMed

The reintroduction of biallelic markers, now in the form of single-nucleotide polymorphisms (SNPs), has again raised concerns about the practicality of the use of markers with low heterozygosity for genomic screening for complex traits, even if thousands of such markers are available. Like the early blood-group markers (e.g., Rh and MNS), tightly linked biallelic SNPs can be combined into composite markers with heterozygosity similar to that of short-tandem-repeat polymorphisms. The assumptions that underlie the equivalence between single-locus multiallelic and composite markers are presented. We used computer simulation to determine the power of the Haseman-Elston test for linkage with composite markers when not all of these assumptions hold. The Genometric Analysis Simulation Program was used to simulate continuous and discrete traits, one single-locus four-allele marker, and six biallelic markers. We studied composite markers created from pairs, trios, and quartets of biallelic markers in nuclear families and in independent sib pairs. The power to detect linkage with a two-point approach for composite markers and with a multipoint approach that incorporated all six biallelic markers was compared with that for a single-locus, four-allele reference marker. Although the power to detect linkage with a single biallelic marker was considerably less than that of the reference marker, the power to detect linkage with two- and three-locus composite markers was quite similar to that of the reference marker. The power to detect linkage with four-locus composite markers was similar to that of a multipoint approach. PMID:10762546

Wilson, A F; Sorant, A J

2000-05-01

167

Equivalence of single- and multilocus markers: power to detect linkage with composite markers derived from biallelic loci.  

PubMed Central

The reintroduction of biallelic markers, now in the form of single-nucleotide polymorphisms (SNPs), has again raised concerns about the practicality of the use of markers with low heterozygosity for genomic screening for complex traits, even if thousands of such markers are available. Like the early blood-group markers (e.g., Rh and MNS), tightly linked biallelic SNPs can be combined into composite markers with heterozygosity similar to that of short-tandem-repeat polymorphisms. The assumptions that underlie the equivalence between single-locus multiallelic and composite markers are presented. We used computer simulation to determine the power of the Haseman-Elston test for linkage with composite markers when not all of these assumptions hold. The Genometric Analysis Simulation Program was used to simulate continuous and discrete traits, one single-locus four-allele marker, and six biallelic markers. We studied composite markers created from pairs, trios, and quartets of biallelic markers in nuclear families and in independent sib pairs. The power to detect linkage with a two-point approach for composite markers and with a multipoint approach that incorporated all six biallelic markers was compared with that for a single-locus, four-allele reference marker. Although the power to detect linkage with a single biallelic marker was considerably less than that of the reference marker, the power to detect linkage with two- and three-locus composite markers was quite similar to that of the reference marker. The power to detect linkage with four-locus composite markers was similar to that of a multipoint approach.

Wilson, A F; Sorant, A J

2000-01-01

168

Development of 1,030 genomic SSR markers in switchgrass.  

PubMed

Switchgrass, Panicum virgatum L., a native to the tall grass prairies in North America, has been grown for soil conservation and herbage production in the USA and recently widely recognized as a promising dedicated cellulosic bioenergy crop. A large amount of codominant molecular markers including simple sequence repeats (SSRs) are required for the construction of linkage maps and implementation of molecular breeding strategies to develop superior switchgrass cultivars. The objectives of this study were (1) to identify SSR-containing clones and to design PCR primer pairs (PPs) in SSR-enriched genomic libraries, and (2) to validate and characterize the designed SSR PPs. Five genomic SSR enriched libraries were constructed using genomic DNA of 'SL93 7 × 15', a switchgrass genotype selected in an Oklahoma State University (OSU) southern lowland breeding population. A total of 3,046 clones from four libraries enriched in (CA/TG)n, (GA/TC)n, (CAG/CTG)n and (AAG/CTT)n SSR repeats were sequenced at the OSU Core Facility. From the sequences, we isolated 1,300 unique SSR-containing clones, from which we designed 1,398 PPs using SSR Locator V.1 software. Among the designed PPs, 1,030 (73.7%) amplified reproducible and strong bands with expected fragment size, and 802 detected polymorphic alleles, in SL93 7 × 15 and 'NL94 16 × 13', two parents of one mapping population. All of the four libraries contained a high rate of perfect SSR repeat types, ranging from 62.7 to 76.2%. Polymorphism of the effective SSR markers was also tested in two lowland and two upland switchgrass cultivars, encompassing 'Alamo' and 'Kanlow', and 'Blackwell' and 'Dacotah', respectively. The developed SSR markers should be useful in genetic and breeding research in switchgrass. PMID:20978736

Wang, Y W; Samuels, T D; Wu, Y Q

2011-03-01

169

Total Parenting  

ERIC Educational Resources Information Center

In this essay, Richard Smith observes that being a parent, like so much else in our late-modern world, is required to become ever more efficient and effective, and is increasingly monitored by the agencies of the state, often with good reason given the many recorded instances of child abuse and cruelty. However, Smith goes on to argue, this begins…

Smith, Richard

2010-01-01

170

Parental Monitoring  

ERIC Educational Resources Information Center

Adolescence is a developmental period during which many youth experiment with risk practices. This paper examined the association of parental monitoring with a range of alcohol and other drug (AOD) use behaviors among high-risk youth, while controlling for other demographic and environmental variables previously found to be associated with AOD…

Shillington, Audrey M.; Lehman, Stephanie; Clapp, John; Hovell, Melbourne; Sipan, Carol; Blumberg, Elaine

2005-01-01

171

Constructive Parenting.  

ERIC Educational Resources Information Center

This book turns important research and theory into essential, easy-to-follow guidelines for new parents and child care providers to help them focus on the critical first 3 years of life to build a strong foundation for the future. All the key areas of child development are covered, including self-esteem, and cognitive, motor and social…

Goldberg, Sally

172

Development of a broad-host-range sacB-based vector for unmarked allelic exchange  

PubMed Central

Background Although genome sequences are available for an ever-increasing number of bacterial species, the availability of facile genetic tools for physiological analysis have generally lagged substantially behind traditional genetic models. Results Here I describe the development of an improved, broad-host-range "in-out" allelic exchange vector, pCM433, which permits the generation of clean, marker-free genetic manipulations. Wild-type and mutant alleles were reciprocally exchanged at three loci in Methylobacterium extorquens AM1 in order to demonstrate the utility of pCM433. Conclusion The broad-host-range vector for marker-free allelic exchange described here, pCM433, has the advantages of a high copy, general Escherichia coli replicon for easy cloning, an IncP oriT enabling conjugal transfer, an extensive set of restriction sites in its polylinker, three antibiotic markers, and sacB (encoding levansucrase) for negative selection upon sucrose plates. These traits should permit pCM433 to be broadly applied across many bacterial taxa for marker-free allelic exchange, which is particularly important if multiple manipulations or more subtle genetic manipulations such as point mutations are desired.

Marx, Christopher J

2008-01-01

173

Marker selection for the transmission/disequilibrium test, in recently admixed populations.  

PubMed Central

Recent admixture between genetically differentiated populations can result in high levels of association between alleles at loci that are <=10 cM apart. The transmission/disequilibrium test (TDT) proposed by Spielman et al. (1993) can be a powerful test of linkage between disease and marker loci in the presence of association and therefore could be a useful test of linkage in admixed populations. The degree of association between alleles at two loci depends on the differences in allele frequencies, at the two loci, in the founding populations; therefore, the choice of marker is important. For a multiallelic marker, one strategy that may improve the power of the TDT is to group marker alleles within a locus, on the basis of information about the founding populations and the admixed population, thereby collapsing the marker into one with fewer alleles. We have examined the consequences of collapsing a microsatellite into a two-allele marker, when two founding populations are assumed for the admixed population, and have found that if there is random mating in the admixed population, then typically there is a collapsing for which the power of the TDT is greater than that for the original microsatellite marker. A method is presented for finding the optimal collapsing that has minimal dependence on the disease and that uses estimates either of marker allele frequencies in the two founding populations or of marker allele frequencies in the current, admixed population and in one of the founding populations. Furthermore, this optimal collapsing is not always the collapsing with the largest difference in allele frequencies in the founding populations. To demonstrate this strategy, we considered a recent data set, published previously, that provides frequency estimates for 30 microsatellites in 13 populations.

Kaplan, N L; Martin, E R; Morris, R W; Weir, B S

1998-01-01

174

A computational workflow to identify allele-specific expression and epigenetic modification in maize.  

PubMed

Allele-specific expression refers to the preferential expression of one of the two alleles in a diploid genome, which has been thought largely attributable to the associated cis-element variation and allele-specific epigenetic modification patterns. Allele-specific expression may contribute to the heterosis (or hybrid vigor) effect in hybrid plants that are produced from crosses of closely-related species, subspecies and/or inbred lines. In this study, using Illumina high-throughput sequencing of maize transcriptomics, chromatic H3K27me3 histone modification and DNA methylation data, we developed a new computational framework to identify allele-specifically expressed genes by simultaneously tracking allele-specific gene expression patterns and the epigenetic modification landscape in the seedling tissues of hybrid maize. This approach relies on detecting nucleotide polymorphisms and any genomic structural variation between two parental genomes in order to distinguish paternally or maternally derived sequencing reads. This computational pipeline also incorporates a modified Chi-square test to statistically identify allele-specific gene expression and epigenetic modification based on the Poisson distribution. PMID:23891706

Wei, Xiaoxing; Wang, Xiangfeng

2013-08-01

175

Parental Power and Adolescents' Parental Identification.  

ERIC Educational Resources Information Center

Combines McDonald's social power of parental identification with sex-linked models of parental identification to account for the identification of daughters (N=199) and sons (N=147) with their parents. Found that because of a halo effect, a gain in identification with one parent is not at the other parent's expense. (JAC)

Acock, Alan C.; Yang, Wen Shan

1984-01-01

176

Allelic analysis of sheath blight resistance with association mapping in rice.  

PubMed

Sheath blight (ShB) caused by the soil-borne pathogen Rhizoctonia solani is one of the most devastating diseases in rice world-wide. Global attention has focused on examining individual mapping populations for quantitative trait loci (QTLs) for ShB resistance, but to date no study has taken advantage of association mapping to examine hundreds of lines for potentially novel QTLs. Our objective was to identify ShB QTLs via association mapping in rice using 217 sub-core entries from the USDA rice core collection, which were phenotyped with a micro-chamber screening method and genotyped with 155 genome-wide markers. Structure analysis divided the mapping panel into five groups, and model comparison revealed that PCA5 with genomic control was the best model for association mapping of ShB. Ten marker loci on seven chromosomes were significantly associated with response to the ShB pathogen. Among multiple alleles in each identified loci, the allele contributing the greatest effect to ShB resistance was named the putative resistant allele. Among 217 entries, entry GSOR 310389 contained the most putative resistant alleles, eight out of ten. The number of putative resistant alleles presented in an entry was highly and significantly correlated with the decrease of ShB rating (r?=?-0.535) or the increase of ShB resistance. Majority of the resistant entries that contained a large number of the putative resistant alleles belonged to indica, which is consistent with a general observation that most ShB resistant accessions are of indica origin. These findings demonstrate the potential to improve breeding efficiency by using marker-assisted selection to pyramid putative resistant alleles from various loci in a cultivar for enhanced ShB resistance in rice. PMID:22427867

Jia, Limeng; Yan, Wengui; Zhu, Chengsong; Agrama, Hesham A; Jackson, Aaron; Yeater, Kathleen; Li, Xiaobai; Huang, Bihu; Hu, Biaolin; McClung, Anna; Wu, Dianxing

2012-01-01

177

Allelic Differences within and among Sister Spores of the Arbuscular Mycorrhizal Fungus Glomus etunicatum Suggest Segregation at Sporulation  

PubMed Central

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae.

St-Arnaud, Marc; Hijri, Mohamed

2013-01-01

178

Variable Number of Tandem Repeat (VNTR) Markers for Human Gene Mapping  

Microsoft Academic Search

A large collection of good genetic markers is needed to map the genes that cause human genetic diseases. Although nearly 400 polymorphic DNA markers for human chromosomes have been described, the majority have only two alleles and are thus uninformative for analysis of genetic linkage in many families. A few known marker systems, however, detect loci that respond to restriction

Yusuke Nakamura; Mark Leppert; Peter O'Connell; Roger Wolff; Tom Holm; Melanie Culver; Cindy Martin; Esther Fujimoto; Mark Hoff; Erika Kumlin; Ray White

1987-01-01

179

Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel Perna viridis.  

PubMed

We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic markers for this species. PMID:18666563

Ong, C C; Teh, C H; Tan, S G; Yusoff, K; Yap, C K

2008-04-01

180

RAPD markers linked to eastern filbert blight resistance in Corylus avellana  

Microsoft Academic Search

A total of 1,110 decamer primers were screened for RAPD markers linked to a dominant allele in hazelnut ( Corylus avellana) that confers resistance to eastern filbert blight caused by Anisogramma anomala. Twenty RAPD markers linked in coupling, and five markers linked in repulsion, were found. A seedling population was used to construct a linkage map of the region flanking

S. A. Mehlenbacher; R. N. Brown; J. W. Davis; H. Chen; N. V. Bassil; D. C. Smith; T. L. Kubisiak

2004-01-01

181

Microsatellite and minisatellite markers based DNA fingerprinting and genetic diversity of blast and ufra resistant genotypes.  

PubMed

A total of 78 alleles and 29 loci were detected from nine microsatellite and three minisatellite markers, respectively across 26 blast and ufra disease resistant genotypes. For blast resistant genotypes, the Polymorphic Information Content (PIC) values ranged from 0.280 to 0.726 and RM21 was considered as the best marker. PIC values ranged from 0.5953 to 0.8296 for ufra resistant genotypes and RM23 was the best marker for characterization of ufra resistant genotypes. The genetic similarity analysis using UPGMA clustering generated nine clusters with coefficient of 0.66 for blast resistant genotypes while five genetic clusters with similarity coefficient of 0.42 for ufra resistant genotypes. In order to develop resistant varieties of two major diseases of rice, hybridisation should be made using the parents, BR29 and NJ70507, BR36 and NJ70507 for blast, while BR11 and Aokazi, BR3 and Aokazi, Rayda and BR3 and Rayda and BR11 for ufra. PMID:21513897

Latif, M A; Rafii Yusop, Mohd; Motiur Rahman, M; Bashar Talukdar, M R

2011-04-01

182

Detection of Parent-of-Origin Effects Using General Pedigree Data  

PubMed Central

Genomic imprinting is an important epigenetic factor in complex traits study, which has generally been examined by testing for parent-of-origin effects of alleles. For a diallelic marker locus, the parental-asymmetry test (PAT) based on case-parents trios and its extensions to incomplete nuclear families (1-PAT and C-PAT) are simple and powerful for detecting parent-of-origin effects. However, these methods are suitable only for nuclear families and thus are not amenable to general pedigree data. Use of data from extended pedigrees, if available, may lead to more powerful methods than randomly selecting one two-generation nuclear family from each pedigree. In this study, we extend PAT to accommodate general pedigree data by proposing the pedigree PAT (PPAT) statistic, which uses all informative family trios from pedigrees. To fully utilize pedigrees with some missing genotypes, we further develop the Monte Carlo (MC) PPAT (MCPPAT) statistic based on MC sampling and estimation. Extensive simulations were carried out to evaluate the performance of the proposed methods. Under the assumption that the pedigrees and their associated affection patterns are randomly drawn from a population of pedigrees with at least one affected offspring, we demonstrated that MCPPAT is a valid test for parent-of-origin effects in the presence of association. Further, MCPPAT is much more powerful compared to PAT for trios or even PPAT for all informative family trios from the same pedigrees if there is missing data. Application of the proposed methods to a rheumatoid arthritis dataset further demonstrates the advantage of MCPPAT.

Zhou, Ji-Yuan; Ding, Jie; Fung, Wing K.; Lin, Shili

2010-01-01

183

Murderous parents.  

PubMed

This article offers observations regarding some of the major manifestations of family violence, neonaticide, infanticide, and filicide with the purpose of aiding in the early identification of parents at risk. They are discussed within the past and present historical and cultural milieu. A brief review of pertinent literature is presented. Pertinent case studies from the forensic psychiatric practice of the author along with psychodynamic reflections are offered. PMID:12113159

Palermo, George B

2002-04-01

184

Multiple alleles for resistance and susceptibility modulate the defense response in the interaction of tetraploid potato (Solanum tuberosum) with Synchytrium endobioticum pathotypes 1, 2, 6 and 18.  

PubMed

The obligate biotrophic, soil-borne fungus Synchytrium endobioticum causes wart disease of potato (Solanum tuberosum), which is a serious problem for crop production in countries with moderate climates. S. endobioticum induces hypertrophic cell divisions in plant host tissues leading to the formation of tumor-like structures. Potato wart is a quarantine disease and chemical control is not possible. From 38 S. endobioticum pathotypes occurring in Europe, pathotypes 1, 2, 6 and 18 are the most relevant. Genetic resistance to wart is available but only few current potato varieties are resistant to all four pathotypes. The phenotypic evaluation of wart resistance is laborious, time-consuming and sometimes ambiguous, which makes breeding for resistance difficult. Molecular markers diagnostic for genes for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 would greatly facilitate the selection of new, resistant cultivars. Two tetraploid half-sib families (266 individuals) segregating for resistance to S. endobioticum pathotypes 1, 2, 6 and 18 were produced by crossing a resistant genotype with two different susceptible ones. The families were scored for five different wart resistance phenotypes. The distribution of mean resistance scores was quantitative in both families. Resistance to pathotypes 2, 6 and 18 was correlated and independent from resistance to pathotype 1. DNA pools were constructed from the most resistant and most susceptible individuals and screened with genome wide simple sequence repeat (SSR), inverted simple sequence region (ISSR) and randomly amplified polymorphic DNA (RAPD) markers. Bulked segregant analysis identified three SSR markers that were linked to wart resistance loci (Sen). Sen1-XI on chromosome XI conferred partial resistance to pathotype 1, Sen18-IX on chromosome IX to pathotype 18 and Sen2/6/18-I on chromosome I to pathotypes 2,6 and 18. Additional genotyping with 191 single nucleotide polymorphism (SNP) markers confirmed the localization of the Sen loci. Thirty-three SNP markers linked to the Sen loci permitted the dissection of Sen alleles that increased or decreased resistance to wart. The alleles were inherited from both the resistant and susceptible parents. PMID:21822548

Ballvora, Agim; Flath, Kerstin; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Gebhardt, Christiane

2011-12-01

185

Parenting an Athlete  

MedlinePLUS

... Living > Sports > Parenting an Athlete Healthy Living Listen Parenting an Athlete Article Body What Parents Can Do ... Experiences (Audio) Healthy Children Radio: Dad to Dad: Parenting Like a Pro (Audio) Healthy Children Radio: Stress ...

186

For Parents and Kids  

MedlinePLUS

... A A A Listen En Español For Parents & Kids Diabetes is a disease that affects the whole ... balance between caring and hovering. Explore: For Parents & Kids Parent's Perspective Parents of children with diabetes share ...

187

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)  

PubMed Central

Background Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. Results The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. Conclusion The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

Upadhyaya, Hari D; Dwivedi, Sangam L; Baum, Michael; Varshney, Rajeev K; Udupa, Sripada M; Gowda, Cholenahalli LL; Hoisington, David; Singh, Sube

2008-01-01

188

Allelic variation of the ?-, ?- and ?-kafirin genes in diverse Sorghum genotypes.  

PubMed

The ?-, ?- and ?-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic diversity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally diverse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic ?-kafirins. Significant diversity was found for each locus, with the cysteine-rich ?-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce ?-kafirin. An analysis of flour viscosity reveals that these ?-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less diversity at the protein level within the cysteine-rich ?-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the ?-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the ?-kafirin locus displayed comparatively low genetic variation. This study has identified genetic diversity in all single copy seed storage protein genes, including a null mutant for ?-kafirin in Sorghum. PMID:20563549

Laidlaw, H K C; Mace, E S; Williams, S B; Sakrewski, K; Mudge, A M; Prentis, P J; Jordan, D R; Godwin, I D

2010-11-01

189

Selection of microsatellite markers for bladder cancer diagnosis without the need for corresponding blood.  

PubMed

Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance. PMID:22927958

van Tilborg, Angela A G; Kompier, Lucie C; Lurkin, Irene; Poort, Ricardo; El Bouazzaoui, Samira; van der Keur, Kirstin; Zuiverloon, Tahlita; Dyrskjot, Lars; Orntoft, Torben F; Roobol, Monique J; Zwarthoff, Ellen C

2012-01-01

190

Selection of Microsatellite Markers for Bladder Cancer Diagnosis without the Need for Corresponding Blood  

PubMed Central

Microsatellite markers are used for loss-of-heterozygosity, allelic imbalance and clonality analyses in cancers. Usually, tumor DNA is compared to corresponding normal DNA. However, normal DNA is not always available and can display aberrant allele ratios due to copy number variations in the genome. Moreover, stutter peaks may complicate the analysis. To use microsatellite markers for diagnosis of recurrent bladder cancer, we aimed to select markers without stutter peaks and a constant ratio between alleles, thereby avoiding the need for a control DNA sample. We investigated 49 microsatellite markers with tri- and tetranucleotide repeats in regions commonly lost in bladder cancer. Based on analysis of 50 blood DNAs the 12 best performing markers were selected with few stutter peaks and a constant ratio between peaks heights. Per marker upper and lower cut off values for allele ratios were determined. LOH of the markers was observed in 59/104 tumor DNAs. We then determined the sensitivity of the marker panel for detection of recurrent bladder cancer by assaying 102 urine samples of these patients. Sensitivity was 63% when patients were stratified for LOH in their primary tumors. We demonstrate that up-front selection of microsatellite markers obliterates the need for a corresponding blood sample. For diagnosis of bladder cancer recurrences in urine this significantly reduces costs. Moreover, this approach facilitates retrospective analysis of archival tumor samples for allelic imbalance.

van Tilborg, Angela A. G.; Kompier, Lucie C.; Lurkin, Irene; Poort, Ricardo; El Bouazzaoui, Samira; van der Keur, Kirstin; Zuiverloon, Tahlita; Dyrskjot, Lars; Orntoft, Torben F.; Roobol, Monique J.; Zwarthoff, Ellen C.

2012-01-01

191

Analysis of Allelic Imbalance on Chromosome 17p13 in Stage I and Stage II Epithelial Ovarian Cancers  

Microsoft Academic Search

Objectives.To determine whether there is evidence for allelic imbalance (AI) on chromosome 17p13 in early-stage epithelial ovarian tumors.Methods.Studies of allelic imbalance were performed on 29 stage I or stage II epithelial ovarian cancers using 5 short tandem repeat polymorphic markers (STRPs) on chromosome 17p13 by polymerase chain reaction (PCR) amplification.Results.Sixteen of 29 (55%) tumors showed AI at one or more

Donald W. Wiper; Kristine M. Zanotti; Alexander W. Kennedy; Jerome L. Belinson; Graham Casey

1998-01-01

192

Inferring Selection Intensity and Allele Age from Multilocus Haplotype Structure  

PubMed Central

It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144?0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories.

Chen, Hua; Slatkin, Montgomery

2013-01-01

193

ALLELE-SPECIFIC EXPRESSION OF APC IN ADENOMATOUS POLYPOSIS FAMILIES  

PubMed Central

Backgound & Aims Germline mutations of the APC gene are the pathogenic cause of most cases of familial adenomatous polyposis (FAP) and a lesser proportion of attenuated FAP (AFAP). Systematic analysis of APC at the RNA level may provide insight into the pathogenicity of identified mutations and uncover the molecular basis of FAP/AFAP in families without identifiable mutations. Here, we analyzed the prevalence of imbalances in the allelic expression of APC in polyposis families with germline mutations in the gene and without detectable mutations in APC or and MUTYH. Methods Allele-specific expression (ASE) was determined by single nucleotide primer extension using an exon 11 polymorphism as an allele-specific marker. In total, 52 APC-mutation-positive (36 families) and 24 APC/MUTYH-mutation-negative (23 families) informative patients were analyzed. Seventy-six controls were also included. Results Of the APC-mutation-positive families, most of those in which the mutation was located before the last exon of the gene (12 of 14) showed ASE imbalance, which is consistent with a mechanism of nonsense-mediated decay (NMD). Of the APC/MUTYH mutation-negative families, two (9%) showed ASE imbalance as a hallmark of the putative pathogenic cause of the disease. Normal allele expression was restored after treatment of short-term cultured lymphocytes with puromycin, supporting the NMD hypothesis. Conclusions ASE analysis may be an indicator of pathogenicity for some cases of FAP and AFAP in which APC mutations are not found. ASE might also be useful for prioritizing the order in which different areas of APC should be tested. Our results underline the importance of RNA-level studies in molecular diagnosis of FAP.

Castellsague, Ester; Gonzalez, Sara; Guino, Elisabet; Stevens, Kristen N.; Borras, Ester; Raymond, Victoria M.; Lazaro, Conxi; Blanco, Ignacio; Gruber, Stephen B.; Capella, Gabriel

2010-01-01

194

Inferring selection intensity and allele age from multilocus haplotype structure.  

PubMed

It is a challenging task to infer selection intensity and allele age from population genetic data. Here we present a method that can efficiently estimate selection intensity and allele age from the multilocus haplotype structure in the vicinity of a segregating mutant under positive selection. We use a structured-coalescent approach to model the effect of directional selection on the gene genealogies of neutral markers linked to the selected mutant. The frequency trajectory of the selected allele follows the Wright-Fisher model. Given the position of the selected mutant, we propose a simplified multilocus haplotype model that can efficiently model the dynamics of the ancestral haplotypes under the joint influence of selection and recombination. This model approximates the ancestral genealogies of the sample, which reduces the number of states from an exponential function of the number of single-nucleotide polymorphism loci to a quadratic function. That allows parameter inference from data covering DNA regions as large as several hundred kilo-bases. Importance sampling algorithms are adopted to evaluate the probability of a sample by exploring the space of both allele frequency trajectories of the selected mutation and gene genealogies of the linked sites. We demonstrate by simulation that the method can accurately estimate selection intensity for moderate and strong positive selection. We apply the method to a data set of the G6PD gene in an African population and obtain an estimate of 0.0456 (95% confidence interval 0.0144-0.0769) for the selection intensity. The proposed method is novel in jointly modeling the multilocus haplotype pattern caused by recombination and mutation, allowing the analysis of haplotype data in recombining regions. Moreover, the method is applicable to data from populations under exponential growth and a variety of other demographic histories. PMID:23797107

Chen, Hua; Slatkin, Montgomery

2013-08-01

195

Cost-effective genome-wide estimation of allele frequencies from pooled DNA in Atlantic salmon (Salmo salar L.)  

PubMed Central

Background New sequencing technologies have tremendously increased the number of known molecular markers (single nucleotide polymorphisms; SNPs) in a variety of species. Concurrently, improvements to genotyping technology have now made it possible to efficiently genotype large numbers of genome-wide distributed SNPs enabling genome wide association studies (GWAS). However, genotyping significant numbers of individuals with large number of SNPs remains prohibitively expensive for many research groups. A possible solution to this problem is to determine allele frequencies from pooled DNA samples, such ‘allelotyping’ has been presented as a cost-effective alternative to individual genotyping and has become popular in human GWAS. In this article we have tested the effectiveness of DNA pooling to obtain accurate allele frequency estimates for Atlantic salmon (Salmo salar L.) populations using an Illumina SNP-chip. Results In total, 56 Atlantic salmon DNA pools from 14 populations were analyzed on an Atlantic salmon SNP-chip containing probes for 5568 SNP markers, 3928 of which were bi-allelic. We developed an efficient quality control filter which enables exclusion of loci showing high error rate and minor allele frequency (MAF) close to zero. After applying multiple quality control filters we obtained allele frequency estimates for 3631 bi-allelic loci. We observed high concordance (r > 0.99) between allele frequency estimates derived from individual genotyping and DNA pools. Our results also indicate that even relatively small DNA pools (35 individuals) can provide accurate allele frequency estimates for a given sample. Conclusions Despite of higher level of variation associated with array replicates compared to pool construction, we suggest that both sources of variation should be taken into account. This study demonstrates that DNA pooling allows fast and high-throughput determination of allele frequencies in Atlantic salmon enabling cost-efficient identification of informative markers for discrimination of populations at various geographical scales, as well as identification of loci controlling ecologically and economically important traits.

2013-01-01

196

Vntr Allele Frequency Distributions under the Stepwise Mutation Model: A Computer Simulation Approach  

PubMed Central

Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). We estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. We then compared our simulation expectations with actual data reported in the literature. We used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, we hypothesize that these three classes of loci are subject to different mutational forces.

Shriver, M. D.; Jin, L.; Chakraborty, R.; Boerwinkle, E.

1993-01-01

197

Multiple origins of Plasmodium falciparum dihydropteroate synthetase mutant alleles associated with sulfadoxine resistance in India.  

PubMed

With the spread of chloroquine (CQ)-resistant malaria in India, sulfadoxine-pyrimethamine (SP) alone or in combination with artesunate is used as an alternative antimalarial drug. Due to continuous drug pressure, the Plasmodium falciparum parasite is exhibiting resistance to antifolates because of mutations in candidate genes dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps). Our earlier study on flanking microsatellite markers of dhfr mutant alleles from India had shown a single origin of the pyrimethamine resistance and some minor haplotypes which shared haplotypes with Southeast Asian (Thailand) strains. In the present study, we have analyzed 193 of these Indian P. falciparum isolates for 15 microsatellite loci around dhps to investigate the genetic lineages of the mutant dhps alleles in different parts of the country. Eighty-one of these samples had mutant dhps alleles, of which 62 were from Andaman and Nicobar Islands and the remaining 19 were from mainland India. Of 112 isolates with a wild-type dhps allele, 109 were from mainland India and only 3 were from Andaman and Nicobar Islands. Consistent with the model of selection, the mean expected heterozygosity (H(e)) around mutant dhps alleles (H(e) = 0.55; n = 81) associated with sulfadoxine resistance was lower (P ? 0.05) than the mean H(e) around the wild-type dhps allele (H(e) = 0.80; n = 112). There was more genetic diversity in flanking microsatellites of dhps than dhfr among these isolates, which confirms the assertion that dhps mutations are at a very early stage of fixation in the parasite population. Microsatellite haplotypes around various mutant dhps alleles suggest that the resistant dhps alleles have multiple independent origins in India, especially in Andaman and Nicobar Islands. Determining the genetic lineages of the resistant dhps alleles on Andaman and Nicobar Islands and mainland India is significant, given the role of Asia in the intercontinental spread of chloroquine- and pyrimethamine-resistant parasites in the past. PMID:21422213

Lumb, Vanshika; Das, Manoj K; Singh, Neeru; Dev, Vas; Khan, Wajihullah; Sharma, Yagya D

2011-06-01

198

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion  

PubMed Central

Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression.

Garcia, Tzintzuni I.; Matos, Isa; Shen, Yingjia; Pabuwal, Vagmita; Coelho, Maria Manuela; Wakamatsu, Yuko; Schartl, Manfred; Walter, Ronald B.

2014-01-01

199

Parents Make a Difference.  

ERIC Educational Resources Information Center

This handbook discusses the following types of parent involvement in education: (1) decision-making; (2) parents as educators; (3) advocacy; (4) school support; and (5) parent education and support. The benefits of parent involvement are outlined. Examples from New York City's 1987-88 Parent Involvement Program (PIP) demonstrate that parent

Institute for Responsive Education, Boston, MA.

200

Identification of Transcriptome SNPs for Assessing Allele-Specific Gene Expression in a Super-Hybrid Rice Xieyou9308  

PubMed Central

Hybridization, a common process in nature, can give rise to a vast reservoir of allelic variants. Combination of these allelic variants may result in novel patterns of gene action and is thought to contribute to heterosis. In this study, we analyzed genome-wide allele-specific gene expression (ASGE) in the super-hybrid rice variety Xieyou9308 using RNA sequencing technology (RNA-Seq). We identified 9325 reliable single nucleotide polymorphisms (SNPs) distributed throughout the genome. Nearly 68% of the identified polymorphisms were CT and GA SNPs between R9308 and Xieqingzao B, suggesting the existence of DNA methylation, a heritable epigenetic mark, in the parents and their F1 hybrid. Of 2793 identified transcripts with consistent allelic biases, only 480 (17%) showed significant allelic biases during tillering and/or heading stages, implying that trans effects may mediate most transcriptional differences in hybrid offspring. Approximately 67% and 62% of the 480 transcripts showed R9308 allelic expression biases at tillering and heading stages, respectively. Transcripts with higher levels of gene expression in R9308 also exhibited R9308 allelic biases in the hybrid. In addition, 125 transcripts were identified with significant allelic expression biases at both stages, of which 74% showed R9308 allelic expression biases. R9308 alleles may tend to preserve their characteristic states of activity in the hybrid and may play important roles in hybrid vigor at both stages. The allelic expression of 355 transcripts was highly stage-specific, with divergent allelic expression patterns observed at different developmental stages. Many transcripts associated with stress resistance were differently regulated in the F1 hybrid. The results of this study may provide valuable insights into molecular mechanisms of heterosis.

Zhan, Xiaodeng; Shen, Xihong; Wu, Weiming; Yu, Ping; Zhang, Yingxin; Chen, Daibo; Wang, Huimin; Lin, Zechuan; Cao, Liyong; Cheng, Shihua

2013-01-01

201

Allelic variation in a willow warbler genomic region is associated with climate clines.  

PubMed

Local adaptation is an important process contributing to population differentiation which can occur in continuous or isolated populations connected by various amounts of gene flow. The willow warbler (Phylloscopus trochilus) is one of the most common songbirds in Fennoscandia. It has a continuous breeding distribution where it is found in all forested habitats from sea level to the tree line and therefore constitutes an ideal species for the study of locally adapted genes associated with environmental gradients. Previous studies in this species identified a genetic marker (AFLP-WW1) that showed a steep north-south cline in central Sweden with one allele associated with coastal lowland habitats and the other with mountainous habitats. It was further demonstrated that this marker is embedded in a highly differentiated chromosome region that spans several megabases. In the present study, we sampled 2,355 individuals at 128 sites across all of Fennoscandia to study the geographic and climatic variables associated with the allele frequency distributions of WW1. Our results demonstrate that 1) allele frequency patterns significantly differ between mountain and lowland populations, 2) these allele differences coincide with extreme temperature conditions and the short growing season in the mountains, and milder conditions in coastal areas, and 3) the northern-allele or "altitude variant" of WW1 occurs in willow warblers that occupy mountainous habitat regardless of subspecies. Finally these results suggest that climate may exert selection on the genomic region associated with these alleles and would allow us to develop testable predictions for the distribution of the genetic marker based on climate change scenarios. PMID:24788148

Larson, Keith W; Liedvogel, Miriam; Addison, Brianne; Kleven, Oddmund; Laskemoen, Terje; Lifjeld, Jan T; Lundberg, Max; Akesson, Susanne; Bensch, Staffan

2014-01-01

202

Allelic Variation in a Willow Warbler Genomic Region Is Associated with Climate Clines  

PubMed Central

Local adaptation is an important process contributing to population differentiation which can occur in continuous or isolated populations connected by various amounts of gene flow. The willow warbler (Phylloscopus trochilus) is one of the most common songbirds in Fennoscandia. It has a continuous breeding distribution where it is found in all forested habitats from sea level to the tree line and therefore constitutes an ideal species for the study of locally adapted genes associated with environmental gradients. Previous studies in this species identified a genetic marker (AFLP-WW1) that showed a steep north-south cline in central Sweden with one allele associated with coastal lowland habitats and the other with mountainous habitats. It was further demonstrated that this marker is embedded in a highly differentiated chromosome region that spans several megabases. In the present study, we sampled 2,355 individuals at 128 sites across all of Fennoscandia to study the geographic and climatic variables associated with the allele frequency distributions of WW1. Our results demonstrate that 1) allele frequency patterns significantly differ between mountain and lowland populations, 2) these allele differences coincide with extreme temperature conditions and the short growing season in the mountains, and milder conditions in coastal areas, and 3) the northern-allele or “altitude variant” of WW1 occurs in willow warblers that occupy mountainous habitat regardless of subspecies. Finally these results suggest that climate may exert selection on the genomic region associated with these alleles and would allow us to develop testable predictions for the distribution of the genetic marker based on climate change scenarios.

Larson, Keith W.; Liedvogel, Miriam; Addison, BriAnne; Kleven, Oddmund; Laskemoen, Terje; Lifjeld, Jan T.; Lundberg, Max; Akesson, Susanne; Bensch, Staffan

2014-01-01

203

Allele-specific gene expression uncovered  

Microsoft Academic Search

Genetic variation in populations can result in variation in levels of gene expression but the extent to which this occurs has been unclear. In this article, recent studies of allele-specific expression among autosomal non-imprinted genes are reviewed. These new data provide evidence that differential expression is relatively common and that allelic differences are heritable and can be highly context specific.

Julian C. Knight

2004-01-01

204

[Analysis of allelic content of genes responsible for baking properties in allocytoplasmic wheat hybrids].  

PubMed

A collection comprised of allocytoplasmic hybrids of mild wheat (ACPH) was screened for the allelic state of genes responsible for baking properties (high-molecular glutenins, puroindolines, and Waxy). The possibility of the introgression of the Waxy gene of T. timopheevii into the mild wheat genome was demonstrated in several ACPH samples using the set of molecular markers. Allelic gene variants responsible for the baking properties were revealed for 22 ACPH samples, which make it possible to detect the most challenging samples for both molecular-genetic research and applied science. PMID:24159803

Klimushina, M V; Divashuk, M G; Mukhammed, T A K; Semenov, O G; Karlov, G I

2013-05-01

205

Allele-specific deletion in exon I of the HRAS1 gene.  

PubMed Central

We have detected a 6-bp deletion in the untranslated first exon of a unique HRAS1 gene cloned from lymphocyte DNA of a familial melanoma patient. The deletion is without apparent functional consequence. Using an RNase protection assay, we have demonstrated the deletion in leukocyte DNAs of individuals unrelated to the patient. In these cases, the deletion marker is specifically associated with one class of common HRAS1 allele, thereby establishing the origin of the unique allele. We discuss the means by which DNA sequence heterogeneity at other loci may be rapidly analyzed. Images Figure 2 Figure 4

Kasperczyk, A; Mermer, B A; Parkinson, D R; Lonergan, J A; Krontiris, T G

1989-01-01

206

Development of simple sequence repeat markers for the soybean rust fungus, Phakopsora pachyrhizi.  

PubMed

Twenty-four simple sequence repeat markers were developed for Phakopsora pachyrhizi, a fungal pathogen of soybean (Glycine max) and other legumes. All 24 of the loci were evaluated on 28 isolates of P. pachyrhizi. Twenty-one loci were polymorphic, with allelic diversity ranging from two to eight alleles, and null alleles were observed for eight of the 24 loci. A preliminary screen with the closely related species, P. meibomiae, indicated that these primer pairs are specific to P. pachyrhizi. PMID:21586030

Anderson, Sharon J; Stone, Christine L; Posada-Buitrago, Martha Lucia; Boore, Jeffrey L; Neelam, Beena A; Stephens, Robert M; Luster, Douglas G; Frederick, Reid D; Pedley, Kerry F

2008-11-01

207

Allelic Diversity and Recombination in Campylobacter jejuni  

PubMed Central

The allelic diversity and population structure of Campylobacter jejuni were studied by multilocus nucleotide sequence analysis. Sequences from seven housekeeping genes were obtained from 32 C. jejuni isolates isolated from enteritis patients in Germany, Hungary, Thailand, and the United States. Also included was strain NCTC 11168, the complete genomic sequence of which has recently been published. For all loci analyzed, multiple strains carried identical alleles. The frequency of synonymous and nonsynonymous sequence polymorphisms was low. The number of unique alleles per locus ranged from 9 to 15. These alleles occurred in 31 different combinations (sequence types), so that all but two pairs of strains could be distinguished from each other. Sequences were analyzed for evidence of recombination by the homoplasy test and split decomposition. These analyses showed that intraspecific recombination is frequent in C. jejuni and has generated extensive diversity of allelic profiles from a small number of polymorphic nucleotides.

Suerbaum, Sebastian; Lohrengel, Marc; Sonnevend, Agnes; Ruberg, Florian; Kist, Manfred

2001-01-01

208

Global RNA sequencing reveals that genotype-dependent allele-specific expression contributes to differential expression in rice F1 hybrids  

PubMed Central

Background Extensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions. Results We report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637–3,824 genes from three rice F1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F1 and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F1 hybrids of rice. Conclusions Analysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F1 hybrids.

2013-01-01

209

Interspecific Backcross Mice Show Sex-Specific Differences in Allelic Inheritance  

PubMed Central

Transmission distortion is identified as a difference in transmission frequency of two alleles from the normal 1:1 Mendelian segregation in diploid organisms. Transmission distortion can extend over part or all of a chromosome. The recent development of interspecific mouse backcrosses has provided a powerful method for multilocus mapping of entire chromosomes in a single cross, and consequently for identifying distortions in allelic inheritance. We used an interspecific backcross of [(C57BL/6J X Mus spretus)F(1) X C57BL/6J] mice to map molecular loci to mouse chromosome 2 and had previously found that the distal region of the chromosome showed distortions in allelic inheritance. We now report the mapping of five loci (Actc-1, D2Hgu1, His-1, Hox-4.1 and Neb) to chromosome 2, which, in addition to the Abl, Ada, B2m, Bmp-2a, Hc, Emv-15, Fshb, Hck-1, Pax-1, Pck-1, Spna-2 and Vim loci previously mapped in our interspecific backcross, serve as markers to measure allelic inheritance along ~75% of mouse chromosome 2. Statistical analyses are used to identify and delimit chromosomal regions showing transmission distortion and to determine whether there are sex-specific differences in allelic inheritance. These studies provide evidence for sex-specific differences in allelic inheritance for chromosome 2 and suggest biological explanations for this form of transmission distortion.

Siracusa, L. D.; Alvord, W. G.; Bickmore, W. A.; Jenkins, N. A.; Copeland, N. G.

1991-01-01

210

Identity-by-Descent Matrix Decomposition Using Latent Ancestral Allele Models  

PubMed Central

Genetic linkage and association studies are empowered by proper modeling of relatedness among individuals. Such relatedness can be inferred from marker and/or pedigree information. In this study, the genetic relatedness among n inbred individuals at a particular locus is expressed as an n × n square matrix Q. The elements of Q are identity-by-descent probabilities, that is, probabilities that two individuals share an allele descended from a common ancestor. In this representation the definition of the ancestral alleles and their number remains implicit. For human inspection and further analysis, an explicit representation in terms of the ancestral allele origin and the number of alleles is desirable. To this purpose, we decompose the matrix Q by a latent class model with K classes (latent ancestral alleles). Let P be an n × K matrix with assignment probabilities of n individuals to K classes constrained such that every element is nonnegative and each row sums to 1. The problem then amounts to approximating Q by PPT, while disregarding the diagonal elements. This is not an eigenvalue problem because of the constraints on P. An efficient algorithm for calculating P is provided. We indicate the potential utility of the latent ancestral allele model. For representative locus-specific Q matrices constructed for a set of maize inbreds, the proposed model recovered the known ancestry.

Braak, Cajo J. F. ter; Boer, Martin P.; Totir, L. Radu; Winkler, Christopher R.; Smith, Oscar S.; Bink, Marco C. A. M.

2010-01-01

211

Interspecific backcross mice show sex-specific differences in allelic inheritance.  

PubMed

Transmission distortion is identified as a difference in transmission frequency of two alleles from the normal 1:1 Mendelian segregation in diploid organisms. Transmission distortion can extend over part or all of a chromosome. The recent development of interspecific mouse backcrosses has provided a powerful method for multilocus mapping of entire chromosomes in a single cross, and consequently for identifying distortions in allelic inheritance. We used an interspecific backcross of [(C57BL/6J x Mus spretus)F1 x C57BL/6J] mice to map molecular loci to mouse chromosome 2 and had previously found that the distal region of the chromosome showed distortions in allelic inheritance. We now report the mapping of five loci (Actc-1, D2Hgu1, His-1, Hox-4.1 and Neb) to chromosome 2, which, in addition to the Abl, Ada, B2m, Bmp-2a, Hc, Emv-15, Fshb, Hck-1, Pax-1, Pck-1, Spna-2 and Vim loci previously mapped in our interspecific backcross, serve as markers to measure allelic inheritance along approximately 75% of mouse chromosome 2. Statistical analyses are used to identify and delimit chromosomal regions showing transmission distortion and to determine whether there are sex-specific differences in allelic inheritance. These studies provide evidence for sex-specific differences in allelic inheritance for chromosome 2 and suggest biological explanations for this form of transmission distortion. PMID:1916246

Siracusa, L D; Alvord, W G; Bickmore, W A; Jenkins, N A; Copeland, N G

1991-08-01

212

An association between Manic-depressive illness and a pseudoautosomal DNA marker  

SciTech Connect

This article reports on the association between manic-depressive illness and a polymorphic DNA marker in the pseudoautosomal region (Xp22.32; Yp11.3). The authors studied two markers in 49 biologically unrelated patients and 119 normal controls. Probe 362A (DXYS20) identified four alleles. Frequencies of the A4 allele were significantly higher in patients than in controls. 9 refs., 1 tab.

Yoneda, Hiroshi; Sakai, Toshiaki; Ishida, Toru; Inayama, Yasuhiro; Nonomura, Yasuhiro; Kono, Yoshihiro; Asaba, Hiroyuki (Osaka Medical Center (Japan))

1992-11-01

213

Cultivar Identification and Genetic Fingerprinting of Guava (Psidium guajava) Using Microsatellite Markers  

Microsoft Academic Search

Guavas (Psidium guajava) are perennial fruit trees cultivated in tropical and subtropical areas of the world. In this study, we have characterized nine guava cultivars using 23 microsatellite markers. The number of alleles ranged from 3 to 12 with a mean of 6.39 alleles per locus. The polymorphic information content of the markers ranged from 0.340 to 0.900 with a

Kanupriya; P. Madhavi Latha; C. Aswath; Laxman Reddy; B. Padmakar; C. Vasugi; M. R. Dinesh

2011-01-01

214

Multiple heterologies increase mitotic double-strand break-induced allelic gene conversion tract lengths in yeast.  

PubMed Central

Spontaneous and double-strand break (DSB)-induced allelic recombination in yeast was investigated in crosses between ura3 heteroalleles inactivated by an HO site and a +1 frameshift mutation, with flanking markers defining a 3.4-kbp interval. In some crosses, nine additional phenotypically silent RFLP mutations were present at approximately 100-bp intervals. Increasing heterology from 0.2 to 1% in this interval reduced spontaneous, but not DSB-induced, recombination. For DSB-induced events, 75% were continuous tract gene conversions without a crossover in this interval; discontinuous tracts and conversions associated with a crossover each comprised approximately 7% of events, and 10% also converted markers in unbroken alleles. Loss of heterozygosity was seen for all markers centromere distal to the HO site in 50% of products; such loss could reflect gene conversion, break-induced replication, chromosome loss, or G2 crossovers. Using telomere-marked strains we determined that nearly all allelic DSB repair occurs by gene conversion. We further show that most allelic conversion results from mismatch repair of heteroduplex DNA. Interestingly, markers shared between the sparsely and densely marked interval converted at higher rates in the densely marked interval. Thus, the extra markers increased gene conversion tract lengths, which may reflect mismatch repair-induced recombination, or a shift from restoration- to conversion-type repair.

Nickoloff, J A; Sweetser, D B; Clikeman, J A; Khalsa, G J; Wheeler, S L

1999-01-01

215

A multicopy dinucleotide marker that maps close to the spinal muscular atrophy gene  

Microsoft Academic Search

Spinal muscular atrophy (SMA) is a common autosomal recessive disorder resulting in loss of motor neurons. The interval containing the SMA gene has been defined by linkage analysis as 5qcen-D5S435-SMA-D5S557-5qter. The authors have isolated a new dinucleotide repeat marker, CATT1, that lies between these two closest markers. The marker CATT1 has 16 alleles and is highly polymorphic. The marker can

A. H. M. Burghes; S. E. Ingraham; Z. Kote-Jarai; J. D. Carpten; C. J. DiDonato; M. McLean; L. Surh; T. G. Thompson; J. D. McPherson; J. E. Ikeda; B. Wirth

1994-01-01

216

Tetranucleotide microsatellite markers in Ctenomys torquatus (Rodentia)  

Microsoft Academic Search

Eleven microsatellite markers were isolated from an enriched library developed specifically for the tuco-tuco Ctenomys torquatus, using tri and tetranucleotide probes. Ten of these were successfully amplified, and only one was monomorphic for the populations\\u000a that have so far been analyzed. Analysis of two different populations yielded a mean of 2.6 (Cachoeira do Sul—CAC) and 4.3\\u000a (Butiá—BUT) alleles per locus,

Paula A. Roratto; Marlise L. Bartholomei-Santos; Thales R. O. de Freitas

217

Transmission of an FMR1 premutation allele in a large family identified through newborn screening: the role of AGG interruptions  

PubMed Central

The CGG repeat within the premutation range in the FMR1 gene can lead to neurodegenerative disorders and intellectual disabilities. An increase in size upon transmission from parent to child is more likely to occur for larger alleles and without AGG interruptions. We describe the molecular structure and the transmission of an FMR1 premutation allele in a multigenerational family, identified through newborn screening for fragile X syndrome. Transmission of the premutation allele was traced through 5 generations in 14 of the 23 individuals who were genotyped through cascade testing. Allele size instability during transmission was observed but no expansions to a full mutation were detected. Clinical and molecular characterizations of the participants lead to the diagnosis of FXTAS in one subject identified as a premutation carrier. A gradual small increase in the size of the premutation allele was observed during transmission through five generations. The relative stability is likely due to the presence of two AGGs within the allele. The detection of AGG interruptions within the premutation alleles is important in genetic counseling to better predict the risk of expansion during transmission from a premutation to a full mutation allele.

Yrigollen, Carolyn M.; Mendoza-Morales, Guadalupe; Hagerman, Randi; Tassone, Flora

2014-01-01

218

Transmission of an FMR1 premutation allele in a large family identified through newborn screening: the role of AGG interruptions.  

PubMed

The CGG repeat within the premutation range in the fragile X mental retardation 1 (FMR1) gene can lead to neurodegenerative disorders and intellectual disabilities. An increase in size upon the transmission from parent to child is more likely to occur for larger alleles and without AGG interruptions. We describe the molecular structure and the transmission of an FMR1 premutation allele in a multigenerational family, identified through newborn screening for fragile X syndrome. Transmission of the premutation allele was traced through five generations in 14 of the 23 individuals who were genotyped through cascade testing. Allele size instability during transmission was observed, but no expansions to a full mutation were detected. Clinical and molecular characterizations of the participants lead to the diagnosis of fragile X-associated tremor ataxia syndrome in one subject identified as a premutation carrier. A gradual small increase in the size of the premutation allele was observed during transmission through five generations. The relative stability is likely due to the presence of two AGGs within the allele. The detection of AGG interruptions within the premutation alleles is important in genetic counseling, to better predict the risk of expansion during transmission from a premutation to a full-mutation allele. PMID:23739124

Yrigollen, Carolyn M; Mendoza-Morales, Guadalupe; Hagerman, Randi; Tassone, Flora

2013-08-01

219

Parental Influences on Adolescent Adjustment: Parenting Styles Versus Parenting Practices  

ERIC Educational Resources Information Center

The study identified distinct patterns of parental practices that differentially influence adolescent behavior using the National Educational Longitudinal Survey (NELS:88) database. Following Brenner and Fox's research model (1999), the cluster analysis was used to classify the four types of parental practices. The clusters of parenting practices…

Lee, Sang Min; Daniels, M. Harry; Kissinger, Daniel B.

2006-01-01

220

Allelic imbalance in selected chromosomal regions in ovarian cancer.  

PubMed

Ovarian cancer (OC) is often asymptomatic at the initial stage. When diagnosed, up to 75% of the patients present grade III or IV tumors with metastasis in nearby organs of the abdomen. Genetic imbalance is abundant in OC, and allelic loss (AL) of specific chromosomal regions is considered an early event. To establish association between genetic markers for early diagnosis/prognosis of OC, our target was to define narrow specific regions of AL. We analyzed 65 ovarian carcinomas by using 19 microsatellite markers located in three different chromosomes. First, a 7.6-Mb region containing the estrogen receptor (ESR1) and the tumor suppressor gene LATS1 was analyzed. Several chromosomal breakpoints flanking ESR1 affecting the region harboring LATS1 were found. Second, we found chromosomal breakpoints on 13q13.1 approximately q13.3 that defined two narrow regions flanking the BRCA2 locus. Third, our ovarian tumors exhibited a very high frequency of AL on 16q and chromosomal breakpoints defining two narrow regions within 16q22.2 approximately q24.3. In this article, we report three new polymorphic microsatellite markers and strong evidence of AL of narrow well-defined regions in hot spots on 6q, 13q, and 16q in ovarian tumors. PMID:12547149

Hansen, Lise Lotte; Jensen, Lise Lind; Dimitrakakis, Constantine; Michalas, Stylianos; Gilbert, Fred; Barber, Hugh R K; Overgaard, Jens; Arzimanoglou, Iordanis I

2002-11-01

221

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles  

PubMed Central

Background Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200?bp (total of 24?kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Results Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Conclusion Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.

2012-01-01

222

Optimal Design for Marker-assisted Gene Pyramiding in Cross Population  

PubMed Central

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A–E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies.

Xu, L. Y.; Zhao, F. P.; Sheng, X. H.; Ren, H. X.; Zhang, L.; Wei, C. H.; Du, L. X.

2012-01-01

223

Parent-Offspring Conflict  

Microsoft Academic Search

synopsis. When parent-offspring relations in sexually reproducing species are viewed from the standpoint of the offspring as well as the parent, conflict is seen to be an expected feature of such relations. In particular, parent and offspring are expected to disagree over how long the period of parental investment should last, over the amount of parental investment that should be

ROBERT L. TRIVERS

1974-01-01

224

Adolescent Violence toward Parents.  

ERIC Educational Resources Information Center

Used National Survey of Youth data to examine extent and cause of adolescent assaults on parents. Found adolescents most likely to assault parents had parent-assaulting friends; approved of delinquent and violent behavior; believed low probability of official sanction for parental assault; were weakly attached to parents; and were White.…

Agnew, Robert; Huguley, Sandra

1989-01-01

225

Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar  

PubMed Central

Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera ‘Chinese Antique’ and N. lutea ‘AL1’, and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of ‘Chinese Antique’. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of ‘Chinese Antique’. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection.

2012-01-01

226

Locus-specific brackets for reliable typing of Y-chromosome short tandem repeat markers.  

PubMed

Short tandem repeat (STR) loci, widely used as genetic markers in disease diagnostic studies and human identity applications, are traditionally genotyped through comparison of allele sizes to a sequenced allelic ladder. Allelic ladders permit a floating bin allele calling method to be utilized, which enables reliable allele calling across laboratories, instrument platforms, and electrophoretic conditions. Precise sizing methods for STR allele calling involving fixed bins can also be used when a high degree of precision has been demonstrated within an instrument platform and a set of electrophoretic conditions. An alternative method for reliable genotyping of STR markers, locus-specific brackets (LSBs), is introduced here. LSBs are artificial alleles created through molecular biology manipulations to be shorter or longer than alleles commonly seen in populations under investigation. The size and repeat number of measured alleles are interpolated between the two LSB products that are mixed with the polymerase chain reaction-amplified STR alleles. The advantages and limitations of the LSB approach are described along with a concordance study between the LSB typing approach and other STR typing methods. Complete agreement was observed with 162 samples studied at 5 Y-chromosome loci. PMID:15934054

Butler, John M; Appleby, Jill E; Duewer, David L

2005-06-01

227

A standardized microsatellite marker panel for parentage and kinship analyses in channel catfish, Ictalurus punctatus.  

PubMed

This research was designed to produce a standardized set of microsatellite loci for parentage and kinship analyses in channel catfish, the leading species of US aquaculture. Three panels of five to six markers each were developed that contained a total of two dinucleotide-, eight trinucleotide- and seven tetranucleotide-microsatellite loci respectively. The loci had a range of nine to 31 alleles per locus in an outbred population. Based on the allele frequencies measured in commercial randomly bred broodstock, the combined probability of non-exclusion of an unrelated candidate parent pair was 5.36e-18. The combined probability of non-exclusion of unrelated identical genotypes was 2.58e-08. The microsatellite panels were validated by parentage and kinship evaluation in three populations. A total of 697 spawns were collected from matings of outbred broodstock over three spawning seasons, and parents were determined unambiguously for all but three spawns. Genotype analysis also enabled the identification of half-sibling and full-sibling families produced by pond spawning. In a second experiment, parentage was unambiguously determined in nine spawns from a population consisting of broodstock derived from only four families. A third experiment demonstrated that all but one of 374 individuals from 10 full-sibling families could be assigned to a family after coculture in an earthen pond for 1 year. The standardized microsatellite panels enable the development of pedigreed catfish populations and large-scale performance evaluations in common environments to support the genetic improvement of cultured catfish through selective breeding. PMID:23216371

Waldbieser, G C; Bosworth, B G

2013-08-01

228

QTL detection power of multi-parental RIL populations in Arabidopsis thaliana  

PubMed Central

A major goal of today's biology is to understand the genetic basis of quantitative traits. This can be achieved by statistical methods that evaluate the association between molecular marker variation and phenotypic variation in different types of mapping populations. The objective of this work was to evaluate the statistical power of quantitative trait loci (QTL) detection of various multi-parental mating designs, as well as to assess the reasons for the observed differences. Our study was based on an empirical data of 20 Arabidopsis thaliana accessions, which have been selected to capture the maximum genetic diversity. The examined mating designs differed strongly with respect to the statistical power to detect QTL. We observed the highest power to detect QTL for the diallel cross with random mating design. The results of our study suggested that performing sibling mating within subpopulations of joint-linkage mapping populations has the potential to considerably increase the power for QTL detection. Our results, however, revealed that using designs in which more than two parental alleles segregate in each subpopulation increases the power even more.

Klasen, J R; Piepho, H-P; Stich, B

2012-01-01

229

Association Between Loci With Deleterious Alleles and Distorted Sex Ratios in an Inbred Line of Tilapia (Oreochromis aureus)  

Microsoft Academic Search

Three microsatellite markers (UNH159, UNH231, and UNH216) were examined for association with both deleterious genes and sex-ratio distortions in a full-sib family of 222 progeny from the fourth generation of a meiogynogenetic tilapia line (Or- eochromis aureus). The three markers were mapped previously to different linkage groups and were shown to be associated with genes with deleterious alleles in this

A. Shirak; Y. Palti; A. Cnaani; A. Korol; G. Hulata; M. Ron; R. R. Avtalion

2002-01-01

230

Evidence of a segregation ratio distortion of SMN1 alleles in spinal muscular atrophy.  

PubMed

Spinal muscular atrophy (SMA) is an autosomal recessive disorder characterised by degeneration and loss of the motor neurons of the anterior horn of the spinal cord. The absence of SMN1 is determinant to have SMA and parents of SMA patients are regarded as carriers of the disease. We compared the segregation ratio of the mutated allele and the wild-type allele of all the confirmed carrier parents assuming Mendelian proportions. Results of transmissions in 235 prenatal tests and in 128 unaffected siblings showed a statistically significant deviation in favour of the wild-type SMN1 allele. The number of affected foetuses and carriers were lower than that expected. No significant differences in the sex ratio or in the progenitor origin of the transmitted allele to the carriers were found. One hypothesis that has been advanced to account for the distortion observed in affected foetuses is the negative postzygote selection due to early miscarriage. However, given that the number of carriers in our series was lower than expected, prezygote events such as meiotic drive, survival of gametes or preferential fertilisation should also be considered. PMID:17625510

Alias, Laura; Barceló, Maria J; Gich, Ignasi; Estapé, Marta; Parra, Juan; Amenedo, Maria; Baiget, Montserrat; Tizzano, Eduardo F

2007-10-01

231

Allelic association at the D14S43 locus in early onset Alzheimer`s disease  

SciTech Connect

The D14S43 marker is closely linked to the major gene for early onset autosomal dominant Alzheimer`s disease on chromosome 14. Allelic frequencies at the D14S43 locus were compared in 113 familial and isolated cases of early onset Alzheimer`s disease (<60 years of age at onset) (EOAD) and 109 unaffected individuals of the same geographic origin. Allele 7 was significantly (P = 0.033) more frequent in type 1 EOAD patients (13.2%), defined by the presence of at least another first degree relative with EOAD, than in controls (4.1%). Since an autosomal dominant gene is probably responsible for type 1 patients, allelic association may reflect linkage disequilibrium at the D14S43 locus. This would mean that some patients share a common ancestral mutation. However, since multiple tests were carried out, this result must be interpreted with caution, and needs confirmation in an independent sample. 16 refs., 2 tabs.

Brice, A.; Tardieu, S.; Campion, D.; Martinez, M. [and others

1995-04-24

232

Allelic variation of the ? -, ? - and ? -kafirin genes in diverse Sorghum genotypes  

Microsoft Academic Search

The ?-, ?- and ?-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic diversity of seed storage proteins. A range of grain sorghums, including inbred parents\\u000a from internationally diverse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus\\u000a exists

H. K. C. Laidlaw; E. S. Mace; S. B. Williams; K. Sakrewski; A. M. Mudge; P. J. Prentis; D. R. Jordan; I. D. Godwin

2010-01-01

233

Questions about Biological Parents  

MedlinePLUS

... About Biological Parents Family Life Listen Questions About Biological Parents Article Body As you raise your adopted ... to her life—the fact that she has biological parents elsewhere—that may make it necessary for ...

234

The Rights of Parents.  

ERIC Educational Resources Information Center

This article describes the rights of parents as they relate to the education of their children. Topics include legal sources of parents' rights; parent involvement; freedom of religion, conscience, and expression; and political rights. (DS)

Fischer, Louis; Schimmel, David

1978-01-01

235

Nucleation and Spread of an Invasive Allele  

NASA Astrophysics Data System (ADS)

We analyze a prototypical discrete spatial model for the spread of an invasive allele when individuals compete preemptively for common limiting resources. Initially, the population is genetically monomorphic with the resident allele at high density. The invasive allele is introduced through rare, but recurrent, mutation. The mutant allele is the better competitor (has an individual-level advantage) but its spread is limited by the local availability of resources. We find that each successful introduction of the mutant leads to strong spatial clustering. Spatial patterns in simulation resemble nucleation and subsequent growth, articulately described by Avrami's law in sufficiently large systemsootnotetextG. Korniss and T. Caraco, J. Theor. Biol. (in press, 2004); http://www.rpi.edu/ korniss/Research/JTB04.pdf.

Korniss, Gyorgy; Caraco, Thomas

2005-03-01

236

Tetranucleotide microsatellite markers in Cryptomeria japonica D. Don  

Microsoft Academic Search

Japanese cedar (Cryptomeria japonica D. Don) is an important ecological and commercial species in Japan. We isolated 11 polymorphic tetranucleotide microsatellite\\u000a markers by using a ligation-mediated suppression PCR technique for Japanese cedar and investigated the polymorphism of these\\u000a markers in 24 individuals from natural populations. The number of alleles ranged from 6 to 20 per locus, and expected heterozygosities\\u000a of the

L. Guan; S. Shiraishi

2011-01-01

237

Paternity analysis using microsatellite markers to identify pollen donors in an olive grove.  

PubMed

Olive (Olea europaea L.) is a wind-pollinated, allogamous species that is generally not considered to be self-compatible. In addition, cross-incompatibilities exist between cultivars that can result in low fruit set if compatible pollinisers are not planted nearby. In this study, microsatellite markers were used to identify 17 genotypes that were potential pollen donors in a commercial olive orchard. DNA typing with the same primers was also applied to 800 olive embryos collected from five cultivars in the grove over 2 years of study. Pollen donors for the cultivars Barnea, Corregiola, Kalamata, Koroneiki, and Mission were estimated by paternity analysis, based on the parental contribution of alleles in the genotypes of the embryos. The exclusion probability for the marker set was 0.998 and paternity was assigned on the basis of the 'most likely method'. Different pollen donors were identified for each of the maternal cultivars indicating that cross-compatibilities and incompatibilities varied between the genotypes studied. Cross-pollination was the principal method of fertilization, as selfing was only observed in two of the embryos studied and both of these were from the cultivar Mission. This is the first report where these techniques have been applied to survey the pollination patterns in an olive grove. The results indicate that careful planning in orchard design is required for efficient pollination between olive cultivars. PMID:16133312

Mookerjee, Sonali; Guerin, Jenny; Collins, Graham; Ford, Chris; Sedgley, Margaret

2005-10-01

238

A set of microsatellite markers for fingerprinting and breeding applications in Pinus radiata.  

PubMed

Fifty microsatellite markers were developed and characterized in Pinus radiata, and from among these, a subset of 10 easily scored and highly polymorphic markers was selected for use in fingerprinting, quality control, and breeding applications. The markers were characterized based on reliable and reproducible amplification, observed and expected heterozygosities, number of alleles, a low frequency of null alleles, and a lack of close linkage with other selected markers. Allele numbers and frequencies were estimated using 24 first-generation breeding clones from Australia and New Zealand. Observed heterozygosities for the selected markers were all greater than 0.67, and there was an average of 10.5 alleles/locus. The occurrence of null alleles was checked with megagametophytes from mother trees for loci that appeared to be homozygous. The 10 markers are not closely linked (r < 0.20 and LOD > 3) to each other. The selected microsatellites fall into three discrete size classes, and with appropriate selection of fluorescent dyes for 5' end labeling, can be multiplexed with up to 6 markers/sample on an ABI PRISM 310 or similar instrument. PMID:12416633

Devey, M E; Bell, J C; Uren, T L; Moran, G F

2002-10-01

239

Resilient Parenting: Overcoming Poor Parental Bonding  

ERIC Educational Resources Information Center

This study identified groups of mothers with varying patterns of adaptive functioning and bonds with their own parents. These patterns were related to mothers' parenting of their own children to understand how some mothers avoid repeating the cycle of poor parenting. Data from 210 new mothers were analyzed before hospital discharge about bonding…

Travis, Wendy J.; Combs-Orme, Terri

2007-01-01

240

Alleles of the Human Mu Opioid Receptor, Diagnostic Methods using said Alleles, and Methods of Treatment Based Thereon.  

National Technical Information Service (NTIS)

Provided herein are variant alleles of a gene encoding a mu opioid receptor, along with cloning vectors for replicating such variant alleles, expressing vectors for expressing the variant alleles to produce variant mu opioid receptors, and antibodies to s...

K. S. LaForge M. J. Kreek

2006-01-01

241

Allelic loss and linkage studies in prostate cancer  

SciTech Connect

Prostate cancer is the most common malignancy in U.S. males. Many examples of familial aggregation have been reported, and segregration analysis suggests that an autosomal dominant gene with a penetrance of 88% by age 85 accounts for 9% of all cases. Because many dominant cancer predisposition syndromes are related to germline mutations in tumor suppressor genes, we analyzed a series of sporadic and hereditary tumors for allelic loss. High grade sporadic, paraffin-embedded, primary prostate tumors were obtained from the archival collection in the Department of Pathology at Yale and hereditary tumors from three families were obtained by an advertisement in the New York Times and from referrals by urologists. PCR analysis showed loss in 4/7 informative sporadic prostate tumors with NEFL (8p21), in 8/22 informative tumors with D10S169 (10q26-qter), in 2/8 informative tumors with D10S108 (10q) and in 4/23 informative tumors with D10S89 (10p) in agreement with previous studies. PYGM on chromosome 11 and D9S127 on chromosome 9 showed no loss. Linkage analysis with NEFL in 3 prostate cancer families gave strongly negative results for close linkage (Z=-2.1 at {theta}=0.01) but LOD scores were very dependent on parameters, e.g. gene frequency, phenocopy rate, and penetrance. Linkage analysis with chromosome 10 markers and systematic analysis of the genome for other area of allelic loss are underway.

Johnson, D.R.; Bale, A.E.; Lytton, B. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

1994-09-01

242

High resolution mapping of trypanosomosis resistance loci Tir2 and Tir3 using F12 advanced intercross lines with major locus Tir1 fixed for the susceptible allele  

PubMed Central

Background Trypanosomosis is the most economically important disease constraint to livestock productivity in Africa. A number of trypanotolerant cattle breeds are found in West Africa, and identification of the genes conferring trypanotolerance could lead to effective means of genetic selection for trypanotolerance. In this context, high resolution mapping in mouse models are a promising approach to identifying the genes associated with trypanotolerance. In previous studies, using F2 C57BL/6J × A/J and C57BL/6J × BALB/cJ mouse resource populations, trypanotolerance QTL were mapped within a large genomic intervals of 20-40 cM to chromosomes MMU17, 5 and 1, and denoted Tir1, Tir2 and Tir3 respectively. Subsequently, using F6 C57BL/6J × A/J and C57BL/6J × BALB/cJ F6 advanced intercross lines (AIL), Tir1 was fine mapped to a confidence interval (CI) of less than 1 cM, while Tir2 and Tir3, were mapped within 5-12 cM. Tir1 represents the major trypanotolerance QTL. Results In order to improve map resolutions of Tir2 and Tir3, an F12 C57BL/6J × A/J AIL population fixed for the susceptible alleles at Tir1 QTL was generated. An F12 C57BL/6J × A/J AIL population, fixed for the resistant alleles at Tir1 QTL was also generated to provide an additional estimate of the gene effect of Tir1. The AIL populations homozygous for the resistant and susceptible Tir1 alleles and the parental controls were challenged with T. congolense and followed for survival times over 180 days. Mice from the two survival extremes of the F12 AIL population fixed for the susceptible alleles at Tir1 were genotyped with a dense panel of microsatellite markers spanning the Tir2 and Tir3 genomic regions and QTL mapping was performed. Tir2 was fine mapped to less than 1 cM CI while Tir3 was mapped to three intervals named Tir3a, Tir3b and Tir3c with 95% confidence intervals (CI) of 6, 7.2 and 2.2 cM, respectively. Conclusions The mapped QTL regions encompass genes that are vital to innate immune response and can be potential candidate genes for the underlying QTL.

2010-01-01

243

Heterogeneity in IBD Allele Sharing among Covariate-Defined Subgroups: Issues and Findings for Affected Relatives  

Microsoft Academic Search

Objectives: Modelling of variation in identical-by-descent (IBD) allele sharing using covariates can increase power to detect linkage, identify covariate-defined subgroups linked to particular marker regions, and improve the design of subsequent studies to localize genes and characterize their effects. In this report, we highlight issues that arise in studies of families with affected relatives. Methods: Mirea et al. [Genet Epidemiol

Shelley B. Bull; Lucia Mirea; Laurent Briollais; Alexander G. Logan

2003-01-01

244

Methods to evaluate populations for alleles to improve an elite hybrid.  

PubMed

Elite hybrids can be improved by the introgression of favorable alleles not already present in the hybrid. Our first objective was to evaluate several estimators derived from quantitative genetic theory that attempt to quantify the relative number of useful alleles in potential donor populations. Secondly, we wanted to evaluate two proposed ways of determining relatedness of donor populations to the parents of the elite hybrid. Two experiments, each consisting of 21 maize populations of known pedigree, were grown at three and four environments in Minnesota in 1991. Yield and plant height means were used to provide estimates of each of the following statistics: (1) LPLU, a minimally biased statistic, (2) UBND, the minimum estimate of an upper bound, (3) NI, the net improvement, (4) PTC, the predicted three-way cross, and (5) TCSC, the testcross of the populations. These statistics are biased estimators of the relative number of unique favorable alleles contained within a population compared to a reference elite hybrid. Based on rank correlations, all statistics except NI ranked populations similarly. The percent novel germplasm relative to the single cross to be improved was positively correlated with the estimates of favorable alleles except when NI was used as the estimator. The relationship estimators agreed with the genetic constitution of the donor populations. Strong positive correlations existed between diversity, based on the relationship rankings, and all the estimator rankings, except NI. Potential donor populations were effectively identified by LPLU, UBND, PTC, and TCSC. NI was not a good estimator of unique favorable alleles. PMID:24186159

Fabrizius, M A; Openshaw, S J

1994-08-01

245

Multi-allelic phenotyping--a systematic approach for the simultaneous analysis of multiple induced mutations.  

PubMed

The zebrafish mutation project (ZMP) aims to generate a loss of function allele for every protein-coding gene, but importantly to also characterise the phenotypes of these alleles during the first five days of development. Such a large-scale screen requires a systematic approach both to identifying phenotypes, and also to linking those phenotypes to specific mutations. This phenotyping pipeline simultaneously assesses the consequences of multiple alleles in a two-step process. First, mutations that do not produce a visible phenotype during the first five days of development are identified, while a second round of phenotyping focuses on detailed analysis of those alleles that are suspected to cause a phenotype. Allele-specific PCR single nucleotide polymorphism (SNP) assays are used to genotype F2 parents and individual F3 fry for mutations known to be present in the F1 founder. With this method specific phenotypes can be linked to induced mutations. In addition a method is described for cryopreserving sperm samples of mutagenised males and their subsequent use for in vitro fertilisation to generate F2 families for phenotyping. Ultimately this approach will lead to the functional annotation of the zebrafish genome, which will deepen our understanding of gene function in development and disease. PMID:23624102

Dooley, Christopher M; Scahill, Catherine; Fényes, Fruzsina; Kettleborough, Ross N W; Stemple, Derek L; Busch-Nentwich, Elisabeth M

2013-08-15

246

Multi-allelic phenotyping - A systematic approach for the simultaneous analysis of multiple induced mutations?  

PubMed Central

The zebrafish mutation project (ZMP) aims to generate a loss of function allele for every protein-coding gene, but importantly to also characterise the phenotypes of these alleles during the first five days of development. Such a large-scale screen requires a systematic approach both to identifying phenotypes, and also to linking those phenotypes to specific mutations. This phenotyping pipeline simultaneously assesses the consequences of multiple alleles in a two-step process. First, mutations that do not produce a visible phenotype during the first five days of development are identified, while a second round of phenotyping focuses on detailed analysis of those alleles that are suspected to cause a phenotype. Allele-specific PCR single nucleotide polymorphism (SNP) assays are used to genotype F2 parents and individual F3 fry for mutations known to be present in the F1 founder. With this method specific phenotypes can be linked to induced mutations. In addition a method is described for cryopreserving sperm samples of mutagenised males and their subsequent use for in vitro fertilisation to generate F2 families for phenotyping. Ultimately this approach will lead to the functional annotation of the zebrafish genome, which will deepen our understanding of gene function in development and disease.

Dooley, Christopher M.; Scahill, Catherine; Fenyes, Fruzsina; Kettleborough, Ross N.W.; Stemple, Derek L.; Busch-Nentwich, Elisabeth M.

2013-01-01

247

Allele-specific silencing of the dominant disease allele in sialuria by RNA interference  

PubMed Central

Dominant disease alleles are attractive therapeutic targets for allele-specific gene silencing by small interfering RNA (siRNA). Sialuria is a dominant disorder caused by missense mutations in the allosteric site of GNE, coding for the rate-limiting enzyme of sialic acid biosynthesis, UDP-GlcNAc 2-epimerase/ManNAc kinase. The resultant loss of feedback inhibition of GNE-epimerase activity by CMP-sialic acid causes excessive production of free sialic acid. For this study we employed synthetic siRNAs specifically targeting the dominant GNE mutation c.797G>A (p.R266Q) in sialuria fibroblasts. We demonstrated successful siRNA-mediated down-regulation of the mutant allele by allele-specific real-time PCR. Importantly, mutant allele-specific silencing resulted in a significant decrease of free sialic acid, to within the normal range. Feedback inhibition of GNE-epimerase activity by CMP-sialic acid recovered after silencing demonstrating specificity of this effect. These findings indicate that allele-specific silencing of a mutated allele is a viable therapeutic strategy for autosomal dominant diseases, including sialuria.—Klootwijk, R. D., Savelkoul, P. J. M., Ciccone, C., Manoli, I., Caplen, N. J., Krasnewich, D. M., Gahl, W. A., Huizing, M. Allele-specific silencing of the dominant disease allele in sialuria by RNA interference.

Klootwijk, Riko D.; Savelkoul, Paul J. M.; Ciccone, Carla; Manoli, Irini; Caplen, Natasha J.; Krasnewich, Donna M.; Gahl, William A.; Huizing, Marjan

2008-01-01

248

Nuclear gene phylogeography using PHASE: dealing with unresolved genotypes, lost alleles, and systematic bias in parameter estimation  

Microsoft Academic Search

BACKGROUND: A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context

Ryan C Garrick; Paul Sunnucks; Rodney J Dyer

2010-01-01

249

Rapid, efficient and precise allele replacement in the fission yeast Schizosaccharomyces pombe.  

PubMed

Gene targeting provides a powerful tool to modify endogenous loci to contain specific mutations, insertions and deletions. Precise allele replacement, with no other chromosomal changes (e.g., insertion of selectable markers or heterologous promoters), maintains physiologically relevant context. Established methods for precise allele replacement in fission yeast employ two successive rounds of transformation and homologous recombination and require genotyping at each step. The relative efficiency of homologous recombination is low and a high rate of false positives during the second round of gene targeting further complicates matters. We report that pop-in, pop-out allele replacement circumvents these problems. We present data for 39 different allele replacements, involving simple and complex modifications at seven different target loci, that illustrate the power and utility of the approach. We also developed and validated a rapid, efficient process for precise allele replacement that requires only one round each of transformation and genotyping. We show that this process can be applied in population scale to an individual target locus, without genotyping, to identify clones with an altered phenotype (targeted forward genetics). It is therefore suitable for saturating, in situ, locus-specific mutation screens (e.g., of essential or non-essential genes and regulatory DNA elements) within normal chromosomal context. PMID:24026504

Gao, Jun; Kan, Fengling; Wagnon, Jacy L; Storey, Aaron J; Protacio, Reine U; Davidson, Mari K; Wahls, Wayne P

2014-05-01

250

Genetically Determined Amerindian Ancestry Correlates with Increased Frequency of Risk Alleles for Systemic Lupus Erythematosus  

PubMed Central

Objectives To analyze if genetically determined Amerindian ancestry predicts the increased presence of risk alleles of known susceptibility genes for systemic lupus erythematosus. Methods Single nucleotide polymorphisms within 16 confirmed genetic susceptibility loci for SLE were genotyped in a set of 804 Mestizo lupus patients and 667 Mestizo normal healthy controls. In addition, 347 admixture informative markers were genotyped. Individual ancestry proportions were determined using STRUCTURE. Association analysis was performed using PLINK, and correlation of the presence of risk alleles with ancestry was done using linear regression. Results A meta-analysis of the genetic association of the 16 SNPs across populations showed that TNFSF4, STAT4, PDCD1, ITGAM, and IRF5 were associated with lupus in a Hispanic-Mestizo cohort enriched for European and Amerindian ancestry. In addition, two SNPs within the MHC region, previously associated in a genome-wide association study in Europeans, were also associated in Mestizos. Using linear regression we predict an average increase of 2.34 risk alleles when comparing a lupus patient with 100% Amerindian ancestry to an SLE patient with 0% American Indian Ancestry (p<0.0001). SLE patients with 43% more Amerindian ancestry are predicted to carry one additional risk allele. Conclusion Amerindian ancestry increased the number of risk alleles for lupus.

Sanchez, E; Webb, R; Rasmussen, A.; Kelly, J.A; Riba, L.; Kaufman, K.M.; Garcia-de la Torre, I.; Moctezuma, J.F.; Maradiaga-Cecena, M.A.; Cardiel, M.; Acevedo, E.; Cucho-Venegas, M.; Garcia, M.A.; Gamron, S.; Pons-Estel, B.A.; Vasconcelos, C.; Martin, J.; Tusie-Luna, T.; Harley, J.B.; Richardson, B.; Sawalha, A.H.; Alarcon-Riquelme, M.E.

2011-01-01

251

Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.  

PubMed

The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(?)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(?)G, rs41525747; -13915(?)G, rs41380347; -14010(?)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(?)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep. PMID:23993196

Jones, Bryony L; Raga, Tamiru O; Liebert, Anke; Zmarz, Pawel; Bekele, Endashaw; Danielsen, E Thomas; Olsen, Anders Krüger; Bradman, Neil; Troelsen, Jesper T; Swallow, Dallas M

2013-09-01

252

Analysis of eight polymorphic human genetic markers in a well-defined Greek population.  

PubMed

The use of DNA in forensic science has become a basic tool for person identification or parentage testing. The use of polymorphic markers permits the formation of a unique profile for each individual. The knowledge of allele frequencies in a given population allows the scientist to estimate the probability of a particular allele combination. For this task, allele databanks are essential. In this report, the authors estimate the frequencies of eight polymorphic markers (namely, HumFES, HumF13A1, HumTHO1, HumVWA, HumFABP2, HumLIPOL, D1S80, and D17S5) in a randomly selected sample from Crete, Greece. The allele profile of all markers, with the exception of D17S5 and HumFABP2, concurs with previous reports and international data. PMID:10871135

Tsopanomichalou, M; Sourvinos, G; Arvanitis, D; Michalodimitrakis, M

2000-06-01

253

Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.)  

PubMed Central

Background Genomic research of cultivated peanut has lagged behind other crop species because of the paucity of polymorphic DNA markers found in this crop. It is necessary to identify additional DNA markers for further genetic research in peanut. Results Microsatellite markers in cultivated peanut were developed using the SSR enrichment procedure. The results showed that the GA/CT repeat was the most frequently dispersed microsatellite in peanut. The primer pairs were designed for fifty-six different microsatellites, 19 of which showed a polymorphism among the genotypes studied. The average number of alleles per locus was 4.25, and up to 14 alleles were found at one locus. This suggests that microsatellite DNA markers produce a higher level of DNA polymorphism than other DNA markers in cultivated peanut. Conclusions It is desirable to isolate and characterize more DNA markers in cultivated peanut for more productive genomic studies, such as genetic mapping, marker-assisted selection, and gene discovery. The development of microsatellite markers holds a promise for such studies.

He, Guohao; Meng, Ronghua; Newman, Melanie; Gao, Guoqing; Pittman, Roy N; Prakash, CS

2003-01-01

254

Molecular Analysis of Chloroquine and Sulfadoxine-Pyrimethamine Resistance-Associated Alleles in Plasmodium falciparum Isolates from Nicaragua.  

PubMed

Abstract. Chloroquine (CQ) is used as a first-line therapy for the treatment of Plasmodium falciparum malaria in Nicaragua. We investigated the prevalence of molecular markers associated with CQ and sulfadoxine-pyrimethamine (SP) resistance in P. falciparum isolates obtained from the North Atlantic Autonomous Region of Nicaragua. Blood spots for this study were made available from a CQ and SP drug efficacy trial conducted in 2005 and also from a surveillance study performed in 2011. Polymorphisms in P. falciparum CQ resistance transporter, dihydrofolate reductase, and dihydropteroate synthase gene loci that are associated with resistance to CQ, pyrimethamine, and sulfadoxine, respectively, were detected by DNA sequencing. In the 2005 dataset, only 2 of 53 isolates had a CQ resistance allele (CVIET), 2 of 52 had a pyrimethamine resistance allele, and 1 of 49 had a sulfadoxine resistance allele. In the 2011 dataset, none of 45 isolates analyzed had CQ or SP resistance alleles. PMID:24615126

Sridaran, Sankar; Rodriguez, Betzabe; Soto, Aida Mercedes; Macedo De Oliveira, Alexandre; Udhayakumar, Venkatachalam

2014-05-01

255

Comparing the van Oosterhout and Chybicki-Burczyk methods of estimating null allele frequencies for inbred populations.  

PubMed

In spite of the usefulness of codominant markers in population genetics, the existence of null alleles raises challenging estimation issues in natural populations that are characterized by positive inbreeding coefficients (F > 0). Disregarding the possibility of F > 0 in a population will generally lead to overestimates of null allele frequencies. Conversely, estimates of inbreeding coefficients (F) may be strongly biased upwards (excess homozygotes), in the presence of nontrivial frequencies of null alleles. An algorithm has been presented for the estimation of null allele frequencies in inbred populations (van Oosterhout method), using external estimates of the F-statistics. The goal of this study is to introduce a modification of this method and to provide a formal comparison with an alternative likelihood-based method (Chybicki-Burczyk). Using simulated data, we illustrate the strengths and limitations of these competing methods. Under most circumstances, the likelihood method is preferable, but for highly inbred organisms, a modified van Oosterhout method offers some advantages. PMID:23227485

Campagne, P; Smouse, P E; Varouchas, G; Silvain, J-F; Leru, B

2012-11-01

256

Analysis of some polymorphic markers of the CFTR gene in cystic fibrosis patients and healthy donors from the Moscow region  

SciTech Connect

Allelic frequencies of three polymorphic markers in the CFTR gene were estimated on chromosomes derived from cystic fibrosis (CF) patients and healthy donors from Moscow and the Moscow region. These polymorphic markers are tetranucleotide tandem repeats GATT in intron 6B, M470V in exon 10, and T854T in exon 14 (fragment A). Frequencies at allele 1 of the M470V marker, along with allele 2 of GATT and T854T, are two times higher for CF patients without {Delta}F508 mutation than for healthy donors, and there is linkage disequilibrium of these alleles of the polymorphic markers analyzed with the CF gene. Allele 1 of M470V and T854T markers, as well as allele 2 of the GATT marker (six repeats), are absolutely linked to mutation F508 of the CFTR gene. Using the polymorphic markers studied, family analysis of CF was carried out in two families. 10 refs., 1 fig., 1 tab.

Amosenko, F.A.; Sazonova, M.A.; Kapranov, N.I.; Trubnikova, I.S.; Kalinin, V.N. [Institute for Human Genetics, Moscow (Russian Federation)

1995-04-01

257

Stochastic Loss of Silencing of the Imprinted Ndn/NDN Allele, in a Mouse Model and Humans with Prader-Willi Syndrome, Has Functional Consequences  

PubMed Central

Genomic imprinting is a process that causes genes to be expressed from one allele only according to parental origin, the other allele being silent. Diseases can arise when the normally active alleles are not expressed. In this context, low level of expression of the normally silent alleles has been considered as genetic noise although such expression has never been further studied. Prader-Willi Syndrome (PWS) is a neurodevelopmental disease involving imprinted genes, including NDN, which are only expressed from the paternally inherited allele, with the maternally inherited allele silent. We present the first in-depth study of the low expression of a normally silent imprinted allele, in pathological context. Using a variety of qualitative and quantitative approaches and comparing wild-type, heterozygous and homozygous mice deleted for Ndn, we show that, in absence of the paternal Ndn allele, the maternal Ndn allele is expressed at an extremely low level with a high degree of non-genetic heterogeneity. The level of this expression is sex-dependent and shows transgenerational epigenetic inheritance. In about 50% of mutant mice, this expression reduces birth lethality and severity of the breathing deficiency, correlated with a reduction in the loss of serotonergic neurons. In wild-type brains, the maternal Ndn allele is never expressed. However, using several mouse models, we reveal a competition between non-imprinted Ndn promoters which results in monoallelic (paternal or maternal) Ndn expression, suggesting that Ndn allelic exclusion occurs in the absence of imprinting regulation. Importantly, specific expression of the maternal NDN allele is also detected in post-mortem brain samples of PWS individuals. Our data reveal an unexpected epigenetic flexibility of PWS imprinted genes that could be exploited to reactivate the functional but dormant maternal alleles in PWS. Overall our results reveal high non-genetic heterogeneity between genetically identical individuals that might underlie the variability of the phenotype.

Unmehopa, Unga; Matarazzo, Valery; Watrin, Francoise; Linke, Matthias; Georges, Beatrice; Bischof, Jocelyn; Dijkstra, Femke; Bloemsma, Monique; Corby, Severine; Michel, Francois J.; Wevrick, Rachel; Zechner, Ulrich; Swaab, Dick; Dudley, Keith; Bezin, Laurent; Muscatelli, Francoise

2013-01-01

258

Segregation and Linkage Analysis of 75 Novel Microsatellite DNA Markers in Pair Crosses of Japanese Abalone ( Haliotis discus hannai ) Using the 5?Tailed Primer Method  

Microsoft Academic Search

We present novel microsatellite markers of the Japanese abalone (Haliotis discus hannai) for general mapping studies in this species. A total of 75 microsatellite markers were developed, and the allele-transmission\\u000a patterns of these markers were studied in three families generated by pair crosses. For allele scoring, we employed the 5?-tailed\\u000a primer polymerase chain reaction (PCR) technique, which substantially reduces the

Masashi Sekino; Toshimasa Kobayashi; Motoyuki Hara

2006-01-01

259

Isolation of polymorphic tetranucleotide microsatellite markers for the masked flowerpiercer Diglossa cyanea  

Microsoft Academic Search

We have isolated 11 polymorphic microsatellite markers for the masked flowerpiercer Diglossa cyanea from a genomic library enriched for (AAGG) n repetitive elements. The number of alleles ranged from eight to 16 per locus with the observed heterozygosity ranging from 0.64 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.

CAROLYNE BARDELEBEN; MELISSA M. GRAY

2005-01-01

260

Isolation of polymorphic tetranucleotide microsatellite markers in the satin bowerbird, Ptilonorhynchus violaceus  

Microsoft Academic Search

We isolated 13 polymorphic microsatellite markers from the satin bowerbird, Ptilonorhynchus violaceus from a genomic library enriched in (AAGG) n repetitive elements and characterized them in 20 individuals. The number of alleles ranged from two to 18 per locus with the observed heterozygosity ranging from 0.15 to 1.00. These markers will be useful for analysing questions concerning parentage, population genetic

CAROLYNE BARDELEBEN; RACHAEL L. MOORE; JAMES A. NICHOLLS; JEREMY J. AUSTIN

2005-01-01

261

Isolation of polymorphic tetranucleotide microsatellite markers for the skink Mabuya affinis  

Microsoft Academic Search

We isolated 10 polymorphic microsatellite markers for the skink Mabuya affinis from genomic libraries enriched for (AAGG) n and (AAAG) n repetitive elements. The number of alleles ranged from eight to 13 per locus with the observed heterozygosity ranging from 0.60 to 0.92 . These markers will be useful for analysis of questions concerning population genetic structure and models of

CAROLYNE BARDELEBEN; RACHAEL L. MOORE; MELISSA M. GRAY

2005-01-01

262

Isolation of polymorphic tetranucleotide microsatellite markers for the black-bellied seedcracker (Pyrenestes ostrinus)  

Microsoft Academic Search

We have isolated 10 polymorphic microsatellite markers for the black-bellied seedcracker ( Pyrenestes ostrinus ) from genomic libraries enriched either for (AAGG) n or (ATCT) n repetitive elements and characterized them in 39 individuals. The number of alleles ranged from two to 27 per locus with the observed heterozygosity ranging from 0.38 to 0.94. These markers will be useful for

KATHLEEN SEMPLE DELANEY; DEBRA PIRES; KAREN HOLDER; CAROLYNE BARDELEBEN; THOMAS SMITH

2005-01-01

263

Consensus genetic structuring and typological value of markers using multiple co-inertia analysis  

Microsoft Academic Search

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the

Denis Laloë; Thibaut Jombart; Anne-Béatrice Dufour; Katayoun Moazami-Goudarzi

2007-01-01

264

Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize  

Microsoft Academic Search

QTLs with flanking markers showing significant allele frequency differences in the BSA studies will indicate The usual method to locate and compare loci regulat- those traits likely to be important in determining yield ing quantitative traits (QTLs) requires a segregating under drought. population of plants with each one genotyped with molecular markers. However, plants from such segreg- Key words: Bulk

Steve A Quarrie; Vesna Lazic; Dragan Kovacevic ´; Andy Steed; Sofija Pekic

1999-01-01

265

A review on SNP and other types of molecular markers and their use in animal genetics  

Microsoft Academic Search

During the last ten years, the use of molecular markers, revealing polymorphism at the DNA level, has been playing an increasing part in animal genetics studies. Amongst others, the microsatellite DNA marker has been the most widely used, due to its easy use by simple PCR, followed by a denaturing gel electrophoresis for allele size determination, and to the high

Alain Vignal; Denis Milan; Magali SanCristobal; André Eggen

2002-01-01

266

Parents Teach Reading, Too.  

ERIC Educational Resources Information Center

Parents and teachers need to be involved in teaching children to read and to enjoy reading. There are three planks in a platform that will help all parents become involved in their children's learning to read. First, parents must set the example. If they want their children to read, parents must read around them and to them. Secondly, they must…

Clary, Linda Mixon

267

Parental Bonding Instrument  

Microsoft Academic Search

The view that those with obsessive compulsive disorder or obsessional personality have been exposed to overcontrolling and overcritical parenting is examined. Two measures of obsessionality (the Maudsley Obsessional-Compulsive Inventory and the Leyton Obsessionality Inventory) were completed by 344 nonclinical subjects. They also scored their parents on the Parental Bonding Instrument (PBI), a measure assessing perceived levels of parental care and

L. C. Cavedo; G. Parker

1994-01-01

268

Involving Latino Parents.  

ERIC Educational Resources Information Center

Describes barriers to Latino parent involvement in educational activities, factors to consider when involving Latino parents, and two examples of Latino involvement programs in California: Family Literacy Workshop at James Monroe Elementary School, Madera Unified School District, and Parents Take P.A.R.T. (Parent Assisted Reading Training) at…

Quezada, Reyes L.; Diaz, Delia M.; Sanchez, Maria

2003-01-01

269

School Parent Involvement Policy  

ERIC Educational Resources Information Center

This school parent involvement policy is divided into three sections: (1) Development and Adoption of the Parent Involvement Policy; (2) Contents of the Parent Involvement Policy; and (3) Distributing and Revising the School's Parent Involvement Policy. This paper presents the provision of the Section 1118 of Title I of the No Child Left Behind…

Center for Law and Education (NJ3), 2005

2005-01-01

270

Parents and Youth Sports.  

ERIC Educational Resources Information Center

Asserts that parents play a critical role in their children's sports and should not be excluded, despite negative press about some "pushy" parents. The paper recommends that youth administrators encourage positive parental involvement in youth sports by acknowledging the important role that each parent plays and empowering them to do the right…

Kanters, Michael

2002-01-01

271

Parent-child Interactions.  

ERIC Educational Resources Information Center

This survey investigates 6 major questions: (1) do adolescents and their parents perceive youth as overindulged; (2) are parent-child communication channels open; (3) has understanding between parents and their children broken down; (4) do children identify with their parents; (5) has discipline been permissive; and (6) do adolescents reject the…

Erlich, A. C., Ed.

272

Partners: Parents & Schools.  

ERIC Educational Resources Information Center

The authors of this collection of essays make the major points that parental participation influences student performance, and that time spent with parents by school personnel results in better learning. Ira J. Gordon explains four models of parent-school-community relationships and cites research evidence of long-term effects of parent

Brandt, Ronald S., Ed.

273

Parent Conferences. Beginnings Workshop.  

ERIC Educational Resources Information Center

Presents six workshop sessions on parent conferences: (1) "Parents' Perspectives on Conferencing" (R. Duffy); (2) "Three Way Conferences" (G. Zeller); (3) "Conferencing with Parents of Infants" (K. Albrecht); (4) "Conferencing with Parents of School-Agers" (L. G. Miller); (5) "Cross Cultural Conferences" (J. Gonzalez-Mena); and (6) "Working with…

Duffy, Roslyn; And Others

1997-01-01

274

Parents, Children, and Alcohol.  

ERIC Educational Resources Information Center

Reports on Soviet parents' responses to a 1986 survey concerning parental influence on children and alcohol use. Points out that most parents perceive the link between their own alcohol use and children's drinking but cultural traditions and alcoholic habits often preclude change. Notes parents' opinions on effectiveness of governmental and school…

Levin, Boris Mikhailovich; Levin, Mikhail Borisovich

1990-01-01

275

STRait Razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data.  

PubMed

Recent studies have demonstrated the capability of second generation sequencing (SGS) to provide coverage of short tandem repeats (STRs) found within the human genome. However, there are relatively few bioinformatic software packages capable of detecting these markers in the raw sequence data. The extant STR-calling tools are sophisticated, but are not always applicable to the analysis of the STR loci commonly used in forensic analyses. STRait Razor is a newly developed Perl-based software tool that runs on the Linux/Unix operating system and is designed to detect forensically-relevant STR alleles in FASTQ sequence data, based on allelic length. It is capable of analyzing STR loci with repeat motifs ranging from simple to complex without the need for extensive allelic sequence data. STRait Razor is designed to interpret both single-end and paired-end data and relies on intelligent parallel processing to reduce analysis time. Users are presented with a number of customization options, including variable mismatch detection parameters, as well as the ability to easily allow for the detection of alleles at new loci. In its current state, the software detects alleles for 44 autosomal and Y-chromosome STR loci. The study described herein demonstrates that STRait Razor is capable of detecting STR alleles in data generated by multiple library preparation methods and two Illumina(®) sequencing instruments, with 100% concordance. The data also reveal noteworthy concepts related to the effect of different preparation chemistries and sequencing parameters on the bioinformatic detection of STR alleles. PMID:23768312

Warshauer, David H; Lin, David; Hari, Kumar; Jain, Ravi; Davis, Carey; Larue, Bobby; King, Jonathan L; Budowle, Bruce

2013-07-01

276

Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates.  

PubMed

Microsatellite loci play an important role as markers for identification, disease gene mapping, and evolutionary studies. Mutation rate, which is of fundamental importance, can be obtained from interspecies comparisons, which, however, are subject to ascertainment bias. This bias arises, for example, when a locus is selected on the basis of its large allele size in one species (cognate species 1), in which it is first discovered. This bias is reflected in average allele length in any noncognate species 2 being smaller than that in species 1. This phenomenon was observed in various pairs of species, including comparisons of allele sizes in human and chimpanzee. Various mechanisms were proposed to explain observed differences in mean allele lengths between two species. Here, we examine the framework of a single-step asymmetric and unrestricted stepwise mutation model with genetic drift. Analysis is based on coalescent theory. Analytical results are confirmed by simulations using the simuPOP software. The mechanism of ascertainment bias in this model is a tighter correlation of allele sizes within a cognate species 1 than of allele sizes in two different species 1 and 2. We present computations of the expected average allele size difference, given the mutation rate, population sizes of species 1 and 2, time of separation of species 1 and 2, and the age of the allele. We show that when the past demographic histories of the cognate and noncognate taxa are different, the rate and directionality of mutations affect the allele sizes in the two taxa differently from the simple effect of ascertainment bias. This effect may exaggerate or reverse the effect of difference in mutation rates. We reanalyze literature data, which indicate that despite the bias, the microsatellite mutation rate estimate in the ancestral population is consistently greater than that in either human or chimpanzee and the mutation rate estimate in human exceeds or equals that in chimpanzee with the rate of allele length expansion in human being greater than that in chimpanzee. We also demonstrate that population bottlenecks and expansions in the recent human history have little impact on our conclusions. PMID:23946335

Li, Biao; Kimmel, Marek

2013-10-01

277

FINDbase: a worldwide database for genetic variation allele frequencies updated  

PubMed Central

Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding.

Georgitsi, Marianthi; Viennas, Emmanouil; Antoniou, Dimitris I.; Gkantouna, Vassiliki; van Baal, Sjozef; Petricoin, Emanuel F.; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P.

2011-01-01

278

Clonal maintenance of imprinted expression of SNRPN and IPW in normal lymphocytes: correlation with allele-specific methylation of SNRPN intron 1 but not intron 7  

Microsoft Academic Search

DNA methylation is a heritable and reversible modification to CpG sites in the mammalian genome. Parental allele-specific methylation is hypothesized to be important in the establishment and maintenance of imprinted gene expression; however, dynamic changes in allele-specific patterns have been observed. The upstream regulatory region of the small nuclear riboprotein N gene (SNRPN) is an important imprinting control region (ICR)

Damina Balmer; Janine M. LaSalle

2001-01-01

279

Pseudoautosomal marker DXYS20 and manic depression  

SciTech Connect

Yoneda et al. (1992) observed a significant association between manic-depressive illness and a 13.5-kb band of the pseudoautosomal marker DXYS20 (probe 362A) in EcoRI digests of 49 Japanese patients compared with 119 controls. The 13.5-kb allele was designated [open quotes]A4 allele[close quotes] and was found on at least one chromosome in 46.9% of the patients, compared with 26.1% of the controls. The relative risk of the A4 allele for the disease was 2.51. The authors have genotyped the EcoRI RFLP in 73 patients (40 females and 33 males) who fulfill DSM-III-R criteria of manic-depressive illness (bipolar affective disorder) and in 79 controls (34 females and 45 males). All subjects included in the study were unrelated and were of German descent. They used the probe 3cos-PP, which, by sequence analysis, was shown to be directly homologous to the independently cloned probe 362A (Rappold et al. 1992). The pseudoautosomal locus DXYS20 represents a VNTR-like minisatellite, and many polymorphic bands are recognized by means of several restriction endonucleases (Page et al. 1987). In EcoRI digests, sizes of bands cluster, and the authors grouped their bands according to allele sizes used by Yoneda et al. In addition to the alleles reported by Yoneda et al., they observed a 10-kb band in five subjects. The results are shown in a table. The frequency of the A4 allele did not differ significantly between patients and controls. Thus, the data do not support a widespread or consistent association between DXYS20 and bipolar affective disorder. A large degree of ethnic variation is seen with DXYS20 (Rappold et al. 1992) and might explain the difference of allele frequencies in controls from Japan and Germany. Since VNTRs evolve rapidly, they may not always be the best markers to detect disease associations, where a positive effect requires linkage disequilibrium. In any case, it should be useful to study larger samples of Japanese patients and controls. 3 refs., 1 tab.

Noethen, M.M.; Cichon, S.; Erdmann, J.; Koerner, J.; Rietschel, M.; Propping, P. (Univ. of Bonn (Germany)); Rappold, G.A. (Univ. of Heidelberg (Germany)); Fritze, J. (Univ. of Wuerzburg (Germany))

1993-04-01

280

Cultural Approaches to Parenting  

PubMed Central

SYNOPSIS This article first introduces some main ideas behind culture and parenting and next addresses philosophical rationales and methodological considerations central to cultural approaches to parenting, including a brief account of a cross-cultural study of parenting. It then focuses on universals, specifics, and distinctions between form (behavior) and function (meaning) in parenting as embedded in culture. The article concludes by pointing to social policy implications as well as future directions prompted by a cultural approach to parenting.

Bornstein, Marc H.

2012-01-01

281

Allele-specific histone modifications regulate expression of the Dlk1-Gtl2 imprinted domain  

PubMed Central

Dlk1 and Gtl2 are reciprocally expressed imprinted genes located on mouse chromosome 12. The Dlk1-Gtl2 locus carries three differentially methylated regions (DMRs), which are methylated only on the paternal allele. Of these, the intergenic (IG) DMR, located 12 kb upstream of Gtl2 is required for proper imprinting of linked genes on the maternal chromosome, while the Gtl2 DMR, located across the promoter of the Gtl2 gene, is implicated in imprinting on both parental chromosomes. In addition to DNA methylation, modification of histone proteins is also an important regulator of imprinted gene expression. Chromatin immunoprecipitation was therefore used to examine the pattern of histone modifications across the IG and Gtl2 DMRs. The data show maternal specific histone acetylation at the Gtl2 DMR, but not at the IG DMR. In contrast, only low levels of histone methylation were observed throughout the region, and there was no difference between the two parental alleles. An existing mouse line mouse line carrying a deletion/insertion upstream of Gtl2 is unable to properly imprint the Dlk1-Gtl2 locus, and demonstrates loss of allele-specific methylation at the Gtl2 DMR. Further analysis of these animals now shows that the loss of allele-specific methylation is accompanied by increased paternal histone acetylation at the Gtl2 DMR, with the activated paternal allele adopting a maternal acetylation pattern. These data indicate that interactions between DNA methylation and histone acetylation are involved in regulating the imprinting of the Dlk1-Gtl2 locus.

Carr, Michael S.; Yevtodiyenko, Aleksey; Schmidt, Claudia L.; Schmidt, Jennifer V.

2007-01-01

282

Fourteen polymorphic microsatellite markers for the fungal banana pathogen Mycosphaerella fijiensis.  

PubMed

Fourteen polymorphic microsatellite markers were developed for Mycosphaerella fijiensis, a fungus causing the black sigatoka disease in banana. The sequenced genome of M. fijiensis was screened for sequences with single sequence repeats (SSRs) using a Perl script. Fourteen SSR loci, evaluated on 48 M. fijiensis isolates from Hawaii, were identified to be highly polymorphic. These markers revealed two to 19 alleles, with an average of 6.43 alleles per locus. The estimated gene diversity ranged from 0.091 to 0.930 across the 14 microsatellite loci. The SSR markers developed would be useful for population genetics studies of M. fijiensis. PMID:21585927

Yang, Bao Jun; Zhong, Shao Bin

2008-07-01

283

Quantitative threefold allele-specific PCR (QuanTAS-PCR) for highly sensitive JAK2 V617F mutant allele detection  

PubMed Central

Background The JAK2 V617F mutation is the most frequent somatic change in myeloproliferative neoplasms, making it an important tumour-specific marker for diagnostic purposes and for the detection of minimal residual disease. Sensitive quantitative assays are required for both applications, particularly for the monitoring of minimal residual disease, which requires not only high sensitivity but also very high specificity. Methods We developed a highly sensitive probe-free quantitative mutant-allele detection method, Quantitative Threefold Allele-Specific PCR (QuanTAS-PCR), that is performed in a closed-tube system, thus eliminating the manipulation of PCR products. QuantTAS-PCR uses a threefold approach to ensure allele-specific amplification of the mutant sequence: (i) a mutant allele-specific primer, (ii) a 3?dideoxy blocker to suppress false-positive amplification from the wild-type template and (iii) a PCR specificity enhancer, also to suppress false-positive amplification from the wild-type template. Mutant alleles were quantified relative to exon 9 of JAK2. Results We showed that the addition of the 3?dideoxy blocker suppressed but did not eliminate false-positive amplification from the wild-type template. However, the addition of the PCR specificity enhancer near eliminated false-positive amplification from the wild-type allele. Further discrimination between true and false positives was enabled by using the quantification cycle (Cq) value of a single mutant template as a cut-off point, thus enabling robust distinction between true and false positives. As 10,000 JAK2 templates were used per replicate, the assay had a sensitivity of 1/10-4 per replicate. Greater sensitivity could be reached by increasing the number of replicates analysed. Variation in replicates when low mutant-allele templates were present necessitated the use of a statistics-based approach to estimate the load of mutant JAK2 copies. QuanTAS-PCR showed comparable quantitative results when validated against a commercial assay. Conclusions QuanTAS-PCR is a simple, cost-efficient, closed-tube method for JAK2 V617F mutation quantification that can detect very low levels of the mutant allele, thus enabling analysis of minimal residual disease. The approach can be extended to the detection of other recurrent single nucleotide somatic changes in cancer.

2013-01-01

284

Development of highly polymorphic tetranucleotide microsatellite markers in Austrocedrus chilensis.  

PubMed

An enriched genomic library was constructed and 9 novel polymorphic tetranucleotide microsatellite markers developed for Austrocedrus chilensis, the most economically important native conifer in the Andean Patagonian region. Polymorphism was investigated for these markers in 48 individuals from two populations. Numbers of alleles ranged from 3 to 19 and levels of observed heterozygosity among the 9 loci ranged from 0.32 to 0.95. No locus combinations exhibited linkage disequilibrium. These polymorphic markers will be useful tools for the study of demography and gene flow and more in general for population and conservation genetics of this species. PMID:21585920

Arana, María Verónica; Buonamici, Anna; Sebastiani, Federico; Alia, Ricardo; Gallo, Leonardo A; Marchelli, Paula; Moreno, Carolina; Vendramin, Giovanni G

2008-07-01

285

HLA alleles and drug hypersensitivity reactions.  

PubMed

The human leucocyte antigen (HLA) system is well known for its association with certain diseases such as ankylosing spondylitis, celiac disease and many others. More recently, severe and even fatal drug hypersensitivity reactions linked to particular HLA alleles have been discovered. The significance of these discoveries has led the European Medicines Agency (EMA) and its member state agencies to recommend HLA gene testing before initiation of drug treatment. To date, the following drugs have been identified as causing significant drug hypersensitivity reactions in patients who have the following HLA alleles: abacavir and HLA-B*57:01, carbamazepine and HLA-B*15:02/A*31:01 and finally allopurinol and HLA-B*58:01. This review will outline and discuss these three drugs and their associated HLA alleles as well as examine the pathogenesis of the drug hypersensitivity reactions. PMID:22136512

Profaizer, T; Eckels, D

2012-04-01

286

The Role of BDNF Genotype, Parental Depression, and Relationship Discord in Predicting Early-Emerging Negative Emotionality  

PubMed Central

The brain-derived neurotrophic factor (BDNF) gene is a plausible candidate for early-emerging negative emotionality (NE), and evidence suggests that the effects of this gene may be especially salient in the context of familial risk for child maladjustment. We therefore examined whether the BDNF val66met polymorphism was associated with child NE in the context of parental depression and relationship discord. A sample of 413 three-year-old children was assessed for NE using standardized laboratory measures. Parents completed clinical interviews and a measure of marital satisfaction. Children with at least one BDNF met allele exhibited elevated NE when a parent had a history of depressive disorder, or when relationship discord was present. In contrast, this allele was associated with especially low NE when parent depression was absent, and when the parental relationship was not discordant. Findings suggest that the BDNF met allele confers increased child sensitivity to both positive and negative familial influences.

Hayden, Elizabeth P.; Klein, Daniel N.; Dougherty, Lea R.; Olino, Thomas M.; Dyson, Margaret W.; Durbin, C. Emily; Sheikh, Haroon I.; Singh, Shiva M.

2012-01-01

287

Development of microsatellite markers for genetic diversity analysis of Dendrobium loddigesii Rolfe, an endangered orchid in China  

Microsoft Academic Search

Dendrobium loddigesii Rolfe is an endangered epiphytic orchid with high medicinal and horticulture value. To estimate genetic diversity and population structure of D. loddigesii, 12 new microsatellite markers of D. loddigesii were developed from an enriched library. A total of 98 alleles were detected with an average of 8.2 alleles per locus. The expected heterozygosity of each SSR locus varied

Xiaoyan Cai; Zhenyu Feng; Beiwei Hou; Wenrui Xing; Xiaoyu Ding

288

To be or not to be the odd one out - Allele-specific transcription in pentaploid dogroses (Rosa L. sect. Caninae (DC.) Ser)  

PubMed Central

Background Multiple hybridization events gave rise to pentaploid dogroses which can reproduce sexually despite their uneven ploidy level by the unique canina meiosis. Two homologous chromosome sets are involved in bivalent formation and are transmitted by the haploid pollen grains and the tetraploid egg cells. In addition the egg cells contain three sets of univalent chromosomes which are excluded from recombination. In this study we investigated whether differential behavior of chromosomes as bivalents or univalents is reflected by sequence divergence or transcription intensity between homeologous alleles of two single copy genes (LEAFY, cGAPDH) and one ribosomal DNA locus (nrITS). Results We detected a maximum number of four different alleles of all investigated loci in pentaploid dogroses and identified the respective allele with two copies, which is presumably located on bivalent forming chromosomes. For the alleles of the ribosomal DNA locus and cGAPDH only slight, if any, differential transcription was determined, whereas the LEAFY alleles with one copy were found to be significantly stronger expressed than the LEAFY allele with two copies. Moreover, we found for the three marker genes that all alleles have been under similar regimes of purifying selection. Conclusions Analyses of both molecular sequence evolution and expression patterns did not support the hypothesis that unique alleles probably located on non-recombining chromosomes are less functional than duplicate alleles presumably located on recombining chromosomes.

2011-01-01

289

Recycling selectable markers in mouse embryonic stem cells.  

PubMed Central

As a result of gene targeting, selectable markers are usually permanently introduced into the mammalian genome. Multiple gene targeting events in the same cell line can therefore exhaust the pool of markers available and limit subsequent manipulations or genetic analysis. In this study, we describe the combined use of homologous and CRE-loxP-mediated recombination to generate mouse embryonic stem cell lines carrying up to four targeted mutations and devoid of exogenous selectable markers. A cassette that contains both positive and negative selectable markers flanked by loxP sites, rendering it excisable by the CRE protein, was constructed. Homologous recombination and positive selection were used to disrupt the Rep-3 locus, a gene homologous to members of the mutS family of DNA mismatch repair genes. CRE-loxP-mediated recombination and negative selection were then used to recover clones in which the cassette had been excised. The remaining allele of Rep-3 was then subjected to a second round of targeting and excision with the same construct to generate homozygous, marker-free cell lines. Subsequently, both alleles of mMsh2, another mutS homolog, were disrupted in the same fashion to obtain cell lines homozygous for targeted mutations at both the Rep-3 and mMsh2 loci and devoid of selectable markers. Thus, embryonic stem cell lines obtained in this fashion are suitable for further manipulation and analysis involving the use of selectable markers.

Abuin, A; Bradley, A

1996-01-01

290

Parent Behavior Importance and Parent Behavior Frequency Questionnaires: Psychometric Characteristics  

ERIC Educational Resources Information Center

This study examined the psychometric characteristics of two parenting measures: the Parent Behavior Importance Questionnaire (PBIQ) and Parent Behavior Frequency Questionnaire (PBFQ). Both research questionnaires are based on the parent development theory (PDT) and offer parent as well as non-parent respondents the opportunity to rate 38 parenting

Mowder, Barbara A.; Sanders, Michelle

2008-01-01

291

Parenting as measured by the Parenting Behaviors Questionnaire  

Microsoft Academic Search

The relationship between parent behaviors, child development and subsequent child behavior outcomes has been examined. However, few tools have been developed and utilized to assess and quantify parenting behaviors in relationship to parent and child demographic characteristics. This study uses the Parenting Behaviors Questionnaire (PBQ), to examine whether parent and child backgrounds influence parents' perceptions of their parenting. Specifically, the

Penni Morganstein

2006-01-01

292

Parents' Education Levels, Parents' Beliefs, and Child Outcomes  

Microsoft Academic Search

Relationships between parents' education levels, parents' beliefs concerning children, children's cognitions related to themselves and their relationships, and academic achievement were investigated in a sample of Turkish fourth-grade children and their parents. Structural equations were used in data analysis. Level of parents' education was a significant predictor of parents' beliefs for both parents. Relationships between parents' beliefs and child outcomes

Nuran Hortaçsu

1995-01-01

293

Using linkage analysis to detect gene-gene interaction by stratifying family data on known disease, or disease-associated, alleles.  

PubMed

Detecting gene-gene interaction in complex diseases is a major challenge for common disease genetics. Most interaction detection approaches use disease-marker associations and such methods have low power and unknown reliability in real data. We developed and tested a powerful linkage-analysis-based gene-gene interaction detection strategy based on conditioning the family data on a known disease-causing allele or disease-associated marker allele. We computer-generated multipoint linkage data for a disease caused by two epistatically interacting loci (A and B). We examined several two-locus epistatic inheritance models: dominant-dominant, dominant-recessive, recessive-dominant, recessive-recessive. At one of the loci (A), there was a known disease-related allele. We stratified the family data on the presence of this allele, eliminating family members who were without it. This elimination step has the effect of raising the "penetrance" at the second locus (B). We then calculated the lod score at the second locus (B) and compared the pre- and post-stratification lod scores at B. A positive difference indicated interaction. We also examined if it was possible to detect interaction with locus B based on a disease-marker association (instead of an identified disease allele) at locus A. We also tested whether the presence of genetic heterogeneity would generate false positive evidence of interaction. The power to detect interaction for a known disease allele was 60-90%. The probability of false positives, based on heterogeneity, was low. Decreasing linkage disequilibrium between the disease and marker at locus A decreased the likelihood of detecting interaction. The allele frequency of the associated marker made little difference to the power. PMID:24690899

Corso, Barbara; Greenberg, David A

2014-01-01

294

Using Linkage Analysis to Detect Gene-Gene Interaction by Stratifying Family Data on Known Disease, or Disease-Associated, Alleles  

PubMed Central

Detecting gene-gene interaction in complex diseases is a major challenge for common disease genetics. Most interaction detection approaches use disease-marker associations and such methods have low power and unknown reliability in real data. We developed and tested a powerful linkage-analysis-based gene-gene interaction detection strategy based on conditioning the family data on a known disease-causing allele or disease-associated marker allele. We computer-generated multipoint linkage data for a disease caused by two epistatically interacting loci (A and B). We examined several two-locus epistatic inheritance models: dominant-dominant, dominant-recessive, recessive-dominant, recessive-recessive. At one of the loci (A), there was a known disease-related allele. We stratified the family data on the presence of this allele, eliminating family members who were without it. This elimination step has the effect of raising the “penetrance” at the second locus (B). We then calculated the lod score at the second locus (B) and compared the pre- and post-stratification lod scores at B. A positive difference indicated interaction. We also examined if it was possible to detect interaction with locus B based on a disease-marker association (instead of an identified disease allele) at locus A. We also tested whether the presence of genetic heterogeneity would generate false positive evidence of interaction. The power to detect interaction for a known disease allele was 60–90%. The probability of false positives, based on heterogeneity, was low. Decreasing linkage disequilibrium between the disease and marker at locus A decreased the likelihood of detecting interaction. The allele frequency of the associated marker made little difference to the power.

Corso, Barbara; Greenberg, David A.

2014-01-01

295

Identification of Markers Linked to a Celery Mosaic Virus Resistance Gene in Celery  

Microsoft Academic Search

Resistance to Celery mosaic virus (CeMV) in celery (Apium graveolens L. var. dulce (Mill.) Pers.) is recessive and determined by the single gene, cmv. We report discovery of two polymerase chain reaction-based dominant markers tightly linked to cmv in segregating F2 and BC1 populations. Marker me1em2 is associated to the dominant (susceptibility allele) and the second marker, me8em2, to the

Juan J. Ruiz; Belen Pico; Genyi Li; Vincent D'Antonio; Bryce Falk; Carlos F. Quiros

296

Eleven novel polymorphic microsatellite DNA markers from the green-lipped mussel, Perna viridis  

Microsoft Academic Search

We report on the characterization of 11 polymorphic microsatellite loci in P. viridis, the first set of such markers developed and characterized for this species. The number of alleles per locus ranged from\\u000a 2 to 7, whereas the observed heterozygosity ranged from 0.0447 to 0.4837. These markers should prove useful as powerful genetic\\u000a markers for this species.

C. C. Ong; C. H. Teh; S. G. Tan; K. Yusoff; C. K. Yap

2008-01-01

297

Expanding the repertoire of gene tools for precise manipulation of the Clostridium difficile genome: allelic exchange using pyrE alleles.  

PubMed

Sophisticated genetic tools to modify essential biological processes at the molecular level are pivotal in elucidating the molecular pathogenesis of Clostridium difficile, a major cause of healthcare associated disease. Here we have developed an efficient procedure for making precise alterations to the C. difficile genome by pyrE-based allelic exchange. The robustness and reliability of the method was demonstrated through the creation of in-frame deletions in three genes (spo0A, cwp84, and mtlD) in the non-epidemic strain 630?erm and two genes (spo0A and cwp84) in the epidemic PCR Ribotype 027 strain, R20291. The system is reliant on the initial creation of a pyrE deletion mutant, using Allele Coupled Exchange (ACE), that is auxotrophic for uracil and resistant to fluoroorotic acid (FOA). This enables the subsequent modification of target genes by allelic exchange using a heterologous pyrE allele from Clostridium sporogenes as a counter-/negative-selection marker in the presence of FOA. Following modification of the target gene, the strain created is rapidly returned to uracil prototrophy using ACE, allowing mutant phenotypes to be characterised in a PyrE proficient background. Crucially, wild-type copies of the inactivated gene may be introduced into the genome using ACE concomitant with correction of the pyrE allele. This allows complementation studies to be undertaken at an appropriate gene dosage, as opposed to the use of multicopy autonomous plasmids. The rapidity of the 'correction' method (5-7 days) makes pyrE(-) strains attractive hosts for mutagenesis studies. PMID:23405251

Ng, Yen Kuan; Ehsaan, Muhammad; Philip, Sheryl; Collery, Mark M; Janoir, Clare; Collignon, Anne; Cartman, Stephen T; Minton, Nigel P

2013-01-01

298

Expanding the Repertoire of Gene Tools for Precise Manipulation of the Clostridium difficile Genome: Allelic Exchange Using pyrE Alleles  

PubMed Central

Sophisticated genetic tools to modify essential biological processes at the molecular level are pivotal in elucidating the molecular pathogenesis of Clostridium difficile, a major cause of healthcare associated disease. Here we have developed an efficient procedure for making precise alterations to the C. difficile genome by pyrE-based allelic exchange. The robustness and reliability of the method was demonstrated through the creation of in-frame deletions in three genes (spo0A, cwp84, and mtlD) in the non-epidemic strain 630?erm and two genes (spo0A and cwp84) in the epidemic PCR Ribotype 027 strain, R20291. The system is reliant on the initial creation of a pyrE deletion mutant, using Allele Coupled Exchange (ACE), that is auxotrophic for uracil and resistant to fluoroorotic acid (FOA). This enables the subsequent modification of target genes by allelic exchange using a heterologous pyrE allele from Clostridium sporogenes as a counter-/negative-selection marker in the presence of FOA. Following modification of the target gene, the strain created is rapidly returned to uracil prototrophy using ACE, allowing mutant phenotypes to be characterised in a PyrE proficient background. Crucially, wild-type copies of the inactivated gene may be introduced into the genome using ACE concomitant with correction of the pyrE allele. This allows complementation studies to be undertaken at an appropriate gene dosage, as opposed to the use of multicopy autonomous plasmids. The rapidity of the ‘correction’ method (5–7 days) makes pyrE? strains attractive hosts for mutagenesis studies.

Philip, Sheryl; Collery, Mark M.; Janoir, Clare; Collignon, Anne; Cartman, Stephen T.; Minton, Nigel P.

2013-01-01

299

Overcoming Allelic Specificity by Immunization with Five Allelic Forms of Plasmodium falciparum Apical Membrane Antigen 1  

PubMed Central

Apical membrane antigen 1 (AMA1) is a leading vaccine candidate, but the allelic polymorphism is a stumbling block for vaccine development. We previously showed that a global set of AMA1 haplotypes could be grouped into six genetic populations. Using this information, six recombinant AMA1 proteins representing each population were produced. Rabbits were immunized with either a single recombinant AMA1 protein or mixtures of recombinant AMA1 proteins (mixtures of 4, 5, or 6 AMA1 proteins). Antibody levels were measured by enzyme-linked immunosorbent assay (ELISA), and purified IgG from each rabbit was used for growth inhibition assay (GIA) with 12 different clones of parasites (a total of 108 immunogen-parasite combinations). Levels of antibodies to all six AMA1 proteins were similar when the antibodies were tested against homologous antigens. When the percent inhibitions in GIA were plotted against the number of ELISA units measured with homologous AMA1, all data points followed a sigmoid curve, regardless of the immunogen. In homologous combinations, there were no differences in the percent inhibition between the single-allele and allele mixture groups. However, all allele mixture groups showed significantly higher percent inhibition than the single-allele groups in heterologous combinations. The 5-allele-mixture group showed significantly higher inhibition to heterologous parasites than the 4-allele-mixture group. On the other hand, there was no difference between the 5- and 6-allele-mixture groups. These data indicate that mixtures with a limited number of alleles may cover a majority of the parasite population. In addition, using the data from 72 immunogen-parasite combinations, we mathematically identified 13 amino acid polymorphic sites which significantly impact GIA activities. These results could be a foundation for the rational design of a future AMA1 vaccine.

Herrera, Raul; Diouf, Ababacar; Zhou, Hong; Mu, Jianbing; Hu, Zonghui; MacDonald, Nicholas J.; Reiter, Karine; Nguyen, Vu; Shimp, Richard L.; Singh, Kavita; Narum, David L.; Long, Carole A.; Miller, Louis H.

2013-01-01

300

Genetic epidemiology of osteoporosis across four microsatellite markers near the VDR gene  

PubMed Central

The large amount of positive genetic association data in a number of bone diseases suggests functional consequences of Vitamin D receptor (VDR) gene polymorphism. In the present study, four microsatellite markers viz., D12S1633, D12S1635, D12S347, and D12S96, that lie in the vicinity of the VDR gene on chromosome 12 were selected to assess the allele distribution pattern and diversity among three groups of individuals - normal, osteopenia and osteoporosis. Genetic association study was performed using allele frequency data. Total genomic DNA was isolated from the whole blood of 226 individuals, after recording their bone mineral density (BMD) using Dual X-ray absorptiometry (DXA). All DNA samples were subjected to multiplex Polymerase Chain Reaction (PCR) - genotyping. Allele frequencies and genetic diversity parameters like - number of alleles, average variance and average heterozygosity across all the four markers among three groups were computed. Effect of population stratification was excluded by investigating population structure. A trend of decreasing genetic diversity across four loci from normal to pre- and post-disease condition has been observed. Lesser recombination rate (?) indicates linkage between studied microsatellite markers and VDR gene. Statistically significant linkage disequilibrium was detected for the allele - 22 of locus D12S96 with osteoporosis. A positive association of allele - 22 suggests susceptibility to disease whereas predominance of allele - 27 among non - diseased group implicates its association with normal bone health.

Raje, Mehrunnisa; Botre, Chaitali; Ashma, Richa

2013-01-01

301

Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry.  

PubMed

Short tandem repeats (STRs) are the primary genetic markers used for the analysis of biological samples in forensic and human identity testing. The discrimination power of a combination of STRs is sufficient in many human identity testing comparisons unless the evidence is substantially compromised and/or there are insufficient relatives or a potential mutation may have arisen in kinship analyses. An automated STR assay system that is based on electrospray ionization mass spectrometry (ESI-MS) has been developed that can increase the discrimination power of some of the CODIS core STR loci and thus provide more information in typical and challenged samples and cases. Data from the ESI-MS STR system is fully backwards compatible with existing STR typing results generated by capillary electrophoresis. In contrast, however, the ESI-MS analytical system also reveals nucleotide polymorphisms residing within the STR alleles. The presence of these polymorphisms expands the number of alleles at a locus. Population studies were performed on the 13 core CODIS STR loci from African Americans, Caucasians and Hispanics capturing both the length of the allele, as well as nucleotide variations contained within repeat motifs or flanking regions. Such additional polymorphisms were identified in 11 of the 13 loci examined whereby several nominal length alleles were subdivided. A substantial increase in heterozygosity was observed, with close to or greater than 5% of samples analyzed being heterozygous with equal-length alleles in at least one of five of the core CODIS loci. This additional polymorphism increases discrimination power significantly, whereby the seven most polymorphic STR loci have a discrimination power equivalent to the 10 most discriminating of the CODIS core loci. An analysis of substructure among the three population groups revealed a higher ? than would be observed compared with using alleles designated by nominal length, i.e., repeats solely. Two loci, D3S1358 and vWA produced ? estimates of 0.0477 and 0.0234, respectively, when the expanded allele complement (i.e., nominal allele and SNPs) was considered compared to 0.0145 and 0.01266, respectively when only nominal repeat number was considered. These differences may indicate underlying population specific allele distributions exist within these populations. A system of nomenclature has been developed that facilitates the databasing, searching and analyses of these combined data forms. PMID:22405515

Planz, John V; Sannes-Lowery, Kristen A; Duncan, David D; Manalili, Sheri; Budowle, Bruce; Chakraborty, Ranajit; Hofstadler, Steven A; Hall, Thomas A

2012-09-01

302

Mutator alleles of yeast DNA polymerase ?  

Microsoft Academic Search

The yeast REV3 gene encodes the catalytic subunit of DNA polymerase zeta (pol ?), a B family polymerase that performs mutagenic DNA synthesis in cells. To probe pol ? mutagenic functions, we generated six mutator alleles of REV3 with amino acid replacements for Leu979, a highly conserved residue inferred to be at the pol ? active site. Replacing Leu979 with

Ayako N. Sakamoto; Jana E. Stone; Grace E. Kissling; Scott D. McCulloch; Youri I. Pavlov; Thomas A. Kunkel

2007-01-01

303

APOE2 allele increased in tardive dyskinesia.  

PubMed

Ninety-seven inpatients with tardive dyskinesia (average AIMS score = 13), the majority of whom were schizophrenic, were studied. Forty patients were Caucasian, and 57 were African-American. The APOE genotypes of these patients were compared to previously published genotypes of controls and with previously published studies of APOE genotypes in patients with schizophrenia. There were no significant differences in APOE allele frequencies comparing the African-American tardive dyskinesia population and the African-American control groups. In contrast, significant (< 0.05) P values were obtained comparing the Caucasian tardive dyskinesia population to the Caucasian controls, when comparing allele frequencies and genotypic frequencies. This study suggests that Caucasians bearing an APOE2 allele are at increased risk of developing tardive dyskinesia, whereas African-Americans are not. APOE genotype-specific risks of both tardive dyskinesia and Alzheimer's disease that vary across populations could be due to recruitment of patients or controls or could be due to modifying effects of differing genetic or environmental backgrounds. The mechanism by which the APOE2 allele increases risk of tardive dyskinesia is not known. Further information about the mechanisms of increased risk of tardive dyskinesia could result in stratification of prescribing practices weighing the costs of medications against the relative risk of side effects. PMID:16261623

Halford, Jonathan; Mazeika, Gandis; Slifer, Susan; Speer, Marcy; Saunders, Ann M; Strittmatter, Warren J; Morgenlander, Joel C

2006-04-01

304

Population stratification and spurious allelic association  

Microsoft Academic Search

3-8 Considerable effort is being expended in attempts to detect genetic loci contributing to complex diseases. 9 Association and linkage studies comprise the two dominant strategies: association studies aim to find disease-predisposing alleles at the population level; and linkage studies focus on familial segregation. Although both strategies have compelling strengths, association analyses are more widely done and likely to spread

Lon R Cardon

305

Expression of human PTPN22 alleles.  

PubMed

Considering the female predominance in most of the autoimmune disorders that associate with the PTPN22 Trp620 variant and the complexity by which this variant influences immunologic tolerance, the objective of this study was to ascertain if the allele-specific expression of the disease-associated Arg620Trp polymorphism is affected by cis-acting or sex-specific trans-acting factor/s (e.g. sex-hormones). The use of the allele-specific transcript quantification of the Arg620Trp encoding 1858T polymorphism revealed no difference in the expression of the 1858C- and T-alleles in non-stimulated peripheral blood mononuclear cells (PBMCs) from non-pregnant female subjects, male subjects or pregnant female subjects in first or third trimester (P=0.70), respectively. While the transcription of PTPN22 in anti-CD3/anti-CD28 stimulated PBMCs increased fourfold (P<0.0001) and 13-fold (P<0.0001) after 48 and 72 h of activation, respectively, the expression of PTPN22 1858C- and T-alleles increased to the same extent (P=0.64). The present result essentially excludes such phenomena as a partial explanation for the female predominance in most of the autoimmune disorders that associate with the PTPN22 Trp620 variant. PMID:17230194

Nielsen, C; Barington, T; Husby, S; Lillevang, S T

2007-03-01

306

Maternal Personality, Parenting Cognitions, and Parenting Practices  

ERIC Educational Resources Information Center

A community sample of 262 European American mothers of firstborn 20-month-olds completed a personality inventory and measures of parenting cognitions (knowledge, self-perceptions, and reports about behavior) and was observed in interaction with their children from which measures of parenting practices (language, sensitivity, affection, and play)…

Bornstein, Marc H.; Hahn, Chun-Shin; Haynes, O. Maurice

2011-01-01

307

Parent to Parent: Giftedness with a Twist  

ERIC Educational Resources Information Center

Discovering that a child is gifted can be both exhilarating and daunting. Parents watch in amazement and awe as their 3-year-old reads a first-grade-level book flawlessly, or they might listen to their preschool child's distress over seeing a homeless person on the street. Parents observe as their 6-year-old dismantles a broken CD player and…

McGee, Christy D.

2012-01-01

308

Associations of HLA alleles with specific language impairment  

PubMed Central

Background Human leukocyte antigen (HLA) loci have been implicated in several neurodevelopmental disorders in which language is affected. However, to date, no studies have investigated the possible involvement of HLA loci in specific language impairment (SLI), a disorder that is defined primarily upon unexpected language impairment. We report association analyses of single-nucleotide polymorphisms (SNPs) and HLA types in a cohort of individuals affected by language impairment. Methods We perform quantitative association analyses of three linguistic measures and case-control association analyses using both SNP data and imputed HLA types. Results Quantitative association analyses of imputed HLA types suggested a role for the HLA-A locus in susceptibility to SLI. HLA-A A1 was associated with a measure of short-term memory (P = 0.004) and A3 with expressive language ability (P = 0.006). Parent-of-origin effects were found between HLA-B B8 and HLA-DQA1*0501 and receptive language. These alleles have a negative correlation with receptive language ability when inherited from the mother (P = 0.021, P = 0.034, respectively) but are positively correlated with the same trait when paternally inherited (P = 0.013, P = 0.029, respectively). Finally, case control analyses using imputed HLA types indicated that the DR10 allele of HLA-DRB1 was more frequent in individuals with SLI than population controls (P = 0.004, relative risk = 2.575), as has been reported for individuals with attention deficit hyperactivity disorder (ADHD). Conclusion These preliminary data provide an intriguing link to those described by previous studies of other neurodevelopmental disorders and suggest a possible role for HLA loci in language disorders.

2014-01-01

309

Parenting and Child DRD4 Genotype Interact to Predict Children's Early Emerging Effortful Control.  

PubMed

Effortful control (EC), or the trait-like capacity to regulate dominant responses, has important implications for children's development. Although genetic factors and parenting likely influence EC, few studies have examined whether they interact to predict its development. This study examined whether the DRD4 exon III variable number tandem repeat polymorphism moderated the relation between parenting and children's EC. Three hundred and eighty-two 3-year-olds and primary caregivers completed behavioral tasks assessing children's EC and parenting. Children's DRD4 genotypes moderated the relation between parenting and EC: Children with at least one 7-repeat allele displayed lower EC in the context of negative parenting than children without this allele. These findings suggest opportunities for modifying early risk for low EC. PMID:22862680

Smith, Heather J; Sheikh, Haroon I; Dyson, Margaret W; Olino, Thomas M; Laptook, Rebecca S; Durbin, C Emily; Hayden, Elizabeth P; Singh, Shiva M; Klein, Daniel N

2012-11-01

310

Modified allelic replication in lymphocytes of patients with neurofibromatosis type 1.  

PubMed

Transcription activity of genes is related to their replication timing, accordingly gene activation is coupled with a shift from late replication to early replication and vice versa. The relationship between replication timing and gene expression is best manifested by monoallelically expressed genes which show an asynchronous pattern of allelic replication, with the active allele replicating earlier than the inactive counterpart. Biallelically expressed genes, which normally replicate highly synchronously, when present in lymphocytes derived from patients with various types of malignancies or premalignancies, replicate highly asynchronously, similar to monoallelically expressed genes. Since neurofibromatosis-type 1 (NF1) patients are at an increased risk to develop malignancies, we used the fluorescence in situ hybridization (FISH) replication assay and evaluated the level of replication synchrony of three cancer-implicated genes (RB1, AML1, and CMYC) in lymphocytes derived from patients with NF1 without malignancy. Each gene, which normally displayed synchrony in allelic replication, in the patients' cells displayed loss of synchrony. The loss of replication synchrony, of each gene, in the patients' cells was achieved by an advanced replication of a single allele, which replicated remarkably earlier than its normal scheduled timing. In addition, the second allele showed slightly earlier replication timing than that normal for the gene. Thus, it is assumed that the NF1 condition is associated with activation of cancer-implicated genes that may be the cause for increased risk of patients to develop malignancies. As loss of synchrony in allelic replication timing differentiates well between NF1 patients and control subjects, this marker may have a potential use for identification of presymptomatic carriers of NF1 disorders. PMID:12781447

Reish, Orit; Orlovski, Ana; Mashevitz, Maya; Sher, Carron; Libman, Vitalia; Rosenblat, Malka; Avivi, Lydia

2003-06-01

311

Evolutionary Dynamics of Sporophytic Self-Incompatibility Alleles in Plants  

PubMed Central

The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act codominantly in both pollen and style (SSIcod), in the second, alleles form a dominance hierarchy in pollen and style (SSIdom). In the third model, alleles interact codominantly in the style and form a dominance hierarchy in the pollen (SSIdomcod). The SSIcod model behaves similarly to the model of gametophytic self-incompatibility, but the selection intensity is stronger. With dominance, dominant alleles invade the population more easily than recessive alleles and have a lower frequency at equilibrium. In the SSIdom model, recessive alleles have both a higher allele frequency and higher expected life span. In the SSIdomcod model, however, loss due to drift occurs more easily for pollen-recessive than for pollen-dominant alleles, and therefore, dominant alleles have a higher expected life span than the more recessive alleles. The process of allelic turnover in the SSIdomcod and SSIdom models is closely approximated by a random walk on a dominance ladder. Implications of the results for experimental studies of sporophytic self-incompatibility in natural populations are discussed.

Schierup, M. H.; Vekemans, X.; Christiansen, F. B.

1997-01-01

312

Gene targeting in the red alga Cyanidioschyzon merolae: single- and multi-copy insertion using authentic and chimeric selection markers.  

PubMed

The unicellular red alga Cyanidioschyzon merolae is an emerging model organism for studying organelle division and inheritance: the cell is composed of an extremely simple set of organelles (one nucleus, one mitochondrion and one chloroplast), and their genomes are completely sequenced. Although a fruitful set of cytological and biochemical methods have now been developed, gene targeting techniques remain to be fully established in this organism. Thus far, only a single selection marker, URA Cm-Gs , has been available that complements the uracil-auxotrophic mutant M4. URA Cm-Gs , a chimeric URA5.3 gene of C. merolae and the related alga Galdieria sulphuraria, was originally designed to avoid gene conversion of the mutated URA5.3 allele in the parental strain M4. Although an early example of targeted gene disruption by homologous recombination was reported using this marker, the genome structure of the resultant transformants had never been fully characterized. In the current study, we showed that the use of the chimeric URA Cm-Gs selection marker caused multicopy insertion at high frequencies, accompanied by undesired recombination events at the targeted loci. The copy number of the inserted fragments was variable among the transformants, resulting in high yet uneven levels of transgene expression. In striking contrast, when the authentic URA5.3 gene (URA Cm-Cm ) was used as a selection marker, efficient single-copy insertion was observed at the targeted locus. Thus, we have successfully established a highly reliable and reproducible method for gene targeting in C. merolae. Our method will be applicable to a number of genetic manipulations in this organism, including targeted gene disruption, replacement and tagging. PMID:24039997

Fujiwara, Takayuki; Ohnuma, Mio; Yoshida, Masaki; Kuroiwa, Tsuneyoshi; Hirano, Tatsuya

2013-01-01

313

Contrasting genetic structures of two parasitic nematodes, determined on the basis of neutral microsatellite markers and selected anthelmintic resistance markers.  

PubMed

For the first time, the neutral genetic relatedness of natural populations of Trichostrongylid nematodes was investigated in relation to polymorphism of the beta-tubulin gene, which is selected for anthelminthic treatments. The aim of the study was to assess the contribution of several evolutionary processes: migration and genetic drift by neutral genetic markers and selection by anthelminthic treatments on the presence of resistance alleles at beta-tubulin. We studied two nematode species (Teladorsagia circumcincta and Haemonchus contortus) common in temperate climatic zones; these species are characterized by contrasting life history traits. We studied 10 isolated populations of goat nematode parasites: no infected adult goat had been exchanged after the herds were established. Beta-tubulin polymorphism was similar in these two species. One and two beta-tubulin alleles from T. circumcincta and H. contortus respectively were shared by several populations. Most of the beta-tubulin alleles were 'private' alleles. No recombination between alleles was detected in BZ-resistant alleles from T. circumcincta and H. contortus. The T. circumcincta populations have not diverged much since their isolation (F(ST) <0.08), whereas H. contortus displayed marked local genetic differentiation (F(ST) ranging from 0.08 to 0.18). These findings suggest that there are severe bottlenecks in the H. contortus populations, possibly because of their reduced abundance during unfavourable periods and their high reproductive rate, which allows the species to persist even after severe population reduction. Overall, the data reported contradict the hypothesis of the origin of beta-tubulin resistance alleles in these populations from a single mutational event, but two other hypotheses (recurrent mutation generating new alleles in isolated populations and the introduction of existing alleles) emerge as equally likely. PMID:19900171

Silvestre, A; Sauve, C; Cortet, J; Cabaret, J

2009-12-01

314

CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells  

PubMed Central

Inter-individual variation in CCAAT/enhancer binding protein gamma (CEBPG) transcript expression in normal human bronchial epithelial cells (NBEC) is associated with predisposition to lung cancer. We hypothesize that this inter-individual variation is in part explained by cis-acting genetic variation in CEBPG. To test this hypothesis we measured transcript expression derived from each parental copy of CEBPG (ie, allele-specific expression; ASE). There was a significant 2.9-fold higher cell cycle-specific variation in ASE of CEBPG rs2772 A compared to C allele (P < 0.001). In 20% of NBEC samples, CEBPG rs2772 A allele was expressed on average 2.10 fold greater than rs2772 C allele. These data support the hypothesis that genetic variation in linkage disequilibrium with rs2772 influences regulation of CEBPG transcript expression through a trans-effect downstream of RNA polymerase II transcription and confirm that cis-acting genetic variation contributes to inter-individual variation in CEBPG transcript expression in NBEC, which is associated with variation in lung cancer risk.

Blomquist, Thomas M.; Brown, Ronald D.; Crawford, Erin L.; de la Serna, Ivana; Williams, Kandace; Yoon, Youngsook; Hernandez, Dawn-Alita; Willey, James C.

2013-01-01

315

A novel hypomorphic Looptail allele at the planar cell polarity Vangl2 gene  

PubMed Central

Vangl2 forms part of the planar cell polarity signalling pathway and is the gene defective in the Looptail (Lp) mouse mutant. Two previously described alleles, Lp and Lpm1Jus, segregate in a semi-dominant fashion, with heterozygotes displaying the looped-tail appearance, while homozygotes show the neural tube defect called craniorachischisis. Here, we report a novel experimentally-induced allele, Lpm2Jus, that carries a missense mutation, R259L, in Vangl2. This mutation was specific to the Lp phenotype and absent from both parental strains and 28 other inbred strains. Notably, this mutation segregates in a recessive manner with all heterozygotes appearing normal and 47% of homozygotes showing a looped-tail. Homozygous Lpm2Jus embryos showed spina bifida in 12%. Lpm2Jus genetically interacts with Lp with 77% of compound heterozygotes displaying craniorachischisis. Vangl2R259L behaved like the wild-type allele in overexpression and morpholino knockdown/rescue assays in zebrafish embryos. These data suggest that Lpm2Jus represents a new hypomorphic allele of Lp.

Guyot, Marie-Claude; Bosoi, Ciprian M.; Kharfallah, Fares; Reynolds, Annie; Drapeau, Pierre; Justice, Monica; Gros, Philippe; Kibar, Zoha

2013-01-01

316

Challenges of Parenting Multiples  

MedlinePLUS

... the American Society for Reproductive Medicine Challenges of Parenting Multiples There are many psychological, social, and economic ... the unique challenges and rewards that come from parenting multiples. For more information on the medical aspects ...

317

Growing Pains (For Parents)  

MedlinePLUS

... Parents Are Reading Q&A: Obamacare Finding Affordable Health Care Eating Well & Staying Fit Flu Vaccine: How Many Doses? Connect With Us: Social Media Pregnant? Your Baby's Growth Growing Pains KidsHealth > Parents > ...

318

When Your Parents Fight  

MedlinePLUS

... many times when parents disagree, they argue. An argument is a fight using words. Most kids worry ... make kids feel scared , sad , or upset. Even arguments that use silence — like when parents act angry ...

319

Parent's Firearm Safety Checklist  

MedlinePLUS

Parent’s Firearm Safety Checklist IN YOUR HOME ? Before you buy a gun, consider less dangerous ways to keep your family ... window locks, dogs, etc. ? Don't buy a gun unless you have the necessary knowledge to use ...

320

Asperger Syndrome (For Parents)  

MedlinePLUS

... history is), kids may benefit from these treatments: parent education and training specialized educational interventions social skills ... Although AS presents challenges for kids and their parents, you can help your child adjust and offer ...

321

Parents, Kids and TV.  

National Technical Information Service (NTIS)

Three articles offer parents suggestions on how to make television a positive experience for their children. An editorial introduces the following themes basic to all the articles: type and amount of television viewing should be regulated by parents, pare...

M. Gaffney

1983-01-01

322

Parent Outreach Success  

NSDL National Science Digital Library

Through the Massachusetts Parent Involvement Project (MassPIP), teams of community businesses, service organizations, school personnel, parents, and children joined together and planned and conducted science, mathematics, and technology related activities

Nitzberg, Joel; Sparrow, Judith

2001-11-01

323

Allele and Haplotype Diversity of 26 X-STR Loci in Four Nationality Populations from China  

PubMed Central

Background Haplotype analysis of closely associated markers has proven to be a powerful tool in kinship analysis, especially when short tandem repeats (STR) fail to resolve uncertainty in relationship analysis. STR located on the X chromosome show stronger linkage disequilibrium compared with autosomal STR. So, it is necessary to estimate the haplotype frequencies directly from population studies as linkage disequilibrium is population-specific. Methodology and Findings Twenty-six X-STR loci including six clusters of linked markers DXS6807-DXS8378-DXS9902(Xp22), DXS7132-DXS10079-DXS10074-DXS10075-DXS981 (Xq12), DXS6801-DXS6809-DXS6789-DXS6799(Xq21), DXS7424-DXS101-DXS7133(Xq22), DXS6804-GATA172D05(Xq23), DXS8377-DXS7423 (Xq28) and the loci DXS6800, DXS6803, DXS9898, GATA165B12, DXS6854, HPRTB and GATA31E08 were typed in four nationality (Han, Uigur, Kazakh and Mongol) samples from China (n?=?1522, 876 males and 646 females). Allele and haplotype frequency as well as linkage disequilibrium data for kinship calculation were observed. The allele frequency distribution among different populations was compared. A total of 5–20 alleles for each locus were observed and altogether 289 alleles for all the selected loci were found. Allele frequency distribution for most X-STR loci is different in different populations. A total of 876 male samples were investigated by haplotype analysis and for linkage disequilibrium. A total of 89, 703, 335, 147, 39 and 63 haplotypes were observed. Haplotype diversity was 0.9584, 0.9994, 0.9935, 0.9736, 0.9427 and 0.9571 for cluster I, II, III, IV, V and VI, respectively. Eighty-two percent of the haplotype of cluster IIwas found only once. And 94% of the haplotype of cluster III show a frequency of <1%. Conclusions These results indicate that allele frequency distribution for most X-STR loci is population-specific and haplotypes of six clusters provide a powerful tool for kinship testing and relationship investigation. So it is necessary to obtain allele frequency and haplotypes data of the linked loci for forensic application.

Quan, Li; Zhao, Hu; Wu, Ye-Da; Huang, Xiao-Ling; Lu, De-Jian

2013-01-01

324

A new and versatile method for the successful conversion of AFLP markers into simple single locus markers  

PubMed Central

Genetic markers can efficiently be obtained by using amplified fragment length polymorphism (AFLP) fingerprinting because no prior information on DNA sequence is required. However, the conversion of AFLP markers from complex fingerprints into simple single locus assays is perceived as problematic because DNA sequence information is required for the design of new locus-specific PCR primers. In addition, single locus polymorphism (SNP) information is required to design an allele-specific assay. This paper describes a new and versatile method for the conversion of AFLP markers into simple assays. The protocol presented in this paper offers solutions for frequently occurring pitfalls and describes a procedure for the identification of the SNP responsible for the AFLP. By following this approach, a high success rate for the conversion of AFLP markers into locus-specific markers was obtained.

Brugmans, Bart; van der Hulst, Ron G. M.; Visser, Richard G. F.; Lindhout, Pim; van Eck, Herman J.

2003-01-01

325

MAOA, Early Experiences of Harsh Parenting, Irritable Opposition, and Bullying-Victimization: A Moderated Indirect-Effects Analysis  

ERIC Educational Resources Information Center

Harsh parenting and child characteristics such as opposition and aggression have been found to relate to bullying, victimization, and bullying-victimization, yet not all children display equal vulnerability to harsh parenting. The monoamine oxidase A gene ("MAOA"; "low-activity" variant) may be a key vulnerability allele as it…

Whelan, Yvonne M.; Kretschmer, Tina; Barker, Edward D.

2014-01-01

326

A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.  

PubMed

Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics. PMID:23688582

Yuasa, Isao; Jin, Feng; Harihara, Shinji; Matsusue, Aya; Fujihara, Junko; Takeshita, Haruo; Akane, Atsushi; Umetsu, Kazuo; Saitou, Naruya; Chattopadhyay, Prasanta K

2013-09-01

327

Allele-specific silencing of the dominant disease allele in sialuria by RNA interference  

Microsoft Academic Search

Dominant disease alleles are attractive therapeutic targets for allele-specific gene silencing by small interfering RNA (siRNA). Sialuria is a dominant disorder caused by missense mutations in the allosteric site of GNE, coding for the rate-limiting enzyme of sialic acid biosynthesis, UDP-GlcNAc 2-epimerase\\/ManNAc kinase. The resultant loss of feedback inhibition of GNE-epimerase activity by CMP-sialic acid causes excessive production of free

Riko D. Klootwijk; Paul J. M. Savelkoul; Carla Ciccone; Irini Manoli; Natasha J. Caplen; Donna M. Krasnewich; William A. Gahl; Marjan Huizing

2008-01-01

328

Allelic or NonAllelic? Complementation Studies with Bacteriophage T4 rII Mutations  

Microsoft Academic Search

An easy-to-perform exercise to demonstrate complementation is presented. Complementation tests are used to determine whether mutations affecting the same phenotype are within the same gene (allelic) or in different genes (non-allelic). In this exercise, mutations in the rII locus of bacteriophage T4 are studied. Host E. coli bacteria are co-infected with different T4 mutant phage. If two mutations are in

Susan J. Karcher

329

ADHD Parents Medication Guide  

MedlinePLUS

... Most doctors recommend that parents and guardians attend parenting classes, particularly those focused on understanding and managing ... PDF: http://www.help4adhd.org/documents/WWK1.pdf Parenting a Child with ADHD HTML: http://www.help4adhd. ...

330

Building Parent Involvement  

ERIC Educational Resources Information Center

Discussed is the rationale behind parent involvement in guidance and educational activities, together with specific suggestions for involving parents with other adults (parent advisory committees, informal coffees, Transactional analysis (groups etc.), with children (story hours, trips, demonstrations, counseling booths, testing, interviewing,…

Nelson, Richard C.; Bloom, John W.

1973-01-01

331

Parental Rights in Education.  

ERIC Educational Resources Information Center

Chapter 15 in a book on school law summarizes court decisions and legislation concerning the rights of parents in the education of children. On purely educational matters, the interest of the parent normally must yield to the dominant interest of the state. Parental arguments are strongest when they can sincerely rely upon religious beliefs that…

Volz, Marlin M.

332

When Parents Argue  

MedlinePLUS

Chances are you've had an argument or twenty with your parents recently — about clothes, homework, your phone, friends, or pretty much anything. But what's going on when your parents fight with each other? When Parents Disagree All couples argue from ...

333

The Parent Needs Inventory.  

ERIC Educational Resources Information Center

The "Parent Needs Inventory" (PNI) is designed to identify needs and concerns of parents of very young handicapped children and to provide an objective measure of program effectiveness. Using the Q-sort process, the PNI compares the parent's "real" and "ideal" perceptions of themselves in three areas--the grieving process, knowledge of child…

DeRosa, Steve

334

Parent Outreach Success.  

ERIC Educational Resources Information Center

Presents the Massachusetts Parent Involvement Project (MassPIP) comprising 59 local community coalitions of businesses, service organizations, school personnel, parents, and children. Describes steps coalitions follow in planning events and presents community success stories. The project developed a set of activities that parents can do at home…

Nitzberg, Joel; Sparrow, Judith

2001-01-01

335

Getting Along with Parents  

MedlinePLUS

... read, you just might grow up carrying a book wherever you go, just like she does. But parents do a lot more than just pass along their hobbies. Moms and dads need to care for their kids from the minute they're born. It's a parent's job to love and guide kids — and most parents ...

336

Parenting Your Adopted Preschooler.  

National Technical Information Service (NTIS)

Parenting an adopted preschooler is very similar to parenting any preschooler. As parents, you should not ignore the fact that your child is adopted or their experiences prior to the adoption. But you need not worry unnecessarily about these issues, eithe...

2009-01-01

337

Relational Responding in Parents  

ERIC Educational Resources Information Center

This study investigated the relationship between parenting stress and relational conditioning. Fourteen students who were not mothers, 14 mothers who reported high parenting stress and 14 mothers with low parenting stress completed two matching-to-sample (MTS) computer tasks, each requiring formation of three 3-member classes. The first MTS task…

Murrell, Amy R.; Wilson, Kelly G.; LaBorde, Cicely T.; Drake, Chad E.; Rogers, Leslie J.

2008-01-01

338

From a Parent's Perspective.  

ERIC Educational Resources Information Center

The series of articles on parenting compiled in this book bridges the gap between educational theory and the everyday problems parents must deal with. The book's perspective encourages parents to be gentle, flexible, observant, and not too attached to expectations. The first chapter, "Surviving Parenthood," discusses topics such as managing…

Gonzalez-Mena, Janet

339

Parenting by Lying  

ERIC Educational Resources Information Center

The present set of studies identifies the phenomenon of "parenting by lying", in which parents lie to their children as a means of influencing their emotional states and behaviour. In Study 1, undergraduates (n = 127) reported that their parents had lied to them while maintaining a concurrent emphasis on the importance of honesty. In Study 2 (n =…

Heyman, Gail D.; Luu, Diem H.; Lee, Kang

2009-01-01

340

Parent Abuse: A Review  

ERIC Educational Resources Information Center

A recent focus of research and clinical practice has been on the issue of abuse of parents by their children (parent abuse). This paper reviews the literature on this phenomenon. While parent abuse falls under the umbrella of family violence, it appears to be qualitatively different from other forms of intra-family abuse. Research has primarily…

Kennair, Nicola; Mellor, David

2007-01-01

341

NYS Foster Parent Manual  

ERIC Educational Resources Information Center

This manual was developed for use in foster parents' day-to-day life with the children in their care. It gives them practical information on topics like medical care, payments, and the role of the court, and also provides guidance on areas like welcoming a child, discipline, and parent visits. The manual emphasizes the role of foster parents in…

McBride, Rebecca

2007-01-01

342

Parental Smoking Modifies the Relation between Genetic Variation in Tumor Necrosis Factor-? (TNF) and Childhood Asthma  

Microsoft Academic Search

RESULTS: The A allele of the TNF-308 SNP was associated with increased risk of asthma (relative risk (RR) = 1.54; 95% confidence interval (CI), 1.04-2.28), especially among children of non- smoking parents (RR = 2.06; 95% CI, 1.19-3.55; p for interaction = 0.09). Similarly, the A allele of the TNF-238 SNP was associated with increased asthma risk among children of

Hao Wu; Isabelle Romieu; Juan-Jose Sienra-Monge; Blanca Estela del Rio-Navarro; Daniel M. Anderson; Erin W. Dunn; Lori L. Steiner; Irma del Carmen Lara-Sanchez; Stephanie J. London

2007-01-01

343

Evaluation of allelic instability in MEN 2A and FMTC tumors  

SciTech Connect

Allelic instability of genomic DNA in tumors derived from individuals with multiple endocrine neoplasia type 2A (MEN 2A) or medullary thyroid carcinoma (MTC) was evaluated. Fourteen highly polymorphic dinucleotide repeat polymorphism markers from 5 different chromosomes were tested. Allelic difference between tumor and peripheral blood leukocyte DNA was observed in 4 of 9 tumors, 2 of which showed allelic instability at more than 1 locus. Pet 1, a sporadic, moderately aggressive MTC, revealed allelic instability at 5 different loci from 4 chromosomes. Rut1, an aggressive MTC from a patient with MEN 2A, revealed genetic instability at 3 different loci, all located on chromosome 10. Microsatellite instability has been associated with hereditary nonpolyposis colon cancer (HNPCC) and has been attributed to germline mutations in hMSH2. In MEN 2A and familial MTC, the initiating event in tumorigenesis is a germline mutation in the receptor tyrosine kinase RET. Progression to full tumor development likely required additional somatic mutations. The presence of microsatellite instability in some MTCs suggests that these additional mutations may affect DNA repair genes such as hMSH2 that has been associated with HNPCC.

Schuster, M.K.; Bratti, L.M.; Rothschild, C.B. [Bowman Gray School of Medicine, Winston-Salem, NC (United States)] [and others

1994-09-01

344

Association between Rdna Alleles and Quantitative Traits in Doubled Haploid Populations of Barley  

PubMed Central

Doubled haploids (DH) were generated from reciprocal F(1) hybrids which were heterozygous for alleles at the Nor-H3 locus on chromosome 5H of barley. The r-DNA alleles did not deviate significantly from the expected 1:1 ratio and the DH progenies were classified into two groups based on the allelic constitution of the Nor-H3 locus. The DHs were grown in a randomized, replicated field experiment and a range of agronomic and quality traits were recorded. The Nor-H3 locus was associated with a significant portion of the genetic variation for: yield, thousand corn weight, water sensitivity and milling energy requirement of the grain. However, the magnitude of the differences between groups was dependent on the direction of the cross. The milling energy requirement of the grain was consistently associated with alleles at the Nor-H3 locus. These results are presented in relation to the dynamics of rDNA evolution and variability. The potential of molecular markers in conjunction with doubled haploids to map quantitative traits in barley is also discussed.

Powell, W.; Thomas, WTB.; Thompson, D. M.; Swanston, J. S.; Waugh, R.

1992-01-01

345

Molecular characterisation of C4 null alleles found in Felty's syndrome.  

PubMed Central

A higher prevalence of C4B null alleles is found in Felty's syndrome. The molecular basis of C4 null alleles was investigated by studying restriction fragment length polymorphisms (RFLPs) obtained with C4 and 21-hydroxylase (21-OH) DNA probes and by pulsed field gel electrophoresis in 30 subjects with Felty's syndrome. C4A null alleles were found in 10 subjects, and in five of these were associated with a deletion that included C4A and adjacent 21-OHA gene sequences. A 6.4 kilobase C4B-5'-specific Taq I fragment usually provided a reliable guide to the presence of a C4A deletion but unusually in one instance this fragment was found to be a marker of a functioning C4A gene. A C4B null allele was found in 17 subjects and was associated with a deletion involving C4B and 21-OHA gene sequences on only two occasions. There were no instances in which deletion of the 21-OHB gene occurred. Images

Hillarby, M C; Strachan, T; Grennan, D M

1990-01-01

346

Null alleles of the X and Y chromosomal amelogenin gene in a Chinese population.  

PubMed

The use of amelogenin locus typing as a gender marker incorporated in short tandem repeat (STR) multiplexes is a common practice in sex typing. Mutations in the X or Y homologue of the amelogenin gene can be misleading and result in serious mistakes in forensic applications and prenatal diagnosis. In these present studies, the amelogenin gene of 8,087 unrelated male individuals from Chinese Han population was genotyped with Powerplex(®)16 system. The samples that showed discordant results were taken for frequency calculation and further validated by re-amplification with different primer sets, Y-STR typing, and sequencing. Our results describe six amelogenin X-allele (AMELX) or amelogenin Y-allele (AMELY) null cases in these studied subjects with an overall prevalence of 0.074%. Further validation revealed point mutations in the amelogenin-priming sites associated with AMELX nulls (three cases, 0.037%) and deletions on the Y chromosome encompassing the AMELY and other Y-STR loci with three AMELY nulls (0.037%). These mutations and failure of the amplification of the AMELX and AMELY alleles have not been reported for the Chinese population. These and previous findings suggest that mutations in the amelogenin gene may result in amplification failure of the AMELX or AMELY allele, and an additional gender test for unambiguous sex determination may be needed. PMID:21735294

Ou, Xueling; Chen, Wenjing; Chen, Hua; Zhao, Fengcang; Zheng, Jianwen; Tong, Dayue; Chen, Yong; Chen, Aiping; Sun, Hongyu

2012-07-01

347

A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae.  

PubMed

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. Using map-based strategy and in silico approach we isolated a new rice (Oryza sativa L.) blast resistance allele of Pid3, designated Pi25, from a stable blast resistance cultivar Gumei2. Over-expression analysis and complementation test showed that Pi25 conferred blast resistance to M. oryzae isolate js001-20. Sequence analysis showed that Pi25 was an intronless gene of 2,772 nucleotides with single nucleotide substitution in comparison to Pid3 at the nucleotide position 459 and predicatively encoded a typical coiled coil--nucleotide binding site--leucine rich repeat (CC--NBS--LRR) protein of 924 amino acid residuals with 100% identity to Pid3 putative protein. The susceptible allele pi25 in Nipponbare contained a nonsense mutation at the nucleotide position 2,209 resulting in a truncated protein with 736 amino acid residuals. In addition, 14 nucleotide substitutions resulting in 10 amino acid substitutions were identified between Pi25 and pi25 upstream the premature stop codon in the susceptible allele. Although the mechanism of Pi25/Pid3-mediated resistance needs to be further investigated, the isolation of the allele would facilitate the utilization of Pi25/Pid3 in rice blast resistance breeding program via transgenic approach and marker assisted selection. PMID:21621742

Chen, Jie; Shi, Yongfeng; Liu, Wenzheng; Chai, Rongyao; Fu, Yaping; Zhuang, Jieyun; Wu, Jianli

2011-05-20

348

Use of allele scores as instrumental variables for Mendelian randomization  

PubMed Central

Background An allele score is a single variable summarizing multiple genetic variants associated with a risk factor. It is calculated as the total number of risk factor-increasing alleles for an individual (unweighted score), or the sum of weights for each allele corresponding to estimated genetic effect sizes (weighted score). An allele score can be used in a Mendelian randomization analysis to estimate the causal effect of the risk factor on an outcome. Methods Data were simulated to investigate the use of allele scores in Mendelian randomization where conventional instrumental variable techniques using multiple genetic variants demonstrate ‘weak instrument’ bias. The robustness of estimates using the allele score to misspecification (for example non-linearity, effect modification) and to violations of the instrumental variable assumptions was assessed. Results Causal estimates using a correctly specified allele score were unbiased with appropriate coverage levels. The estimates were generally robust to misspecification of the allele score, but not to instrumental variable violations, even if the majority of variants in the allele score were valid instruments. Using a weighted rather than an unweighted allele score increased power, but the increase was small when genetic variants had similar effect sizes. Naive use of the data under analysis to choose which variants to include in an allele score, or for deriving weights, resulted in substantial biases. Conclusions Allele scores enable valid causal estimates with large numbers of genetic variants. The stringency of criteria for genetic variants in Mendelian randomization should be maintained for all variants in an allele score.

Burgess, Stephen; Thompson, Simon G

2013-01-01

349

Utilization of a ts-sacB selection system for the generation of a Mycobacterium avium serovar-8 specific glycopeptidolipid allelic exchange mutant  

PubMed Central

Background Mycobacterium avium are ubiquitous environmental organisms and a cause of disseminated infection in patients with end-stage AIDS. The glycopeptidolipids (GPL) of M. avium are proposed to participate in the pathogenesis of this organism, however, establishment of a clear role for GPL in disease production has been limited by the inability to genetically manipulate M. avium. Methods To be able to study the role of the GPL in M. avium pathogenesis, a ts-sacB selection system, not previously used in M. avium, was employed as a means to achieve homologous recombination for the rhamnosyltransferase (rtfA) gene of a pathogenic serovar 8 strain of M. avium to prevent addition of serovar-specific sugars to rhamnose of the fatty acyl-peptide backbone of GPL. The genotype of the resultant rtfA mutant was confirmed by polymerase chain reaction and southern hybridization. Disruption in the proximal sugar of the haptenic oligosaccharide resulted in the loss of serovar specific GPL with no change in the pattern of non-serovar specific GPL moieties as shown by thin layer chromatography and gas chromatography/mass spectrometry. Complementation of wild type (wt) rtfA in trans through an integrative plasmid restored serovar-8 specific GPL expression identical to wt serovar 8 parent strain. Results In this study, we affirm our results that rtfA encodes an enzyme responsible for the transfer of Rha to 6d-Tal and provide evidence of a second allelic exchange mutagenesis system suitable for M. avium. Conclusion We report the second allelic exchange system for M. avium utilizing ts-sacB as double-negative and xylE as positive counter-selection markers, respectively. This system of allelic exchange would be especially useful for M. avium strains that demonstrate significant isoniazid (INH) resistance despite transformation with katG. Through the construction of mutants in GPL or other mycobacterial components, their roles in M. avium pathogenesis, biosynthesis, or drug resistance can be studied in a consistent manner.

Irani, Vida R; Lee, Sun-Hwa; Eckstein, Torsten M; Inamine, Julia M; Belisle, John T; Maslow, Joel N

2004-01-01

350

Allele frequency of resistance to Bacillus thuringiensis Cry1ab corn in Louisiana populations of sugarcane borer (Lepidoptera: Crambidae).  

PubMed

Transgenic Bacillus thuringiensis (Bt) corn, Zea mays L., has been widely used to manage a corn borer complex in the mid-southern region of the United States. The sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), has become a dominant cornstalk boring species in some areas of this region, especially in Louisiana. Therefore, management of sugarcane borer resistance to Bt corn is critical to ensure the long-term sustainability of Bt corn for the region. This study screened 280 two-parent family-lines of sugarcane borer from four geographical populations in Louisiana during 2005 to determine whether Bt resistance allele frequency in sugarcane borer is sufficiently low to meet the rare resistance assumption of the current "high dose/refuge" resistance management strategy for Bt corn. These sugarcane borer family-lines were examined for Bt resistance by using novel F2 screening procedures. No major Bt resistance alleles were detected in these four populations. The estimated frequency of major Bt resistance alleles was < 0.0027, with a 95% probability and a detection power of 94%. The estimated minor resistance allele frequency was 0.0063, with a 95% CI of 0.0025-0.0117. During a previous study, a major Bt resistance allele was detected in one individual from 213 family-lines of another Louisiana population of sugarcane borer. Combining these data with the current screen, the frequency of major Bt resistance alleles across the five populations was 0.001, with a 95% credibility interval of 0.0001-0.0028 and a detection power of 95%. Major Bt resistance allele frequencies in Louisiana sugarcane borer populations seem to be low, and they should support the rare resistance allele requirement of the high dose/refuge strategy. PMID:18459416

Huang, Fangneng; Leonard, B Rogers; Moore, Steven H; Cook, Donald R; Baldwin, Jack; Tindall, Kelly V; Lee, Donna R

2008-04-01

351

Marker assisted breeding for transformability in maize  

Microsoft Academic Search

Corn lines with improved culturability and transformability were produced using Marker Assisted Breeding (MAB) to introgress specific regions from the highly transformable hybrid, Hi-II, into the elite line, FBLL that responds very poorly in culture. FBLL is a female inbred parental stiff-stalk line that has been used to produce a series of some of DEKALB’s historically best selling hybrids. Five

Brenda A. Lowe; Jennifer M. Kumpf; Jyoti Rout; Dave Warner; Richard Johnson; Charles L. Armstrong; Michael T. Spencer; Paul S. Chomet

2006-01-01

352

Parenting Beliefs, Parental Stress, and Social Support Relationships  

ERIC Educational Resources Information Center

The present study built on prior research by examining the relationship of parental stress and social support to parenting beliefs and behaviors. A sample of 87 parents provided their views concerning the importance of parenting characteristics as well as their level of parental stress and perceived social support. These parents completed the…

Respler-Herman, Melissa; Mowder, Barbara A.; Yasik, Anastasia E.; Shamah, Renee

2012-01-01

353

Personality and Parenting Style in Parents of Adolescents  

ERIC Educational Resources Information Center

Since parental personality traits are assumed to play a role in parenting behaviors, the current study examined the relation between parental personality and parenting style among 688 Dutch parents of adolescents in the SMILE study. The study assessed Big Five personality traits and derived parenting styles (authoritative, authoritarian,…

Huver, Rose M. E.; Otten, Roy; de Vries, Hein; Engels, Rutger C. M. E.

2010-01-01

354

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers.  

PubMed

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding. PMID:24301794

Khaing, A A; Moe, K T; Hong, W J; Park, C S; Yeon, K H; Park, H S; Kim, D C; Choi, B J; Jung, J Y; Chae, S C; Lee, K M; Park, Y J

2013-01-01

355

Evaluation of Allele-Specific Somatic Changes of Genome-Wide Association Study Susceptibility Alleles in Human Colorectal Cancers  

PubMed Central

Background Tumors frequently exhibit loss of tumor suppressor genes or allelic gains of activated oncogenes. A significant proportion of cancer susceptibility loci in the mouse show somatic losses or gains consistent with the presence of a tumor susceptibility or resistance allele. Thus, allele-specific somatic gains or losses at loci may demarcate the presence of resistance or susceptibility alleles. The goal of this study was to determine if previously mapped susceptibility loci for colorectal cancer show evidence of allele-specific somatic events in colon tumors. Methods We performed quantitative genotyping of 16 single nucleotide polymorphisms (SNPs) showing statistically significant association with colorectal cancer in published genome-wide association studies (GWAS). We genotyped 194 paired normal and colorectal tumor DNA samples and 296 paired validation samples to investigate these SNPs for allele-specific somatic gains and losses. We combined analysis of our data with published data for seven of these SNPs. Results No statistically significant evidence for allele-specific somatic selection was observed for the tested polymorphisms in the discovery set. The rs6983267 variant, which has shown preferential loss of the non-risk T allele and relative gain of the risk G allele in previous studies, favored relative gain of the G allele in the combined discovery and validation samples (corrected p-value?=?0.03). When we combined our data with published allele-specific imbalance data for this SNP, the G allele of rs6983267 showed statistically significant evidence of relative retention (p-value?=?2.06×10?4). Conclusions Our results suggest that the majority of variants identified as colon cancer susceptibility alleles through GWAS do not exhibit somatic allele-specific imbalance in colon tumors. Our data confirm previously published results showing allele-specific imbalance for rs6983267. These results indicate that allele-specific imbalance of cancer susceptibility alleles may not be a common phenomenon in colon cancer.

Gerber, Madelyn M.; Hampel, Heather; Schulz, Nathan P.; Fernandez, Soledad; Wei, Lai; Zhou, Xiao-Ping; de la Chapelle, Albert; Toland, Amanda Ewart

2012-01-01

356

Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations  

PubMed Central

The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans.

Vina, Marcelo A. Fernandez; Hollenbach, Jill A.; Lyke, Kirsten E.; Sztein, Marcelo B.; Maiers, Martin; Klitz, William; Cano, Pedro; Mack, Steven; Single, Richard; Brautbar, Chaim; Israel, Shosahna; Raimondi, Eduardo; Khoriaty, Evelyne; Inati, Adlette; Andreani, Marco; Testi, Manuela; Moraes, Maria Elisa; Thomson, Glenys; Stastny, Peter; Cao, Kai

2012-01-01

357

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon  

PubMed Central

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (FST coefficients) to the present database ranged from FST = 0.0016 between Macapá and Belém to FST = 0.0036 between Macapá and the Iberian Peninsula.

da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazao, Gleycianne Furtado; dos Reis Borges, Nathalia Danielly; dos Santos, Sidney Emanuel Batista

2011-01-01

358

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon.  

PubMed

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula. PMID:21637540

da Costa Francez, Pablo Abdon; Rodrigues, Elzemar Martins Ribeiro; Frazão, Gleycianne Furtado; Dos Reis Borges, Nathalia Danielly; Dos Santos, Sidney Emanuel Batista

2011-01-01

359

Strong allelic association between Sjoegren-Larsson syndrome and D17S805  

SciTech Connect

Sjoegren-Larsson Syndrom (SLS) is characterized by congenital ichthyosis, spastic di- or tetraplegia and mental retardation. It is an autosomal recessive trait that has been described in many populations, but is particularly frequent in the northern part of Sweden. A defect in the enzyme fatty alcohol: NAD+ oxidoreductase (FAD) has been suggested, but the molecular mechanism has not been elucidated. Based on linkage analysis and allelic association, the disorder has now been mapped to chromosome 17. Meiotic recombinations suggests that the gene is flanked by D17S805 on the centromeric and D17S783 and D17S925 on the telomeric side. These three markers map to the same location in reference pedigrees. Strong allelic association (chi-square 60.28, p<0.0003) to D17S805 suggests that the mutation is located at a limited distance on the telomeric side of this marker. It is possible that the gene can be identified by functional complementation of SLS cells using YACs from this region. Alternatively, positional cloning should be possible in this presumable small area. The markers identified are close and informative enough to allow accurate genetic diagnosis.

Pigg, M.; Jagell, S.; Sillen, A. [University Hospital, Uppsala (Sweden)] [and others

1994-09-01

360

Eighteen new tetranucleotide microsatellite DNA markers for Coregonus lavaretus cloned from an alpine lake population  

Microsoft Academic Search

We developed 18 polymorphic microsatellite markers for Coregonus lavaretus from genomic libraries enriched for (GACA)n and (GATA)n repeat sequences. Emphasis was placed on developing highly polymorphic, perfect repeats. These loci were screened in 69 individuals from two alpine populations in Austria. Allelic variation was high with nine to 37 alleles per locus and expected heterozygosities ranging from 0.37 to 0.95.

KATHRIN A. WINKLER; STEVEN WEISS

2008-01-01

361

Mutant maize variety containing the glt1-1 allele  

DOEpatents

A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

Nelson, Oliver E. (Cross Plains, WI); Pan, David (Madison, WI)

1994-01-01

362

Mutant maize variety containing the glt1-1 allele  

DOEpatents

A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating. 2 figs.

Nelson, O.E.; Pan, D.

1994-07-19

363

Common allele on chromosome 9 associated with coronary heart disease  

US Patent & Trademark Office Database

Disclosed are methods and compositions for determining whether a person carries an allele associated with increased risk for coronary atherosclerosis by determining whether the person has had RA-CHR9 allele, such as by determining whether the person has an RA-CHR9 allele-associated single nucleotide polymorphism (SNP).

2011-02-08

364

Leveraging Information Across HLA Alleles\\/Supertypes Improves Epitope Prediction  

Microsoft Academic Search

We present a model for predicting HLA class I restricted CTL epitopes. In contrast to almost all other work in this area, we train a single model on epitopes from all HLA alleles and supertypes, yet re- tain the ability to make epitope predictions for specific HLA alleles. We are therefore able to leverage data across all HLA alleles and\\/or

David Heckerman; Carl Myers Kadie; Jennifer Listgarten

2006-01-01

365

A Newly Characterized HLA DQbeta Allele Associated with Pemphigus Vulgaris  

Microsoft Academic Search

The inheritance of particular alleles of major histocompatibility complex class II genes increases the risk for various human autoimmune diseases; however, only a small percentage of individuals having an allele associated with susceptibility develop disease. The identification of allelic variants more precisely correlated with disease susceptibility would greatly facilitate clinical screening and diagnosis. Oligonucleotide-primed gene amplification in vitro was used

Animesh A. Sinha; Chaim Brautbar; Fanny Szafer; Adam Friedmann; Eli Tzfoni; John A. Todd; Lawrence Steinman; Hugh O. McDevitt

1988-01-01

366

Comparative Anatomy of Chromosomal Domains with Imprinted and Non-Imprinted Allele-Specific DNA Methylation  

PubMed Central

Allele-specific DNA methylation (ASM) is well studied in imprinted domains, but this type of epigenetic asymmetry is actually found more commonly at non-imprinted loci, where the ASM is dictated not by parent-of-origin but instead by the local haplotype. We identified loci with strong ASM in human tissues from methylation-sensitive SNP array data. Two index regions (bisulfite PCR amplicons), one between the C3orf27 and RPN1 genes in chromosome band 3q21 and the other near the VTRNA2-1 vault RNA in band 5q31, proved to be new examples of imprinted DMRs (maternal alleles methylated) while a third, between STEAP3 and C2orf76 in chromosome band 2q14, showed non-imprinted haplotype-dependent ASM. Using long-read bisulfite sequencing (bis-seq) in 8 human tissues we found that in all 3 domains the ASM is restricted to single differentially methylated regions (DMRs), each less than 2kb. The ASM in the C3orf27-RPN1 intergenic region was placenta-specific and associated with allele-specific expression of a long non-coding RNA. Strikingly, the discrete DMRs in all 3 regions overlap with binding sites for the insulator protein CTCF, which we found selectively bound to the unmethylated allele of the STEAP3-C2orf76 DMR. Methylation mapping in two additional genes with non-imprinted haplotype-dependent ASM, ELK3 and CYP2A7, showed that the CYP2A7 DMR also overlaps a CTCF site. Thus, two features of imprinted domains, highly localized DMRs and allele-specific insulator occupancy by CTCF, can also be found in chromosomal domains with non-imprinted ASM. Arguing for biological importance, our analysis of published whole genome bis-seq data from hES cells revealed multiple genome-wide association study (GWAS) peaks near CTCF binding sites with ASM.

Kerkel, Kristi; Yale, Alexander; Yotova, Iveta; Drost, Natalia; Lax, Simon; Nhan-Chang, Chia-Ling; Powell, Charles; Borczuk, Alain; Aviv, Abraham; Wapner, Ronald; Chen, Xiaowei; Nagy, Peter L.; Schork, Nicholas; Do, Catherine; Torkamani, Ali; Tycko, Benjamin

2013-01-01

367

Characterization of a PDR1 mutant allele from a clotrimazole-resistant sake yeast mutant with improved fermentative activity  

Microsoft Academic Search

Clotrimazole-resistant mutants from various sake yeasts show improved fermentative activity in sake mash while retaining their parental advantages for sake making. These mutants also exhibit pleiotropic drug resistance (PDR) phenotypes. To investigate the relationship between the improvement of fermentative activity and PDR phenotypes, a PDR1 mutant allele (pdr1-h176) encoding a transcription factor was cloned from a clotrimazole-resistant mutant, HL176 (MATa\\/MAT?),

Hiroko Mizoguchi; Mutsumi Watanabe; Akira Nishimura

1999-01-01

368

Di and tetranucleotide microsatellite markers for the Alpine newt (Triturus alpestris): characterization and cross-priming in five congeners  

Microsoft Academic Search

We developed a set of di- and tetranucleotide microsatellite markers for the Alpine newt, Triturus alpestris . Polymorphism as detected in 39 individuals ranged from 3 to 32 alleles at a locus. Cross-priming with samples of five other Triturus species showed extremely poor levels of cross-species utility. Still, these markers are suitable for studies of inter- and intrapopulation genetic diversity

Trenton W. J. Garner; Benedikt R. Schmidt; Paquita Hoeck; Josh Van Buskirk

2003-01-01

369

Marker-assisted selection to improve drought adaptation in maize: the backcross approach, perspectives, limitations, and alternatives  

Microsoft Academic Search

A number of different marker-assisted selection (MAS) approaches do exist for the improvement of polygenic traits. Results of a marker-assisted backcross (MABC) selection experiment aimed at improving grain yield under drought conditions in tropical maize are pre- sented and compared with alternative MAS strategies. The introgression of favourable alleles at five target regions involved in the expression of yield compo-

Jean-Marcel Ribaut; Michel Ragot

2006-01-01

370

Parental Effect of DNA (Cytosine-5) Methyltransferase 1 on Grandparental-Origin-Dependent Transmission Ratio Distortion in Mouse Crosses and Human Families  

PubMed Central

Transmission ratio distortion (TRD) is a deviation from the expected Mendelian 1:1 ratio of alleles transmitted from parents to offspring and may arise by different mechanisms. Earlier we described a grandparental-origin-dependent sex-of-offspring-specific TRD of maternal chromosome 12 alleles closely linked to an imprinted region and hypothesized that it resulted from imprint resetting errors in the maternal germline. Here, we report that the genotype of the parents for loss-of-function mutations in the Dnmt1 gene influences the transmission of grandparental chromosome 12 alleles. More specifically, maternal Dnmt1 mutations restore Mendelian transmission ratios of chromosome 12 alleles. Transmission of maternal alleles depends upon the presence of the Dnmt1 mutation in the mother rather than upon the Dnmt1 genotype of the offspring. Paternal transmission mirrors the maternal one: live-born offspring of wild-type fathers display 1:1 transmission ratios, whereas offspring of heterozygous Dnmt1 mutant fathers tend to inherit grandpaternal alleles. Analysis of allelic transmission in the homologous region of human chromosome 14q32 detected preferential transmission of alleles from the paternal grandfather to grandsons. Thus, parental Dnmt1 is a modifier of transmission of alleles at an unlinked chromosomal region and perhaps has a role in the genesis of TRD.

Yang, Lanjian; Andrade, Moises Freitas; Labialle, Stephane; Moussette, Sanny; Geneau, Genevieve; Sinnett, Donna; Belisle, Alexandre; Greenwood, Celia M. T.; Naumova, Anna K.

2008-01-01

371

Parent-child relationship and parental well-being of Chinese parents in Hong Kong  

Microsoft Academic Search

This study examines the impact of parental characteristics, family attributes, and parent-child relationship (parent-child relational quality and parent-child relational demands) on parental well-being (psychiatric morbidity, midlife crisis symptoms, positive mental health, and perceived health status) in 1501 Chinese parents. Results showed that amongst the various predictors under focus, parent-child relationship variables were found to have the strongest effects on parental

Daniel T. L Shek

1997-01-01

372

Genetic Introgression and Species Boundary of Two Geographically Overlapping Pine Species Revealed by Molecular Markers  

PubMed Central

Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.

Dai, Xiaogang; Xu, Jin; Li, Shuxian; Yin, Tongming

2014-01-01

373

Genes of the Unfolded Protein Response Pathway Harbor Risk Alleles for Primary Open Angle Glaucoma  

PubMed Central

The statistical power of genome-wide association (GWA) studies to detect risk alleles for human diseases is limited by the unfavorable ratio of SNPs to study subjects. This multiple testing problem can be surmounted with very large population sizes when common alleles of large effects give rise to disease status. However, GWA approaches fall short when many rare alleles may give rise to a common disease, or when the number of subjects that can be recruited is limited. Here, we demonstrate that this multiple testing problem can be overcome by a comparative genomics approach in which an initial genome-wide screen in a genetically amenable model organism is used to identify human orthologues that may harbor risk alleles for adult-onset primary open angle glaucoma (POAG). Glaucoma is a major cause of blindness, which affects over 60 million people worldwide. Several genes have been associated with juvenile onset glaucoma, but genetic factors that predispose to adult onset primary open angle glaucoma (POAG) remain largely unknown. Previous genome-wide analysis in a Drosophila ocular hypertension model identified transcripts with altered regulation and showed induction of the unfolded protein response (UPR) upon overexpression of transgenic human glaucoma-associated myocilin (MYOC). We selected 16 orthologous genes with 62 polymorphic markers and identified in two independent human populations two genes of the UPR that harbor POAG risk alleles, BIRC6 and PDIA5. Thus, effectiveness of the UPR in response to accumulation of misfolded or aggregated proteins may contribute to the pathogenesis of POAG and provide targets for early therapeutic intervention.

Carbone, Mary Anna; Chen, Yuhong; Hughes, Guy A.; Weinreb, Robert N.; Zabriskie, Norman A.; Zhang, Kang; Anholt, Robert R. H.

2011-01-01

374

Allelic dimorphism of Plasmodium vivax gam-1 in the Indian subcontinent  

PubMed Central

Background Genetic polymorphism is an inevitable component of a complex organism especially in multistage infectious organisms such as malaria parasites. Understanding the population genetic structure of the parasites would provide valuable information for effective malaria control strategies. Recently, the development of molecular tools like PCR has made analysis of field samples possible and easier and research on Plasmodium vivax has also been strengthened. Not many reports are available on the genetic polymorphism of P. vivax from the Indian sub-continent. This study evaluates the extent of diversity in field isolates of India with respect to Pvgam-1. Methods A study was designed to assess the diversity of Pvgam-1 among field isolates from India, using a nested PCR assay. Field isolates were collected from different regions of the country and the observed variability was confirmed by sequencing data. Results Both Belem and Chesson type alleles were present either exclusively or in mixed form among isolates of all 10 study sites. The Belem type allele was predominant, occurring in 67% of isolates. The proportion of isolates showing the mixed form (both Belem and Chesson type alleles occurring together in the same isolate) was about 13 overall (up to 38.5% in some isolates). Sequencing of the PCR-amplified Belem and Chesson type alleles confirmed the PCR results. Among the 10 study sequences, 11 polymorphic sites and four singleton variations were observed. All the nucleotide substitutions were non-synonymous. Conclusion Study shows limited diversity of Pvgam-1 marker in Indian isolates with well representation of both Belem and Chesson type alleles.

Prajapati, Surendra K; Verma, Anju; Adak, Tridibes; Yadav, Rajpal S; Kumar, Ashwini; Eapen, Alex; Das, Manoj K; Singh, Neeru; Sharma, Surya K; Rizvi, Moshahid A; Dash, Aditya P; Joshi, Hema

2006-01-01

375

Active Parenting Today: For Parents of 2 to 12 Year Olds. Parent's Guide.  

ERIC Educational Resources Information Center

This book is designed for parents participating in discussion groups utilizing the Active Parenting Today video-based parent education program. The book is divided into six chapters, each of which is integrated with a 26-minute video to be shown at a parent meeting. Chapter 1, the Active Parent, discusses the purpose and roles of parents, while…

Popkin, Michael H.

376

Parenting attitudes, foster parenting attitudes, and motivations of adoptive and nonadoptive foster parent trainees  

Microsoft Academic Search

The purpose of this study was to examine attitudes and motivations of adoptive and nonadoptive foster parent trainees toward parenting and foster parenting. Subjects were 44 adoptive female participants and 149 nonadoptive female trainees. Multivariate Analysis of Covariance revealed significant differences between adoptive and nonadoptive trainees in parenting attitudes, foster parenting attitudes, and motivations for foster parenting. Inspection of adjusted

Renee Gillis-Arnold; Sedahlia Jasper Crase; Dahlia F. Stockdale; Mack C. Shelley

1998-01-01

377

Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives  

PubMed Central

Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species.

Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

2011-01-01

378

Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives.  

PubMed

Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species. PMID:21768136

Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

2011-10-01

379

Linkage maps of grapevine displaying the chromosomal locations of 420 microsatellite markers and 82 markers for R -gene candidates  

Microsoft Academic Search

Genetic maps functionally oriented towards disease resistance have been constructed in grapevine by analysing with a simultaneous\\u000a maximum-likelihood estimation of linkage 502 markers including microsatellites and resistance gene analogs (RGAs). Mapping\\u000a material consisted of two pseudo-testcrosses, ‘Chardonnay’  ‘Bianca’ and ‘Cabernet Sauvignon’  ‘20\\/3’ where the seed parents\\u000a were Vitis vinifera genotypes and the male parents were Vitis hybrids carrying resistance to mildew diseases.

G. Di Gaspero; G. Cipriani; A.-F. Adam-Blondon; R. Testolin

2007-01-01

380

Development of microsatellite markers for Pythium helicoides.  

PubMed

A strategy combining dual-suppression PCR and thermal asymmetric interlaced PCR was used to determine sequences flanking microsatellite regions in Pythium helicoides. The primer pairs were designed to amplify loci containing (AC)n, (GA)n, (AGC)n, (CAC)n(CAA)n, (TCA)n and (CTTT)n repeats from the P. helicoides nuclear genome. The PCR products of each primer pair, amplified from three representative isolates collected from different hosts and locations, were cloned and sequenced. Different degrees of polymorphism were detected among these microsatellite markers. The numbers of alleles were 6, 2, 4, 11, 4 and 4 in YL-AC, YL-AGC, YL-CAA, YL-CTTT, YL-GA and YL-TCA, respectively. Allele analysis of 30 P. helicoides isolates showed length polymorphisms in all loci, except for YL-AC, using capillary electrophoresis. Thus, we have developed a simple method for designing PCR primers to amplify microsatellite markers from P. helicoides. PMID:19278526

Yin-Ling; Zhou, Wei; Motohashi, Keiichi; Suga, Haruhisa; Fukui, Hirokazu; Kageyama, Koji

2009-04-01

381

Cycle pattern of a R allelic variation. Progress report, 1 November 1978-31 January 1980  

SciTech Connect

Two R alleles vary in cycle fashion. The original, intensely pigmenting forms change to weakly acting ones which revert in turn to the original. Neither direction of change is correlated with recombination of flanking markers. The reversion frequencies do not differ from the respective frequencies of change in the forward direction. The changes are restricted in the life cycle to about the time of meiosis. Modifying tthe incidence of crossing over in the R region altered the frequency of reversion proportionately. These features of instability could result from switching by intrachromosomal recombination between alternative arrangements of an R segment associated with an inverted duplication.

Kermicle, J.L.

1980-01-01

382

Parents Come to Class  

NSDL National Science Digital Library

Are you challenged to involve parents in your school's science curriculum? Ridgecrest Elementary School in Hyattsville, Maryland, tackled that issue and found a successful solution in an exciting program called "Playtime Is Science" (Sprung, Froschl, and Colon 1997). This program trains parent volunteers as "coteachers" to help classroom teachers facilitate learning in specific science units and also encourages parental participation in the school at all levels.

Gooden, Kelly

2003-01-01

383

Parent Abuse: A Review  

Microsoft Academic Search

A recent focus of research and clinical practice has been on the issue of abuse of parents by their children (parent abuse).\\u000a This paper reviews the literature on this phenomenon. While parent abuse falls under the umbrella of family violence, it appears\\u000a to be qualitatively different from other forms of intra-family abuse. Research has primarily focused on prevalence rates and

Nicola Kennair; David Mellor

2007-01-01

384

Kappa chain monoallelic demethylation and the establishment of allelic exclusion.  

PubMed

Allelic exclusion in kappa light-chain synthesis is thought to result from a feedback mechanism by which the expression of a functional kappa light chain on the surface of the B cell leads to an intracellular signal that down-regulates the V(D)J recombinase, thus precluding rearrangement of the other allele. Whereas such a feedback mechanism clearly plays a role in the maintenance of allelic exclusion, here we provide evidence suggesting that the initial establishment of allelic exclusion involves differential availability of the two kappa alleles for rearrangement. Analysis of kappa+ B-cell populations and of individual kappa+ B cells that have rearranged only one allele demonstrates that in these cells, critical sites on the rearranged allele are unmethylated, whereas the nonrearranged allele remains methylated. This pattern is apparently generated by demethylation that is initiated at the small pre-B cell stage, on a single allele, in a process that occurs prior to rearrangement and requires the presence in cis of both the intronic and 3' kappa enhancers. Taken together with data demonstrating that undermethylation is required for rearrangement, these results indicate that demethylation may actually underly the process of allelic exclusion by directing the initial choice of a single kappa allele for rearrangement. PMID:9637682

Mostoslavsky, R; Singh, N; Kirillov, A; Pelanda, R; Cedar, H; Chess, A; Bergman, Y

1998-06-15

385

Allelic genealogies in sporophytic self-incompatibility systems in plants.  

PubMed Central

Expectations for the time scale and structure of allelic genealogies in finite populations are formed under three models of sporophytic self-incompatibility. The models differ in the dominance interactions among the alleles that determine the self-incompatibility phenotype: In the SSIcod model, alleles act codominantly in both pollen and style, in the SSIdom model, alleles form a dominance hierarchy, and in SSIdomcod, alleles are codominant in the style and show a dominance hierarchy in the pollen. Coalescence times of alleles rarely differ more than threefold from those under gametophytic self-incompatibility, and transspecific polymorphism is therefore expected to be equally common. The previously reported directional turnover process of alleles in the SSIdomcod model results in coalescence times lower and substitution rates higher than those in the other models. The SSIdom model assumes strong asymmetries in allelic action, and the most recessive extant allele is likely to be the most recent common ancestor. Despite these asymmetries, the expected shape of the allele genealogies does not deviate markedly from the shape of a neutral gene genealogy. The application of the results to sequence surveys of alleles, including interspecific comparisons, is discussed.

Schierup, M H; Vekemans, X; Christiansen, F B

1998-01-01

386

Parenting and plasticity  

PubMed Central

As any new parent knows, having a baby provides opportunities for enrichment, learning and stress –experiences known to change the adult brain. Yet surprisingly little is known about the effects of maternal experience, and even less about the effects of paternal experience, on neural circuitry not directly involved in parenting. Here we discuss how caregiving and the accompanying experiential and hormonal changes influence the hippocampus and prefrontal cortex, brain regions involved in cognition and mood regulation. A better understanding of how parenting impacts the brain is likely to help in devising strategies for treating parental depression, a condition that can have serious cognitive and mental health consequences for children.

Leuner, Benedetta; Glasper, Erica R.; Gould, Elizabeth

2010-01-01

387

Characterization of polymorphic microsatellite markers for the blowfly Chrysomya albiceps (Diptera: Calliphoridae).  

PubMed

Chrysomya albiceps is a blowfly of great medical, sanitary and forensic importance widely distributed in the Afrotropical, southern Palaearctic, northern Oriental regions and, recently, in Central and South Americas. Here, we report the characterization of 13 polymorphic microsatellite markers for C. albiceps. The number of alleles ranged from three to 13 alleles with expected heterozygosities ranging from 0.4668 to 0.8408. These markers will be extremely useful for investigating many important aspects of this species such as population structure, dispersal and colonization dynamics. PMID:21585758

Torres, Tatiana Teixeira; DE Azeredo-Espin, Ana Maria Lima

2008-01-01

388

Development of EST-based new SSR markers in seabuckthorn.  

PubMed

EST-based SSR markers were developed by screening a collection of 1584 clustered ESTs of seabuckthorn (Hippophae rhamnoides). PCR primers were designed for the amplification of 30 microsatellite loci. Two to five allelic bands were displayed by nine primer pairs in H. rhamnoides genotypes and by eleven primer pairs in H. salicifolia genotypes. None of the thirty primer pairs detected polymorphism in H. tibetana genotypes. Considering the high polymorphism detected in the tested genotypes and their direct origin from the genic regions, these EST-SSR markers hold immense promise in seabuckthorn genome analysis, molecular breeding and population genetics. PMID:23572988

Jain, Ankit; Ghangal, Rajesh; Grover, Atul; Raghuvanshi, Saurabh; Sharma, Prakash C

2010-12-01

389

Common Allelic Variants of Exons 10, 12, and 33 of the Thyroglobulin Gene Are Not Associated with Autoimmune Thyroid Disease in the United Kingdom  

Microsoft Academic Search

Thyroglobulin (Tg) is a major autoantigen for autoimmune thyroid disease (AITD). The Tg gene (Tg) has been mapped to chromosome 8q24, which has recently been linked in two in- dependent studies to AITD. Association of specific alleles of microsatellite markers within Tg itself supports a role for Tg as a good candidate susceptibility locus for AITD. Resequenc- ing of the

J. E. Collins; J. M. HEWARD; J. M. M. HOWSON; H. FOXALL; J. CARR-SMITH; J. A. FRANKLYN

2004-01-01

390

Reduced Life- and Healthspan in Mice Carrying a Mono-Allelic BubR1 MVA Mutation  

PubMed Central

Mosaic Variegated Aneuploidy (MVA) syndrome is a rare autosomal recessive disorder characterized by inaccurate chromosome segregation and high rates of near-diploid aneuploidy. Children with MVA syndrome die at an early age, are cancer prone, and have progeroid features like facial dysmorphisms, short stature, and cataracts. The majority of MVA cases are linked to mutations in BUBR1, a mitotic checkpoint gene required for proper chromosome segregation. Affected patients either have bi-allelic BUBR1 mutations, with one allele harboring a missense mutation and the other a nonsense mutation, or mono-allelic BUBR1 mutations combined with allelic variants that yield low amounts of wild-type BubR1 protein. Parents of MVA patients that carry single allele mutations have mild mitotic defects, but whether they are at risk for any of the pathologies associated with MVA syndrome is unknown. To address this, we engineered a mouse model for the nonsense mutation 2211insGTTA (referred to as GTTA) found in MVA patients with bi-allelic BUBR1 mutations. Here we report that both the median and maximum lifespans of the resulting BubR1+/GTTA mice are significantly reduced. Furthermore, BubR1+/GTTA mice develop several aging-related phenotypes at an accelerated rate, including cataract formation, lordokyphosis, skeletal muscle wasting, impaired exercise ability, and fat loss. BubR1+/GTTA mice develop mild aneuploidies and show enhanced growth of carcinogen-induced tumors. Collectively, these data demonstrate that the BUBR1 GTTA mutation compromises longevity and healthspan, raising the interesting possibility that mono-allelic changes in BUBR1 might contribute to differences in aging rates in the general population.

Wijshake, Tobias; Malureanu, Liviu A.; Baker, Darren J.; Jeganathan, Karthik B.; van de Sluis, Bart; van Deursen, Jan M.

2012-01-01

391

Characterization and multiplex genotyping of alpaca tetranucleotide microsatellite markers  

Microsoft Academic Search

Hybridisation-capture was used to create 12 unique alpaca DNA libraries each enriched for a different tetranucleotide microsatellite motif. Two hundred and forty-nine microsatellites were found, of which 26 were polymorphic (motifs GGAT, GTTT and GCAC). Nine markers were fully characterised on 45 samples. Allele numbers ranged from 6 (locus P135) to 12 (loci P149 and PCTD17). There was no evidence

K. A. Munyard; J. M. Ledger; C. Y. Lee; C. Babra; D. M. Groth

2009-01-01

392

High-density Integrated Linkage Map Based on SSR Markers in Soybean  

PubMed Central

A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding.

Hwang, Tae-Young; Sayama, Takashi; Takahashi, Masakazu; Takada, Yoshitake; Nakamoto, Yumi; Funatsuki, Hideyuki; Hisano, Hiroshi; Sasamoto, Shigemi; Sato, Shusei; Tabata, Satoshi; Kono, Izumi; Hoshi, Masako; Hanawa, Masayoshi; Yano, Chizuru; Xia, Zhengjun; Harada, Kyuya; Kitamura, Keisuke; Ishimoto, Masao

2009-01-01

393

A Modified Janus Cassette (Sweet Janus) to Improve Allelic Replacement Efficiency by High-Stringency Negative Selection in Streptococcus pneumoniae  

PubMed Central

The Janus cassette permits marker-free allelic replacement or knockout in streptomycin-resistant Streptococcus pneumoniae (pneumococcus) through sequential positive and negative selection. Spontaneous revertants of Janus can lead to high level of false-positives during negative selection, which necessitate a time-consuming post-selection screening process. We hypothesized that an additional counter-selectable marker in Janus would decrease the revertant frequency and reduce false-positives, since simultaneous reversion of both counter-selectable makers is much less likely. Here we report a modified cassette, Sweet Janus (SJ), in which the sacB gene from Bacillus subtilis conferring sucrose sensitivity is added to Janus. By using streptomycin and sucrose simultaneously as selective agents, the frequency of SJ double revertants was about 105-fold lower than the frequency of Janus revertants. Accordingly, the frequency of false-positives in the SJ-mediated negative selection was about 100-fold lower than what was seen for Janus. Thus, SJ enhances negative selection stringency and can accelerate allelic replacement in pneumococcus, especially when transformation frequency is low due to strain background or suboptimal transformation conditions. Results also suggested the sacB gene alone can function as a counter-selectable marker in the Gram-positive pneumococcus, which will have the advantage of not requiring a streptomycin-resistant strain for allelic replacement.

Li, Yuan; Thompson, Claudette M.; Lipsitch, Marc

2014-01-01

394

Handbook of Parenting. Volume 2: Biology and Ecology of Parenting.  

ERIC Educational Resources Information Center

Concerned with social settings and correlates of parenting, this volume, the second of four volumes on parenting deals specifically with the biology and the ecology of parenting. The volume consists of 12 chapters as follows: (1) "Hormonal Basis of Parenting in Mammals" (Jay S. Rosenblatt); (2) "Parenting in Primates" (Kim A. Bard); (3)…

Bornstein, Marc H., Ed.

395

Parent Choice and Empowerment: New Roles for Parents.  

ERIC Educational Resources Information Center

Describes New York City initiatives for parent participation in education, including the Parent Involvement Program (PIP), the Parent Orientation Program (POP), and the Parent Leadership Assistance Network (PLAN). These programs incorporate commitment to the family, broadened definitions of parent involvement, varied involvement strategies, and…

Jackson, Barbara L.; Cooper, Bruce S.

1989-01-01

396

Dismay and Disappointment: Parental Involvement of Latino Immigrant Parents  

Microsoft Academic Search

Parental involvement in schools has become more popular over the past decade due to Goals 2000 and research suggesting that student academic success increases when parents are included in the education of their children. Although researchers have examined the issue of parents and schools, limited research on parental involvement has been conducted within immigrant communities. Latino immigrant parents within a

A. Y. Fred Ramirez

2003-01-01

397

Personal Health Practices in Single Parent and Two Parent Families.  

ERIC Educational Resources Information Center

Examined the differences in personal health practices by family type--single-parent versus two-parent--and the relationship of family characteristics--socialization practices, extent of social networks, health training efforts by parents, family socioeconomic status to personal health practices in single-parent and two-parent families (N=41).…

Loveland-Cherry, Carol J.

1986-01-01

398

A Novel Class of Simple PCR Markers with SNP-Level Sensitivity for Mapping and Haplotype Characterization in Solanum Species  

Microsoft Academic Search

The RB gene from wild potato Solanum bulbocastanum imparts broad-spectrum late blight resistance to cultivated potato. To explore marker associations and haplotype frequencies\\u000a near RB, we developed, optimized, validated, and employed a set of markers specific to the haplotype associated with the RB resistance allele. Our markers, developed using a mismatch amplification mutation assay (MAMA)-PCR approach, have single\\u000a nucleotide polymorphism-level

Ryan L. Syverson; James M. Bradeen

2011-01-01

399

Transposon-based high sequence diversity in Avr-Pita alleles increases the potential for pathogenicity of Magnaporthe oryzae populations.  

PubMed

Magnaporthe oryzae causes rice blast that is one of the most devastating diseases of rice worldwide. Highly variable nature of this fungus has evolved itself against major resistance genes in newly released rice varieties. Understanding the population structure of this fungus is essential for proper utilization of the rice blast resistance genes in rice crop plants. In the present study, we analyzed 133 isolates of M. oryzae from ten countries to find the allelic variation of Avr-Pita gene that is triggering Pita-mediated resistance in rice plant. The diversity analysis of these alleles showed higher level of nucleotide variation in the coding regions than the noncoding regions. Evolutionary analysis of these alleles indicates that Avr-Pita gene is under purifying selection to favor its major alleles in 133 isolates analyzed in this study. We hypothesize that the selection of favorable Avr-Pita allele in these isolates may occur through a genetic mechanism known as recurrent selective sweeps. A total of 22 functional Avr-Pita protein variants were identified in this study. Insertion of Pot3 transposable element into the promoter of Avr-Pita gene was identified in virulent isolates and was suggested that mobility of repeat elements in avirulence genes of M. oryzae seems to help in emergence of new virulent types of the pathogen. Allele-specific markers developed in this study will be helpful to identify a particular type of Avr-Pita allele from M. oryzae population which can form the basis for the deployment of Pita gene in different epidemiological regions. PMID:24633351

Singh, P K; Thakur, S; Rathour, R; Variar, M; Prashanthi, S K; Singh, A K; Singh, U D; Sharma, V; Singh, N K; Sharma, T R

2014-06-01

400

Demography can favour female-advantageous alleles.  

PubMed

When female fecundity is relatively independent of male abundance, while male reproduction is proportional to female abundance, females have a larger effect on population dynamics than males (i.e. female demographic dominance). This population dynamic phenomenon might not appear to influence evolution, because male and female genomes still contribute equally much to the next generation. However, here we examine two evolutionary scenarios to provide a proof of principle that spatial structure can make female demographic dominance matter. Our two simulation models combine dispersal evolution with local adaptation subjected to intralocus sexual conflict and environmentally driven sex ratio biases, respectively. Both models have equilibria where one environment (without being intrinsically poorer) has so few reproductive females that trait evolution becomes disproportionately determined by those environments where females survive better (intralocus sexual conflict model), or where daughters are overproduced (environmental sex determination model). Surprisingly, however, the two facts that selection favours alleles that benefit females, and population growth is improved when female fitness is high, together do not imply that all measures of population performance are improved. The sex-specificity of the source-sink dynamics predicts that populations can evolve to fail to persist in habitats where alleles do poorly when expressed in females. PMID:25056617

Harts, Anna M F; Schwanz, Lisa E; Kokko, Hanna

2014-09-01