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1

Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers  

Microsoft Academic Search

Linkage maps for the apple cultivars ‘Prima’ and ‘Fiesta’ were constructed using RFLP, RAPD, isozyme, AFLP, SCAR and microsatellite\\u000a markers in a ‘Prima’?‘Fiesta’ progeny of 152 individuals. Seventeen linkage groups, putatively corresponding to the seventeen\\u000a haploid apple chromosomes, were obtained for each parent. These maps were aligned using 67 multi-allelic markers that were\\u000a heterozygous in both parents. A large number

C. Maliepaard; F. H. Alston; G. van Arkel; L. M. Brown; E. Chevreau; F. Dunemann; K. M. Evans; S. Gardiner; P. Guilford; A. W. van Heusden; J. Janse; F. Laurens; J. R. Lynn; A. G. Manganaris; A. P. M. den Nijs; N. Periam; E. Rikkerink; P. Roche; C. Ryder; S. Sansavini; H. Schmidt; S. Tartarini; J. J. Verhaegh; M. Vrielink-van Ginkel; G. J. King

1998-01-01

2

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

3

Analysis of allelic association between D6S461 marker and multiple sclerosis in Ashkenazi and Iraqi Jewish patients  

Microsoft Academic Search

A genetic factor contributing to multiple sclerosis (MS) disease risk is evident by the increased prevalence of disease among\\u000a siblings of probands. A recent genome screen on Canadian sib pairs suffering from MS identified linkage between the genetic\\u000a marker D6S461 and MS, and showed disequilibrium in transmission of its 260-bp allele from heterozygous parents to affected\\u000a siblings (Ebers et al.,

Yael Shinar; Elon Pras; Itzhak Siev-Ner; Dorit Gamus; Chaim Brautbar; Shoshana Israel; Anat Achiron

1998-01-01

4

Analysis of the methylation profiles in imprinted genes applicable to parental allele discrimination  

Microsoft Academic Search

This study investigated the distribution of methylated CpGs around several SNPs in five imprinted genes, which are useful to discriminate the differentially methylated parental allele (DMPA), by bisulfite-sequencing method. The genomic DNAs from peripheral blood, saliva and relatively fresh postmortem tissues except for testis showed a differentially methylated status in each parental allele, however, DNAs from the other sources (nail,

Nori Nakayashiki; Masataka Takamiya; Kirito Shimamoto; Yasuhiro Aoki

2009-01-01

5

Analysis of mechanisms regulating the expression of parental alleles at the GPD locus in mule erythrocytes  

Microsoft Academic Search

Erythrocyte glucose-6-phosphate dehydrogenase (G6PD) was examined by 13% starch gel electrophoresis in 74 mules (42 females and 32 males), 35 donkeys, and ten horses. The quantitative expression of the parental alleles at the Gpd locus varies greatly in female mules from the hemizygous expression of the maternal allele to that of the paternal. The data obtained indicate that the X

O. L. Serov; S. M. Zakijan; V. A. Kulichkov

1978-01-01

6

Development of a CAPS marker system for genotyping European pear cultivars harboring 17 S alleles.  

PubMed

The full-length cDNAs of eight S ribonucleases (S-RNases) were cloned from stylar RNA of European pear cultivars that could not be characterized by the cleaved amplified polymorphic sequences (CAPS) marker system for genotyping European pear cultivars harboring nine S alleles Sa, Sb, Sd, Se, Sh, Sk, Sl, Sq, and Sr. Comparison of the nucleotide sequences between these cDNAs and six putative S-RNase alleles previously amplified by genomic PCR revealed that five corresponded to the putative Sc-, Si-, Sm-, Sn-, and Sp-RNase alleles and the other three corresponded new S-RNase alleles (designated as putative Sg-, Ss-, and St-RNase alleles). Genomic PCR with a new set of primers was used to amplify 17 S-RNase alleles: 1906 bp (Sg), 1642 bp (St), 1414 bp (Sl), ca. 1.3 kb (Sk and Sq), 998 bp (Se), 440 bp (Sb), and ca. 350 bp (Sa, Sc, Sd, Sh, Si, Sm, Sn, Sp, Sr, and Ss). Among them, S-RNase alleles of similar size were discriminated by digestion with 11 restriction endo-nucleases. The PCR amplification of 17 S-RNase alleles following digestion with the restriction endonucleases provided a new CAPS marker system for rapid S-genotyping of European pear cultivars harboring 17 S alleles. Using the CAPS analysis, Sc, Sg, Si, Sm, Sn, Sp, Ss, and St alleles were found in 32 cultivars, which were classified into 23 S-genotypes. PMID:17061100

Moriya, Yuki; Yamamoto, Kentaro; Okada, Kazuma; Iwanami, Hiroshi; Bessho, Hideo; Nakanishi, Tetsu; Takasaki, Takeshi

2006-10-24

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

2013-07-12

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

High Resolution Analysis of Parent-of-Origin Allelic Expression in the Mouse Brain  

PubMed Central

Genomic imprinting results in preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain. This approach uncovered parent-of-origin allelic effects in over 1300 loci. We identified parental bias in the expression of individual genes and of specific transcript isoforms, with differences between brain regions. Many imprinted genes are expressed in neural systems associated with feeding and motivated behaviors, and parental biases preferentially target genetic pathways governing metabolism and cell adhesion. We observed a preferential maternal contribution to gene expression in the developing brain and a major paternal contribution in the adult brain. Thus, parental expression bias emerges as a major mode of epigenetic regulation in the brain.

Gregg, Christopher; Zhang, Jiangwen; Weissbourd, Brandon; Luo, Shujun; Schroth, Gary P.; Haig, David; Dulac, Catherine

2010-01-01

10

Allele capture by selection for flanking markers: A new method for analyzing multigenic traits  

SciTech Connect

in complex living organisms like mammals, most important processes are controlled by sets of interacting genes organized in biological pathways. A vital area of research during the coming decades will be to identify the genes that regulate such pathways and to analyze their functions. We here outline a new procedure to accomplish this: allele capture using flanking markers. Here illustrated for mice, it should be useful for all organisms in which adequate numbers of marker genes are available. This procedure combines mankind`s oldest and best proven logical technique, selective breeding, with the modern technologies of molecular markers, linkage analyses and computer programs. 7 refs.

Harrison, D.E.; Roderick, T.H.; Paigen, K. [Jackson Lab., Bar Harbor, ME (United States)

1995-12-31

11

Sex-specific parent-of-origin allelic expression in the mouse brain.  

PubMed

Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific imprinting features. In the hypothalamus, sex-specific imprinted genes were mostly found in females, which suggests parental influence over the hypothalamic function of daughters. We show that interleukin-18, a gene linked to diseases with sex-specific prevalence, is subject to complex, regional, and sex-specific parental effects in the brain. Parent-of-origin effects thus provide new avenues for investigation of sexual dimorphism in brain function and disease. PMID:20616234

Gregg, Christopher; Zhang, Jiangwen; Butler, James E; Haig, David; Dulac, Catherine

2010-07-08

12

Sex-Specific Parent-of-Origin Allelic expression in the Mouse Brain  

PubMed Central

Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific imprinting features. In the hypothalamus, sex-specific imprinted genes were mostly found in females, suggesting parental influence over the hypothalamic function of daughters. We show that Interleukin 18, a gene linked to diseases with sex-specific prevalence, is subject to complex, regional, and sex-specific parental effects in the brain. Parent of origin effects thus provide new avenues for investigation of sexual dimorphism in brain function and disease.

Gregg, Christopher; Zhang, Jiangwen; Butler, James E.; Haig, David; Dulac, Catherine

2010-01-01

13

Sex-Specific Parent-of-Origin Allelic Expression in the Mouse Brain  

Microsoft Academic Search

Genomic imprinting results in preferential gene expression from paternally versus maternally inherited chromosomes. We used a genome-wide approach to uncover sex-specific parent-of-origin allelic effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Moreover, analysis of the cortex and hypothalamus identified 347 autosomal genes with sex-specific

Christopher Gregg; Jiangwen Zhang; James E. Butler; David Haig; Catherine Dulac

2010-01-01

14

Analysis of simple tandem repeat (STR) marker allele distributions in a Balinese population  

SciTech Connect

Genotypes for 53 simple tandem repeat (STR) markers distributed at greater than 39 cM intervals throughout the genome were determined for 46 individuals from the village of Bengkala, Bali. This village dates to at least the thirteenth century, has approximately 2,200 individuals and has an oral and written tradition suggesting genetic bottlenecks. The allele frequency distributions in Bengkala were compared with distributions obtained by typing individuals in the CEPH data base using a Kolmogorov-Smirnov two sample test. Twenty-eight of the 53 markers showed differences (p<0.05) in distribution between the two populations. Allele frequencies of tetranucleotide STRs were much more similar between the two populations than were those of dinucleotide STRs (p < 0.0043). This may be due to the higher mutation rate of tetranucleotide STRs, combining with selection on repeat lengths, to produce a {open_quotes}stable{close_quotes} allele distribution. Population heterogeneity in Bengkala was indicated by an excess of observed homozygosity, deviations from Hardy-Weinberg equilibrium at seven loci, and significant genotypic disequilibrium between physically unlinked loci. These analyses serve as a resource to map a gene causing non-syndromal autosomal recessive deafness in Bengkala, and to corroborate the anthropological study of the history and social structure of the village.

Morell, R.; Ashler, J.H.; Friedman, T.B. [Michigan State Univ., East Lansing, MI (United States)] [and others

1994-09-01

15

High-throughput retrotransposon-based fluorescent markers: improved information content and allele discrimination  

PubMed Central

Background Dense genetic maps, together with the efficiency and accuracy of their construction, are integral to genetic studies and marker assisted selection for plant breeding. High-throughput multiplex markers that are robust and reproducible can contribute to both efficiency and accuracy. Multiplex markers are often dominant and so have low information content, this coupled with the pressure to find alternatives to radio-labelling, has led us to adapt the SSAP (sequence specific amplified polymorphism) marker method from a 33P labelling procedure to fluorescently tagged markers analysed from an automated ABI 3730 xl platform. This method is illustrated for multiplexed SSAP markers based on retrotransposon insertions of pea and is applicable for the rapid and efficient generation of markers from genomes where repetitive element sequence information is available for primer design. We cross-reference SSAP markers previously generated using the 33P manual PAGE system to fluorescent peaks, and use these high-throughput fluorescent SSAP markers for further genetic studies in Pisum. Results The optimal conditions for the fluorescent-labelling method used a triplex set of primers in the PCR. These included a fluorescently labelled specific primer together with its unlabelled counterpart, plus an adapter-based primer with two bases of selection on the 3' end. The introduction of the unlabelled specific primer helped to optimise the fluorescent signal across the range of fragment sizes expected, and eliminated the need for extensive dilutions of PCR amplicons. The software (GeneMarker Version 1.6) used for the high-throughput data analysis provided an assessment of amplicon size in nucleotides, peak areas and fluorescence intensity in a table format, so providing additional information content for each marker. The method has been tested in a small-scale study with 12 pea accessions resulting in 467 polymorphic fluorescent SSAP markers of which 260 were identified as having been mapped previously using the radio-labelling technique. Heterozygous individuals from pea cultivar crosses were identifiable after peak area data analysis using the fluorescent SSAP method. Conclusion As well as developing a rapid, and high-throughput marker method for genetic studies, the fluorescent SSAP system improved the accuracy of amplicon scoring, increased the available marker number, improved allele discrimination, and was sensitive enough to identify heterozygous loci in F1 and F2 progeny, indicating the potential to develop high-throughput codominant SSAPs.

Knox, Maggie; Moreau, Carol; Lipscombe, James; Baker, David; Ellis, Noel

2009-01-01

16

Phylogenetic relationship analysis of Iranians and other world populations using allele frequencies at 12 polymorphic markers.  

PubMed

The estimation of genetic distance between populations could improve our viewpoint about human migration and its genetic origin. In this study, we used allele frequency data of 12 polymorphic markers on 250 individuals (500 alleles) from the Iranian population to estimate genetic distance between the Iranians and other world populations. The phylogenetic trees for three different sets of allele frequency data were constructed. Our results revealed the genetic similarity between the Iranians and European populations. The lowest genetic distance was observed between the Iranians and some populations reside in Russia. Furthermore, the high genetic distance was observed between the Iranians and East Asian populations. The data suggested that the Iranians might have relatively close evolutionary history with Europeans, but historically independent from East Asian populations. The evaluation of genetic distance between Indians populations and Iranians was also performed. The Indian groups showed low genetic distance with others, but high genetic distance with the Iranians. This study could provide a new insight into the evolutionary history of the Iranian population. PMID:23065267

Fazeli, Zahra; Vallian, Sadeq

2012-10-14

17

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

PubMed

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. PMID:23990759

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

2013-08-07

18

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

19

Assessing paternities with inconclusive STR results: The suitability of bi-allelic markers.  

PubMed

In paternity testing the genetic profiles of the individuals are used to compare the relative likelihoods of the alleged father and the child being related as father/offspring against, usually, being unrelated. In the great majority of the cases, analyses with the widely used sets of short tandem repeat markers (STRs) provide powerful statistical evidence favouring one of the alternative hypotheses. Nevertheless, there are situations where the final statistical result is ambiguous, mostly because the alleged father shows incompatible genotypes at a few loci along with a very high paternity index in the remaining systems. In these cases, the possibility that the alleged father is actually a close relative of the real one (son, father or brother) can reasonably be raised. In such cases, when the statistical evidence obtained is considered as insufficient, the common practice is to extend the set of analysed markers. In this context, many authors have suggested that bi-allelic markers, such as single nucleotide (SNP) or insertion/deletion (Indel) polymorphisms, are markers of choice, as they are incomparably less prone to mutation than STRs. In this work we address the soundness of this claim and the consequences of this strategy, analyzing the a priori odds both for (a) expected number of Mendelian incompatibilities, and (b) expected values for the final likelihood ratios. Moreover, one hundred real pairs of second degree relatives, typed for two sets of markers: 15 STRs plus 38 Indels, were used to simulate paternity testing. Our data show that, for the number of markers commonly considered, the results from an extended battery of SNPs or Indels should be interpreted with caution when relatives are possibly involved. PMID:22658886

Pinto, Nádia; Magalhães, Marta; Conde-Sousa, Eduardo; Gomes, Cláudia; Pereira, Rui; Alves, Cíntia; Gusmão, Leonor; Amorim, António

2012-06-01

20

Detection of bovine leukocyte antigen DRB3 alleles as candidate markers for clinical mastitis resistance in Holstein x Zebu.  

PubMed

Bovine leukocyte antigen DRB3 alleles from Holstein x Zebu crossbred dairy cows (n = 409) were analyzed using the PCR-RFLP technique. Exon II of DRB3 was amplified using locus-specific primers (HLO30/HLO32), followed by digestion with 3 restriction enzymes (RsaI, BstyI, and HaeIII). Forty alleles were found with frequency ranging from 0.005 to 0.139. The most frequently detected alleles of Holstein x Zebu were DRB3*16, *51, *23, *11, *8, and *1, accounting for 61.12% of the alleles in the population. Detection of candidate alleles for clinical mastitis occurrence was performed by logistic regression. It was found that percentage of Holstein fraction in crossbred cows had a nonsignificant effect (P > 0.05). However, parity had a significant effect on mastitis occurrence. In addition, DRB3*1 and *52 were the most associated with the occurrence of clinical mastitis, whereas *15, *51, and *22 were associated with resistance in crossbred populations. This is the first report of association of DRB3*15 and *51 with mastitis resistance. The association was validated by examining the candidate alleles in another commercial population. Highly susceptible (n = 43) and resistant (n = 42) groups of Holstein x Zebu cows were investigated. The result confirmed that DRB3*1 and *52 could be considered as susceptibility alleles, whereas *15, *51, and *22 could be considered as resistant alleles in Holstein x Zebu raised under tropical conditions. In addition, allele effects on 305-d milk production were estimated by BLUP. It was shown that most alleles associated with high clinical mastitis occurrence were related to increased milk yield. This study revealed that allele DRB3*10 had the greatest effect on increasing milk yield with moderate resistance to clinical mastitis, which could be used as a potential marker for selection in dairy genetic evaluation. PMID:18820165

Duangjinda, M; Buayai, D; Pattarajinda, V; Phasuk, Y; Katawatin, S; Vongpralub, T; Chaiyotvittayakul, A

2008-09-26

21

Parent-child concordance of Taq1 A1 allele predicts similarity of parent-child weight loss in behavioral family-based treatment programs?  

PubMed Central

Family-based treatments show positive relationships between parent and child weight losses. One mechanism for similar parent–child changes may be a common genetic predisposition to respond similarly to a structured weight loss program. We examined whether concordance of the Taq1 A1 allele of the dopamine D2 receptor (DRD2) predicts similarities in zBMI change in 26 families with obese parents and overweight/obese 8–12-year-old children. Results showed a relationship between parent and child zBMI change over 6 and 12 months (rs = .69, .77, ps < 0.001), and concordance for the number of Taq1 A1 alleles predicted the similarity in parent and child weight loss at 6 (p = 0.003) and 12 (p = 0.025) months. These results show concordance of the Taq1 A1 allele of the DRD2 between parents and children may be one mechanism for the similar response to family-based treatments within families.

Epstein, Leonard H.; Dearing, Kelly K.; Erbe, Richard W.

2011-01-01

22

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

23

Allelic diversity of a beer haze active protein gene in cultivated and Tibetan wild barley and development of allelic specific markers.  

PubMed

The formation of haze is a serious quality problem in beer production. It has been shown that the use of silica elute (SE)-ve malt (absence of molecular weight (MW) ?14000 Da) for brewing can improve haze stability in the resultant beer, and the protein was identified as a barley trypsin inhibitor of the chloroform/methanol type (BTI-CMe). The objectives of this study were to determine (1) the allelic diversity of the gene controlling BTI-CMe in cultivated and Tibetan wild barley and (2) allele-specific (AS) markers for screening SE protein type. A survey of 172 Tibetan annual wild barley accessions and 71 cultivated barley genotypes was conducted, and 104 wild accessions and 35 cultivated genotypes were identified as SE+ve and 68 wild accessions and 36 cultivated genotypes as SE-ve. The allelic diversity of the gene controlling BTI-CMe was investigated by cloning, alignment, and association analysis. It was found that there were significant differences between the SE+ve and SE-ve types in single-nucleotide polymorphisms at 234 (SNP(234)), SNP(313), and SNP(385.) Furthermore, two sets of AS markers were developed to screen SE protein type based on SNP(313). AS-PCR had results very similar to those obtained by immunoblot method. Mapping analysis showed that the gene controlling the MW?14 kDa band was located on the short arm of chromosome 3H, at the position of marker BPB-0527 (33.302 cM) in the Franklin/Yerong DH population. PMID:21608526

Ye, Lingzhen; Dai, Fei; Qiu, Long; Sun, Dongfa; Zhang, Guoping

2011-06-03

24

Genomic Analysis of Parent-of-Origin Allelic Expression in Arabidopsis thaliana Seeds  

PubMed Central

Differential expression of maternally and paternally inherited alleles of a gene is referred to as gene imprinting, a form of epigenetic gene regulation common to flowering plants and mammals. In plants, imprinting primarily occurs in the endosperm, a seed tissue that supports the embryo during its growth and development. Previously, we demonstrated that widespread DNA demethylation at remnants of transposable elements accompanies endosperm development and that a subset of these methylation changes are associated with gene imprinting. Here we assay imprinted gene expression genome-wide by performing high-throughput sequencing of RNA derived from seeds of reciprocal intraspecific crosses. We identify more than 200 loci that exhibit parent-of-origin effects on gene expression in the endosperm, including a large number of transcription factors, hormone biosynthesis and response genes, and genes that encode regulators of epigenetic information, such as methylcytosine binding proteins, histone methyltransferases, and chromatin remodelers. The majority of these genes are partially, rather than completely, imprinted, suggesting that gene dosage regulation is an important aspect of imprinted gene expression.

Gehring, Mary; Missirian, Victor; Henikoff, Steven

2011-01-01

25

Allelic database and accession divergence of a Brazilian mango collection based on microsatellite markers.  

PubMed

Allelic patterns and genetic distances were examined in a collection of 103 foreign and Brazilian mango (Mangifera indica) accessions in order to develop a reference database to support cultivar protection and breeding programs. An UPGMA dendrogram was generated using Jaccard's coefficients from a distance matrix based on 50 alleles of 12 microsatellite loci. The base pair number was estimated by the method of inverse mobility. The cophenetic correlation was 0.8. The accessions had a coefficient of similarity from 30 to 100%, which reflects high genetic variability. Three groups were observed in the UPGMA dendrogram; the first group was formed predominantly by foreign accessions, the second group was formed by Brazilian accessions, and the Dashehari accession was isolated from the others. The 50 microsatellite alleles did not separate all 103 accessions, indicating that there are duplicates in this mango collection. These 12 microsatellites need to be validated in order to establish a reliable set to identify mango cultivars. PMID:23096906

Dos Santos Ribeiro, I C N; Lima Neto, F P; Santos, C A F

2012-12-19

26

Influence of sex of the transmitting parent as well as of parental allel size on the CTG expansion in myotonic dystrophy (DM)  

SciTech Connect

In patients with myotonic dystrophy (DM), the severity of clinical signs is correlated with the length of a (CTG)[sub n] trinucleotide repeat sequence. This sequence tends to expand in subsequent generations. In order to examine the kinetics of this process and, in particular, the influence of the mutant-allele size and the sex of the transmitting parent, the authors have studied (CTG)[sub n] repeat lengths in the offspring of 38 healthy carriers with small mutations (less than 100 CTG trinucleotides, mean length [CTG][sub 67]). In these studies, the authors found a weakly positive correlation between the size of the mutation in the carrier parents and that in their offspring. Furthermore, the authors observed that, in the offspring of male transmitters, repeat lengths exceeding 100 CTG trinucleotides were much more frequent than in the offspring of carrier females (48 [92%] of 52 vs. 7 [44%] of 16, P = .0002). Similarly, in genealogical studies performed in 38 Dutch DM kindreds, an excess of nonmanifesting male transmitters was noted, which was most conspicuous in the generation immediately preceding that with phenotypic expression of DM. Thus, two separate lines of evidence suggest that the sex of the transmitting parent is an important factor that determines DM allele size in the offspring. On the basis of the data, the authors estimate that when both parents are asymptomatic, the odds are approximately 2:1 that the father carries the DM mutation. Because expansion of the CTG repeat is more rapid with male transmission, negative selection during spermatogenesis may be required to explain the exclusive maternal inheritance of severe congenital onset DM. 42 refs., 1 fig., 2 tabs.

Brunner, H.G.; Brueggenwirth, H.T.; Nillesen, W.; Hamel, B.C.J.; Hoppe, R.L.E.; Oost, B.A. van; Ropers, H.H.; Smeets, H.J.M.; Jansen, G.; Die, C.E.M. de; Hoeweler, C.J. Wieringa, B.

1993-11-01

27

Synchronous activation of both parental alleles at the 6-PGD locus of Japanese quail embryos  

Microsoft Academic Search

The gene locus for the enzyme 6-phosphogluconate dehydrogenase belongs to that part of the genome which is activated at the beginning of embryonic development. The present experiment, utilizing three alleles at this autosomally inherited locus of the Japanese quail, was designed to show whether exhaustion of maternally stored 6-PGD is followed by maternally hemizygous de novo synthesis of the same

S. Ohno; C. Stenius; L. C. Christian; C. Harris

1968-01-01

28

A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.).  

PubMed

Single nucleotide polymorphism (SNP) detection has become a marker system of choice, because of the high abundance of source polymorphisms and the ease with which allele calls are automated. Various technologies exist for the evaluation of SNP loci and previously we validated two medium throughput technologies. In this study, our goal was to utilize a 768 feature, Illumina GoldenGate assay for common bean (Phaseolus vulgaris L.) developed from conserved legume gene sequences and to use the new technology for (1) the evaluation of parental polymorphisms in a mini-core set of common bean accessions and (2) the analysis of genetic diversity in the crop. A total of 736 SNPs were scored on 236 diverse common bean genotypes with the GoldenGate array. Missing data and heterozygosity levels were low and 94 % of the SNPs were scorable. With the evaluation of the parental polymorphism genotypes, we estimated the utility of the SNP markers in mapping for inter-genepool and intra-genepool populations, the latter being of lower polymorphism than the former. When we performed the diversity analysis with the diverse genotypes, we found Illumina GoldenGate SNPs to provide equivalent evaluations as previous gene-based SNP markers, but less fine-distinctions than with previous microsatellite marker analysis. We did find, however, that the gene-based SNPs in the GoldenGate array had some utility in race structure analysis despite the low polymorphism. Furthermore the SNPs detected high heterozygosity in wild accessions which was probably a reflection of ascertainment bias. The Illumina SNPs were shown to be effective in distinguishing between the genepools, and therefore were most useful in saturation of inter-genepool genetic maps. The implications of these results for breeding in common bean are discussed as well as the advantages and disadvantages of the GoldenGate system for SNP detection. PMID:23124389

Blair, Matthew W; Cortés, Andrés J; Penmetsa, R Varma; Farmer, Andrew; Carrasquilla-Garcia, Noelia; Cook, Doug R

2012-11-03

29

Parent psychological states predict changes in inflammatory markers in children with asthma and healthy children  

Microsoft Academic Search

Previous research has shown that parent mental health is associated with asthma morbidity in children. However, the biological pathways explaining these relationships are not known. The present study tested whether parent psychological characteristics could predict longitudinal changes in inflammatory markers in children with asthma and a comparison group of healthy children.For this, 33 healthy children (17m\\/16f; 13.5years) and 50 children

Jutta M. Wolf; Gregory E. Miller; Edith Chen

2008-01-01

30

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

31

Early Markers of Language and Attention: Mutual Contributions and the Impact of Parent–Infant Interactions  

Microsoft Academic Search

This study of was conducted to explore the contribution of attentional skills to early language, and the influence of early\\u000a language markers on the development of attention, simultaneously examining the impact of parent–child interaction factors\\u000a (reciprocity\\/synchrony and sensitivity\\/responsivity), including their potential moderator effects. All children were between\\u000a 6 months and 12 months of age, and about equally distributed between genders (33 males,

Maria A. Gartstein; Jennifer Crawford; Christopher D. Robertson

2008-01-01

32

The Dopamine Receptor D4 Gene 7-Repeat Allele Interacts with Parenting Quality to Predict Effortful Control in Four-Year-Old Children  

PubMed Central

The dopamine receptor D4 gene (DRD4) 7-repeat allele has been found to interact with environmental factors such as parenting in children and peer attitudes in adults to influence aspects of behavior such as risk taking. We previously found that in toddlers, lower-quality parenting in combination with the 7-repeat allele of the DRD4 gene was associated with greater parent-reported Sensation Seeking (SS), but was unrelated to Effortful Control (EC). We now report findings from a followup assessment with the same sample of children showing that parenting quality interacts with the presence of the 7-repeat allele to predict EC in 3-to 4-year-old children. The change in these patterns of results may reflect the increased role of the executive attention network in older children and adults. However, due to the small sample size (N = 52) and the novelty of the results, these findings should be treated with caution and considered preliminary until they are replicated in an independent sample.

Sheese, Brad E.; Rothbart, Mary K.; Voelker, Pascale M.; Posner, Michael I.

2012-01-01

33

RNA-Seq Analysis of Allele-Specific Expression, Hybrid Effects, and Regulatory Divergence in Hybrids Compared with Their Parents from Natural Populations  

PubMed Central

Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed. Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative single-nucleotide polymorphism sites, respectively. Of the 17% of sites exhibiting both cis- and trans-effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele, whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations.

Bell, Graeme D.M.; Kane, Nolan C.; Rieseberg, Loren H.; Adams, Keith L.

2013-01-01

34

RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations.  

PubMed

Hybridization is a prominent process among natural plant populations that can result in phenotypic novelty, heterosis, and changes in gene expression. The effects of intraspecific hybridization on F1 hybrid gene expression were investigated using parents from divergent, natural populations of Cirsium arvense, an invasive Compositae weed. Using an RNA-seq approach, the expression of 68,746 unigenes was quantified in parents and hybrids. The expression levels of 51% of transcripts differed between parents, a majority of which had less than 1.25× fold-changes. More unigenes had higher expression in the invasive parent (P1) than the noninvasive parent (P2). Of those that were divergently expressed between parents, 10% showed additive and 81% showed nonadditive (transgressive or dominant) modes of gene action in the hybrids. A majority of the dominant cases had P2-like expression patterns in the hybrids. Comparisons of allele-specific expression also enabled a survey of cis- and trans-regulatory effects. Cis- and trans-regulatory divergence was found at 70% and 68% of 62,281 informative single-nucleotide polymorphism sites, respectively. Of the 17% of sites exhibiting both cis- and trans-effects, a majority (70%) had antagonistic regulatory interactions (cis x trans); trans-divergence tended to drive higher expression of the P1 allele, whereas cis-divergence tended to increase P2 transcript abundance. Trans-effects correlated more highly than cis with parental expression divergence and accounted for a greater proportion of the regulatory divergence at sites with additive compared with nonadditive inheritance patterns. This study explores the nature of, and types of mechanisms underlying, expression changes that occur in upon intraspecific hybridization in natural populations. PMID:23677938

Bell, Graeme D M; Kane, Nolan C; Rieseberg, Loren H; Adams, Keith L

2013-07-01

35

Use of RFLP markers for the identification of alleles of the Pm3 locus conferring powdery mildew resistance in wheat ( Triticum aestivum L.)  

Microsoft Academic Search

The objective of this study was to identify molecular markers linked to genes for resistance to powdery mildew (Pm) in wheat using a series of ‘Chancellor’ near-isogenic-lines (NILs), each having one powdery mildew resistance gene. A total of 210 probes were screened for their ability to detect polymorphism between the NILs and the recurrent parent. One of these restriction fragment

L. Hartl; H. Weiss; F. J. Zeller; A. Jahoor

1993-01-01

36

Bayesian estimation of marker dosage in sugarcane and other autopolyploids  

Microsoft Academic Search

In sugarcane or other autopolyploids, after generating the data, the first step in constructing molecular marker maps is to\\u000a determine marker dosage. Improved methods for correctly allocating marker dosage will result in more accurate maps and increased\\u000a efficiency of QTL linkage detection. When employing dominant markers like AFLPs, single-dose markers represent alleles present\\u000a as one copy in one parent and

Peter Baker; Phillip Jackson; Karen Aitken

2010-01-01

37

Prediction of hybrid biomass in Arabidopsis thaliana by selected parental SNP and metabolic markers.  

PubMed

A recombinant inbred line (RIL) population, derived from two Arabidopsis thaliana accessions, and the corresponding testcrosses with these two original accessions were used for the development and validation of machine learning models to predict the biomass of hybrids. Genetic and metabolic information of the RILs served as predictors. Feature selection reduced the number of variables (genetic and metabolic markers) in the models by more than 80% without impairing the predictive power. Thus, potential biomarkers have been revealed. Metabolites were shown to bear information on inherited macroscopic phenotypes. This proof of concept could be interesting for breeders. The example population exhibits substantial mid-parent biomass heterosis. The results of feature selection could therefore be used to shed light on the origin of heterosis. In this respect, mainly dominance effects were detected. PMID:19911163

Steinfath, Matthias; Gärtner, Tanja; Lisec, Jan; Meyer, Rhonda C; Altmann, Thomas; Willmitzer, Lothar; Selbig, Joachim

2009-11-13

38

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

39

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.  

PubMed

Polyphenol oxidase (PPO) activity is highly related to the undesirable browning of wheat-based end products, especially Asian noodles. Characterization of PPO genes and the development of their functional markers are of great importance for marker-assisted selection in wheat breeding. In the present study, complete genomic DNA sequences of two PPO genes, one each located on chromosomes 2A and 2D and their allelic variants were characterized by means of in silico cloning and experimental validation. Sequences were aligned at both DNA and protein levels. Two haplotypes on chromosome 2D showed 95.2% sequence identity at the DNA level, indicating much more sequence diversity than those on chromosome 2A with 99.6% sequence identity. Both of the PPO genes on chromosomes 2A and 2D contain an open reading frame (ORF) of 1,731 bp, encoding a PPO precursor peptide of 577 amino acids with a predicted molecular mass of approximately 64 kD. Two complementary dominant STS markers, PPO16 and PPO29, were developed based on the PPO gene haplotypes located on chromosome 2D; they amplify a 713-bp fragment in cultivars with low PPO activity and a 490-bp fragment in those with high PPO activity, respectively. The two markers were mapped on chromosome 2DL using a doubled haploid population derived from the cross Zhongyou 9507/CA9632, and a set of nullisomic-tetrasomic lines and ditelosomic line 2DS of Chinese Spring. QTL analysis indicated that the PPO gene co-segregated with the two STS markers and was closely linked to SSR marker Xwmc41 on chromosome 2DL, explaining from 9.6 to 24.4% of the phenotypic variance for PPO activity across three environments. In order to simultaneously detect PPO loci on chromosomes 2A and 2D, a multiplexed marker combination PPO33/PPO16 was developed and yielded distinguishable DNA patterns in a number of cultivars. The STS marker PPO33 for the PPO gene on chromosome 2A was developed from the same gene sequences as PPO18 that we reported previously, and can amplify a 481-bp and a 290-bp fragment from cultivars with low and high PPO activity, respectively. A total of 217 Chinese wheat cultivars and advanced lines were used to validate the association between the polymorphic fragments and grain PPO activity. The results showed that the marker combination PPO33/PPO16 is efficient and reliable for evaluating PPO activity and can be used in wheat breeding programs aimed for noodle and other end product quality improvement. PMID:17426955

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

2007-04-11

40

Detection of Parent-of-Origin Effects in Complete and Incomplete Nuclear Families with Multiple Affected Children Using Multiple Tightly Linked Markers  

Microsoft Academic Search

For a diallelic marker locus, the parental-asymmetry test (PAT) based on case-parents trios and its extensions to accommodate incomplete unclear families (1-PAT and C-PAT) are simple and powerful approaches to test for parent-of-origin effects. However, haplotype analysis is generally regarded as advantageous over single-marker analysis in genetic study of common complex diseases. This is mainly due to the fact that

Ji-Yuan Zhou; Shili Lin; Wing K. Fung; Yue-Qing Hu

2009-01-01

41

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

ERIC Educational Resources Information Center

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 non-normative parenting. In addition, salivary cortisol samples were obtained to examine whether parents of children…

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

2009-01-01

42

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

43

Utility testing of an apple skin color MdMYB1 marker in two progenies  

Technology Transfer Automated Retrieval System (TEKTRAN)

A reported allele-specific dCAP PCR marker associated with apple fruit red skin color was tested in 18 elite breeding parents and two apple cross populations. Among all tested cultivars except one, a consistent relationship was observed between red fruit color and the presence of allele. In both pop...

44

Psychosocial and biological markers of daily lives of midlife parents of children with disabilities.  

PubMed

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. PMID:19413131

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

2009-03-01

45

A Life-Course Study on Effects of Parental Markers of Morbidity and Mortality on Offspring's Suicide Attempt  

PubMed Central

Background Research on the temporal relationship of parental risk factors with offspring’s suicide attempt is scarce and a life course approach has not been applied to date. We investigated the temporal relationship of parental morbidity and mortality with offspring’s suicide attempt and whether any such association was modified by offspring’s age at attempt. Methods We designed a case-control study through linkage of Swedish registers. Cases comprised all individuals in Sweden born 1973–1983 with inpatient care due to suicide attempt (15–31 years of age) and with information on both biological parents (N?=?15 193). Ten controls were matched to each case (National Patient register with national complete coverage). Conditional logistic and spline regressions were applied. Results Particularly for women, most parental markers showed the strongest effect sizes if exposure was short-term (within 2 years after exposure) and related to the mother. Especially short-term exposure to maternal inpatient care due to psychiatric diagnoses had a significantly stronger effect on suicide attempt risk in women compared to men. Regarding exposure to parental inpatient care due to psychiatric diagnoses, short-term as opposed to long-term (exceeding 2 years after exposure) effects were highest during adolescence and decreased significantly with age for female and male offspring, respectively. Conclusions Although limited by the fact that data on parental morbidity and the outcome of suicidality were based on in-patient data only, the data suggest that the high risks of suicide attempt in case of exposure to parental psychopathology and suicidal behavior particularly during adolescence and the strong short-term effects associated with maternal psychopathology for female offspring are of direct clinical importance.

Mittendorfer-Rutz, Ellenor; Rasmussen, Finn; Lange, Theis

2012-01-01

46

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

47

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

48

Parents.  

ERIC Educational Resources Information Center

|This document contains the fifth volume of "Today's Delinquent," an annual publication of the National Center for Juvenile Justice. This volume deals with the issue of the family and delinquency, examining the impact of parental behavior on the production of delinquent behavior. "Parents: Neglectful and Neglected" (Laurence D. Steinberg) posits…

Hurst, Hunter, Ed.; And Others

1986-01-01

49

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

50

The normal huntington disease (HD) allele, or a closely linked gene, influences age at onset of HD  

SciTech Connect

The authors evaluated the hypothesis that Huntington disease (HD) is influenced by the normal HD allele by comparing transmission patterns of genetically linked markers at the D4S10 locus in the normal parent against age at onset in the affected offspring. Analysis of information from 21 sibships in 14 kindreds showed a significant tendency for sibs who have similar onset ages to share the same D4S10 allele from the normal parent. Affected sibs who inherited different D4S10 alleles from the normal parent tended to have more variable ages at onset. These findings suggest that the expression of HD is modulated by the normal HD allele or by a closely linked locus. 38 refs., 2 figs., 1 tab.

Farrer, L.A. (Boston Univ., MA (United States) Harvard Medical School, Boston, MA (United States)); Cupples, L.A. (School of Public Health, Boston Univ., MA (United States)); Conneally, P.M. (Indiana Univ. School of Medicine, Indianapolis, IN (United States)); Gusella, J.F. (Harvard Medical School and Massachusetts General Hospital, Boston, MA (United States)); Myers, R.H. (Harvard Medical School, Boston, MA (United States))

1993-07-01

51

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

52

Parenting.  

ERIC Educational Resources Information Center

Various aspects of child-rearing are covered in this transcript of a program broadcast in the National Public Radio weekly series, "Options in Education." Authors of current popular books on parenting are interviewed. Benjamin Spock discusses changes (including sex role revisions) in his "Baby and Child Care" since the 1946 first edition. Eda…

Spock, Benjamin; And Others

53

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

Microsoft Academic Search

Forty clinic-referred mothers completed questionnaires describing their children’s problems and the mothers’ parenting styles.\\u000a In addition, each mother told three stories about their personal experiences in child care and one story about being cared\\u000a for in their families of origin. Each story was transcribed and rated for coherence on six dimensions describing narrative\\u000a clarity and richness. Results showed the narrative

Katherine S. RowinskiRobert; Robert G. Wahler

2010-01-01

54

Allele-Specific Expression Patterns Reveal Biases and Embryo-Specific Parent-of-Origin Effects in Hybrid Maize[W  

PubMed Central

We employed allele-specific expression (ASE) analyses to document biased allelic expression in maize (Zea mays). A set of 316 quantitative ASE assays were used to profile the relative allelic expression in seedling tissue derived from five maize hybrids. The different hybrids included in this study exhibit a range of heterosis levels; however, we did not observe differences in the frequencies of allelic bias. Allelic biases in gene expression were consistently observed for ?50% of the genes assayed in hybrid seedlings. The relative proportion of genes that exhibit cis- or trans-acting regulatory variation was very similar among the different genotypes. The cis-acting regulatory variation was more prevalent and resulted in greater expression differences than trans-acting regulatory variation for these genes. The ASE assays were further used to compare the relative expression of the B73 and Mo17 alleles in three tissue types (seedling, immature ear, and embryo) derived from reciprocal hybrids. These comparisons provided evidence for tissue-specific cis-acting variation and for a slight maternal expression bias in ?20% of genes in embryo tissue. Collectively, these data provide evidence for prevalent cis-acting regulatory variation that contributes to biased allelic expression between genotypes and between tissues.

Springer, Nathan M.; Stupar, Robert M.

2007-01-01

55

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

Microsoft Academic Search

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC),

M. W. Blair; M. C. Giraldo; H. F. Buendía; E. Tovar; M. C. Duque; S. E. Beebe

2006-01-01

56

Characterisation and marker development for low molecular weight glutenin genes from Glu-A3 alleles of bread wheat ( Triticum aestivum. L)  

Microsoft Academic Search

PCR was used to amplify low-molecular-weight (LMW) glutenin genes from the Glu-A3 loci of hexaploid wheat cultivars containing different Glu-A3 alleles. The complete coding sequence of one LMW glutenin gene was obtained for each of the seven alleles Glu-A3a to Glu-A3g. Chromosome assignment of PCR products using Chinese Spring nulli-tetrasomic lines confirmed the amplified products were from chromosome 1A. All

W. Zhang; M. C. Gianibelli; L. R. Rampling; K. R. Gale

2004-01-01

57

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

Microsoft Academic Search

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

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

1994-01-01

58

Parental somatic and germ-line mosaicism for a multiexon deletion with unusual endpoints in a type III collagen (COL3Al) allele produces ehlers-danlos syndrome type IV in the heterozygous offspring  

SciTech Connect

Ehlers-Danlos syndrome (EDS) type IV is a dominantly inherited disorder that results from mutation in the type III collagen gene (COL3A1). The authors studied the structure of the COL3A1 gene of an individual with EDS type IV and that of her phenotypically normal parents. The proband was heterozygous for a 2-kb deletion in COL3A1, while her father was mosaic for the same deletion in somatic and germ cells. In fibroblasts from the father, approximately two-fifths of the COL3A1 alleles carried the deletion, but only 10% of the COL3A1 alleles in white blood cells were of the mutant species. The deletion in the mutant allele extended from intron 7 into intron 11. There was a 12-bp direct repeat in intron 7 and intron 11, the latter about 60 bp 5' to the junction. At the breakpoint there was a duplication of 10 bp from intron 11 separated by an insertion of 4 bp contained within the duplicated sequence. The father was mosaic for the deletion so that the gene rearrangement occurred during his early embryonic development prior to lineage allocation. These findings suggest that at least some of the deletions seen in human genes may occur during replication, rather than as a consequence of meiotic crossing-over, and that they thus have a risk for recurrence when observed de novo. 71 refs., 4 figs., 2 tabs.

McGookey Milewicz, D.; Witz, A.M.; Byers, P.H. (Univ of Washington, Seattle (United States)); Smith, A.C.M.; Manchester, D.K.; Waldstein, G. (Children's Hospital, Denver, CO (United States))

1993-07-01

59

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

60

Generation and characterization of a novel neural crest marker allele, Inka1-LacZ, reveals a role for Inka1 in mouse neural tube closure  

PubMed Central

Previous studies identified Inka1 as a gene regulated by AP-2? in the neural crest required for craniofacial morphogenesis in fish and frog. Here, we extend the analysis of Inka1 function and regulation to the mouse by generating a LacZ knock-in allele. Inka1-LacZ allele expression occurs in the cephalic mesenchyme, heart, and paraxial mesoderm prior to E8.5. Subsequently, expression is observed in the migratory neural crest cells and their derivatives. Consistent with expression of Inka1 in tissues of the developing head during neurulation, a low percentage of Inka1?/? mice show exencephaly while the remainder are viable and fertile. Further studies indicate that AP-2? is not required for Inka1 expression in the mouse, and suggest that there is no significant genetic interaction between these two factors during embryogenesis. Together, these data demonstrate that while the expression domain of Inka1 is conserved among vertebrates, its function and regulation are not.

Reid, Bethany S.; Sargent, Thomas D.; Williams, Trevor

2010-01-01

61

The haplotype runs test: the parent-parent-affected offspring trio design.  

PubMed

The increasing availability of maps of dense polymorphic markers makes use of haplotype data in family-based association analyses an attractive alternative to single marker association tests. We describe a novel class of statistics designed to test for an association between marker haplotypes and a qualitative trait using the parent-parent-affected-offspring trio design. Our haplotype runs test (HRT) is based on consecutive allele-sharing between pairs of haplotypes. We assign weights according to the relative frequencies of the alleles for which the two haplotypes match. Herein, we compare the HRT to the maximum-identity-length-contrast (MILC) statistic, the single-locus transmission/disequilibrium test (TDT), and the generalized test of transmission disequilibrium for haplotype data, as implemented in the software TRANSMIT, using both simulated data and published haplotype data from the recessive disorder ataxia-telangiectasia. Our simulation results suggest that the HRT outperforms the MILC and that the HRT provides comparable power to the TDT and TRANSMIT when the number of distinct founder haplotypes with a disease susceptibility allele is small but substantially outperforms the TDT and TRANSMIT when the number of distinct founder haplotypes with a disease susceptibility allele is even of modest size. PMID:15305328

Lange, Ethan M; Boehnke, Michael

2004-09-01

62

Gene knock-outs and allelic replacements in Toxoplasma gondii: HXGPRT as a selectable marker for hit-and-run mutagenesis  

Microsoft Academic Search

The hypoxanthine-xanthine-guanine phosphoribosyl transferase (HXGPRT) gene of the protozoan parasite Toxoplasma gondii encodes a safe, practical genetic marker suitable for both positive and negative selection. Taking advantage of the ability to control homologous versus nonhomologous recombination in haploid T. gondii tachyzoites by manipulating the length of homologous DNA sequence, we have explored the possibility of ‘hit-and-run’ mutagenesis to introduce gene

Robert G. K Donald; David S Roos

1998-01-01

63

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

64

Association between AgI-CA alleles and severity of autosomal recessive proximal spina lmuscular atrophy  

SciTech Connect

The gene for autosomal recessive proximal spinal muscular atrophy (SMA) has been mapped to an 850-kb interval on 5q11.2-q13.3, between the centromeric D5S823 and telomeric D5S557 markers. We report a new complex marker, Ag1-CA, that lies in this interval, whose primers produce one, two, or rarely three amplification-fragment-length variants (AFLVs) per allele. Class I chromosomes are those which amplify a single AFLV allele, and class II chromosomes are those which amplify an allele with two or three AFLVs. Ag1-CA shows highly significant allelic association with type I SMA in both the French Canadian (Hopital Sainte-Justine (HSJ)) and American (Ohio State University (OSU)) populations (P < .0001). Significant association between the Ag1-CA genotype and disease severity was also observed. Type I patients were predominantly homozygous for class I chromosomes (P = .0003 OSU; P = 0.0012 HSJ), whereas the majority of type II patients were heterozygous for class I and II chromosomes (P = .0014 OSU; P = .001 HSJ). There was no significant difference in Ag1-CA genotype frequencies between type III patients (P = .5 OSU; P = .25 HSJ) and the paired normal chromosomes from both carrier parents. Our results indicate that Ag1-CA is the most closely linked marker to SMA and defines the critical candidate-gene region. Finally, we have proposed a model that should be taken into consideration when screening candidates SMA genes.

DiDonato, C.J.; Carpten, J.D.; Fuerst, P.; Ingraham, S.E.; Mendell, J.R.; Burghes, A.H.M. [Ohio State Univ., Columbus, OH (United States); Morgan, K. [McGill Univ. (Canada); Prescott, G.; Simard, L.R. [Hopital Sainte-Justine, Montreal (Canada); McPherson, J.D. [Univ. of California, Irvine, CA (United States)] [and others

1994-12-01

65

Allelic Variation of Gene Expression in Maize HybridsW?  

PubMed Central

Allelic expression variation of nonimprinted autosomal genes has recently been uncovered in mouse hybrids and humans. The allelic expression variation is attributed to differences in noncoding DNA sequences and does not involve epigenetic regulation or gene imprinting. This expression variation is suggested to play important roles in determining phenotypic diversity. Virtually nothing is known about such allele-specific expression variation in a hybrid plant where two alleles are compared in the same genetic context. We examined parental transcript accumulation in maize (Zea mays) hybrids using allele-specific RT-PCR analysis. Among 15 genes analyzed, 11 showed differences at the RNA level, ranging from unequal expression of the two alleles (biallelic) to expression of a single allele (monoallelic). Maternal or paternal transmission had little effect on the allele-specific transcript ratio of nearly all genes analyzed, suggesting that parent-of-origin effect was minimal. We analyzed the allelic difference in genetically contrasting hybrids and hybrids under high planting density and drought stress. Whereas a genetically improved modern hybrid expressed both alleles, a less improved old hybrid frequently showed mono-allelic expression. Furthermore, the two alleles in the hybrid responded differentially to abiotic stresses. The results of allele-specific regulation in different tissues in responding to environment and stress suggest an unequivalent function of the parental alleles in the hybrid, which may have an impact on heterosis.

Guo, Mei; Rupe, Mary A.; Zinselmeier, Christopher; Habben, Jeffrey; Bowen, Benjamin A.; Smith, Oscar S.

2004-01-01

66

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

67

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

68

[Selective elimination of alleles in rice anther cultures].  

PubMed

The nature of heterosis is discussed and selective elimination of alleles (introduced in the hybrid genotype by the parental forms) in anther culture is shown. This supports the possibility of removing viability-reducing alleles (lethal, semilethal, and less effective alleles) from the genotypes of heterotic hybrids in anther culture. PMID:23668085

Goncharova, Iu K

2013-02-01

69

Abnormal segregation of alleles in CEPH pedigree DNAs arising from allele loss in lymphoblastoid DNA  

SciTech Connect

Somatic events that result in the reduction to hemior homozygosity at all loci affected by the event have been identified in lymphoblastoid DNA from mothers of two CEPH families. Using suitably informative probes, the allele deficiencies were detected by the abnormal transmission of alleles from grandparents to grandchildren, with the apparent absence of the alleles from the parent. Undetected somatic deficiencies in family DNAs could result in misscoring of recombination events and consequently introduce errors into linkage analysis. 15 refs., 2 figs.

Royle, N.J.; Armour, J.A.L.; Crosier, M.; Jeffreys, A.J. (Univ. of Leicester (United Kingdom))

1993-01-01

70

Development of polysomic microsatellite markers for characterization of population structuring and phylogeography in the shortnose sturgeon (Acipenser brevirostrum)  

USGS Publications Warehouse

Shortnose sturgeon Acipenser brevirostrum is an endangered polyploid fish species for which no nuclear DNA markers previously existed. To address this need, 86 polysomic loci were developed and characterized in 20 A. brevirostrum from five river systems and eight members (parents and six progeny) of a captive-bred family. All markers proved to be polymorphic, polysomic, and demonstrated direct inheritance when tested in a captive family. Eleven loci were included in a range-wide survey of 561 fish sampled from 17 geographic collections. Allelic diversity at these markers ranged from 7 to 24 alleles/locus and averaged 16.5 alleles/locus; sufficient diversity to produce unique multilocus genotypes. In the range-wide survey, a Mantel comparison of an ecological (1-Jaccard’s) and genetic (?PT; an analog to FST) distance metrics, identified a strong positive correlation (r = 0.98, P PT represents a viable metric for assessing genetic relatedness using this class of marker.

Henderson, Anne P.; King, Tim L.

2012-01-01

71

Tight clustering and hemizygosity of apomixis-linked molecular markers in Pennisetum squamulatum implies genetic control of apospory by a divergent locus that may have no allelic form in sexual genotypes  

PubMed Central

Apomixis is a naturally occurring mode of reproduction that results in embryo formation without the involvement of meiosis or fertilization of the egg. Seed-derived progeny of an apomictic plant are genetically identical to the maternal parent. We are studying a form of apomixis called apospory that occurs in the genus Pennisetum, a taxon in the grass family. A cultivated member of this genus, pearl millet (Pennisetum glaucum), reproduces sexually. A wild relative of pearl millet, Pennisetum squamulatum, that is an obligate aposporous species, is cross-compatible with pearl millet when used as a pollen donor in the interspecific cross. We present herein the genetic mapping of 13 molecular markers in an interspecific hybrid population of 397 individuals that segregates for apomixis and sexuality. Surprisingly, 12 of the 13 markers strictly cosegregated with aposporous embryo sac development, clearly defining a contiguous apospory-specific genomic region in which no genetic recombination was detected. Lack of or suppression of recombination may be coincidentally associated with the chromosomal context of the apomixis locus or it may be a consequence of its evolution that is essential for preservation of gene function as has been previously shown in studies of complex loci in both plant and animal species.

Ozias-Akins, Peggy; Roche, Dominique; Hanna, Wayne W.

1998-01-01

72

Transmission/Disequilibrium Test Based on Haplotype Sharing for Tightly Linked Markers  

PubMed Central

Studies using haplotypes of multiple tightly linked markers are more informative than those using a single marker. However, studies based on multimarker haplotypes have some difficulties. First, if we consider each haplotype as an allele and use the conventional single-marker transmission/disequilibrium test (TDT), then the rapid increase in the degrees of freedom with an increasing number of markers means that the statistical power of the conventional tests will be low. Second, the parental haplotypes cannot always be unambiguously reconstructed. In the present article, we propose a haplotype-sharing TDT (HS-TDT) for linkage or association between a disease-susceptibility locus and a chromosome region in which several tightly linked markers have been typed. This method is applicable to both quantitative traits and qualitative traits. It is applicable to any size of nuclear family, with or without ambiguous phase information, and it is applicable to any number of alleles at each of the markers. The degrees of freedom (in a broad sense) of the test increase linearly as the number of markers considered increases but do not increase as the number of alleles at the markers increases. Our simulation results show that the HS-TDT has the correct type I error rate in structured populations and that, in most cases, the power of HS-TDT is higher than the power of the existing single-marker TDTs and haplotype-based TDTs.

Zhang, Shuanglin; Sha, Qiuying; Chen, Huann-Sheng; Dong, Jianping; Jiang, Renfang

2003-01-01

73

Genetic Marker for Endocrine Disorders.  

National Technical Information Service (NTIS)

A genetic marker associated with polycystic ovary syndrome is disclosed. The presence or absence of the allele is highly predictive of whether an individual is at risk from polycystic ovary syndrome. Methods of diagnosis, markers, and primers are disclose...

A. E. Dunaif

2003-01-01

74

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population  

PubMed Central

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ?200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance.

Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B

2012-01-01

75

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

PubMed

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. PMID:24065982

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

2013-09-18

76

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

77

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

78

Molecular mechanisms of alpha 1-antitrypsin null alleles  

Microsoft Academic Search

Alpha1-antitrypsin (?1-AT) is the most abundant circulating inhibitor of serine proteases and therefore is essential to normal protease–anti-protease homeostasis. Inheritance of two parental ?1-AT deficiency alleles is associated with a substantially increased risk for development of emphysema and liver disease. In very rare circumstances individuals may inherit ?1-AT null alleles. Null?1 -AT alleles are characterized by the total absence of

J. H LEE; M BRANTLY

2000-01-01

79

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

80

Child dopamine active transporter 1 genotype and parenting: evidence for evocative gene-environment correlations.  

PubMed

The dopamine active transporter 1 (DAT1) gene is implicated in psychopathology risk. Although the processes by which this gene exerts its effects on risk are poorly understood, a small body of research suggests that the DAT1 gene influences early emerging negative emotionality, a marker of children's psychopathology risk. As child negative emotionality evokes negative parenting practices, the DAT1 gene may also play a role in gene-environment correlations. To test this model, children (N = 365) were genotyped for the DAT1 gene and participated in standardized parent-child interaction tasks with their primary caregiver. The DAT1 gene 9-repeat variant was associated with child negative affect expressed toward the parent during parent-child interactions, and parents of children with a 9-repeat allele exhibited more hostility and lower guidance/engagement than parents of children without a 9-repeat allele. These gene-environment associations were partially mediated by child negative affect toward the parent. The findings implicate a specific polymorphism in eliciting negative parenting, suggesting that evocative associations play a role in elevating children's risk for emotional trajectories toward psychopathology risk. PMID:23398760

Hayden, Elizabeth P; Hanna, Brigitte; Sheikh, Haroon I; Laptook, Rebecca S; Kim, Jiyon; Singh, Shiva M; Klein, Daniel N

2013-02-01

81

Identification of Null Alleles and Deletions from SNP Genotypes for an Intercross Between Domestic and Wild Chickens  

PubMed Central

We analyzed genotypes from ~10K single-nucleotide polymorphisms (SNPs) in two families of an F2 intercross between Red Junglefowl and White Leghorn chickens. Possible null alleles were found by patterns of incompatible and missing genotypes. We estimated that 2.6% of SNPs had null alleles compared with 2.3% with genotyping errors and that 40% of SNPs in which a parent and offspring were genotyped as different homozygotes had null alleles. Putative deletions were identified by null alleles at adjacent markers. We found two candidate deletions that were supported by fluorescence intensity data from a 60K SNP chip. One of the candidate deletions was from the Red Junglefowl, and one was present in both the Red Junglefowl and White Leghorn. Both candidate deletions spanned protein-coding regions and were close to a previously detected quantitative trait locus affecting body weight in this population. This study demonstrates that the ~50K SNP genotyping arrays now available for several agricultural species can be used to identify null alleles and deletions in data from large families. We suggest that our approach could be a useful complement to linkage analysis in experimental crosses.

Crooks, Lucy; Carlborg, Orjan; Marklund, Stefan; Johansson, Anna M.

2013-01-01

82

Allele-specific gene targeting in Candida albicans results from heterology between alleles  

Microsoft Academic Search

The opportunistic fungal pathogen Candida albicans is asexual and diploid. Thus, introduction of recessive mutations requires targeted gene replacement of two alleles to effect expression of a recessive phenotype. This is often performed by recycling of a URA3 marker gene that is flanked by direct repeats of hisG. After targeting to a locus, recombination between the repeats excises URA3 leaving

Kyle Yesland; William A. Fonzi

2000-01-01

83

Multipoint Linkage-Disequilibrium-Mapping Approach Based on the Case-Parent Trio Design  

PubMed Central

In the present study we propose a multipoint approach, for the mapping of genes, that is based on the case-parent trio design. We first derive an expression for the expected preferential–allele-transmission statistics for transmission, from either parent to an affected child, for an arbitrary location within a chromosomal region demarcated by several genetic markers. No assumption about genetic mechanism is needed in this derivation, beyond the assumption that no more than one disease gene lies in the region framed by the markers. When one builds on this representation, the way in which one may maximize the genetic information from multiple markers becomes obvious. This proposed method differs from the popular transmission/disequilibrium test (TDT) approach for fine mapping, in the following ways: First, in contrast with the TDT approach, all markers contribute information, regardless of whether the parents are heterozygous at any one marker, and incomplete trio data can be utilized in our approach. Second, rather than performing the TDT at each marker separately, we propose a single test statistic that follows a ?2 distribution with 1 df, under the null hypothesis of no linkage or linkage disequilibrium to the region. Third, in the presence of linkage evidence, we offer a means to estimate the location of the disease locus along with its sampling uncertainty. We illustrate the proposed method with data from a family study of asthma, conducted in Barbados.

Liang, Kung-Yee; Hsu, Fang-Chi; Beaty, Terri H.; Barnes, Kathleen C.

2001-01-01

84

Genetic Tools for Allelic Replacement in Burkholderia Species  

Microsoft Academic Search

Allelic replacement in the Burkholderia genus has been problematic due to the lack of appropriate counter- selectable and selectable markers. The counter-selectable marker sacB, commonly used in gram-negative bacteria, is nonselective on sucrose in many Burkholderia species. In addition, the use of antibiotic resistance markers of clinical importance for the selection of desirable genetic traits is prohibited in the United

Ashley R. Barrett; Yun Kang; Ken S. Inamasu; Mike S. Son; Joseph M. Vukovich; Tung T. Hoang

2008-01-01

85

Systematic search for markers linked to insulin-dependent diabetes on chromosome 17  

SciTech Connect

We tested 19 microsatellite markers on chromosome 17 for linkage with insulin-dependent diabetes mellitus (IDDM). Nuclear families (N = 235) with at least two affected offspring were provided by the British Diabetic Association, Human Biological Data Interchange, and our own lab. The mean interval ({plus_minus}sd) between markers was 8 {plus_minus} 3 cM. For each parent heterozygous at the marker locus being studied, we determined whether the same or different alleles were transmitted to the two affected sibs. The {open_quotes}degree of sharing{close_quotes} for each marker is the frequency with which the same parental allele is transmitted to both affected sibs. Linkage with IDDM susceptibility leads to values higher than 0.50 for degree of sharing. Unlike lods, this approach makes no assumption about mode of inheritance. Mean sharing for the 19 markers was 0.51 (range 0.460 to 0.557; sd = .03). Three markers on 17q (all mutually unlinked) showed sharing of {approximately}0.55. The degree of sharing was 228/414 = 0.551 for D17A807 ({chi}{sup 2} = 4.26, p = .04), 172/309 = 0.557 for D17S784 ({chi}{sup 2} = 3.96, p = .04), and 218/398 = 0.548 for D17S798 ({chi}{sup 2} = 3.63, p =.06). We also looked for evidence of linkage disequilibrium between IDDM and alleles of each of these markers, by means of the transmission/disequilibrium test of Spielman. No significant linkage disequilibrium was found for D17S784 or D17S798. However, allele 6 of D17S807 was transmitted from heterozygous parents to IDDM offspring with frequency 131/230 = 0.57 ({chi}{sup 2} = 4.45, p = .035), supporting linkage with IDDM. We are currently investigating other markers and candidate genes in the region of D17S807.

Williams, S.R.; Shephard, J.M.; Berger, J.S. [Univ. of Pennsylvania, Philadelphia, PA (United States)] [and others

1994-09-01

86

Investigation of parent-of-origin effects in ADHD candidate genes.  

PubMed

Attention deficit hyperactivity disorder (ADHD) is a common early-onset childhood disorder with a strong genetic component. Results from previous studies have suggested that there may be a parent-of-origin effect for ADHD candidate genes. In particular, a recent investigation identified a pattern of paternal over-transmission of risk alleles for nine ADHD candidate genes. We examined this phenomenon in a sample of 291 trios for five genes previously associated with ADHD (HTR1B, SNAP-25, DRD5, DAT1, and BDNF). Using a dense map of markers and two analytic methods in this relatively large family-based sample, we do not find any evidence for significant paternal over-transmission of risk alleles in these candidate loci. Thus, we conclude that a substantial parent-of-origin effect is unlikely for these leading ADHD candidate genes. PMID:17427194

Kim, Jang Woo; Waldman, Irwin D; Faraone, Stephen V; Biederman, Joseph; Doyle, Alysa E; Purcell, Shaun; Arbeitman, Lori; Fagerness, Jesen; Sklar, Pamela; Smoller, Jordan W

2007-09-01

87

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

88

The relationship between parental genetic or phenotypic divergence and progeny variation in the maize nested association mapping population.  

PubMed

Appropriate selection of parents for the development of mapping populations is pivotal to maximizing the power of quantitative trait loci detection. Trait genotypic variation within a family is indicative of the family's informativeness for genetic studies. Accurate prediction of the most useful parental combinations within a species would help guide quantitative genetics studies. We tested the reliability of genotypic and phenotypic distance estimators between pairs of maize inbred lines to predict genotypic variation for quantitative traits within families derived from biparental crosses. We developed 25 families composed of ~200 random recombinant inbred lines each from crosses between a common reference parent inbred, B73, and 25 diverse maize inbreds. Parents and families were evaluated for 19 quantitative traits across up to 11 environments. Genetic distances (GDs) among parents were estimated with 44 simple sequence repeat and 2303 single-nucleotide polymorphism markers. GDs among parents had no predictive value for progeny variation, which is most likely due to the choice of neutral markers. In contrast, we observed for about half of the traits measured a positive correlation between phenotypic parental distances and within-family genetic variance estimates. Consequently, the choice of promising segregating populations can be based on selecting phenotypically diverse parents. These results are congruent with models of genetic architecture that posit numerous genes affecting quantitative traits, each segregating for allelic series, with dispersal of allelic effects across diverse genetic material. This architecture, common to many quantitative traits in maize, limits the predictive value of parental genotypic or phenotypic values on progeny variance. PMID:22027895

Hung, H-Y; Browne, C; Guill, K; Coles, N; Eller, M; Garcia, A; Lepak, N; Melia-Hancock, S; Oropeza-Rosas, M; Salvo, S; Upadyayula, N; Buckler, E S; Flint-Garcia, S; McMullen, M D; Rocheford, T R; Holland, J B

2011-10-26

89

Paternally transmitted FMR1 alleles are less stable than maternally transmitted alleles in the common and intermediate size range.  

PubMed

Fragile X syndrome, a form of X-linked mental retardation, results from the hyperexpansion of a CGG trinucleotide repeat located in the 5' untranslated region of the fragile X mental retardation (FMR1) gene. Relatively little is known about the initial mutation that causes a stable allele to become unstable and, eventually, to expand to the full mutation. In the present study, we have examined 1,452 parent-child transmissions of alleles of common (< or =39 repeats) or intermediate (40-59 repeats) sizes to study the initial mutation events. Of these, 201 have been sequenced and haplotyped. Using logistic regression analysis, we found that parental origin of transmission, repeat size (for unsequenced alleles), and number of the 3' CGGs (for sequenced alleles) were significant risk factors for repeat instability. Interestingly, transmission of the repeat through males was less stable than that through females, at the common- and intermediate-size level. This pattern differs from that seen for premutation-size alleles: paternally transmitted alleles are far more stable than maternally transmitted alleles. This difference that depends on repeat size suggests either a different mutational mechanism of instability or an increase in selection against sperm as their repeat size increases. PMID:11992259

Sullivan, Amy K; Crawford, Dana C; Scott, Elizabeth H; Leslie, Mary L; Sherman, Stephanie L

2002-05-03

90

A genetic analysis of parent-offspring conflict  

Microsoft Academic Search

1.When there is no cost to the selfish behavior, selection favors the spread of selfish alleles at offspring loci when the ratio of cost c to the parents' future offspring to benefit b to the selfish offspring is less than 2 for full-sibs and 4 for half-sibs. Selection on the parent favors offspring alleles where c\\/b?1. For monogamous parents, parent-offspring

Judy A. Stamps; Robert A. Metcalf; V. V. Krishnan

1978-01-01

91

The molecular mechanism underlying the “rare allele phenomenon” in a subspecific hybrid zone of the California field mouse, Peromyscus californicus  

Microsoft Academic Search

Natural hybrid zones are known to have unusually high levels of novel or otherwise rare electrophoretic variants (the “rare allele phenomenon”). These variant alleles are most likely the result either of high levels of unique mutations in hybrids or of intragenic recombination between divergent alleles from the parental populations. This study uses DNA sequence comparisons to determine which process has

S. M. G. Hoffman; W. M. Brown

1995-01-01

92

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

2013-09-11

93

Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles?  

Microsoft Academic Search

We developed multivatiate analytical models to predict the probability of assigning offspring to parental cou- ples as a function of population size, number of loci, and allelic diversity and the relationships between the probability of allocating individuals to their population of origin as a function of number of loci and allelic diversity. The parent- age model predicts that the number

Louis Bernatchez; Pierre Duchesne

2000-01-01

94

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

95

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.  

PubMed

Genotyping by sequencing (GBS) is the latest application of next-generation sequencing protocols for the purposes of discovering and genotyping SNPs in a variety of crop species and populations. Unlike other high-density genotyping technologies which have mainly been applied to general interest "reference" genomes, the low cost of GBS makes it an attractive means of saturating mapping and breeding populations with a high density of SNP markers. One barrier to the widespread use of GBS has been the difficulty of the bioinformatics analysis as the approach is accompanied by a high number of erroneous SNP calls which are not easily diagnosed or corrected. In this study, we use a 384-plex GBS protocol to add 30,984 markers to an indica (IR64) × japonica (Azucena) mapping population consisting of 176 recombinant inbred lines of rice (Oryza sativa) and we release our imputation and error correction pipeline to address initial GBS data sparsity and error, and streamline the process of adding SNPs to RIL populations. Using the final imputed and corrected dataset of 30,984 markers, we were able to map recombination hot and cold spots and regions of segregation distortion across the genome with a high degree of accuracy, thus identifying regions of the genome containing putative sterility loci. We mapped QTL for leaf width and aluminum tolerance, and were able to identify additional QTL for both phenotypes when using the full set of 30,984 SNPs that were not identified using a subset of only 1,464 SNPs, including a previously unreported QTL for aluminum tolerance located directly within a recombination hotspot on chromosome 1. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research. PMID:23918062

Spindel, Jennifer; Wright, Mark; Chen, Charles; Cobb, Joshua; Gage, Joseph; Harrington, Sandra; Lorieux, Mathias; Ahmadi, Nourollah; McCouch, Susan

2013-08-06

96

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

97

Genetic diversity analysis in Opal cotton hybrids based on SSR, ISSR, and RAPD markers.  

PubMed

Cotton is one of the most economically important crops in Iran; hybridization is a means to increase the genetic diversity and obtain new elite cultivars in this crop. We examined agronomic characteristics and molecular genetic diversity in the Opal cotton (Gossypium hirsutum) cultivar and in F(2) progenies. Ten homo-primers and seven hetero-primers of 26 RAPD primers produced 261 reproducible bands, with an average of 4.18 bands per primer and 22% polymorphism. The OPB12/OPH08 primer gave the highest effective number of alleles (N(E)), and the largest Shannon index (I), Nei's genetic diversity (H), and polymorphism information content (PIC) values. Some RAPD bands were present in the parental genotypes but were absent in their hybrids. Ten ISSR primers produced 206 reproducible bands, with 49.4% polymorphism. The UBC807 locus gave the highest N(E), I, H, and PIC values. Some ISSR bands occurred only in the parental genotype, while others were only present in the hybrid genotypes. Four microsatellite loci produced 12 alleles, ranging from 181 to 236 bp, with 54% polymorphism. The TMB1421 locus, with a monomorphic allele, was digested with three restriction enzymes (CAP-microsatellite) to evaluate sequence variations among samples. Association analysis between molecular markers and agronomic data revealed a significant correlation between ISSR-UBC807-1500 and yield. The Mantel test performed among the genetic distance matrices obtained from RAPD, ISSR and SSR showed a non-significant regression between RAPD versus ISSR and ISSR versus SSR, while RAPD versus SSR showed a significant regression; regression for ISSR and RAPD+ISSR+SSR combined data was also significant. Cluster analysis (UPGMA) based on these three types of molecular markers differentiated cotton genotypes and their progenies. Among the molecular markers, ISSR revealed more genetic variation among the genotypes. However, using all three types of molecular markers provided a better overall view of cotton genome polymorphism. PMID:23408413

Noormohammadi, Z; Hasheminejad-Ahangarani Farahani, Y; Sheidai, M; Ghasemzadeh-Baraki, S; Alishah, O

2013-01-30

98

Allelic loss in colorectal carcinoma  

SciTech Connect

Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes' classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis.

Kern, S.E.; Fearon, E.R.; Tersmette, K.W.F.; Enterline, J.P.; Vogelstein, B.; Hamilton, S.R. (Johns Hopkins Medical Institutions, Baltimore, MD (USA)); Leppert, M.; Nakamura, Yusuke; White, R. (Univ. of Utah School of Medicine, Salt Lake City (USA))

1989-06-02

99

Bisulfite sequencing of cloned alleles.  

PubMed

Bisulfite sequencing of cloned alleles is a widely used method for capturing the methylation profiles of single alleles. This method combines PCR amplification of the bisulfite-modified DNA with the subcloning of the amplicons into plasmids followed by transformation into bacteria and plating on selective media. The resulting colony forming units are each comprised of bacterial clones containing the same plasmid reflecting a single allele in the original PCR reaction. Following whole cell PCR and sequencing, the results provide highly detailed information about the status of each CG site within an allele. Sequencing of a large number of individual clones can provide quantitative information, assuming unbiased PCR, subcloning and clone selection. The proportion of methylated cytosine at a particular position within the sequenced alleles can be determined by counting the number of alleles showing methylation at the position of interest and dividing this by the total number of clones sequenced. PMID:23913211

Huang, Zhiqing; Bassil, Christopher F; Murphy, Susan K

2013-01-01

100

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

101

Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait  

PubMed Central

Background Infectious pancreatic necrosis (IPN) is one of the most prevalent and economically devastating diseases in Atlantic salmon (Salmo salar) farming worldwide. The disease causes large mortalities at both the fry- and post-smolt stages. Family selection for increased IPN resistance is performed through the use of controlled challenge tests, where survival rates of sib-groups are recorded. However, since challenge-tested animals cannot be used as breeding candidates, within-family selection is not performed and only half of the genetic variation for IPN resistance is being exploited. DNA markers linked to quantitative trait loci (QTL) affecting IPN resistance would therefore be a powerful selection tool. The aim of this study was to identify and fine-map QTL for IPN-resistance in Atlantic salmon, for use in marker-assisted selection to increase the rate of genetic improvement for this trait. Results A genome scan was carried out using 10 large full-sib families of challenge-tested Atlantic salmon post-smolts and microsatellite markers distributed across the genome. One major QTL for IPN-resistance was detected, explaining 29% and 83% of the phenotypic and genetic variances, respectively. This QTL mapped to the same location as a QTL recently detected in a Scottish Atlantic salmon population. The QTL was found to be segregating in 10 out of 20 mapping parents, and subsequent fine-mapping with additional markers narrowed the QTL peak to a 4 cM region on linkage group 21. Challenge-tested fry were used to show that the QTL had the same effect on fry as on post-smolt, with the confidence interval for QTL position in fry overlapping the confidence interval found in post-smolts. A total of 178 parents were tested for segregation of the QTL, identifying 72 QTL-heterozygous parents. Genotypes at QTL-heterozygous parents were used to determine linkage phases between alleles at the underlying DNA polymorphism and alleles at single markers or multi-marker haplotypes. One four-marker haplotype was found to be the best predictor of QTL alleles, and was successfully used to deduce genotypes of the underlying polymorphism in 72% of the parents of the next generation within a breeding nucleus. A highly significant population-level correlation was found between deduced alleles at the underlying polymorphism and survival of offspring groups in the fry challenge test, parents with the three deduced genotypes (QQ, Qq, qq) having mean offspring mortality rates of 0.13, 0.32, and 0.49, respectively. The frequency of the high-resistance allele (Q) in the population was estimated to be 0.30. Apart from this major QTL, one other experiment-wise significant QTL for IPN-resistance was detected, located on linkage group 4. Conclusion The QTL confirmed in this study represents a case of a major gene explaining the bulk of genetic variation for a presumed complex trait. QTL genotypes were deduced within most parents of the 2005 generation of a major breeding company, providing a solid framework for linkage-based MAS within the whole population in subsequent generations. Since haplotype-trait associations valid at the population level were found, there is also a potential for MAS based on linkage disequilibrium (LD). However, in order to use MAS across many generations without reassessment of linkage phases between markers and the underlying polymorphism, the QTL needs to be positioned with even greater accuracy. This will require higher marker densities than are currently available.

Moen, Thomas; Baranski, Matthew; Sonesson, Anna K; Kj?glum, Sissel

2009-01-01

102

Non-Mendelian inheritance revealed in a genetic analysis of sexual progeny of Phytophthora cinnamomi with microsatellite markers.  

PubMed

We report the development of four microsatellite loci into genetic markers for the diploid oomycete plant pathogen Phytophthora cinnamomi and that (AC)(n) and (AG)(n) microsatellites are significantly less frequent than in plant and mammal genomes. A minisatellite motif 14 bp long was also discovered. The four microsatellite loci were used to analyze sexual progeny from four separate crosses of P. cinnamomi. A large proportion of non-Mendelian inheritance was observed across all loci in all four crosses, including inheritance of more than two alleles at a locus and noninheritance of alleles from either parent at a locus. The aberrant inheritance is best explained by nondisjunction at meiosis in both the A1 parent and the A2 trisomic parents, resulting in aneuploid progeny. Two loci on the putative trisomic chromosome showed linkage and no loci were linked to mating type. One aneuploid offspring was shown to have lost alleles at two loci following subculture over 4 years, indicating that aneuploid progeny may not be mitotically stable. PMID:11929210

Dobrowolski, Mark P; Tommerup, I C; Blakeman, Harley D; O'Brien, Philip A

2002-04-01

103

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.

104

Parent Drug Use, Parent Personality, and Parenting  

Microsoft Academic Search

This study examined the relationship of parent drug use and specific parent personality traits with four indicators of the parent-child bond: affection, child-centeredness, involvement, and nonconflictual relations. The participants (N = 71) were young mothers or fathers who have participated in a longitudinal study of 1,000 children and their parents from 1975 to the present. They answered a self-administered questionnaire

Judith S. Brook; Martin Whiteman; Elinor B. Balka; Patricia Cohen

1995-01-01

105

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers  

PubMed Central

Background The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. Results The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19?cM, with a marker density of 8.87?cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72?cM, with an estimated average length of 52.64?cM. The greatest distance between two adjacent markers was 48.25?cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5?cM, and was observed on five CGs, suggesting a clustered organization. Conclusions Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

2012-01-01

106

The use of association data to identify family members at high risk for marker-linked diseases.  

PubMed Central

The study of genetic markers linked and associated with disease has provided important evidence of a genetic contribution to numerous diseases and has helped to establish their modes of inheritance. However, this information has not been fully utilized in counseling individuals at risk for these disorders. In the case of recessive, marker-linked diseases, such as idiopathic hemochromatosis linked to HLA in family studies and associated with specific HLA alleles in population surveys, the only current clinical application has been to identify siblings who share both HLA-marker haplotypes with the affected proband. They are considered to be presymptomatically affected, and more definitive invasive investigations are considered appropriate. All other relatives, including parents, offspring, and other siblings, who share only one marker with the proband, have been counseled only that their risk is equivalent to the gene frequency of the disease allele, for example, 3%-6% for hemochromatosis. We have developed a generally applicable method to utilize population association data to derive more specific and accurate risk figures for these other relatives of patients with marker-linked and associated diseases. We have applied this method to idiopathic hemochromatosis. If the offspring of a patient with hemochromatosis lacks A3, B7, and B14, the risk to that offspring for developing hemochromatosis is less than 2%. On the other hand, if they receive HLA A3 from their unaffected parent, their risk climbs to 9%-10%; if they receive an A3-B14 haplotype, their risk increases to virtually 100%. As demonstrated by our example, the application of association data to family members already at a basal increased risk for marker-linked disease can significantly refine the disease risk estimates given to those relatives. This information can be utilized to select individuals in whom invasive diagnostic testing or preventative intervention is indicated.

Conte, W J; Rotter, J I

1984-01-01

107

What Is a Recessive Allele?  

ERIC Educational Resources Information Center

|Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)|

American Biology Teacher, 1991

1991-01-01

108

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome  

PubMed Central

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1265-1) contains supplementary material, which is available to authorized users.

Nayak, Spurthi N.; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jungling, Ruth; Singh, Jagbir; Kavi Kishor, P. B.; Sivaramakrishnan, S.; Hoisington, Dave A.; Kahl, Gunter; Winter, Peter; Cook, Douglas R.

2010-01-01

109

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome.  

PubMed

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 x C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM-ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2-21 alleles and polymorphic information content value 0.04-0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago. PMID:20098978

Nayak, Spurthi N; Zhu, Hongyan; Varghese, Nicy; Datta, Subhojit; Choi, Hong-Kyu; Horres, Ralf; Jüngling, Ruth; Singh, Jagbir; Kishor, P B Kavi; Sivaramakrishnan, S; Hoisington, Dave A; Kahl, Günter; Winter, Peter; Cook, Douglas R; Varshney, Rajeev K

2010-01-23

110

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

2013-04-29

111

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

112

Recombination of 4p16 DNA markers in an unusual family with Huntington disease  

PubMed Central

The Huntington disease (HD) mutation has been localized to human chromosome 4p16, in a 6-Mb region between the D4S10 locus and the 4p telomere. In a report by Robbins et al., a family was identified in which an affected individual failed to inherit three alleles within the 6-Mb region originating from the parental HD chromosome. To explain these results, it was suggested that the HD locus (HD) lies close to the telomere and that a recombination event took place between HD and the most telomeric marker examined, D4S90. As a test of this telomere hypothesis, we examined six members of this family, five of whom are affected with HD, for the segregation of 12 polymorphic markers from 4p16, including D4S169, which lies within 80 kb of the 4p telomere. We separated, in somatic cell hybrids, the chromosomes 4 from each family member, to determine the phase of marker alleles on each chromosome. We excluded nonpaternity by performing DNA fingerprint analyses on all six family members, and we found no evidence for chromosomal rearrangements when we used high-resolution karyotype analysis. We found that two affected siblings, including one of the patients originally described by Robbins et al., inherited alleles from the non-HD chromosome 4 of their affected parents, throughout the 6-Mb region. We found that a third affected sibling, also studied by Robbins et al., inherited alleles from the HD chromosome 4 of the affected parent, throughout the 6-Mb region. Finally, we found that a fourth sibling, who is likely affected with HD, has both a recombination event within the 6-Mb region and an additional recombination event in a more centromeric region of the short arm of chromosome 4. Our results argue against a telomeric location for HD and suggest that the HD mutation in this family is either associated with DNA predisposed to double recombination and/or gene conversion within the 6-Mb region or is in a gene that is outside this region and that is different from that mutated in most other families with HD. ImagesFigure 4Figure 3

Pritchard, Catrin; Zhu, Ning; Zuo, Jian; Bull, Laura; Pericak-Vance, Margaret A.; Vance, Jeffery M.; Roses, Allen D.; Milatovich, Athena; Francke, Uta; Cox, David R.; Myers, Richard M.

1992-01-01

113

Rare allelic forms of PRDM9 associated with childhood leukemogenesis  

PubMed Central

One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis.

Hussin, Julie; Sinnett, Daniel; Casals, Ferran; Idaghdour, Youssef; Bruat, Vanessa; Saillour, Virginie; Healy, Jasmine; Grenier, Jean-Christophe; de Malliard, Thibault; Busche, Stephan; Spinella, Jean-Francois; Lariviere, Mathieu; Gibson, Greg; Andersson, Anna; Holmfeldt, Linda; Ma, Jing; Wei, Lei; Zhang, Jinghui; Andelfinger, Gregor; Downing, James R.; Mullighan, Charles G.; Awadalla, Philip

2013-01-01

114

Allele-dependent barley grain beta-amylase activity.  

PubMed

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 beta-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 beta-amy1 gene characterization to demonstrate that the high beta-amylase trait in the backcross line is co-inherited with the beta-amy1 gene from the H. spontaneum parent. We have analyzed the beta-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct beta-amy1 alleles. Two of these beta-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 beta-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated beta-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of beta-amylase activity in barley grain is proposed. PMID:9625721

Erkkilä, M J; Leah, R; Ahokas, H; Cameron-Mills, V

1998-06-01

115

Distribution of FMR-1 and associated microsatellite alleles in a normal Chinese population  

SciTech Connect

The CGG repeat size distribution of the fragile X mental retardation gene (FMR-1) was studied in a population of normal Chinese X chromosomes along with that of two proximal microsatellite polymorphic markers: FRAXAC1 and DXS548. The most common CGG repeat allele was 29 (47.2%) with 30 being second most common (26%). This distribution was different from that seen in Caucasian controls, where the most common allele was 30 repeats. Other differences with Caucasian controls included a secondary model peak at 36 repeats and the absence of peaks at 20 or 23 repeats. There were only two FRAXAC1 and five DXS548 alleles found in the Chinese sample. A striking linkage disequilibrium of FMR-1 alleles with FRAXAC1 alleles was observed, in that 90% of the 29 CGG repeat alleles but only 41% of the 30 CGG repeat alleles had the FRAXAC1 152 bp allele (18 AC repeats). This disequilibrium suggests that slippage between the closely spaced normal CGG repeat alleles, 29 and 30, and between 152 and 154 FRAXAC1 alleles is very rare. This study lays the groundwork for an understanding of founder chromosome effects in comparing Asian and Caucasian populations. 29 refs., 5 tabs.

Zhong, N.; Houck, G.E. Jr.; Li, S.; Dobkin, C.; Brown, W.T. [New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY (United States); Xixian Liu; Shen Gou [Tongji Medical Univ., Wuhan (China)

1994-07-15

116

Increasing the denaturation temperature during the first cycles of amplification reduced allele dropout from single cells for preimplantation genetic diagnosis  

Microsoft Academic Search

Single cell polymerase chain reaction (PCR) for preimplantation genetic diagnosis (PGD) needs to be highly efficient and accurate. In some single cells from human embryos presumed to be heterozygous for the AF508 deletion causing cystic fibrosis (CF), we recently observed random amplification failure of one of the two parental alleles following nested PCR. To investigate allele dropout (ADO), we have

Pierre F. Ray; Alan H. Handyside

1996-01-01

117

Parent of origin effects.  

PubMed

A major weakness of most genome-wide association studies has been their inability to fully explain the heritable component of complex disease. Nearly all such studies consider the two parental alleles to be functionally equivalent. However, the existence of imprinted genes demonstrates that this assumption can be wrong. In this review, we describe a wide variety of different mechanisms that underlie many other parent of origin and trans-generational effects that are known to operate in both humans and model organisms, suggesting that these phenomena are perhaps not uncommon in the genome. We propose that the consideration of alternative models of inheritance will improve our understanding of the heritability and causes of human traits and could have significant impacts on the study of complex disorders. PMID:21933173

Guilmatre, A; Sharp, A J

2011-10-30

118

Bone Markers  

MedlinePLUS

... Procollagen Type 1 N-Terminal Propeptide Formal name: Biochemical Markers of Bone Remodeling Related tests: Calcium , Phosphorus , ... 2013. Singer, F. and Eyre, D. (2008). Using biochemical markers of bone turnover in clinical practice. [On- ...

119

Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes  

PubMed Central

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F2 lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species.

Saxena, Rachit K.; Varma Penmetsa, R.; Upadhyaya, Hari D.; Kumar, Ashish; Carrasquilla-Garcia, Noelia; Schlueter, Jessica A.; Farmer, Andrew; Whaley, Adam M.; Sarma, Birinchi K.; May, Gregory D.; Cook, Douglas R.; Varshney, Rajeev K.

2012-01-01

120

Large-scale development of cost-effective single-nucleotide polymorphism marker assays for genetic mapping in pigeonpea and comparative mapping in legumes.  

PubMed

Single-nucleotide polymorphisms (SNPs, >2000) were discovered by using RNA-seq and allele-specific sequencing approaches in pigeonpea (Cajanus cajan). For making the SNP genotyping cost-effective, successful competitive allele-specific polymerase chain reaction (KASPar) assays were developed for 1616 SNPs and referred to as PKAMs (pigeonpea KASPar assay markers). Screening of PKAMs on 24 genotypes [23 from cultivated species and 1 wild species (Cajanus scarabaeoides)] defined a set of 1154 polymorphic markers (77.4%) with a polymorphism information content (PIC) value from 0.04 to 0.38. One thousand and ninety-four PKAMs showed polymorphisms between parental lines of the reference mapping population (C. cajan ICP 28 × C. scarabaeoides ICPW 94). By using high-quality marker genotyping data on 167 F(2) lines from the population, a comprehensive genetic map comprising 875 PKAMs with an average inter-marker distance of 1.11 cM was developed. Previously mapped 35 simple sequence repeat markers were integrated into the PKAM map and an integrated genetic map of 996.21 cM was constructed. Mapped PKAMs showed a higher degree of synteny with the genome of Glycine max followed by Medicago truncatula and Lotus japonicus and least with Vigna unguiculata. These PKAMs will be useful for genetics research and breeding applications in pigeonpea and for utilizing genome information from other legume species. PMID:23103470

Saxena, Rachit K; Penmetsa, R Varma; Upadhyaya, Hari D; Kumar, Ashish; Carrasquilla-Garcia, Noelia; Schlueter, Jessica A; Farmer, Andrew; Whaley, Adam M; Sarma, Birinchi K; May, Gregory D; Cook, Douglas R; Varshney, Rajeev K

2012-10-26

121

Estimation of genetic marker effects for CAPN1, CAST, and GHR on carcass quality traits in Angus cattle selected to increase minor marker frequencies  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic marker effects and interactions cannot be accurately estimated when minor marker allele frequencies (MAF) are low. To increase the accuracy of estimation for three marker systems in commercial use, an Angus population at USMARC was subjected to marker assisted-selection for multiple years t...

122

Gene-environment interaction and the intergenerational transmission of parenting: testing the differential-susceptibility hypothesis.  

PubMed

The current study evaluated the differential-susceptibility hypothesis in explaining the intergenerational transmission of parenting, using data from the National Longitudinal Study of Adolescent Health (Add Health). Exposure to maternal parenting was measured prospectively when respondents were adolescents and parental stress was measured when they were parents themselves, some 14 years later, on average. Cumulative-genetic plasticity was measured by dominantly coding the presence of putative plasticity alleles from four genes: the 10R allele of DAT1, the A1 allele of DRD2, the 7R allele of DRD4, and the short allele of 5HTTLPR. Results showed that the more plasticity alleles individuals carried (range 0-4), the more that parenting experienced in adolescence predicted future parenting experience. Those respondents with the most plasticity alleles not only experienced the highest levels of parental stress when exposed to negative maternal parenting in adolescence but the lowest levels when exposed to positive maternal parenting in adolescence. These results indicate that differential susceptibility is operative in the case of the intergenerational transmission of parenting, which could explain why estimates of such transmission have proven so modest in studies which fail to consider GXE interactions. PMID:21553075

Beaver, Kevin M; Belsky, Jay

2012-03-01

123

Parenting Education  

Microsoft Academic Search

Television advertising offers a preventive tool that can influence behavior in positive directions. This paper reports on the evaluation of a television campaign on parenting designed to foster more positive emotional environments for young children (under 5) and to teach and remind parents of basic child-rearing skills. The results of a limited test-market campaign revealed positive changes in parenting beliefs

William D. Ratcliffe; William P. Wittman

1983-01-01

124

Identification of three distinct regions of allelic deletions on the short arm of chromosome 8 in hepatocellular carcinoma  

Microsoft Academic Search

The chromosome 8p is associated with a large number of allelic imbalances in epithelial tumors including hepatocellular carcinoma (HCC). However, no tumor suppressor gene has been identified so far in this particular region of the genome. To further clarify the pattern of allelic deletions on chromosome 8p in HCC, we have undertaken high-density polymorphic marker analysis of 109 paired normal

Pascal Pineau; Hisaki Nagai; Sylvie Prigent; Yu Wei; Gabor Gyapay; Jean Weissenbach; Pierre Tiollais; Marie-Annick Buendia; Anne Dejean

1999-01-01

125

A proposal for standardization in forensic canine DNA typing: allele nomenclature of six canine-specific STR loci.  

PubMed

In this study a proposal for the allele nomenclature of six polymorphic short tandem repeat (STR) loci (PEZ3, PEZ6, PEZ8, PEZ10, FHC2161, and FHC2328) for canine genotyping (Canis lupus familiaris) is presented. The nomenclature is based on the sequence data of the polymorphic region of the microsatellite markers as recommended by the DNA commission of the International Society of Forensic Haemogenetics (ISFH) in 1994 for human DNA typing. To cover commonly and rarely occurring alleles, a selection of homozygous and heterozygous animals were analyzed and subjected to sequence studies. The alleles consisted of simple tri- and tetra-nucleotide repeat patterns as well as compound and highly complex repeat patterns. Several alleles revealing the same fragment size but different repeat structures were found. The allele designation described here was adopted to the number of repeats, including all variable regions within the amplified fragment. In a second step the most commonly occurring alleles were added to an allelic ladder for each marker allowing a reliable typing of all alleles differing in size. A total number of 142 unrelated dogs from surrounding municipal animal homes, private households, and canines in police duty were analyzed. The data were added to a population database providing allele frequencies for each marker. PMID:16566760

Hellmann, Andreas P; Rohleder, Udo; Eichmann, Cordula; Pfeiffer, Ina; Parson, Walther; Schleenbecker, Uwe

2006-03-01

126

Segregation of isozyme markers and cold tolerance in an interspecific backcross of tomato  

Microsoft Academic Search

An interspecific backcross was obtained between the cultivated tomato, L. esculentum, and a high-altitude, cold-tolerant L. hirsutum, using the former as the recurrent pistillate parent. An individual plant of L. hirsutum which possessed maximum allelic differences for enzyme loci, with respect to those of L. esculentum, was selected as the staminate parent. Allelic differences were found at seventeen enzyme loci,

C. E. Vallejos; S. D. Tanksley

1983-01-01

127

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

128

Parenting Stress and Parental Bonding  

Microsoft Academic Search

Attachment experiences are thought to be important because of their implications for later development. The authors' aim with the questionnaire-based study was to investigate the differences between recalled parental bonding regarding 4 types of maternal and paternal bonding with respect to experienced parenting stress caused by child characteristics, parent attributes, and life events under the consideration of the child's gender

Ulrike Willinger; Gabriela Diendorfer-Radner; Ruth Willnauer; Gudrun Jörgl; Veronika Hager

2005-01-01

129

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

130

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

2012-06-25

131

Distribution of the photoperiod insensitive Ppd-D1a allele in Chinese wheat cultivars  

Microsoft Academic Search

Photoperiod response is of great importance for optimal adaptation of bread wheat cultivars to specific environments, and\\u000a variation is commonly associated with allelic differences at the Ppd-D1 locus on chromosome 2D. A total of 926 Chinese wheat landraces and improved cultivars collected from nine wheat growing zones\\u000a were tested for their genotypes at the Ppd-D1 locus using allele-specific markers. The

F. P. Yang; X. K. Zhang; X. C. Xia; D. A. Laurie; W. X. Yang; Z. H. He

2009-01-01

132

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

2013-02-27

133

PARENT DEVELOPMENT  

PubMed Central

Today's parents tend to be overwhelmed with advice from many sources. In his role as family counselor, the pediatrician must understand and consider the emotional development of parents in relation to their child's development; otherwise, his advice and counsel do not “take” and he becomes tired and frustrated and angry. Parents progress through definite stages of development: Stage 1: Learning the cues—the struggle of the parents to interpret the infant's needs. Stage 2: Learning to accept growth and development—the parent learning to accept some loss of control of the toddler. Stage 3: Learning to separate—the parent learning to allow the child to develop independently. Stage 4: Learning to accept rejection, without deserting—the struggle of the parents not to intrude and yet to be there when needed. Stage 5: Learning to build a new life having been thoroughly discredited by one's teenager—the parent learning to live independently while the teenager struggles to develop his own identity. The pediatrician who is accepting, sensitive and a good listener and who keeps in mind that parents as well as children have capacities for growth and development, will be a potent factor in promoting good parent-child relationships and many times more effective in dealing with the child in health and disease.

Friedman, David Belais

1957-01-01

134

Concordance between parental origin of chromosome 13q loss and chromosome 6p duplication in sporadic retinoblastoma  

SciTech Connect

Two hypotheses are capable of explaining nonrandom loss of one parent's alleles at tumor suppressor loci in sporadic cases of several pediatric cancers, including retinoblastoma - namely, preferential germ-line mutation or chromosome imprinting. The authors have examined 74 cases of sporadic retinoblastoma for tumors in which at least two genetic events - loss of heterozygosity for chromosome 13q markers and formation of an isochromosome 6p - have occurred. Sixteen cases were found to contain both events. In 13 of 16 such tumors, the chromosomes 13q that were lost and chromosomes 6p that were duplicated are derived from the same parent. These data may be explained within the framework of the genome imprinting model but are not predicted by preferential germ-line mutation. 39 refs., 3 figs., 5 tabs.

Naumova, A.; Sapienza, C. (Univ. of California-San Diego, La Jolla, CA (United States)); Hansen, M.; Strong, L. (M.D. Anderson Cancer Center, Houston, TX (United States)); Jones, P.A. (Univ. of Southern California, Los Angeles, CA (United States)); Hadjistilianou, D.; Mastrangelo, D. (Univ. of Siena (Italy)); Griegel, S.; Rajewsky, M.F. (Univ. of Essen Medical School, Essen (Germany)); Shields, J. (Wills Eye Hospital, Philadelphia, PA (United States)) (and others)

1994-02-01

135

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

136

Allelic variation in paralogs of GDP-L-galactose phosphorylase is a major determinant of vitamin C concentrations in apple fruit.  

PubMed

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. PMID:23001142

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

2012-09-21

137

Genetic Tools for Allelic Replacement in Burkholderia Species? †  

PubMed Central

Allelic replacement in the Burkholderia genus has been problematic due to the lack of appropriate counter-selectable and selectable markers. The counter-selectable marker sacB, commonly used in gram-negative bacteria, is nonselective on sucrose in many Burkholderia species. In addition, the use of antibiotic resistance markers of clinical importance for the selection of desirable genetic traits is prohibited in the United States for two potential bioterrorism agents, Burkholderia mallei and Burkholderia pseudomallei. Here, we engineered a mutated counter-selectable marker based on the B. pseudomallei PheS (the ?-subunit of phenylalanyl tRNA synthase) protein and tested its effectiveness in three different Burkholderia species. The mutant PheS protein effectively killed 100% of the bacteria in the presence of 0.1% p-chlorophenylalanine. We assembled the mutant pheS on several allelic replacement vectors, in addition to constructing selectable markers based on tellurite (Telr) and trimethoprim (Tpr) resistance that are excisable by flanking unique FLP recombination target (FRT) sequences. As a proof of concept, we utilized one of these gene replacement vectors (pBAKA) and the Telr-FRT cassette to produce a chromosomal mutation in the Burkholderia thailandensis betBA operon, which codes for betaine aldehyde dehydrogenase and choline dehydrogenase. Chromosomal resistance markers could be excised by the introduction of pFLP-AB5 (Tpr), which is one of two constructed flp-containing plasmids, pFLP-AB4 (Telr) and pFLP-AB5 (Tpr). These flp-containing plasmids harbor the mutant pheS gene and allow self curing on media that contain p-chlorophenylalanine after Flp-FRT excision. The characterization of the ?betBA::Telr-FRT and ?betBA::FRT mutants indicated a defect in growth with choline as a sole carbon source, while these mutants grew as well as the wild type with succinate and glucose as alternative carbon sources.

Barrett, Ashley R.; Kang, Yun; Inamasu, Ken S.; Son, Mike S.; Vukovich, Joseph M.; Hoang, Tung T.

2008-01-01

138

GENOPROB: COMPUTATION OF GENOTYPE AND GRANDPARENTAL ORIGIN PROBABILITIES IN COMPLEX PEDIGREES WITH MISSING MARKER DATA  

Technology Transfer Automated Retrieval System (TEKTRAN)

GenoProb analyzes genetic marker data in complex pedigrees with missing marker data using an iterative allelic peeling algorithm. Its output has been used for QTL detection, marker assisted selection, and identification and correction of errors in marker data and pedigrees. It computes the approxima...

139

Estimating Y-STR allelic drop-out rates and adjusting for interlocus balances.  

PubMed

Y chromosome short tandem repeats (Y-STRs) are valuable genetic markers in certain areas of forensic case-work. However, when the Y-STR DNA profile is weak, the observed Y-STR profile may not be complete--i.e. locus drop-out may have occurred. Another explanation could be that the stain DNA did not have a Y-STR allele that was detectable with the method used (the allele is a 'null allele'). If the Y-STR profile of a stain is strong, one would be reluctant to consider drop-out as a reasonable explanation of lack of a Y-STR allele and would maybe consider 'null allele' as an explanation. On the other hand, if the signal strengths are weak, one would most likely accept drop-out as a possible explanation. We created a logistic regression model to estimate the probability of allele drop-out with the Life Technologies/Applied Biosystems AmpFlSTR(®) Yfiler(®) kit such that the trade-off between drop-outs and null alleles could be quantified using a statistical model. The model to estimate the probability of drop-out uses information about locus imbalances, signal strength, the number of PCR cycles, and the fragment size of Yfiler. We made two temporarily separated experiments and found no evidence of temporal variation in the probability of drop-out. Using our model, we found that for 30 PCR cycles with a 150 bp allele, the probability of drop-out was 1:5000 corresponding to the average estimate of the probability of Y-STR null alleles at a signal strength of 1249 RFU. This means that the probability of a null allele is higher than that of an allele drop-out at e.g. 4000 RFU and the probability of drop-out is higher than that of a null allele at e.g. 75 RFU. PMID:23453365

Andersen, Mikkel Meyer; Mogensen, Helle Smidt; Eriksen, Poul Svante; Olofsson, Jill Katharina; Asplund, Maria; Morling, Niels

2013-02-27

140

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

2011-10-17

141

SNP-based large-scale identification of allele-specific gene expression in human B cells.  

PubMed

Polymorphism and variations in gene expression provide the genetic basis for human variation. Allelic variation of gene expression, in particular, may play a crucial role in phenotypic variation and disease susceptibility. To identify genes with allelic expression in human cells, we genotyped genomic DNA and cDNA isolated from 31 immortalized B cell lines from three Centre d'Etude du Polymorphisme Humain (CEPH) families using high-density single-nucleotide polymorphism (SNP) chips containing 13,900 exonic SNPs. We identified seven SNPs in five genes with monoallelic expression, 146 SNPs in 125 genes with allelic imbalance in expression with preferentially higher expression of one allele in a heterozygous individual. The monoallelically expressed genes (ERAP2, MDGA1, LOC644422, SDCCAG3P1 and CLTCL1) were regulated by cis-acting, non-imprinted differential allelic control. In addition, all monoallelic gene expression patterns and allelic imbalances in gene expression in B cells were transmitted from parents to offspring in the pedigree, indicating genetic transmission of allelic gene expression. Furthermore, frequent allele substitution, probably due to RNA editing, was also observed in 21 genes in 23 SNPs as well as in 48 SNPs located in regions containing no known genes. In this study, we demonstrated that allelic gene expression is frequently observed in human B cells, and SNP chips are very useful tools for detecting allelic gene expression. Overall, our data provide a valuable framework for better understanding allelic gene expression in human B cells. PMID:22178530

Song, Min-Young; Kim, Hye-Eun; Kim, Sun; Choi, Ick-Hwa; Lee, Jong-Keuk

2011-12-08

142

Segregation distortion of T-DNA markers linked to the self-incompatibility (S) locus in Petunia hybrida.  

PubMed Central

In plants with a gametophytic self-incompatibility system the specificity of the pollen is determined by the haploid genotype at the self-incompatibility (S) locus. In certain crosses this can lead to the exclusion of half the gametes from the male parent carrying a particular S-allele. This leads to pronounced segregation distortion for any genetic markers that are linked to the S-locus. We have used this approach to identify T-DNA insertions carrying a maize transposable element that are linked to the S-locus of Petunia hybrida. A total of 83 T-DNA insertions were tested for segregation distortion of the selectable marker used during transformation with Agrobacterium. Segregation distortion was observed for 12 T-DNA insertions and at least 8 of these were shown to be in the same linkage group by intercrossing. This indicates that differential transmission of a single locus (S) is probably responsible for all of these examples of T-DNA segregation distortion. The identification of selectable markers in coupling with a functional S-allele will allow the preselection of recombination events around the S-locus in petunia. Our approach provides a general method for identifying transgenes that are linked to gametophytic self-incompatibility loci and provides an opportunity for transposon tagging of the petunia S-locus.

Harbord, R M; Napoli, C A; Robbins, T P

2000-01-01

143

Parent training  

Microsoft Academic Search

Parent training programmes are a very well replicated, effective treatment for conduct problems. The most effective include a strong element of practising skills, combined with understanding the parents' predicament and helping them alter this. However, they don't always improve behaviour in the school setting, which is an important predictor of poor outcomes. The focus therefore is now on also adding

Stephen Scott

2005-01-01

144

Virtual Parentalism  

Microsoft Academic Search

Parents, not Laws, ultimately protect children both online and offline. If legislation places adults at legal risk because of the presence of children in virtual worlds, adults will exit those worlds, and children will be isolated into separate spaces. This will not improve safety for children. Instead, this Article suggests that Congress enact measures that encourage filtering technology and parental

Joshua A. T. Fairfield

2009-01-01

145

Preliminary genetic linkage map of Miscanthus sinensis with RAPD markers.  

PubMed

We have used an "offspring cross" mapping strategy in combination with the random amplified polymorphic DNA (RAPD) assay to construct the first genetic map of the species Miscanthus sinensis (2 n = 2 x = 38). This map is based on an outbred population of 89 individuals resulting from the cross between two genotypes from a previously designed cross. Consequently, both parents are fullsibs. The same proportion of bi-parental markers (heterozygotic in both parents) and pseudo-testcross markers (heterozygotic in one parent and null in the other), mono-parental markers, have been obtained. A total of 383 RAPD markers were analysed within the 89 F1 plants. Out of these markers, 257 were mapped into 28 linkage groups which spanned a total map length of around 1,074.5 cM with an average density of 4.2 cM per marker. Out of 257 mapped markers, 62 were inherited from F1.1 (P1), 63 from F1.7 (P7) and 132 were bi-parental markers. The contribution to the map was equal from both parents. This map provides a useful tool for genetic analyses of agronomically interesting characters in M. sinensis such as flowering, yield, plant height, stem diameter and mineral constitution. The offspring cross mapping strategy is proposed to obtain a higher efficiency in developing integrated maps including both parents. PMID:12582920

Atienza, G.; Satovic, Z.; Petersen, K.; Dolstra, O.; Martín, A.

2002-06-19

146

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh  

PubMed Central

Background Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. Results In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ?18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. Conclusion We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.

2011-01-01

147

KIR allele and gene polymorphism group (KAG).  

PubMed

Recent research presented at this meeting verifies the extent of the polymorphism of KIR genes and their alleles and shows their association with various diseases. Methods were described for the determination of alleles of several of the KIR genes in different populations including a novel allele formed by an unequal recombination event. Associations of KIR genes were found with several diseases: type I diabetes; psoriatic arthritis; and hepatitis C infection. Discussion took place on nomenclature issues of the KIR genes and their alleles, and a website has been developed to collect frequencies of KIR genes and alleles in various diverse populations. PMID:15607798

Middleton, D

2005-02-01

148

Molecular background of novel silent RHCE alleles.  

PubMed

BACKGROUND: The absence of expression of C/c and E/e antigens has been associated with rare variant RHCE alleles, referred to as silent RHCE alleles, classically identified among individuals with a rare D-?- or Rh(null) phenotype. This work reports on different molecular mechanisms identified in three novel silent RHCE alleles. STUDY DESIGN AND METHODS: Samples from D-?- or Rh(null) individuals and their family members, from families for whom Rh phenotype and/or serologic data were unexplained by inheritance of conventional RH alleles, were analyzed. Genomic DNA and transcripts were tested by sequencing analysis. RESULTS: The first silent allele was a RHCE*cE allele carrying an intronic IVS3+5G>A mutation. The second was a RHCE*ce allele carrying an intronic IVS7-2A>G mutation, whereas the third was a silent RHCE*ce allele carrying a 5-bp deletion (Nucleotides 679-683) in Exon?5. CONCLUSION: In addition to hybrid alleles and nucleotide deletion, intronic mutations may be associated with the nonexpression of RhCE antigens. Regarding the RH system, silent alleles may not be investigated among D-?- or Rh(null) individuals only. Rh phenotype and/or serologic data unexplained by inheritance of conventional RH alleles should lead to molecular investigations. PMID:23252593

Pham, Bach-Nga; Ramelet, Stéphanie; Wibaut, Bénédicte; Juszczak, Genevieve; Loukil, Chawki; Dubeaux, Isabelle; Gien, Dominique; Kappler-Gratias, Sandrine; Rouger, Philippe; Le Pennec, Pierre-Yves

2012-12-17

149

Allelic relationships between genes for resistance to tomato spotted wilt tospovirus in Capsicum chinense  

Microsoft Academic Search

Pepper (Capsicum chinense Jacq.) has been reported to be an important reservoir of resistance genes to tomato spotted wilt virus (TSWV). The genes for TSWV resistance present in three C. chinense lines (‘PI 152225’, ‘PI 159236’ and ‘Panca’) were investigated for allelism. All resistant lines were crossed with each other. Parents, F1, backcrosses and F2 populations (including reciprocals) developed from

L. S. Boiteux

1995-01-01

150

Differential chromatin packaging of genomic imprinted regions between expressed and non-expressed alleles  

Microsoft Academic Search

Chromosomal regions subject to genomic imprinting comprise a functional domain exhibiting parental- specific expression of genes and hence may take a unique chromatin structure. Here we have examined the chromatin packaging state of allelic sites in the Zfp127\\/Snrpn locus on mouse chromosome 7 and in the Igf2r locus on mouse chromosome 17 with an assay consisting of chromatin fractionation and

Takuya Watanabe; Akira Yoshimura; Yukio Mishima; Yoshiro Endo; Toshihiko Shiroishi; Tuyoshi Koide; Hiroyuki Sasaki; Hitoshi Asakura; Ryo Kominami

2000-01-01

151

Evidence of Allelic Suppression for Transcripts Expressed in Day 30 Pig Embryos by SNP Genotyping  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genomic imprinting results in alleles being differentially expressed in a parent-of-origin specific manner. Parthenogenetic and biparental pig embryo gene expression profiles were compared using three cDNA microarray platforms. Comparison of the profiles of the two tissue types indicated different...

152

Identification of linkage phase by parental genotypes  

SciTech Connect

The possibility of using the phenotypic characteristics of parents for identifying the linkage phase in offspring is analyzed. It is demonstrated that parents with similar phenotypes (or marker genotypes) carry no information about the gene linkage phase in diheterozygous offspring. The probability of a certain linkage phase remains the same in all informative crossings. It depends on the model of inheritance of the analyzed alternative trait and is similar for di- and polyallelic markers. The frequencies of informative crossings and the probability of the linkage phase for different models of inheritance of the analyzed and marker traits are estimated. 17 refs., 2 tabs.

Aksenovich, T.I. [Institute of Cytology and Genetics, Novosibirsk (Russian Federation)

1995-08-01

153

Premutation and intermediate-size FMR1 alleles in 10572 males from the general population: loss of an AGG interruption is a late event in the generation of fragile X syndrome alleles.  

PubMed

We previously reported a 1:259 prevalence of female carriers of FMR1 premutation-size alleles (greater than 54 triplet repeats) in the general population. We now have screened 10 572 independent males from the same population for similar alleles using high-throughput Southern blotting. We identified 13 male carriers of an allele with more than 54 repeats. This corresponds to a prevalence of 1:813 males (95% confidence interval 1:527 to 1:1781). Haplotype analysis of four markers flanking the triplet array revealed that the prevalence of the major fragile X mutation-associated haplotype was increased among FMR1 alleles of 40-54 repeats. Although sequencing of highly unstable premutation alleles from fragile X families revealed only pure CGG tracts, this was not the case for alleles of similar size that were identified in males from the general population. Forty-eight out of forty-nine alleles of 40 or more triplets had one or two AGG interruptions. This observation, combined with the observation of the enrichment of major fragile X syndrome haplotypes in all alleles of this size, is evidence that the loss of an AGG interruption in the triplet repeat array is not necessary for expansion of normal alleles of 29-30 triplets to intermediate size. The loss of AGG interruptions thus appears to be a late event that leads to greatly increased instability and may be related to the haplotype background of specific FMR1 alleles. PMID:11854169

Dombrowski, C; Lévesque, S; Morel, M L; Rouillard, P; Morgan, K; Rousseau, F

2002-02-15

154

Prediction of deleterious human alleles.  

PubMed

Single nucleotide polymorphisms (SNPs) constitute the bulk of human genetic variation, occurring with an average density of approximately 1/1000 nucleotides of a genotype. SNPs are either neutral allelic variants or are under selection of various strengths, and the impact of SNPs on fitness remains unknown. Identification of SNPs affecting human phenotype, especially leading to risks of complex disorders, is one of the key problems of medical genetics. SNPs in protein-coding regions that cause amino acid variants (non-synonymous cSNPs) are most likely to affect phenotypes. We have developed a straightforward and reliable method based on physical and comparative considerations that estimates the impact of an amino acid replacement on the three-dimensional structure and function of the protein. We estimate that approximately 20% of common human non-synonymous SNPs damage the protein. The average minor allele frequency of such SNPs in our data set was two times lower than that of benign non-synonymous SNPs. The average human genotype carries approximately 10(3) damaging non-synonymous SNPs that together cause a substantial reduction in fitness. PMID:11230178

Sunyaev, S; Ramensky, V; Koch, I; Lathe, W; Kondrashov, A S; Bork, P

2001-03-15

155

Abusive Parents.  

National Technical Information Service (NTIS)

Presents, with commentary, a panel of women incarcerated for child abuse. These women belong to a prison chapter of Parents Anonymous. Also offers commentary from a social worker on the social, personal, and family dynamics of child abuse. Primary audienc...

1994-01-01

156

Wheat breeding assisted by markers: CIMMYT’s experience  

Microsoft Academic Search

Significant progress has been made in the characterization of loci controlling traits of importance using molecular markers.\\u000a A number of markers are currently available in wheat for genes of interest to the breeders. Markers can be used to better\\u000a characterize parental material, thereby improving the efficiency and effectiveness of parental selection for crossing and\\u000a to track genes in segregating progenies

H. M. William; R. Trethowan; E. M. Crosby-Galvan

2007-01-01

157

Sixteen polymorphic microsatellite markers from Zizania latifolia Turcz. (Poaceae).  

PubMed

Sixteen polymorphic microsatellite markers were isolated and identified in Zizania latifolia Turcz. (Poaceae), a perennial aquatic plant widespread in Eastern Asia. The microsatellite-enriched library was constructed using the fast isolation by AFLP of sequences containing repeats method. These markers revealed two to 14 alleles, with an average of 5.6 alleles per locus. The observed and expected heterozygosities varied from 0.071 to 0.690 and from 0.174 to 0.812, respectively. These markers will be useful for studying of gene flow and evaluating the genetic diversity of the Zizania latifolia population. PMID:21564779

Quan, Zhiwu; Pan, Lei; Ke, Weidong; Liu, Yiman; Ding, Yi

2009-02-03

158

Increased Frequency of the S-allele of the L-myc Oncogene in Breast Cancer  

Microsoft Academic Search

Background: Association between restriction fragment length polymorphisms (RFLP) of known oncogenes and a predisposition to develop cancer have been postulated. The L-myc gene is a potential molecular marker associ- ated with cancer susceptibility as well as metastasis, prognosis, and adverse survival. Our aim was to test the hypothesis that there was an association between L-myc S allele in breast cancer

Ilhan Yaylim; Soykan Arîkan; Seden Küçücük; Hakan Çamlíca

2002-01-01

159

Molecular mapping of the mutant fap4(A24) allele for elevated palmitate concentration in soybean  

Technology Transfer Automated Retrieval System (TEKTRAN)

Soybean [Glycine max L. Merr.] oil with an elevated palmitate concentration is useful for some food and industrial applications. The objective of this study was to map the genetic location of the fap4(A24) allele that controls an increase in palmitate concentration and to identify molecular marker...

160

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

161

The structure of allelic diversity in the presence of purifying selection  

PubMed Central

In the absence of selection, the structure of equilibrium allelic diversity is described by the elegant sampling formula of Ewens. This formula has helped shape our expectations of empirical patterns of molecular variation. Along with coalescent theory, it provides statistical techniques for rejecting the null model of neutrality. However, we still do not fully understand the statistics of the allelic diversity expected in the presence of natural selection. Earlier work has described the effects of strongly deleterious mutations linked to many neutral sites, and allelic variation in models where offspring fitness is unrelated to parental fitness, but it has proven difficult to understand allelic diversity in the presence of purifying selection at many linked sites. Here, we study the population genetics of infinitely many perfectly linked sites, some neutral and some deleterious. Our approach is based on studying the lineage structure within each class of individuals of similar fitness in the deleterious mutation-selection balance. Consistent with previous observations, we find that for moderate and weak selection pressures, the patterns of allelic diversity cannot be described by a neutral model for any choice of the effective population site. We compute precisely how purifying selection at many linked sites distorts the patterns of allelic diversity, by developing expressions for the likelihood of any configuration of allelic types in a sample analogous to the Ewens sampling formula.

Desai, Michael M.; Nicolaisen, Lauren E.; Walczak, Aleksandra M.; Plotkin, Joshua B.

2013-01-01

162

Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes  

PubMed Central

In different eukaryotic model systems, chromatin and gene expression are modulated by post-translational modification of histone tails. In this in vivo study, histone methylation and acetylation are investigated along the imprinted mouse genes Snrpn, Igf2r and U2af1-rs1. These imprinted genes all have a CpG-rich regulatory element at which methylation is present on the maternal allele, and originates from the female germ line. At these ‘differentially methylated regions’ (DMRs), histone H3 on the paternal allele has lysine-4 methylation and is acetylated. On the maternally inherited allele, in contrast, chromatin is marked by hypermethylation on lysine-9 of H3. Allele-specific patterns of lysine-4 and lysine-9 methylation are also detected at other regions of the imprinted loci. For the DMR at the U2af1-rs1 gene, we establish that the methyl-CpG-binding-domain (MBD) proteins MeCP2, MBD1 and MBD3 are associated with the maternal allele. These data support the hypothesis that MBD protein-associated histone deacetylase/chromatin-remodelling complexes are recruited to the parental allele that has methylated DNA and H3-K9 methylation, and are prevented from binding to the opposite allele by H3 lysine-4 methylation.

Fournier, Cecile; Goto, Yuji; Ballestar, Esteban; Delaval, Katia; Hever, Ann M.; Esteller, Manel; Feil, Robert

2002-01-01

163

Expansion to full mutation of a FMR1 intermediate allele over two generations.  

PubMed

Fragile X syndrome is due to an expanded CGG repeat in the 5' UTR of the FMR1 gene. According to repeat size, we distinguish four allele categories: normal (<40 CGG), intermediate (46-60 CGG), premutated (55-200 CGG) and full mutated (>200 CGG). However, the boundaries among these categories are unclear, making it difficult to classify unstable alleles and to estimate the risk of expansion. We report a family with a proband, carrying a methylated full mutation with an amplification of 1.2 kb. PCR analysis demonstrated two alleles of 29 and 61 CGGs in the mother. Sequencing of the 61 CGG allele showed no AGG interruptions. Both mother's sisters had two alleles of 31 and 44 CGGs, and the daughter of one of these had two alleles of 22 and 44 repeats, demonstrating stable transmission of the 44 CGG allele. The maternal grandfather was deceased, but haplotype reconstruction using markers DXS548 and FRAXAC1 demonstrated that he was carrier of the premutated allele. Furthermore, molecular analysis confirmed the same paternity with a probability of 99.79% for all the three sisters. According to these findings, it is likely that the maternal grandfather carried the 44 CGG allele, showing unstable transmission, given that it expanded first to 61 CGGs in one daughter, and then to full mutation in her child. Although we cannot exclude paternal mosaicism, it is likely that a rare event of progression from an intermediate to a premutated and on to a full mutated allele occurred in this family over two generations. PMID:14735162

Terracciano, Alessandra; Pomponi, Maria Grazia; Marino, Grazia Maria Elisabetta; Chiurazzi, Pietro; Rinaldi, Maria Michela; Dobosz, Marina; Neri, Giovanni

2004-04-01

164

Allelic Analysis of Sheath Blight Resistance with Association Mapping in Rice  

PubMed Central

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.

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

165

The use of microsatellite markers for the detection of genetic similarity among winter bread wheat lines for chromosome 3A.  

PubMed

Previous studies with chromosome substitution and recombinant inbred chromosome lines identified that chromosome 3A of wheat cv. Wichita contains alleles that influence grain yield, yield components and agronomic performance traits relative to alleles on chromosome 3A of Cheyenne, a cultivar believed to be the founder parent of many Nebraska developed cultivars. This study was carried out to examine the genetic similarity among wheat cultivars based on the variation in chromosome 3A. Forty-eight cultivars, two promising lines and four substitution lines (in duplicate) were included in the study. Thirty-six chromosome 3A-specific and 12 group-3 barley simple sequence repeat (SSR) primer pairs were used. A total of 106 polymorphic bands were scored. Transferability of barley microsatellite markers to wheat was 73%. The coefficient of genetic distance (D) among the genotypes ranged from 0.40 to 0.91 and averaged D=0.66. Cluster analysis by the unweighted pair-group method with arithmetic averages showed one large and one small cluster with eight minor clusters in the large cluster. Several known pedigree relationships largely corresponded with the results of SSR clusters and principal coordinate analysis. Cluster analysis was also carried out by using 22 alleles that separate Wichita 3A from Cheyenne 3A, and three clusters were identified (a small cluster related to Cheyenne of mainly western Nebraska wheat cultivars; a larger, intermediate cluster with many modern Nebraska wheat cultivars; a large cluster related to Wichita with many modern high-yielding or Kansas wheat cultivars). Using three SSR markers that identify known agronomically important quantitative trait loci (QTL) regions, we again separated the cultivars into three main clusters that were related to Cheyenne or Wichita, or had a different 3A lineage. These results suggest that SSR markers linked to agronomically important QTLs are a valuable asset for estimating both genetic similarity for chromosome 3A and how the chromosome has been used in cultivar improvement. PMID:15290051

Mahmood, A; Baenziger, P S; Budak, H; Gill, K S; Dweikat, I

2004-07-29

166

Comparative analysis of Hoxa5 allelic series.  

PubMed

Analysis of the Hoxa5(-/-) mutants has revealed the critical role of Hoxa5 in survival, specification of axial identity, and ontogeny of organs, including the respiratory tract. The presence of the selection cassette in the original Hoxa5(-/-) mutation may interfere with the interpretation of the phenotypes. To circumvent this aspect and to bypass the lethality of the Hoxa5 mutation, we have designed a conditional approach and generated Hoxa5 allelic variants. The conditional allele (Hoxa5(floxed)) behaves as a wild-type allele. In contrast, both the Hoxa5(Delta) and the Hoxa5(floxneo) alleles are characterized by the loss of the functional transcript and protein, the lethality due to lung defects and the skeletal homeotic transformations similar to those of the Hoxa5(-/-) mutants. Analysis of neighboring Hox gene expression patterns in the Hoxa5 mutants produced further confirmed that the Hoxa5 allelic variants are true null alleles. PMID:17417799

Tabariès, Sébastien; Lemieux, Margot; Aubin, Josée; Jeannotte, Lucie

2007-04-01

167

Maximum likelihood estimation of individual inbreeding coefficients and null allele frequencies.  

PubMed

In this paper, we developed and compared several expectation-maximization (EM) algorithms to find maximum likelihood estimates of individual inbreeding coefficients using molecular marker information. The first method estimates the inbreeding coefficient for a single individual and assumes that allele frequencies are known without error. The second method jointly estimates inbreeding coefficients and allele frequencies for a set of individuals that have been genotyped at several loci. The third method generalizes the second method to include the case in which null alleles may be present. In particular, it is able to jointly estimate individual inbreeding coefficients and allele frequencies, including the frequencies of null alleles, and accounts for missing data. We compared our methods with several other estimation procedures using simulated data and found that our methods perform well. The maximum likelihood estimators consistently gave among the lowest root-mean-square-error (RMSE) of all the estimators that were compared. Our estimator that accounts for null alleles performed particularly well and was able to tease apart the effects of null alleles, randomly missing genotypes and differing degrees of inbreeding among members of the datasets we analysed. To illustrate the performance of our estimators, we analysed previously published datasets on mice (Mus musculus) and white-tailed deer (Odocoileus virginianus). PMID:22805896

Hall, Nathan; Mercer, Laina; Phillips, Daisy; Shaw, Jonathan; Anderson, Amy D

2012-07-18

168

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

169

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.).  

PubMed

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2-20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics. PMID:21384113

Gujaria, Neha; Kumar, Ashish; Dauthal, Preeti; Dubey, Anuja; Hiremath, Pavana; Bhanu Prakash, A; Farmer, Andrew; Bhide, Mangla; Shah, Trushar; Gaur, Pooran M; Upadhyaya, Hari D; Bhatia, Sabhyata; Cook, Douglas R; May, Greg D; Varshney, Rajeev K

2011-03-08

170

A genetic map of potato ( Solanum tuberosum ) integrating molecular markers, including transposons, and classical markers  

Microsoft Academic Search

A genetic map of potato (Solanum tuberosum L.) integrating molecular markers with morphological and isozyme markers was constructed using a backcross population of 67 diploid potato plants. A general method for map construction is described that differs from previous methods employed in potato and other outbreeding plants. First, separate maps for the female and male parents were constructed. The female

J. M. E. Jacobs; H. J. Van Eek; P. F. P. Arens; B. Verkerk-Bakker; B. te Lintel Hekkert; H. J. M. Bastiaanssen; A. El-Kharbotly; A. Pereira; E. Jacobsen; W. J. Stiekema

1995-01-01

171

Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences  

PubMed Central

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker’s sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known.

Barthe, Stephanie; Gugerli, Felix; Barkley, Noelle A.; Maggia, Laurent; Cardi, Celine; Scotti, Ivan

2012-01-01

172

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays  

Microsoft Academic Search

Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and\\/or increase the number of individuals contribut- ing to a study where hundreds of thousands of genetic markers need to be genotyped in very large popula- tions sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from

Jesper Brohede; Rob Dunne; James D. McKay; Garry N. Hannan

2005-01-01

173

RAPD MARKERS LINKED TO EASTERN FILBERT BLIGHT RESISTANCE IN CORYLUS AVELLANA  

Technology Transfer Automated Retrieval System (TEKTRAN)

A total of 1420 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 additional markers linked in repulsion were fou...

174

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers  

Microsoft Academic Search

Genetic diversity of 36 rice entries from the United States Department of Agriculture (USDA) rice collection was assessed using 103 ILP (intron length polymorphism) and 54 SSR (simple sequence repeats) markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number

Ming HUANG; Fang-min XIE; Li-yun CHEN; Xiang-qian ZHAO; L. JOJEE; D. MADONNA

2010-01-01

175

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

176

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

177

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

178

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…

Smith, Richard

2010-01-01

179

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

180

A limited association of generalized osteoarthritis with alleles at the type II collagen locus: COL2A1.  

PubMed

A significant genetic influence in osteoarthritis has been observed in the combination of Heberden's nodes and generalized osteoarthritis. We examined whether mutation in the gene encoding the major cartilage matrix protein type II collagen was responsible by comparing allele frequencies at the locus (COL2A1) in a group of 61 patients with nodal GOA with a control population and by analysing the COL2A1 genotypes of 21 affected sibling pairs. There were no significant allele differences but a slightly increased tendency over chance alone for affected siblings to have inherited the same COL2A1 alleles from their parents. PMID:1863823

Priestley, L; Fergusson, C; Ogilvie, D; Wordsworth, P; Smith, R; Pattrick, M; Doherty, M; Sykes, B

1991-08-01

181

Allelic loss mapping and physical delineation of a region harboring a putative thymic lymphoma suppressor gene on mouse chromosome 12  

Microsoft Academic Search

Our previous allelic loss analysis of ?-ray induced thymic lymphomas in F1 hybrid and backcross mice between BALB\\/c and MSM strains mapped the Tlsr4 region exhibiting a high frequency of allelic loss (62%) to a 2.9 cM interval between the markers D12Mit53 and D12Mit279 on mouse chromosome 12. To narrow further the interval harboring a putative tumor suppressor gene, a

Toshimitsu Shinbo; Atsushi Matsuki; Yasuo Matsumoto; Shin-ichi Kosugi; Yoshiaki Takahashi; Ohtsura Niwa; Ryo Kominami

1999-01-01

182

A comparison of the effects of parental risk markers on pre- and perinatal variables in multiple patient cohorts with fetal alcohol syndrome, autism, Tourette syndrome, and sudden infant death syndrome: an enviromic analysis  

Microsoft Academic Search

The prevalence and magnitude of effect of individual risk markers for specific developmental disorders vary widely across diagnostic category. The four study cohorts for this project were patients from four diagnostic registries in North Dakota for fetal alcohol syndrome (FAS), autism, sudden infant death syndrome (SIDS), and Tourette syndrome. These four cohorts were used to estimate prevalence and magnitude of

Marilyn G. Klug; Larry Burd; Jacob Kerbeshian; Becky Benz; John T. Martsolf

2003-01-01

183

Multiple Origins of Plasmodium falciparum Dihydropteroate Synthetase Mutant Alleles Associated with Sulfadoxine Resistance in India?†  

PubMed Central

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 (He) around mutant dhps alleles (He = 0.55; n = 81) associated with sulfadoxine resistance was lower (P ? 0.05) than the mean He around the wild-type dhps allele (He = 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.

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

2011-01-01

184

Caution! Analyze transcripts from conditional knockout alleles.  

PubMed

A common strategy for conditional knockout alleles is to "flox" (flank with loxP sites) a 5' exon within the target gene. Typically, the floxed exon does not contain a unit number of codons so that the Cre-mediated recombination event yields a frameshift and a null allele. Documenting recombination within the genomic DNA is often regarded as sufficient proof of a frameshift, and the analysis of transcripts is neglected. We evaluated a previously reported conditional knockout allele for the beta-subunit of protein farnesyltransferase. The recombination event in that allele-the excision of exon 3-was predicted to yield a frameshift. However, following the excision of exon 3, exon 4 was skipped by the mRNA splicing machinery, and the predominant transcript from the mutant allele lacked exon 3 and exon 4 sequences. The "Deltaexon 3-4 transcript" does not contain a frameshift but rather is predicted to encode a protein with a short in-frame deletion. This represents a significant concern when studying an enzyme, since an enzyme with partial function could lead to erroneous conclusions. With thousands of new conditional knockout alleles under construction within mouse mutagenesis consortiums, the protein farnesyltransferase allele holds an important lesson-to characterize knockout alleles at both the DNA and RNA levels. PMID:19093225

Yang, Shao H; Bergo, Martin O; Farber, Emily; Qiao, Xin; Fong, Loren G; Young, Stephen G

2008-12-18

185

Caution! Analyze transcripts from conditional knockout alleles  

PubMed Central

A common strategy for conditional knockout alleles is to “flox” (flank with loxP sites) a 5? exon within the target gene. Typically, the floxed exon does not contain a unit number of codons so that the Cre-mediated recombination event yields a frameshift and a null allele. Documenting recombination within the genomic DNA is often regarded as sufficient proof of a frameshift, and the analysis of transcripts is neglected. We evaluated a previously reported conditional knockout allele for the ?-subunit of protein farnesyltransferase. The recombination event in that allele—the excision of exon 3—was predicted to yield a frameshift. However, following the excision of exon 3, exon 4 was skipped by the mRNA splicing machinery, and the predominant transcript from the mutant allele lacked exon 3 and exon 4 sequences. The “?exon 3–4 transcript” does not contain a frameshift but rather is predicted to encode a protein with a short in-frame deletion. This represents a significant concern when studying an enzyme, since an enzyme with partial function could lead to erroneous conclusions. With thousands of new conditional knockout alleles under construction within mouse mutagenesis consortiums, the protein farnesyltransferase allele holds an important lesson—to characterize knockout alleles at both the DNA and RNA levels.

Yang, Shao H.; Bergo, Martin O.; Farber, Emily; Qiao, Xin; Fong, Loren G.; Young, Stephen G.

2008-01-01

186

Generation of new Notch2 mutant alleles  

Microsoft Academic Search

The Notch signaling pathway is an evolutionarily conserved intercellular signaling mechanism, and mutations in its components disrupt embryonic development in many organisms and cause inherited diseases in humans. We previously described construction and analysis of a hypomorphic allele of the Notch2 gene. Homozygosity for this allele leads to embryonic and perinatal lethality due to cardiovascular and kidney defects. We report

B McCright; J Lozier; T Gridley

2006-01-01

187

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

188

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

189

Identification of transcriptome SNPs for assessing allele-specific gene expression in a super-hybrid rice Xieyou9308.  

PubMed

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. PMID:23613738

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

2013-04-17

190

Generation of new Notch2 mutant alleles.  

PubMed

The Notch signaling pathway is an evolutionarily conserved intercellular signaling mechanism, and mutations in its components disrupt embryonic development in many organisms and cause inherited diseases in humans. We previously described construction and analysis of a hypomorphic allele of the Notch2 gene. Homozygosity for this allele leads to embryonic and perinatal lethality due to cardiovascular and kidney defects. We report here novel Notch2 mutant alleles generated by gene targeting in embryonic stem cells, including a conditional null allele in which exon 3 of the Notch2 gene is flanked by loxP sequences. These new Notch2 mutant alleles expand the set of tools available for studying the myriad roles of the Notch pathway during mammalian development and will enable analysis of Notch2 function at additional stages of embryogenesis and in adult mice. PMID:16397869

McCright, Brent; Lozier, Julie; Gridley, Thomas

2006-01-01

191

Marker-assisted selection for early-season cold tolerance in sorghum: QTL validation across populations and environments.  

PubMed

Sorghum [Sorghum bicolor (L.) Moench] landraces from China generally exhibit excellent emergence and seedling vigor under cool conditions, and are being used as sources of genes for improvement of seedling cold tolerance in other cultivars. Marker-assisted selection (MAS) could expedite the introgression of genes from landraces into elite lines, however, only a few studies have empirically demonstrated efficacy of MAS for quantitatively inherited agronomic traits. In a preceding study we identified quantitative trait loci (QTL) for early-season performance in a recombinant inbred (RI) population, one parent of which was a cold-tolerant Chinese line, 'Shan Qui Red' (SQR). In this study, three SSR markers (Xtxp43, Xtxp51, and Xtxp211), each representing a QTL, were tested in two new populations: (Tx2794 x SQR F(3)) and (Wheatland x SQR BC(1)F(3)). Individual families were genotyped, and early-season field performance was measured for two years. Statistical analyses showed that the SQR allele of Xtxp43 had favorable effects on seedling vigor in both populations, and on emergence in the Tx2794 population. A large positive effect of the SQR allele of Xtxp51 was observed in the Tx2794 population for vigor and emergence. Slight genotype by environment interaction was observed for Xtxp51 in the Wheatland population. Marker Xtxp211 had small but significant effects on seedling vigor and emergence in both populations. Various interactions between loci were also significant. This study validated QTL markers in various genetic backgrounds, and demonstrated the utility of MAS for a quantitative trait, early-season cold tolerance, evaluated in the field. PMID:18092147

Knoll, Joseph; Ejeta, Gebisa

2007-12-19

192

Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.  

PubMed

Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within-locus polymorphism is not known. PMID:22808236

Barthe, Stéphanie; Gugerli, Felix; Barkley, Noelle A; Maggia, Laurent; Cardi, Céline; Scotti, Ivan

2012-07-13

193

The Interplay between Parental Monitoring and the Dopamine D4 Receptor Gene in Adolescent Cannabis Use  

PubMed Central

Background Both environmental risk and genetic variation is believed to play a role in substance use. A candidate environmental variable is parenting. Recent studies have found support for the idea that the dopamine system affects the susceptibility to environmental influences. In the present study we will examine the interplay between effects of parental monitoring and the presence of the DRD4 7-repeat allele in adolescent lifetime cannabis use and the developmental course of cannabis use. Methods A total of 311 adolescents participated in a five-wave longitudinal design. First, we conducted logistic regression analyses to examine the prospective associations between parental monitoring, the DRD4 polymorphism, their interaction and lifetime cannabis use. Second, individual growth parameters were calculated for frequency of cannabis use. Linear regression was used to assess the relationship between parental monitoring, the DRD4 polymorphism, their interaction, and the frequency of cannabis use. Results There were no significant main effects of parental monitoring or the DRD4 polymorphism. However, both analyses showed that over a period of four years, a) when experiencing low levels of parental monitoring, individuals with the 7-repeat allele were more likely to show lifetime cannabis use and a stronger increase in frequency of cannabis use than individuals without this allele; b) when experiencing high levels of parental monitoring, individuals with the 7-repeat allele were less likely to show lifetime cannabis use and they showed a smaller increase in frequency of cannabis use than individuals without the 7-repeat allele. Conclusions This study shows that carriers of the DRD4 7-repeat allele are disproportionally affected by the negative and positive effects of parental monitoring such that carriers of the DRD4 7-repeat allele, as compared to non-carriers, are more likely to use cannabis when levels of parental monitoring are low, and less likely to use cannabis when parental monitoring levels are high.

Otten, Roy; Barker, Edward D.; Huizink, Anja C.; Engels, Rutger C. M. E.

2012-01-01

194

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

195

Testing the rare-alleles model of quantitative variation by artificial selection  

PubMed Central

The rare-alleles model of quantitative variation posits that a common allele (the `wild-type') and one or more rare alleles segregate at each locus affecting a quantitative trait; a scenario predicted by several distinct evolutionary hypotheses. Single locus arguments suggest that artificial selection should substantially increase the genetic variance (Vg) if the rare-alleles model is accurate. This paper tests the `?Vg prediction' using a large artificial selection experiment on flower size of Mimulus guttatus. Vg for flower size does evolve, increasing with selection for larger flower while decreasing in the other direction. These data are consistent with a model in which flower size variation is caused by rare, partially dominant alleles. However, this explanation becomes increasingly tenuous when considered with other data (correlated responses to selection and the effects of inbreeding). A combination of modern (marker-based mapping) and classical (biometric) techniques will likely to be required to determine the distribution of allele frequencies at loci influencing quantitative traits.

Kelly, John K.

2009-01-01

196

Survey of allelic expression using EST mining  

PubMed Central

Cis-acting allelic variation in gene regulation is a source of phenotypic variation. Consequently, recent studies have experimentally screened human genes in an attempt to initiate a catalog of genes possessing cis-acting variants. In this study, we use human EST data in dbEST as the source of allelic expression data, and the HapMap database to provide expected allele frequencies in human populations. We demonstrate a greater concordance of allele frequencies estimated from human ESTs in dbEST with those derived from the CEPH HapMap sample representing Caucasians from northern and western Europe, than population samples obtained in Asia and Africa. Deviations between allele frequencies observed in EST databases and the ones obtained from the CEPH HapMap samples may result from common heritable cis-acting variants altering the relative allele distribution in RNA. We provide in silico as well as experimental evidence that this strategy does allow significant enrichment of genes harboring common heritable cis-acting polymorphisms in linkage disequilibrium with expressed alleles.

Ge, Bing; Gurd, Scott; Gaudin, Tiffany; Dore, Carole; Lepage, Pierre; Harmsen, Eef; Hudson, Thomas J.; Pastinen, Tomi

2005-01-01

197

Characterization of the treefrog null allele  

SciTech Connect

As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

Guttman, S.I. (Miami Univ., Oxford, OH (USA). Dept. of Zoology)

1990-12-01

198

Identification of repeat sequence heterogeneity at the polymorphic short tandem repeat locus HUMTH01[AATG][sub n] and reassignment of alleles in population analysis by using a locus-specific allelic ladder  

SciTech Connect

An allelic ladder containing amplified sequences of seven alleles of the polymorphic human tyrosine hydroxylase locus, HUMTH01, was constructed and employed as a standard marker. Sequence analysis of each ladder component indicates that fragments differ by integral multiples of the AATG core repeat sequence characteristic of this locus. Individual alles are designated [open quotes]5[close quotes] through [open quotes]11,[close quotes] according to the number of complete reiterations of the core repeat contained within them. Comparison of the HUMTH01 allelic ladder with DNA samples amplified at this locus revealed core repeat length heterogeneity (i.e., deletions or insertions shorter than one core repeat) within the human population. In particular, a common allele was identified which migrates more quickly than allele 10, but more slowly than allele 9, on electrophoresis through a denaturing polyacrylamide gel. Sequence analysis of this allele, designated [open quotes]10-1,[close quotes] reveals lack of a single adenine normally present in the seventh copy of the AATG. The allelic ladder was used to reevaluate previously published population data. Results of testing for Hardy-Weinberg equilibrium and population substructure were not altered significantly by these modifications. 29 refs., 1 fig., 3 tabs.

Puers, C. (Institute for Forensic Medicine, Muenster (Germany)); Schumm, J.W. (Promega Corp., Madison, WI (United States)); Hammond, H.A.; Caskey, C.T.; Jin, L.

1993-10-01

199

Assessment of genetic diversity and relationships among Coix lacryma-jobi accessions using microsatellite markers  

Microsoft Academic Search

The present study describes the assessment of genetic diversity and relationships among 79 Job’s tears (Coix lacrymajobi L.) accessions collected from China and Korea using 17 microsatellite markers. A total of 57 alleles were detected with an\\u000a average of 3.4 alleles per locus. A high frequency of rare alleles (36.3 %) was observed within the collection. Values for\\u000a observed (HO),

K.-H. Ma; K.-H. Kim; A. Dixit; I.-M. Chung; J.-G. Gwag; T.-S. Kim; Y.-J. Park

2010-01-01

200

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans  

PubMed Central

The extent to which variation in chromatin structure and transcription factor binding may influence gene expression, and thus underlie or contribute to variation in phenotype, is unknown. To address this question, we cataloged both individual-to-individual variation and differences between homologous chromosomes within the same individual (allele-specific variation) in chromatin structure and transcription factor binding in lymphoblastoid cells derived from individuals of geographically diverse ancestry. Ten percent of active chromatin sites were individual-specific; a similar proportion were allele-specific. Both individual-specific and allele-specific sites were commonly transmitted from parent to child, which suggests that they are heritable features of the human genome. Our study shows that heritable chromatin status and transcription factor binding differ as a result of genetic variation and may underlie phenotypic variation in humans.

McDaniell, Ryan; Lee, Bum-Kyu; Song, Lingyun; Liu, Zheng; Boyle, Alan P.; Erdos, Michael R.; Scott, Laura J.; Morken, Mario A.; Kucera, Katerina S.; Battenhouse, Anna; Keefe, Damian; Collins, Francis S.; Willard, Huntington F.; Lieb, Jason D.; Furey, Terrence S.; Crawford, Gregory E.; Iyer, Vishwanath R.; Birney, Ewan

2010-01-01

201

Development and Characterization of Novel, Polymorphic Microsatellite Markers for Oat Crown Rust, Puccinia coronata  

Technology Transfer Automated Retrieval System (TEKTRAN)

We report the development of 37 novel and polymorphic microsatellite markers for oat crown rust, Puccinia coronata. The allelic diversity ranged from 2 to 16 alleles per locus. Observed heterozygosity ranged from 0.000 to 0.971, and expected heterozygosity ranged from 0.057 to 0.848. Twenty-two of t...

202

Genetic Structure of Wild Rice Oryza Glumaepatula Populations in Three Brazilian Biomes Using Microsatellite Markers  

Microsoft Academic Search

The existence of Oryza glumaepatula is threatened by devastation and, thus, the implementation of conservation strategies is extremely relevant. This study aimed to characterize the genetic variability and estimate population parameters of 30 O. glumaepatula populations from three Brazilian biomes using 10 microsatellite markers. The levels of allelic variability for the SSR loci presented a mean of 10.3 alleles per

Rosana Pereira Vianello Brondani; Maria Imaculada Zucchi; Claudio Brondani; Paulo Hideo Nakano Rangel; Tereza Cristina De Oliveira Borba; Priscila Nascimento Rangel; Mara Rubia Magalhães; Roland Vencovsky

2005-01-01

203

Analysis of forensically used autosomal short tandem repeat markers in Polish and neighboring populations  

Microsoft Academic Search

The purpose of this study was to evaluate the homogeneity of Polish populations with respect to STRs chosen as core markers of the Polish Forensic National DNA Intelligence Database, and to provide reference allele frequencies and to explore the genetic interrelationship between Poland and neighboring countries. The allele frequency distribution of 10 STRs included in the SGMplus kit was analyzed

Ireneusz Soltyszewski; Andrzej Plocienniczak; Hans Åke Fabricius; Igor Kornienko; Dmitrij Vodolazhsky; Walther Parson; Roman Hradil; Hermann Schmitter; Pavel Ivanov; Piotr Kuzniar; Boris A. Malyarchuk; Tomasz Grzybowski; Marcin Wo?niak; J?rgen Henke; Lotte Henke; Sergiv Olkhovets; Vladimir Voitenko; Vita Lagus; Andrej Ficek; Gabriel Minárik; Peter de Knijff; Krzysztof R?ba?a; Joanna Wysocka; Ewa Kapi?ska; Lidia Cybulska; Alexei I. Mikulich; Iosif S. Tsybovsky; Zofia Szczerkowska; Pawe? Krajewski; Rafa? Ploski

2008-01-01

204

Neutrality of miniSTR D22S1045 marker by Ewing's sarcoma phenotype.  

PubMed

Neutrality investigations of markers with forensic use are important to see if a phenotypic trait is being expressed in relation to the alleles of the marker. MiniSTR marker D22S1045 (locus 22q12.3) is localized near the breakpoint region of the EWS gene (22q12.2), which leads to the development of Ewing's Sarcoma. Analyzing allele frequencies and linkage disequilibrium in Ewing's sarcoma patients and non-affected populations, we found that the marker mD22S1045 was neutral when related to Ewing's Sarcoma. PMID:24112992

Silva, Deborah S B S; Raimann, Paulo E; Moro, Tatiane; Picanço, Juliane B; Abujamra, Ana L; de Farias, Caroline B; Roesler, Rafael; Brunetto, Algemir L; Alho, Clarice S

2013-09-10

205

Allelic diagnosis of susceptibility to compulsive disorder  

US Patent & Trademark Office Database

In an important embodiment, the present invention concerns a method for diagnosing and detecting compulsive disorder susceptibility of an individual. The method comprises initially obtaining a DNA sample of said individual and then determining the presence or absence of particular human D.sub.2 receptor gene alleles in said sample. Detection of said alleles in the sample are indicative of predilection to compulsive disorder. A most preferred embodiment is to detect predisposition to impulsive, addictive, and compulsive disorders such as, but not limited to, alcoholism, obesity, smoking, polysubstance abuse and drug addiction, particularly because said alleles have been found to be present in a majority of individuals clinically diagnosed with these compulsive disorders. The human D.sub.2 receptor gene A1, B1, and .sup.In6-Ex7 haplotype I alleles are most preferably detected in said sample.

1996-08-27

206

Characterization of the treefrog null allele, 1991.  

National Technical Information Service (NTIS)

Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was fou...

S. I. Guttman

1992-01-01

207

Brazilian population profile of 15 STR markers.  

PubMed

Allele frequencies for 15 STR markers included in the AmpFISTR Identifiler kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, and FGA) were obtained from a sample of 561 unrelated individuals from São Paulo, Brazil. PMID:19083795

Fridman, Cintia; dos Santos, Paulo César Costa; Kohler, Priscila; Garcia, Claudia Figaro; Lopez, Luis Fernandez; Massad, Eduardo; Gattás, Gilka Jorge Figaro

2007-11-19

208

Protein markers for anther culturability in barley  

Microsoft Academic Search

Two-dimensional electrophoresis of proteins from a recombinant population of anther culture-derived doubled haploid lines identified 4 loci or linkage groups showing a deviation from an expected 1:1 segregation. It was hypothesized that these markers are linked to genes involved in the process of haploid plant production and that the deviation was due to a selection for alleles conferring higher anther

P. Devaux; M. Zivy

1994-01-01

209

Efficiency of typing unaffected relatives in an affected-sib-pair linkage study with single-locus and multiple tightly linked markers  

SciTech Connect

In an affected-sib-pair study, the parents are often unavailable for typing, particularly for diseases of late onset. In many cases, however, it is possible to sample unaffected siblings. It is therefore desirable to assess the contribution of such siblings to the power of such a study. The likelihood ratio introduced by Risch and improved by Holmans was extended to incorporate data from unaffected siblings. Tests based on two likelihoods were considered: the full likelihood of the data, based on the identity-by-descent (IBD) sharing states of the entire sibship, and a pseudolikelihood based on the IBD sharing states of the affected pair only, using the unaffected siblings to infer parental genotypes. The latter approach was found to be more powerful, except when penetrance was high. Typing an unaffected sibling, or just one parent, was found to give only a small increase in power except when the PIC of the marker was low. Even then, typing an unaffected relative increased the overall number of individuals that had to be typed to achieve a given power. If there is no highly informative marker locus in the area under study, it may be possible to {open_quotes}build{close_quotes} one by combining the alleles from two or more neighboring tightly linked loci into haplotypes. Typing two loci gave a sizeable power increase over a single locus, but typing further loci gave much smaller gains. Building haplotypes will introduce phase uncertainties, with the result that such a system will yield less power than will a single locus with the same number of alleles. This power loss was small, however, and did not affect the conclusions regarding the worth of typing unaffected relatives. 14 refs., 2 figs., 11 tabs.

Holmans, P.; Clayton, D.

1995-11-01

210

Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders  

PubMed Central

Background Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders. Results At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (GNAT1) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects. Conclusion While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.

Fitzpatrick, Benjamin M; Johnson, Jarrett R; Kump, D Kevin; Shaffer, H Bradley; Smith, Jeramiah J; Voss, S Randal

2009-01-01

211

Linking Parent to Parent: A Case Study.  

ERIC Educational Resources Information Center

Describes an innovative approach to building a school community taking hold at a Winston-Salem, North Carolina, elementary school. Called Parents in Partnership, the program uses a Big Brother/Big Sister model to link parents of incoming kindergarten children with more experienced parents at the school. The parents form informal, personal networks…

Oberle, Sylvia Ingle

1991-01-01

212

Parenting Matters: What Works in Parenting Education?  

ERIC Educational Resources Information Center

Because the expansion of parenting education is likely to continue, it is important to ensure that methods involved in parenting education are effective. This report summarizes research on the effectiveness of parenting education and provides information to help practitioners develop methods of working with parents that are based on sound research…

Lloyd, Eva, Ed.

213

Parent-Teacher Conferences: Suggestions for Parents  

Microsoft Academic Search

Parent-teacher conferences sometimes become a cause for concern for everyone involved—children, parents, and teachers. Children just beginning their school experience may be wary of the idea of parents and teachers talking about them behind closed doors. Parents may feel uncomfortable about going inside their child's classroom, sitting in small chairs, and listening to reports of their child's conduct and class

Ann-Marie Clark; ERIC DIGEST

214

Chinese Parenting Reconsideration: Parenting Practices in Taiwan.  

ERIC Educational Resources Information Center

|This study examined authoritative and authoritarian parenting and specific parenting practices among Chinese mothers with preschoolers. The final sample consisted of 463 mothers with their 3 to 7 year-olds from 11 preschools, in Taiwan. Mothers completed a Chinese translation of the Parenting Behavior Questionnaire that assessed their parenting

Chen, Fu-mei; Luster, Tom

215

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

Microsoft Academic Search

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.

Hiroshi Yoneda; Toshiaki Sakai; Toru Ishida; Yasuhiro Inayama; Yasuhiro Nonomura; Yoshihiro Kono; Hiroyuki Asaba

1992-01-01

216

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

217

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

218

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

219

Gene identification and allele-specific marker development for two allelic low phytic acid mutations in rice ( Oryza sativa L.)  

Microsoft Academic Search

Phytic acid (PA, myo-inositol 1,2,3,4,5,6-hexakisphosphate) is an important anti-nutritional component in cereal and legume grains. PA forms of phosphorus (P) and its salts\\u000a with micronutrient cations, such as iron and zinc, are indigestible in humans and non-ruminant animals, and hence could affect\\u000a food\\/feed nutritional value and cause P pollution of ground water from animal waste. We previously developed a set

Hai-Jun Zhao; Qing-Long Liu; Xue-Liang Ren; Dian-Xing Wu; Qing-Yao Shu

2008-01-01

220

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

221

Chromosome 11q in sporadic colorectal carcinoma: patterns of allele loss and their significance for tumorigenesis.  

PubMed Central

AIMS: To analyse the frequency of loss of heterozygosity (allele loss, LOH) in a large sample of colorectal carcinomas using highly informative markers along chromosome 11q. METHODS: One hundred paired samples of colorectal cancer and normal tissue were genotyped at six microsatellite markers on chromosome 11q (cen-D11S1313-D11S901-DRD2/NCAM-D11S29- D11S968-tel). The high levels of heterozygosity at these markers allow allele loss to be determined in about 80% of cases at any one locus. The frequency of replication errors (RERs, microsatellite instability) has also been determined. RESULTS: LOH was found at frequencies of 25% and 29% at the distal D11S968 (11qter) and D11S29 (11q23.3) loci, slightly above the accepted baseline of 0-20%. Allele loss at NCAM, DRD2, D11S901, and D11S1313 was not raised above baseline levels. The probable genetic mechanism of allele loss--chromosomal non-disjunction, mitotic recombination, deletion, or gene conversion--seemed to vary between tumours and no consistent mechanism of mutation was found. Microsatellite instability was found in 23 (23%) tumours. No associations were found between LOH and clinical data (patient sex, age at presentation, tumour site, and Duke's stage). CONCLUSIONS: Although gene(s) on 11q may have a role in the development of a minority of colorectal carcinomas, this study provides evidence against the general importance of allele loss on chromosome 11q in the pathogenesis of colorectal cancer. The results also have implications for the importance of 11q in other cancers: it seems less likely that a single tumour supressor gene at this location promotes the growth of all types of tumour when lost. Rather, one or more genes with tissue specific effects may be involved. Images

Tomlinson, I P; Bodmer, W F

1996-01-01

222

Apolipoprotein E4 allele as a predictor of cholinergic deficits and treatment outcome in Alzheimer disease.  

PubMed Central

Apolipoprotein E (apoE) is critical in the modulation of cholesterol and phospholipid transport between cells of different types. Human apoE is a polymorphic protein with three common alleles, APO epsilon 2, APO epsilon 3, and APO epsilon 4. ApoE4 is associated with sporadic and late-onset familial Alzheimer disease (AD). Gene dose was shown to have an effect on risk of developing AD, age of onset, accumulation of senile plaques in the brain, and reduction of choline acetyltransferase (ChAT) activity in the hippocampus of AD subjects. To characterize the possible impact of the apoE4 allele on cholinergic markers in AD, we examined the effect of apoE4 allele copy number on pre- and postsynaptic markers of cholinergic activity. ApoE4 allele copy number showed an inverse relationship with residual brain ChAT activity and nicotinic receptor binding sites in both the hippocampal formation and the temporal cortex of AD subjects. AD cases lacking the apoE4 allele showed ChAT activities close or within age-matched normal control values. The effect of the apoE4 allele on cholinomimetic drug responsiveness was assessed next in a group (n = 40) of AD patients who completed a double-blind, 30-week clinical trial of the cholinesterase inhibitor tacrine. Results showed that > 80% of apoE4-negative AD patients showed marked improvement after 30 weeks as measured by the AD assessment scale (ADAS), whereas 60% of apoE4 carriers had ADAS scores that were worse compared to baseline. These results strongly support the concept that apoE4 plays a crucial role in the cholinergic dysfunction associated with AD and may be a prognostic indicator of poor response to therapy with acetylcholinesterase inhibitors in AD patients. Images Fig. 2

Poirier, J; Delisle, M C; Quirion, R; Aubert, I; Farlow, M; Lahiri, D; Hui, S; Bertrand, P; Nalbantoglu, J; Gilfix, B M

1995-01-01

223

Allele frequencies of 14 STR loci in the population of Malta.  

PubMed

Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest power of discrimination (PD) values while TPOX was the least informative marker. Allele frequencies observed in the Maltese population were also compared with those of other populations from the Mediterranean region, Europe and Africa. Our data is useful for anthropological and other comparative studies of populations and is powerful for forensic and paternity testing in the Maltese islands. PMID:18039589

Cassar, M; Farrugia, C; Vidal, C

2007-11-26

224

Haplotype study of intermediate-length alleles at the fragile X (FMR1) gene: ATL1, FMRb, and microsatellite haplotypes differ from those found in common-size FMR1 alleles.  

PubMed

The CGG repeat within the X-chromosome-linked FMR1 gene, which in hyperexpansion (> 200 copies) results in fragile X syndrome, is highly polymorphic. The mechanism of expansion is not well understood, but CGG repeats called intermediate-length or gray zone alleles (approximately equal 35-60 repeats) are thought to make up the FMR1 alleles showing initial steps in this expansion process. It has been hypothesized that the background haplotype of these alleles plays a role in their susceptibility to expansion. In this study we investigate whether or not the frequencies of alleles and haplotypes at four marker loci in the FMR1 gene region (microsatellites DXS548 and FRAXAC1 and SNPs ATL1 and FMRb) in 84 intermediate-length male chromosomes differ from those in 94 common-size male alleles. The ATL1*G and FMRB*A alleles were more frequent among intermediate-length alleles than among common alleles. In addition, the DXS548-FRAXAC1 T50-T42 and T40-T42 haplotypes were strongly associated with intermediate-length alleles between 41 and 60 CGG repeats (p < 0.001). Two extended haplotypes, DXS548-FRAXAC1-ATL1-FMRb T50-T42-G-A and T40-T42-G-A, are strongly associated (p < 0.001) with intermediate-length alleles between 41 and 60 CGG repeats, and these haplotypes have also been reported as fragile X associated haplotypes in European populations. These data suggest that these haplotypes are among the most susceptible to further expansion among the intermediate-length alleles. T50-T42-G-A was also much more prevalent in males with 35-40 CGG repeats than in males with common-size alleles. ATL1 did not increase discrimination among intermediate-length alleles beyond that detected by DXS548-FRAXAC1 haplotypes, but the FMRb locus did, particularly for the DXS548-FRAXAC1-ATL1 T50-T42-G and T40-T42-G haplotypes. Comparison with fragile X associated haplotypes, from the literature, suggests that repeat hyperexpansion occurs most frequently on chromosomes carrying FMRB*A. Within the intermediate-length allele category, however, there were some significant differences in haplotype frequencies between smaller and larger alleles, and this finding has implications for future studies. PMID:16114822

Curlis, Yvette; Zhang, Cuiling; Holden, Jeanette J A; Loesch, P Ken Kirkby Danuta; Mitchell, R John

2005-02-01

225

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

2012-12-06

226

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

227

Allelic losses and DNA methylation at DNA mismatch repair loci in sporadic colorectal cancer  

Microsoft Academic Search

Normal and tumor DNA samples of 35 patients with sporadic colorectal carcinoma were analyzed for micro- satellite alterations at 12 markers linked to mismatch repair loci: hMLH1, hMSH2, hMSH3, hMSH6, hPMS1 and hPMS2. Remarkably, no correlation was observed between the replication error phenotype (RERF) and allelic losses at these loci. Hemizygous deletions, seen in 6\\/35 (17%) informative cases at hMLH1,

N. Benachenhou; S. Guiral; I. Gorska-Flipot; R. Michalski; D. Labuda; D. Sinnett

1998-01-01

228

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

229

Allele-Biased Expression in Differentiating Human Neurons: Implications for Neuropsychiatric Disorders  

PubMed Central

Stochastic processes and imprinting, along with genetic factors, lead to monoallelic or allele-biased gene expression. Stochastic monoallelic expression fine-tunes information processing in immune cells and the olfactory system, and imprinting plays an important role in development. Recent studies suggest that both stochastic events and imprinting may be more widespread than previously considered. We are interested in allele-biased gene expression occurring in the brain because parent-of-origin effects suggestive of imprinting appear to play a role in the transmission of schizophrenia (SZ) and autism spectrum disorders (ASD) in some families. In addition, allele-biased expression could help explain monozygotic (MZ) twin discordance and reduced penetrance. The ability to study allele-biased expression in human neurons has been transformed with the advent of induced pluripotent stem cell (iPSC) technology and next generation sequencing. Using transcriptome sequencing (RNA-Seq) we identified 801 genes in differentiating neurons that were expressed in an allele-biased manner. These included a number of putative SZ and ASD candidates, such as A2BP1 (RBFOX1), ERBB4, NLGN4X, NRG1, NRG3, NRXN1, and NLGN1. Overall, there was a modest enrichment for SZ and ASD candidate genes among those that showed evidence for allele-biased expression (chi-square, p?=?0.02). In addition to helping explain MZ twin discordance and reduced penetrance, the capacity to group many candidate genes affecting a variety of molecular and cellular pathways under a common regulatory process – allele-biased expression – could have therapeutic implications.

Lin, Mingyan; Hrabovsky, Anastasia; Pedrosa, Erika; Wang, Tao; Zheng, Deyou; Lachman, Herbert M.

2012-01-01

230

Allelic discrimination of the Restorer-of-fertility gene and its inheritance in peppers (Capsicum annuum L.).  

PubMed

Cytoplasmic male sterility (CMS), one of the most important traits in crop breeding, is used for commercial F(1)-hybrid seed production in peppers (Capsicum annuum L.). A nuclear gene, Restorer-of-fertility (Rf), can induce normal pollen production in CMS plants resulting in fertility. Since the first report of fertility restoration in peppers, various inheritance modes have been suggested, including the presence of a third haplotype of the locus. The pepper Rf gene has not been cloned, and calculated genetic distances of linked markers have varied between research groups. A more precise allelic test and additional genetic mapping are needed to accurately select recombinants for use in marker-assisted backcrossing (MAB). Therefore, the reliability and application of these markers for allelic selection of the Rf gene was tested. Two different F(2) populations, Buja and Tamna, were used for the construction of a linkage map. From these linkage groups, anew closely linked flanking marker of the Rf gene were identified. Previous allelic testing revealed the existence of a third haplotype, Rfls(7701), which can function as dominant (Rf) or recessive (rf). In a previous report, Rfls(7701) was considered to be linked to unstable male sterility (MS). However, our results suggest that unstable MS was induced by a gene residing at another locus rather than by Rfls(7701) haplotype- linked allele. PMID:19727656

Min, Woong-Ki; Kim, Sunggil; Sung, Soon-Kee; Kim, Byung-Dong; Lee, Sanghyeob

2009-11-01

231

Incorporating Allelic Variation for Reconstructing the Evolutionary History of Organisms from Multiple Genes: An Example from Rosa in North America  

Microsoft Academic Search

Allelic variation within individuals holds information regarding the relationships of organisms, which is expected to be particularly important for reconstructing the evolutionary history of closely related taxa. However, little effort has been committed to incorporate such information for reconstructing the phylogeny of organisms. Haplotype trees represent a solution when one nonrecombinant marker is considered, but there is no satisfying method

Simon Joly; Anne Bruneau

2006-01-01

232

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

233

Effect of parental family history of Alzheimer's disease on serial position profiles  

PubMed Central

Background An exaggerated recency effect (i.e., disproportionate recall of last-presented items) has been consistently observed in the word list learning of patients with Alzheimer’s disease (AD). Our study sought to determine if there were similar alterations in serial position learning among asymptomatic persons at risk for AD due to parental family history. Methods Subjects included 623 asymptomatic middle-aged children of patients with AD (median = 53 years) and 157 control participants whose parents survived to at least age 70 without AD or other memory disorders. All participants were administered the Rey Auditory Verbal Learning Test which requires learning and recall of 15 unrelated nouns. Results There was no significant difference in total words recalled between the AD children and control groups. However, compared to controls, AD children showed a significantly greater tendency to recall words from the end (recency) versus beginning (primacy) of the list. Serial position effects were unrelated to apolipoprotein allele epsilon 4 (APOE ?4) or depressive symptoms. Conclusions Asymptomatic persons at risk for AD by virtue of family history do not show a difference in total words recalled compared to controls, but exhibit a distinctly different serial position curve suggesting greater reliance on immediate as opposed to episodic memory. This is the same serial position pattern observed in mild AD, seen here in reduced severity. Longitudinal follow-up is planned to determine whether changes in serial position patterns are a meaningful marker for preclinical detection of AD.

La Rue, Asenath; Hermann, Bruce; Jones, Jana E.; Johnson, Sterling; Asthana, Sanjay; Sager, Mark A.

2009-01-01

234

Allele-specific DNA methylation: beyond imprinting  

PubMed Central

Allele-specific DNA methylation (ASM) and allele-specific gene expression (ASE) have long been studied in genomic imprinting and X chromosome inactivation. But these types of allelic asymmetries, along with allele-specific transcription factor binding (ASTF), have turned out to be far more pervasive—affecting many non-imprinted autosomal genes in normal human tissues. ASM, ASE and ASTF have now been mapped genome-wide by microarray-based methods and NextGen sequencing. Multiple studies agree that all three types of allelic asymmetries, as well as the related phenomena of expression and methylation quantitative trait loci, are mostly accounted for by cis-acting regulatory polymorphisms. The precise mechanisms by which this occurs are not yet understood, but there are some testable hypotheses and already a few direct clues. Future challenges include achieving higher resolution maps to locate the epicenters of cis-regulated ASM, using this information to test mechanistic models, and applying genome-wide maps of ASE/ASM/ASTF to pinpoint functional regulatory polymorphisms influencing disease susceptibility.

Tycko, Benjamin

2010-01-01

235

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

2013-08-29

236

Diversity of Lactase Persistence Alleles in Ethiopia: Signature of a Soft Selective Sweep  

PubMed Central

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.

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

2013-01-01

237

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

238

Proactive Parent Communication.  

ERIC Educational Resources Information Center

Presents examples of teacher-parent interactions designed to help teachers communicate with parents. The scenarios involve a teacher communicating with parents about a struggling student, a teacher communicating with parents about a student's behavior problems, and a teacher attempting to communicate with a confrontational parent. Teacher prompts…

Babcock, Sharel; Backlund, Judy

2001-01-01

239

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

240

Infant zygosity can be assigned by parental report questionnaire data  

Microsoft Academic Search

A parental report questionnaire posted to a population sample of 18-month-old twins correctly assigned zygosity in 95%of cases when validated against zygosity determined by identity of polymorphic DNA markers. The questionnaire was as accurate when readministered at 3 years of age, with 96% of children being assigned the same zygosity on both occasions. The results validate the use of parental

Thomas S Price; Bernard Freeman; Ian Craig; Stephen A Petrill; Lorna Ebersole; Robert Plomin

2000-01-01

241

Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene  

SciTech Connect

At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

Pena, S.D.J.; De Souza, K.T. (Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte (Brazil)); De Andrade, M.; Chakraborty, R. (Univ. of Texas Graduate School of Biomedical Sciences, Houston, TX (United States))

1994-01-18

242

Consecutive Mutational Events in a TSHR Allele of Arab Families with Resistance to Thyroid Stimulating Hormone  

PubMed Central

Background Our laboratory identified six distinct inactivating TSHR gene mutations in Arab tribes living in Israel. We recently reported three nucleotide substitutions in exon 3 producing p.[L89L;Q90P] and one in exon 9 of the same allele producing p.P264S in Family A. Family B, reported herein, harbors the identical mutation in exon 3 only. We set to determine whether the mutations have common ancestral origin. Methods Coding regions of the TSHR were sequenced and flanking microsatellite markers spanning 5.3 cM were used for haplotyping. Results Two siblings of Family B were compound heterozygous for TSHR gene mutations. The paternal allele contained the exon 3 mutation and the maternal allele harbored a mutation in exon 10 (p.L653V). We investigated the possibility of a founder effect with subsequent mutational events for the presence of the same exon 3 mutation in different families. The haplotype of the allele harboring the exon 3 mutation in Family B was identical to that of Family A, also harboring the exon 9 mutation on the same allele, indicating that the latter occurred subsequently. The ancestral wild-type TSHR was present in Family B, suggesting that the mutation in exon 3 was also new in the history of that population. Conclusions It is more likely that two consecutive mutational events occurred on the ancestral wild-type allele instead of a recombination bringing exon 3 and exon 9 mutations together on the same allele. New mutational events contribute to the high prevalence of TSHR mutations in this population in addition to a founder effect and limited gene pool due to inbreeding.

Sriphrapradang, Chutintorn; German, Alina; Dumitrescu, Alexandra M.

2012-01-01

243

Initial frequency of alleles conferring resistance to Bacillus thuringiensis poplar in a field population of Chrysomela tremulae.  

PubMed Central

Globally, the estimated total area planted with transgenic plants producing Bacillus thuringiensis (Bt) toxins was 12 million hectares in 2001. The risk of target pests becoming resistant to these toxins has led to the implementation of resistance-management strategies. The efficiency and sustainability of these strategies, including the high-dose plus refuge strategy currently recommended for North American maize, depend on the initial frequency of resistance alleles. In this study, we estimated the initial frequencies of alleles conferring resistance to transgenic Bt poplars producing Cry3A in a natural population of the poplar pest Chrysomela tremulae (Coleoptera: Chrysomelidae). We used the F(2) screen method developed for detecting resistance alleles in natural pest populations. At least three parents of the 270 lines tested were heterozygous for a major Bt resistance allele. We estimated mean resistance-allele frequency for the period 1999-2001 at 0.0037 (95% confidence interval = 0.00045-0.0080) with a detection probability of 90%. These results demonstrate that (i) the F(2) screen method can be used to detect major alleles conferring resistance to Bt-producing plants in insects and (ii) the initial frequency of alleles conferring resistance to Bt toxin can be close to the highest theoretical values that are expected prior to the use of Bt plants if considering fitness costs and typical mutation rates.

Genissel, Anne; Augustin, Sylvie; Courtin, Claudine; Pilate, Gilles; Lorme, Philippe; Bourguet, Denis

2003-01-01

244

D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies.  

PubMed

The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas. PMID:19083860

Phillips, C; Rodriguez, A; Mosquera-Miguel, A; Fondevila, M; Porras-Hurtado, L; Rondon, F; Salas, A; Carracedo, A; Lareu, M V

2008-08-26

245

A powerful test of parent-of-origin effects for quantitative traits using haplotypes  

Technology Transfer Automated Retrieval System (TEKTRAN)

Imprinting is an epigenetic phenomenon where the same alleles have unequal transcriptions and thus contribute differently to a trait depending on their parent of origin. This mechanism has been found to affect a variety of human disorders. Although various methods for testing parent-of-origin effect...

246

Three allele combinations associated with Multiple Sclerosis  

PubMed Central

Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGF?1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGF?1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5?32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles.

Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

2006-01-01

247

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

2013-05-16

248

Exploring of tri-allelic SNPs using Pyrosequencing and the SNaPshot methods for forensic application.  

PubMed

Tri-allelic single nucleotide polymorphisms (SNPs) are potential forensic markers for DNA analysis. Currently, only a limited number of tri-allelic SNP loci have been proved to be fit for forensic application. In this study, we aimed to develop an effective method to select and genotype tri-allelic SNPs based on both Pyrosequencing (PSQ) and the SNaPshot methods. 50 candidate SNPs were chosen from NCBI's dbSNP database and were analyzed by PSQ. The results revealed that 20 SNPs were tri-allelic and were located on 16 autosomal chromosomes. Then 20 SNP loci were combined in one multiplex polymerase chain reaction to develop a single base extension (SBE)-based SNP-typing assay. A total of 100 unrelated Chinese individuals were genotyped by this assay and allele frequencies were estimated. The total discrimination power was 0.999999999975 and the cumulative probability of exclusion was 0.9937. These data demonstrated that the strategy is a rapid and effective method for seeking and typing tri-allelic SNPs. In addition, the 20 tri-allelic SNP multiplex typing assay may be used to supplement paternity testing and human identification. PMID:22437649

Zha, Lagabaiyila; Yun, Libing; Chen, Pengyu; Luo, Haibo; Yan, Jing; Hou, Yiping

2012-03-21

249

Exploring of tri-allelic SNPs using pyrosequencing and the SNaPshot methods for forensic application.  

PubMed

Tri-allelic single nucleotide polymorphisms (SNPs) are potential forensic markers for DNA analysis. Currently, only a limited number of tri-allelic SNP loci have been proved to be fit for forensic application. In this study, we aimed to develop an effective method to select and genotype tri-allelic SNPs based on both Pyrosequencing (PSQ) and the SNaPshot methods. 50 candidate SNPs were chosen from NCBI's dbSNP database and were analyzed by PSQ. The results revealed that 20 SNPs were tri-allelic and were located on 16 autosomal chromosomes. Then 20 SNP loci were combined in one multiplex polymerase chain reaction to develop a single base extension (SBE)-based SNP-typing assay. A total of 100 unrelated Chinese individuals were genotyped by this assay and allele frequencies were estimated. The total discrimination power was 0.999999999975 and the cumulative probability of exclusion was 0.9937. These data demonstrated that the strategy is a rapid and effective method for seeking and typing tri-allelic SNPs. In addition, the 20 tri-allelic SNP multiplex typing assay may be used to supplement paternity testing and human identification. PMID:22522538

Zha, Lagabaiyila; Yun, Libing; Chen, Pengyu; Luo, Haibo; Yan, Jing; Hou, Yiping

2012-03-01

250

The role of HLA-DRB1 alleles on susceptibility of Chinese patients with anti-GBM disease.  

PubMed

Anti-glomerular basement membrane (GBM) disease, a rare autoimmune disorder, is associated with HLA-DR15 genotype in Caucasian and Japanese populations. But the distribution of HLA-DRB1 alleles in Chinese patients with anti-GBM disease and their association with clinical characteristics of anti-GBM disease are to be determined. The present study analyzed the HLA-DRB1 alleles by sequence based typing in 44 Chinese patients with anti-GBM disease and 200 healthy controls. The effects of DRB1 alleles on susceptibility to anti-GBM disease were examined by a relative predispositional effects (RPEs) method. The clinical and pathological data of the patients were collected and analyzed. The DRB1*1501 allele was significantly associated with anti-GBM disease (p=1.597 x 10(-7)). The RPEs test also showed a significant increased frequency of DRB1*0404 in anti-GBM disease (p=0.037). Interestingly, the patients with DRB1*1501 or 0404 had more crescent formation in glomeruli than those without the two alleles (p=0.021). But the DRB1*0404 was rare in both patients and control groups, which indicates that the importance of the *0404 allele is limited in anti-GBM disease. We conclude that the HLA-DRB1*1501 allele is a genetic marker for susceptibility to anti-GBM disease. PMID:19654074

Yang, Rui; Cui, Zhao; Zhao, Juan; Zhao, Ming-Hui

2009-08-04

251

Differences in allele frequencies of autosomal dominant hypercholesterolemia SNPs in the Malaysian population.  

PubMed

Hypercholesterolemia is caused by different interactions of lifestyle and genetic determinants. At the genetic level, it can be attributed to the interactions of multiple polymorphisms, or as in the example of familial hypercholesterolemia (FH), it can be the result of a single mutation. A large number of genetic markers, mostly single nucleotide polymorphisms (SNP) or mutations in three genes, implicated in autosomal dominant hypercholesterolemia (ADH), viz APOB (apolipoprotein B), LDLR (low density lipoprotein receptor) and PCSK9 (proprotein convertase subtilisin/kexin type-9), have been identified and characterized. However, such studies have been insufficiently undertaken specifically in Malaysia and Southeast Asia in general. The main objective of this study was to identify ADH variants, specifically ADH-causing mutations and hypercholesterolemia-associated polymorphisms in multiethnic Malaysian population. We aimed to evaluate published SNPs in ADH causing genes, in this population and to report any unusual trends. We examined a large number of selected SNPs from previous studies of APOB, LDLR, PCSK9 and other genes, in clinically diagnosed ADH patients (n=141) and healthy control subjects (n=111). Selection of SNPs was initiated by searching within genes reported to be associated with ADH from known databases. The important finding was 137 mono-allelic markers (44.1%) and 173 polymorphic markers (55.8%) in both subject groups. By comparing to publicly available data, out of the 137 mono-allelic markers, 23 markers showed significant differences in allele frequency among Malaysians, European Whites, Han Chinese, Yoruba and Gujarati Indians. Our data can serve as reference for others in related fields of study during the planning of their experiments. PMID:22534770

Alex, Livy; Chahil, Jagdish Kaur; Lye, Say Hean; Bagali, Pramod; Ler, Lian Wee

2012-04-26

252

Molecular characterization of diverse CIMMYT maize inbred lines from eastern and southern Africa using single nucleotide polymorphic markers  

PubMed Central

Background Knowledge of germplasm diversity and relationships among elite breeding materials is fundamentally important in crop improvement. We genotyped 450 maize inbred lines developed and/or widely used by CIMMYT breeding programs in both Kenya and Zimbabwe using 1065 SNP markers to (i) investigate population structure and patterns of relationship of the germplasm for better exploitation in breeding programs; (ii) assess the usefulness of SNPs for identifying heterotic groups commonly used by CIMMYT breeding programs; and (iii) identify a subset of highly informative SNP markers for routine and low cost genotyping of CIMMYT germplasm in the region using uniplex assays. Results Genetic distance for about 94% of the pairs of lines fell between 0.300 and 0.400. Eighty four percent of the pairs of lines also showed relative kinship values ? 0.500. Model-based population structure analysis, principal component analysis, neighbor-joining cluster analysis and discriminant analysis revealed the presence of 3 major groups and generally agree with pedigree information. The SNP markers did not show clear separation of heterotic groups A and B that were established based on combining ability tests through diallel and line x tester analyses. Our results demonstrated large differences among the SNP markers in terms of reproducibility, ease of scoring, polymorphism, minor allele frequency and polymorphic information content. About 40% of the SNPs in the multiplexed chip-based GoldenGate assays were found to be uninformative in this study and we recommend 644 of the 1065 for low to medium density genotyping in tropical maize germplasm using uniplex assays. Conclusions There were high genetic distance and low kinship coefficients among most pairs of lines, clearly indicating the uniqueness of the majority of the inbred lines in these maize breeding programs. The results from this study will be useful to breeders in selecting best parental combinations for new breeding crosses, mapping population development and marker assisted breeding.

2012-01-01

253

Babesia bovis biological clones and the inter-strain allelic diversity of the Bv80 gene support subpopulation selection as a mechanism involved in the attenuation of two virulent isolates.  

PubMed

The virulence phenotype of Babesia bovis subpopulations was evaluated using biological clones derived from the high-virulence BboS2P and the low-virulence BboR1A strain and two original virulent isolates, BboL15 and BboL17, multiplied extensively in vitro or attenuated by successive passages in splenectomized calves. The virulence phenotype was assessed both by inoculation of normal Holstein adult steers and by analyses of polymorphic fragments of the single-copy Bv80 gene as a subpopulation marker. BboS2P and its nine derived clones contained a single 750 bp fragment with identical nucleotide sequences and numbers of repeats. A single fragment of approximately 850 bp was observed in BboR1A and its derived clones (Ca3B1, Ca2B1). Ca3B1 and Ca2B1 were differentiated by a stable deletion of 15 contiguous nucleotides in the Bv80 allele of Ca3B1. Both alleles were identified in the parental strain. Original isolates BboL15 and BboL17 contained two Bv80 fragments of different sizes. Interestingly, the heavy and light fragments persisted in the in vivo-attenuated strains and the virulent in vitro-multiplied strains, respectively. Despite the inter-strain allelic diversity of the Bv80 gene, the fragments had identical nucleotide sequences and numbers of repeats compared to their respective parental Bv80 genes. The high-virulence and low-virulence phenotypes remained unchanged after they were multiplied in vitro. In conclusion, the polymorphic B. bovis Bv80 gene, was a useful marker for differentiating subpopulations with different phenotypes. The brevity of the procedure to isolate one parasite from the original isolate or strain before in vitro cloning and the fact that the continuous in vitro multiplication did not modify the virulence phenotype of B. bovis clones strongly suggest that the in vivo-attenuated subpopulations existed in the original isolates before they were selected by passages in splenectomized calves. PMID:22820058

Baravalle, M E; Thompson, C; Valentini, B; Ferreira, M; Torioni de Echaide, S; Christensen, M Florín; Echaide, I

2012-07-04

254

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

255

Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377  

Microsoft Academic Search

X-linked DNA markers are increasingly used in forensic kinship testing. This paper presents sequencing data of the short tandem repeats (STRs) DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423, DXS8377 and proposes an allele nomenclature. Alleles were assigned according to the recommendations of the International Society of Forensic Genetics (ISFG) Commission.

Jeanett Edelmann; Danilo Deichsel; Sandra Hering; Ines Plate; Reinhard Szibor

2002-01-01

256

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

257

The Affected-/Discordant-Sib-Pair Design Can Guarantee Validity of Multipoint Model-Free Linkage Analysis of Incomplete Pedigrees When There Is Marker-Marker Disequilibrium  

PubMed Central

Genomewide linkage studies are tending toward the use of single-nucleotide polymorphisms (SNPs) as the markers of choice. However, linkage disequilibrium (LD) between tightly linked SNPs violates the fundamental assumption of linkage equilibrium (LE) between markers that underlies most multipoint calculation algorithms currently available, and this leads to inflated affected-relative-pair allele-sharing statistics when founders’ multilocus genotypes are unknown. In this study, we investigate the impact that the degree of LD, marker allele frequency, and association type have on estimating the probabilities of sharing alleles identical by descent in multipoint calculations and hence on type I error rates of different sib-pair linkage approaches that assume LE. We show that marker-marker LD does not inflate type I error rates of affected sib pair (ASP) statistics in the whole parameter space, and that, in any case, discordant sib pairs (DSPs) can be used to control for marker-marker LD in ASPs. We advocate the ASP/DSP design with appropriate sib-pair statistics that test the difference in allele sharing between ASPs and DSPs.

Xing, Chao; Sinha, Ritwik; Xing, Guan; Lu, Qing; Elston, Robert C.

2006-01-01

258

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

259

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

260

Parentage determination of Kuruma shrimp Penaeus ( Marsupenaeus) japonicus using microsatellite markers (Bate)  

Microsoft Academic Search

The application of microsatellite markers for parentage determination is gaining both acceptance and popularity in aquaculture. In this study we used simulations and controlled matings to examine the potential of microsatellite markers in assigning parentage to Kuruma shrimp (Penaeus japonicus) progeny. Simulations based on allele frequency data from a captive population of P. japonicus demonstrated that at least five loci

Dean R Jerry; Nigel P Preston; Peter J Crocos; Sandy Keys; Jennifer R. S Meadows; Yutao Li

2004-01-01

261

Estimation of allele frequencies at isoloci.  

PubMed

In some polyploid animals and plants, pairs of duplicated loci occur that share alleles encoding proteins with identical electrophoretic mobilities. Except in cases where these "isoloci" are known to be inherited tetrasomically, individual genotypes cannot be determined unambiguously, and there is no direct way to assign observed variation to a particular locus of the pair. For a pair of diallelic isoloci, nine genotypes are possible but only five phenotypes can be identified, corresponding to individuals with 0-4 doses of the variant allele. A maximum likelihood (ML) approach is used here to identify the set of allele frequencies (p, q) at the individual gene loci with the highest probability of producing the observed phenotypic distribution. A likelihood ratio test is used to generate the asymmetrical confidence intervals around ML estimates. Simulations indicate that the standard error of p is typically about twice the binomial sampling error associated with single locus allele frequency estimates. ML estimates can be used in standard indices of genetic diversity and differentiation and in goodness-of-fit tests of genetic hypotheses. The noncentral chi 2 distribution is used to evaluate the power of a test of apparent heterozygote deficiency that results from attributing all variation to one locus when both loci are polymorphic. PMID:3360307

Waples, R S

1988-02-01

262

Selection Against Recessive Deleterious and Lethal Alleles  

Microsoft Academic Search

For a fully recessive allele with mutation rate to it ?, from it v and complete selection against homozygous recessives, the equilibrium frequency is approximately ?1\\/2. It is possible to reduce the equilibrium by eliminating from the breeding population all homozygous recessives and all individuals identified as heterozygous on the basis of having produced one or more homozygous progeny. The

J. F. Kidwell; G. W. Hagy

1971-01-01

263

Overcoming allelic specificity by immunization with five allelic forms of Plasmodium falciparum apical membrane antigen 1.  

PubMed

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. PMID:23429537

Miura, Kazutoyo; 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

2013-02-19

264

S -allele Diversity in Lycium andersonii: Implications for the Evolution of S Allele Age in the Solanaceae  

Microsoft Academic Search

We evaluate competing explanations for striking differences in the average age of self-incompatibility (S -) alleles in population samples. The age of alleles is inferred from evidence for trans-generic evolution (TGE), in which an allele sampled from one species is more closely related to an allele found in another genus than any con-generic allele, as determined by phylogenetic analysis. Whereas

Adam D. Richman

2000-01-01

265

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

266

A parental combination analysis for ABO-HP interaction in a Bengali population.  

PubMed

Blood samples from 577 couples and their 657 offspring of Bengali caste group derivation were used to study interactions between ABO blood groups and haptoglobin (HP) systems. There was no significant sex difference in HP distribution among the parents. Significantly higher incidences of HP*1 allele were noted in the offspring of ABO-incompatible parental combinations in comparison with those in the offspring of ABO-compatible parents. PMID:8500792

Bandyopadhyay, A R

1993-05-01

267

A comparative survey of genetic diversity among a set of Caricaceae accessions using microsatellite markers.  

PubMed

A preliminary survey of genetic diversity among 34 commercially popular Carica papaya cultivars from India and abroad, 6 accessions of Vasconcellea species and 1 accession of Jacaratia spinosa, was done using 20 simple sequence repeat (SSR) markers. The SSR profiles were used to find out total number of alleles, null and rare alleles, Polymorphism Information Content (PIC) values and to calculate similarity matrix using Jaccard's coefficient. The subsequent dendrogram was made by unweighted pair-group method of arithmetic average (UPGMA) and neighbor-joining method. Based on these parameters a comparison was made between the Indian papaya cultivars and the rest of the accessions. All the markers showed polymorphism and a total of 140 alleles were identified. The average number of alleles was 7 alleles/locus. Categorically the Vasconcellea and Jacaratia species had 54 alleles, the 7 non-Indian Carica papaya accessions had 70 and the 27 Indian accessions had 102 alleles. The average PIC value was 0.735 per marker. A total of 37 rare alleles were identified. Jacaratia spinosa had 17 rare alleles. Nineteen null alleles were detected among the Carica papaya accessions. A Carica papaya accession from South Africa, Hortus Gold had 5 null alleles. The genetic similarity among the accessions ranged from 7% to 67%. In the dendrogram, the Vasconcellea and Jacaratia spinosa accessions separated as a distinct cluster from the rest of the Carica papaya accessions. The study indicated that the accessions of Indian Carica papaya cultivars included in this survey are genetically more diverse than the non-Indian Carica papaya cultivars. PMID:23961410

Sengupta, Samik; Das, Basabdatta; Prasad, Manoj; Acharyya, Pinaki; Ghose, Tapas Kumar

2013-07-26

268

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

SciTech Connect

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 have 1 to 4 (or more) copies per chromosome, giving rise to individuals with up to 8 (or more) alleles. All of the subloci map between the markers D5S557 and D5S435 and lie in close proximity to one another. The marker CATT1 is linked to the SMA gene with a lod score of Z[sub max] = 34.42 at [theta] = 0 and crosses all available recombinants. Certain alleles occurred more frequently in either the SMA or normal populations, indicating significant allelic association between CATT1 and the SMA locus. Haplotype analysis combining US and Canadian SMA families reveals that one haplotype group (VII) occurs significantly more frequently in the SMA population than in the normal. This confirms the allelic association of CATT1 with the SMA locus. 37 refs., 4 figs., 3 tabs.

Burghes, A.H.M.; Ingraham, S.E.; Kote-Jarai, Z.; Carpten, J.D.; DiDonato, C.J. (Ohio State Univ., Columbus, OH (United States)); McLean, M.; Surh, L. (Children's Hospital of Eastern Ontario, Ottawa (Canada)); Thompson, T.G.; McPherson, J.D. (Univ. of California, Irvine, CA (United States)); Ikeda, J.E. (Tokhai Univ. School of Medicine, Isehara City (Japan)); Wirth, B. (Institute for Human Genetics, Bonn (Germany)) (and others)

1994-05-15

269

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

270

MHC class I chain-related gene alleles 5 and 5.1 are transmitted more frequently to type 1 diabetes offspring in HBDI families.  

PubMed

Type 1 diabetes mellitus (T1DM) is an autoimmune disease characterized by autoimmune destruction of pancreatic beta cells. Genetic and environmental factors contribute in this disease. There is evidence that MHC class I chain-related gene (MIC-A) plays a role in the susceptibility to this and other autoimmune diseases. There are five alleles of the MIC-A gene, which consist of different repetitions of GCT. In particular, MIC-A alleles 5 and 5.1 (the former with five repetitions of GCT, the latter with five repetitions and one additional insertion of nucleotide G) have been found to be associated with susceptibility to and age at onset of T1DM. The aim of our study was to analyze the transmission of these MIC-A alleles to T1DM-affected offsprings in HBDI families. These are multiplex families with affected offsprings and unaffected parents. DNA samples were amplified for MIC-A using fluorescence-labeled primers and analyzed on an ABI prism DNA sequencer. The transmission of alleles was then analyzed using pedigrees of families also obtained from HBDI. We analyzed 78 families and found that MIC-A alleles 5 and 5.1 are present and transmitted more frequently than expected. Heterozygotic parents for MIC-A alleles 5 and 5.1 were excluded from the study. Our results suggest that MIC-A alleles 5 and 5.1 are associated with susceptibility to T1DM in family studies. PMID:12021130

Zake, L Nikitina; Ghaderi, M; Park, Y S; Babu, S; Eisenbarth, G; Sanjeevi, C B

2002-04-01

271

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

2012-03-08

272

Sympathovagal Imbalance in Prehypertensive Offspring of Two Parents versus One Parent Hypertensive  

PubMed Central

Objective. Though prehypertension has strong familial predisposition, difference in pathophysiological mechanisms in its genesis in offspring of both parents and single parent hypertensive have not been elucidated. Methods. Body mass index (BMI), waist-hip ratio (WHR), basal heart rate (BHR), blood pressure (BP), HR and BP response to standing, deep breathing difference, BP response to handgrip and spectral indices of heart rate variability (HRV) were analyzed in normotensive offspring of two parents hypertensive (Group I), normotensive offspring of one parent hypertensive (Group II), prehypertensive offspring of two parents hypertensive (Group III) and prehypertensive offspring of one parent hypertensive (Group IV). Results. Sympathovagal imbalance (SVI) in prehypertensive offspring was observed due to increased sympathetic and decreased vagal activity. In group III, SVI was more prominent with greater contribution by vagal withdrawal. LF-HF ratio, the marker of SVI was correlated more with diastolic pressure, 30?:?15 ratio and E?:?I ratio in prehypertensives and the degree of correlation was more in group III prehypertensives. Conclusion. Vagal withdrawal plays a critical role in development of SVI in prehypertensive offspring of hypertensive parents. The intensity of SVI was more in offspring of two parents hypertensive compared to single parent hypertensive.

Pal, G. K.; Pal, Pravati; Nanda, Nivedita; Lalitha, V.; Dutta, T. K.; Adithan, C.

2011-01-01

273

Patterns of Parental Help  

Microsoft Academic Search

This research explores the nature of the relationship between parental attitudes and children's school performance. Particular emphasis is placed upon the parents' own perspective on the situation that occurs when their children start at infant school and the way in which parental expectations are confirmed or altered during this first term. The parents (usually mothers only) of 50 children were

Jill Cohen

1979-01-01

274

Questionnaire for Parents.  

ERIC Educational Resources Information Center

|The 116-item parent questionnaire is designed for parents of elementary school children. It is intended to be used with the child's mother, or the person acting as the child's mother. The questionnaire consists of a section devoted to demographic variables and scales measuring 14 parent variables: (1) parent's achievement aspirations for the…

Purdue Univ., Lafayette, IN. Educational Research Center.

275

Parent Interview Schedule.  

ERIC Educational Resources Information Center

|This 116-item interview schedule designed for parents who failed to respond to the Questionnaire for Parents, is individually administered to the mother of the child of elementary school age. It consists of scales measuring 14 parent variables plus a section devoted to demographic variables: (1) parent's achievement aspirations for the child, (2)…

Purdue Univ., Lafayette, IN. Educational Research Center.

276

Teens Parenting. Project Seed.  

ERIC Educational Resources Information Center

One of eight papers from Project Seed, this paper describes Teens Parenting, a program that brings together a group of parenting teenagers for a 20-week learning experience using the "Nurturing Program for Teenage Parents and Their Families." It is noted that the program is open to all teenage parents in the area, whether or not they are currently…

Drasby, Gail; And Others

277

Customizing Parenting Education  

ERIC Educational Resources Information Center

|The authors of this article discuss customizing parent education which requires customized assessment. At Auburn University, Kreg Edgmon and Wally Goddard developed a parent assessment based on the National Extension Parent Education Model (NEPEM) (Smith, Cudaback, Goddard, & Myers-Walls, 1994). All items in the parent assessment were tested with…

Goddard, H. Wallace; Dennis, Steven A.

2004-01-01

278

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

279

Parental Rights in Schooling.  

ERIC Educational Resources Information Center

|Parental rights in schooling, which protect parents' entitlement to provide for the education of their children, are discussed in this chapter. The courts and legislatures are being forced to deal with these rights. Further, churches, schools, and parents are pressed to define and better protect parental rights, because of the following…

Ball, William Bentley

280

Parent Hearing Aid Experiences  

ERIC Educational Resources Information Center

|This study addresses parent experiences in obtaining and managing hearing aids for their young child. The purpose was to identify challenges parents encounter to determine what state agencies can do to improve parent access to amplification. Data were collected July through September of 2010; 40 parents of children ages birth to 3 years old…

Munoz, Karen; Roberts, Mallory; Mullings, Day; Harward, Richard

2012-01-01

281

Parents and the media  

Microsoft Academic Search

In this study we analysed the effects of parental social background and family composition on various types of parental media socialization. We employed the Family Survey Dutch Population 1998, 2000 and 2003 (N=2608), and analysed respondents’ reports of socialization practices in their parental home. Respondents from high-status families report more extensive parental media socialization in all highbrow and guidance activities.

Natascha Notten; Gerbert Kraaykamp

2009-01-01

282

Cultural Approaches to Parenting  

Microsoft Academic Search

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

Marc H. Bornstein

2012-01-01

283

Children of Incarcerated Parents.  

ERIC Educational Resources Information Center

|The arrest and imprisonment of a parent is significant trauma for children, and children of incarcerated parents are at high risk for juvenile delinquency. This book for social workers, psychologists, and others who work with children whose parents are incarcerated examines parental incarceration, its impact on children, care and placement of…

Gabel, Katherine, Ed.; Johnston, Denise, Ed.

284

Parental Involvement. IDRA Focus.  

ERIC Educational Resources Information Center

|This newsletter contains seven articles about meaningful participation by parents, particularly Hispanic and other minority parents, in the education of their children. "Parents Reclaiming Their Schools: New Initiative Brings Parents Together for Better Schools" (Aurelio M. Montemayor) describes objectives and activities of a Texas-based…

IDRA Newsletter, 1994

1994-01-01

285

Ideas: Working with Parents.  

ERIC Educational Resources Information Center

Collaboration of teachers and parents can strengthen school and home ties. The key ingredients in teachers' efforts to promote parent involvement are communication and education. Forms of one-way and two-way communication with parents are described. Educational strategies discussed include parent instruction and the use of support groups and…

Silliman, Benjamin; Royston, Karen

1990-01-01

286

A Chance to Parent  

ERIC Educational Resources Information Center

|While parents with disabilities may face big challenges, with appropriate supports, many can be great parents. Just like other parents, they do not have to be responsible for every part of childrearing all by themselves. All parents rely on supports to help raise their children, such as day care, carpools, schools, babysitting co-ops, or advice…

Yuan, Susan; Brillhart, Lindsay; Lightfoot, Elizabeth

2012-01-01

287

Codependency and Parenting Styles  

Microsoft Academic Search

This study examined the association between the parent-child relationship (as perceived by late adolescent-early adult children) and the adolescent's codependency. College students 17through 22 years of age (N = 175) reported the parenting style of their mother and father (via ratings of perceived parental support and coercive control) and completed a scale assessing their own level of codependency. Parenting style

Judith L. Fischer; Duane W. Crawford

1992-01-01

288

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

289

Turn Parents into Partners.  

ERIC Educational Resources Information Center

|Focuses on how music teachers can improve their interaction with parents and involve them in their child's music education. States that teachers should meet with parents early in the year and inform parents about their child's accomplishments. Offers ideas about discipline issues and how parents can become involved in the music program. (CMK)|

Bobetsky, Victor V.

2003-01-01

290

Meet the Parents  

ERIC Educational Resources Information Center

|Notification tools can do more than alert the school community to an emergency. New systems are cultivating parental involvement by sending home daily reports on students' behavior, attendance, and performance. South El Monte High School's new parent notification system, a service from TeleParent, contacts parents personally by text message or…

Villano, Matt

2008-01-01

291

Parents, Kids and TV.  

ERIC Educational Resources Information Center

|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, parents should discuss television with their children, and parents must become aware of the…

Gaffney, Maureen, Ed.

1983-01-01

292

Template mixing: a method of enhancing detection and interpretation of codominant RAPD markers  

Microsoft Academic Search

Ten codominant RAPD markers, ranging in size from about 300 to about 1350 bp, were identified in mapping populations of chickpea (Cicer arietinum L.) and diploid strawberry (Fragaria vesca L.). A distinguishing feature of all ten markers, and perhaps of codominant RAPD markers in general, was the presence in heterozygous individuals of a non-parental, heteroduplex band migrating more slowly than

T. M. Davis; H. Yu; K. M. Haigis; P. J. McGowan

1995-01-01

293

Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map  

PubMed Central

Background Triticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches aimed at enhancing breeding progress in cereals require high-quality genetic linkage maps. Consensus maps are genetic maps that are created by a joint analysis of the data from several segregating populations and different approaches are available for their construction. The phenomenon that alleles at a locus deviate from the Mendelian expectation has been defined as segregation distortion. The study of segregation distortion is of particular interest in doubled haploid (DH) populations due to the selection pressure exerted on the plants during the process of their establishment. Results The final consensus map, constructed out of six segregating populations derived from nine parental lines, incorporated 2555 DArT markers mapped to 2602 loci (1929 unique). The map spanned 2309.9 cM with an average number of 123.9 loci per chromosome and an average marker density of one unique locus every 1.2 cM. The R genome showed the highest marker coverage followed by the B genome and the A genome. In general, locus order was well maintained between the consensus linkage map and the component maps. However, we observed several groups of loci for which the colinearity was slightly uneven. Among the 2602 loci mapped on the consensus map, 886 showed distorted segregation in at least one of the individual mapping populations. In several DH populations derived by androgenesis, we found chromosomes (2B, 3B, 1R, 2R, 4R and 7R) containing regions where markers exhibited a distorted segregation pattern. In addition, we observed evidence for segregation distortion between pairs of loci caused either by a predominance of parental or recombinant genotypes. Conclusions We have constructed a reliable, high-density DArT marker consensus genetic linkage map as a basis for genomic approaches in triticale research and breeding, for example for multiple-line cross QTL mapping experiments. The results of our study exemplify the tremendous impact of different DH production techniques on allele frequencies and segregation distortion covering whole chromosomes.

2011-01-01

294

Differential ACE expression among tissues in allele-specific Wistar rat lines.  

PubMed

In humans, the insertion/deletion polymorphism in the angiotensin converting enzyme (ACE) gene accounts for half of the variance in plasma ACE activity. The deletion allele is associated with high plasma ACE activity, cardiovascular disease, and renal disease. In rat, a similar association is found between the B and L alleles of a microsatellite marker in the ACE gene. We identified the B/L variation in the Wistar outbred rat and bred two lines homozygous for the two alleles (WU-B and WU-L). ACE activity was measured in serum, heart, kidney, and aorta homogenates. Immunohistochemistry and ACE mRNA expression were performed in heart, kidney, and aortic tissue. Aortic rings were collected and stimulated with AngI, AngII, and AngI with Lisinopril to measure ACE functional activity by vasoconstrictor response. Serum, heart, and kidney ACE activity and kidney mRNA expression were two-fold higher in WU-B. Kidney staining showed a clear difference in tubular ACE expression, with more staining in WU-B. While in aorta ACE activity and mRNA expression was twofold higher in WU-L, functional conversion of AngI was higher in WU-B, indicating either a functional difference in AngI to AngII conversion between the two alleles due to different splicing or the presence of other factors involved in the conversion that are differentially expressed as the result of differences in the ACE alleles. The newly developed WU-B and WU-L lines show tissue-specific differences in ACE expression and activity. This provides an experimental tool to study the pathophysiologic consequences of differences in ACE alleles in renal and cardiovascular disease. PMID:19255705

Kamilic, Jelena; Lely, A Titia; van Goor, Harry; Buikema, Hendrik; Tent, Hilde; Navis, Gerjan J; Korstanje, Ron

2009-03-03

295

Catalogue of alleles of gliadin-coding loci in durum wheat (Triticum durum Desf.).  

PubMed

Gliadins are seed storage proteins which are characterized by high intervarietal polymorphism and can be used as genetic markers. As a result of our work, a considerably extended catalogue of allelic variants of gliadin component blocks was compiled for durum wheat; 74 allelic variants for four gliadin-coding loci were identified for the first time. The extended catalogue includes a total of 131 allelic variants: 16 for locus Gli-A1(d), 19 for locus Gli-B1(d), 41 for locus Gli-A2(d), and 55 for locus Gli-B2(d). The electrophoretic pattern of the standard cultivar and a diagram are provided for every block identified. The number of alleles per family is quite small for loci Gli-A1(d) and Gli-B1(d) of durum wheat, as contrasted to loci Gli-A2(d) and Gli-B2(d) that are characterized by large families including many alleles. The presence of large block families determines a higher diversity of durum wheat for loci Gli-A2(d) and Gli-B2(d) as compared to Gli-A1(d) and Gli-B1(d). The catalogue of allelic variants of gliadin component blocks can be used by seed farmers to identify durum wheat cultivars and evaluate their purity; by breeders, to obtain homogenous cultivars and control the initial stages of selection; by gene bank experts, to preserve native varieties and the original biotypic composition of cultivars. PMID:21946233

Melnikova, N V; Kudryavtseva, A V; Kudryavtsev, A M

2011-09-17

296

No evidence for a preferential transmission of the methylenetetrahydrofolate reductase 677T allele in families with schizophrenia offspring.  

PubMed

The methylenetetrahydrofolate reductase (MTHFR) 677C > T polymorphism has been associated with an increased risk of schizophrenia in various case-control studies. However, case-control studies are sensitive to population stratification, which is not an issue in family-based studies. We conducted a family-based study comprising 120 families with a schizophrenic family member to explore the association between the parental MTHFR 677C > T polymorphism and schizophrenia risk in offspring. In addition, a meta-analysis was performed using the available studies with data on this subject. Transmission Disequilibrium Test (TDT) analysis showed no preferential transmission of the 677T allele from parents heterozygous for the MTHFR 677C > T polymorphism to schizophrenia offspring (P = 0.27). The genotype relative risks were 1.43 (95% CI: 0.83-2.47) for the 677TT and 1.42 (95% CI: 0.54-3.78) for the 677CT genotype, relative to the 677CC genotype. A meta-analysis using data from family-based studies comprising a total of 416 parent-child triads yielded no evidence implicating the 677T allele in schizophrenia risk (P = 0.58). By applying a log-linear model, we found no asymmetry within parental mating type. Our data provided no evidence that transmission of the MTHFR 677T allele is associated with schizophrenia risk. In addition, we found no evidence that the maternal genotype influences the risk of having schizophrenia offspring substantially. PMID:17503473

Muntjewerff, Jan-Willem; Hoogendoorn, Mechteld L C; Aukes, Maartje F; Kahn, René S; Sinke, Richard J; Blom, Henk J; den Heijer, Martin

2007-10-01

297

HLA-B alleles of the Cayapa of Ecuador: New B39 and B15 alleles  

SciTech Connect

Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles. 70 refs., 2 figs., 2 tabs.

Garber, T.L.; Butler, L.M.; Watkins, D.I. [Univ. of Wisconsin, Madison, WI (United States)] [and others

1995-05-01

298

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

299

Gene therapy by allele selection in a mouse model of beta-thalassemia.  

PubMed

To be of therapeutic use, autologous stem cells derived from patients with inherited genetic disorders require genetic modification via gene repair or insertion. Here, we present proof of principle that, for diseases associated with dominant alleles (gain-of-function or haploinsufficient loss-of-function), disease allele–free ES cells can be derived from afflicted individuals without genome manipulation. This approach capitalizes on the derivation of uniparental cells, such as parthenogenetic (PG) ES cell lines from disease allele–free gametes. Diploid mammalian uniparental embryos with only maternally (oocyte-) or paternally (sperm-)derived genomes fail early in development due to the nonequivalence of parental genomes caused by genomic imprinting. However, these uniparental embryos develop to the blastocyst stage, allowing the derivation of ES cell lines. Using a mouse model for dominant beta-thalassemia, we developed disease allele–free PG ES cell lines from the oocytes of affected animals. Phenotype correction was obtained in donor-genotype recipients after transplantation of in vitro hematopoietic ES cell derivatives. This genetic correction strategy without gene targeting is potentially applicable to any dominant disease. It could also be the sole approach for larger or more complex mutations that cannot be corrected by homologous recombination. PMID:21293060

Eckardt, Sigrid; Leu, N Adrian; Yanchik, Ashley; Hatada, Seigo; Kyba, Michael; McLaughlin, K John

2011-02-01

300

CEBPG Exhibits Allele-Specific Expression in Human Bronchial Epithelial Cells.  

PubMed

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. PMID:23888109

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

2013-07-04

301

Discourse Markers across Language.  

ERIC Educational Resources Information Center

|This paper discusses discourse markers (e.g., "and, so, anyway") and offers an overview of their characteristics and occurrence, using English for illustration. The role of discourse markers is to signal speaker comment on the current utterance. The discourse marker is not part of the sentence's propositional content. While absence of markers

Fraser, Bruce

302

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

303

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

304

Allele frequency distribution for 15 autosomal STR loci in Afridi Pathan population of Uttar Pradesh, India.  

PubMed

Allele frequencies of the 15 autosomal short tandem repeat (STR) loci D8S1179, D21S11, D7S820, CSF1PO D19S433, vWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818 and FGA were determined in Afridi Pathan population of Uttar Pradesh, India. All the 15 STR loci studied were found to be highly polymorphic with respect to observed heterozygosity values. Adherence to the expectations of the Hardy-Weinberg equilibrium (HWE) was confirmed for all the loci with an exception of TPOX and FGA. The allele 12 in CSF1PO was found to be most frequent. The power of discrimination was found to be high ranging from a minimum of 0.858 for the locus CSFIPO to maximum of 0.962 for the locus FGA, thereby facilitating the validation and efficiency of these STR markers in human identification. Population differentiation test between the studied and neighboring populations revealed significant differences at several loci suggesting the endogamous nature of the studied population. To the best of our knowledge, Afridi Pathan population has not been explored genetically for generating forensic data on STR markers. Therefore, STR allele frequency data of this unique population is a valuable contribution to the existing DNA database on Indian populations. PMID:19740691

Noor, Sabahat; Ali, Shahnaz; Eaaswarkhanth, Muthukrishnan; Haque, Ikramul

2009-09-08

305

High-density Integrated Linkage Map Based on SSR Markers in Soybean  

Microsoft Academic Search

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

TAE-YOUNG Hwang; T AKASHI Sayama; M ASAKAZU Takahashi; Y. Takada; Y. Nakamoto; H. Funatsuki; H. Hisano; S. Sasamoto; S. Sato; S. Tabata; I. Kono; M. Hoshi; M. Hanawa; C. Yano; Z. Xia; K. Harada; K. Kitamura; M. Ishimoto

2009-01-01

306

Development of a microsatellite DNA parentage marker suite for black tiger shrimp Penaeus monodon  

Microsoft Academic Search

Twenty-three published Penaeus monodon microsatellites were screened for inclusion in a DNA parentage marker suite by examining their ease of amplification, reliability of allele calling and Mendelian inheritance in an Australian captive population. Seven highly polymorphic markers (mean He=0.87 and PIC=0.84) were identified from the original 23 as being suitable for inclusion in the parentage marker suite. These seven microsatellites

Dean R. Jerry; Brad S. Evans; Matt Kenway; Kate Wilson

2006-01-01

307

Maternal Personality, Parenting Cognitions and Parenting Practices  

PubMed Central

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) were independently coded. Factor analyses of the personality inventory replicated extraction of the Five-Factor model of personality (Openness, Neuroticism, Extraversion, Agreeableness, and Conscientiousness). Controlling for sociodemographic characteristics, the five personality factors qua variables and in patterns qua clusters related differently to diverse parenting cognitions and practices, supporting the multidimensional, modular, and specific nature of parenting. Maternal personality in the normal range, a theoretically important but empirically neglected factor in everyday parenting, has meaning in studies of parenting, child development, and family process.

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

2011-01-01

308

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

309

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

310

Recovery of Heritable, Transposon-Induced, Mutant Alleles of the Rf2 Nuclear Restorer of T-Cytoplasm Maize  

PubMed Central

T (Texas) cytoplasm is associated with a mitochondrial disruption that is phenotypically expressed during microsporogenesis resulting in male sterility. Restoration of pollen fertility in T-cytoplasm maize is controlled by dominant alleles at two unlinked, complementary, nuclear-encoded genes, rf1 and rf2. As a first step in the molecular isolation of the rf2 gene, 178,300 gametes derived from plants that carried the Mutator, Cy or Spm transposon families were screened for rf2 mutant alleles (rf2-m) via their inability to restore pollen fertility to T-cytoplasm male-sterile maize. Seven heritable rf2-m alleles were recovered from these transposon populations. Pedigrees and restriction fragment length polymorphism (RFLP)-based analyses indicated that all seven rf2-m alleles were derived independently. The ability to obtain rf2-m derivatives from Rf2 suggests that Rf2 alleles produce a functional product necessary to restore pollen fertility to cmsT. Molecular markers flanking the rf1 and rf2 loci were used to decipher segregation patterns in progenies segregating for the rf2-m alleles. These analyses provided preliminary evidence of a weak, third restorer gene of cmsT that can substitute for Rf1.

Schnable, P. S.; Wise, R. P.

1994-01-01

311

Linker histone subtypes and their allelic variants.  

PubMed

Members of histone H1 family bind to nucleosomal and linker DNA to assist in stabilization of higher-order chromatin structures. Moreover, histone H1 is involved in regulation of a variety of cellular processes by interactions with cytosolic and nuclear proteins. Histone H1, composed of a series of subtypes encoded by distinct genes, is usually differentially expressed in specialized cells and frequently non-randomly distributed in different chromatin regions. Moreover, a role of specific histone H1 subtype might be also modulated by post-translational modifications and/or presence of polymorphic isoforms. While the significance of covalently modified histone H1 subtypes has been partially recognized, much less is known about the importance of histone H1 polymorphic variants identified in various plant and animal species, and human cells as well. Recent progress in elucidating amino acid composition-dependent functioning and interactions of the histone H1 with a variety of molecular partners indicates a potential role of histone H1 polymorphic variation in adopting specific protein conformations essential for chromatin function. The histone H1 allelic variants might affect chromatin in order to modulate gene expression underlying some physiological traits and, therefore could modify the course of diverse histone H1-dependent biological processes. This review focuses on the histone H1 allelic variability, and biochemical and genetic aspects of linker histone allelic isoforms to emphasize their likely biological relevance. PMID:23075301

Kowalski, Andrzej; Pa?yga, Jan

2012-11-01

312

Marker reconstitution mutagenesis: a simple and efficient reverse genetic approach.  

PubMed

A novel reverse genetic approach termed 'marker reconstitution mutagenesis' was designed to generate mutational allelic series in genes of interest. This approach consists of two simple steps which utilize two selective markers. First, using one selective marker, a partial fragment of another selective marker gene is inserted adjacently to a gene of interest by homologous recombination. Second, random mutations are introduced precisely into the gene of interest, together with the reconstitution of the latter selective marker by homologous recombination. This approach was successfully tested for several genes in the fission yeast Schizosaccharomyces pombe. It circumvents the problems encountered with other methods and should be adaptable to any organism that incorporates exogenous DNA by homologous recombination. PMID:21360732

Tang, Xie; Huang, Junqi; Padmanabhan, Anup; Bakka, Kavya; Bao, Yun; Tan, Brenda Yuelin; Cande, W Zacheus; Balasubramanian, Mohan K

2010-11-22

313

Parenting Regarding Children with Special Needs: Parental Perceptions and Stress  

Microsoft Academic Search

Parenting is an important part of a child's development that begins before the child is born and extends throughout parents' and children's lives. Previous research has shown that parenting is an important indicator of children's later psychological adjustment. According to the parent development theory (PDT), parenting behaviors are generally consistent with individuals' parenting beliefs and perceptions of the parenting role.

Devorah Neuhaus

2011-01-01

314

Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a 'thrifty' allele?  

PubMed

Apolipoprotein E (APOE = gene, apoE = protein) plays a central role in plasma lipoprotein metabolism and in lipid transport within tissues. The APOE shows a genetic polymorphism determined by three common alleles, APOE*2, APOE*3, APOE*4 and the product of the three alleles differs in several functional properties. APOE is involved in the development of certain pathological conditions. In particular, the APOE*4 allele is a risk factor for susceptibility to coronary artery disease (CAD) and Alzheimer's Disease (AD). In the present study we analyzed the APOE allele distribution in the world. The APOE*3 is the most frequent in all the human groups, especially in populations with a long-established agricultural economy like those of the Mediterranean basin (0.849-0.898). The frequency of APOE*4, the ancestral allele, remains higher in populations like Pygmies (0.407) and Khoi San (0.370), aborigines of Malaysia (0.240) and Australia (0.260), Papuans (0.368), some Native Americans (0.280), and Lapps (0.310) where an economy of foraging still exists, or food supply is (or was until the recent past) scarce and sporadically available. The APOE*2 frequency fluctuates with no apparent trend (0.145-0.02) and is absent in Native Americans. We suggest that the APOE*4, based on some functional properties it has and on its distribution among human populations, could be identified as a 'thrifty' allele. The exposure of APOE*4 to the contemporary environmental conditions (Western diet, longer lifespans) could have rendered it a susceptibility allele for CAD and AD. The absence of the association of APOE*4 with CAD and AD in Sub-Saharan Africans, and its presence in African Americans, seems to confirm this hypothesis. PMID:10738542

Corbo, R M; Scacchi, R

1999-07-01

315

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, URACm-Gs , has been available that complements the uracil-auxotrophic mutant M4. URACm-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 URACm-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 (URACm-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

2013-09-05

316

Gene Targeting in the Red Alga Cyanidioschyzon merolae: Single- and Multi-Copy Insertion Using Authentic and Chimeric Selection Markers  

PubMed Central

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, URACm-Gs, has been available that complements the uracil-auxotrophic mutant M4. URACm-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 URACm-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 (URACm-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.

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

2013-01-01

317

Parental authority questionnaire.  

PubMed

A questionnaire was developed for the purpose of measuring Baumrind's (1971) permissive, authoritarian, and authoritative parental authority prototypes. It consists of 30 items per parent and yields permissive, authoritarian, and authoritative scores for both the mother and the father; each of these scores is derived from the phenomenological appraisals of the parents' authority by their son or daughter. The results of several studies have supported the Parental Authority Questionnaire as a psychometrically sound and valid measure of Baumrind's parental authority prototypes, and they have suggested that this questionnaire has considerable potential as a valuable tool in the investigation of correlates of parental permissiveness, authoritarianism, and authoritativeness. PMID:16370893

Buri, J R

1991-08-01

318

Parenting by lying  

PubMed Central

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 = 127), parents reported lying to their children and considered doing so to be acceptable under some circumstances, even though they also reported teaching their children that lying is unacceptable. As compared to European American parents, Asian American parents tended to hold a more favourable view of lying to children for the purpose of promoting behavioural compliance.

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

2010-01-01

319

Microsatellite markers for the diploid basidiomycete fungus Armillaria mellea.  

PubMed

We isolated and characterized 12 microsatellite markers for two North American populations (California, Pennsylvania) of Armillaria mellea, a fungal pathogen responsible for Armillaria root disease of numerous woody plants. Allele frequency ranged from two to nine alleles per locus, and gene diversity ranged from 0.05 to 0.86. Of the 12 loci, eight loci were polymorphic in the California and Pennsylvania populations, and showed no evidence of heterozygote deficiencies or severe linkage disequilibrium. Our results suggest that we have isolated and characterized variable loci to estimate genotypic diversity, gene flow and migration, and to determine population structure of North American A. mellea. PMID:21564799

Baumgartner, K; Grubisha, L C; Fujiyoshi, P; Garbelotto, M; Bergemann, S E

2009-01-22

320

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

321

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

322

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

323

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

324

Parenting Curriculum for Language Minority Parents.  

ERIC Educational Resources Information Center

The curriculum consists of a workbook for language minority parents learning English as a Second Language and parenting skills, and a teaching activities guide for instructors. The guide, developed for both literate and non-literate adults, serves three purposes: (1) as a visual aid for the classroom, with pictures introducing English in…

Holt, Grace D.

325

Fragile X full mutation alleles composed of few alleles: implications for CGG repeat expansion.  

PubMed

Southern analysis of the FMR1 repeat region has suggested that individuals with the full mutation usually carry a heterogeneous array of FMR1 alleles in somatic tissue that can range from 200 to more than 1,000 repeats. Our studies indicate that this heterogeneity is an artifact generated by ethidium bromide commonly used in Southern analysis. When analyzed in the absence of ethidium bromide, nearly all full mutation individuals carried only one to four major alleles and did not exhibit the heterogeneity often referred to as a "smear" in the literature. Full mutations in chorionic villi, however, exhibited much greater heterogeneity. Nine transmissions from mothers with full mutation alleles to offspring indicated that the full mutations continued to expand in transmission to the next generation. In contrast, analysis of leukocyte DNA from three full mutation males revealed no change in somatic full mutation alleles over many years. Our studies support the hypothesis that the FMR1 CGG repeat instability is limited to very early embryogenesis in the soma. These studies also have clinical importance because the omission of ethidium bromide will facilitate the diagnosis of females with full mutation alleles. PMID:18074381

Nolin, Sarah L; Ding, Xiao-hua; Houck, George E; Brown, W Ted; Dobkin, Carl

2008-01-01

326

Evaluation of 16 SNPs allele-specific to quantify post hSCT chimerism by SYBR green-based qRT-PCR.  

PubMed

The importance of monitoring post haematopoietic stem cell transplantation (hSCT) chimerism has been defined in numerous publications. Single-nucleotide polymorphisms (SNPs) are molecular markers that vary significantly among different populations. Allied to a very sensible technique, SNP assays seem to be very sensitive (0.001%) when post hSCT chimerism is measured. However, well known SNP frequencies are limited to certain populations, mainly in countries where there is a high level of diversity in its population, therefore restricting their use worldwide. Amplification by SYBR green based quantitative real time PCR of eight pairs of allele-specific SNPs (MLH-1, PECAM-1, ICAM-1, SUR-1, HA-1, rs715405, rs713503, rs2296600) was conducted in 88 patient/donor pairs, who underwent allogeneic myeloablative or non-myeloablative hSCT. One informative allele was detected in at least 42% (n=37) of the samples; 20% (n=18) had at least two informative alleles; 10% (n=9) had at least three informative alleles; 9% (n=8) had more than three informative alleles and 18% (n=16) showed no informative allele at all. Overall, the frequency of informative alleles for these SNPs in the Brazilian population was very low. Consequently, the amount of information attained reached 9% of those expected, being able to discriminate only eight pairs of donor/recipient samples with more than three informative alleles, making them useless for the quantification of chimerism in our routine. PMID:23288918

Almeida, Carlos Arthur Cardoso; Dreyfuss, Juliana Luporini; Azevedo-Shimmoto, Marily Maria; Figueiredo, Maria Stela; de Oliveira, José Salvador Rodrigues

2013-01-02

327

Human immunoglobulin allotypes: previously unrecognized determinants and alleles defined with monoclonal antibodies.  

PubMed Central

The highly polymorphic system of serologically defined genetic markers on human IgG heavy chains (Gm allotypes) is second only to the HLA complex in terms of the large number of determinants, alleles, and haplotypes that can be used for analyses of disease associations and other genetic studies. However, present typing methods are based on the use of anti-Gm antisera that are derived mainly from fortuitously immunized human donors, often requiring processing before use, and must be used in a hemagglutination-inhibition assay that cannot be used in typing for isoallotypic determinants (currently termed "non-markers"). In studies presented here, we describe an allotyping system that utilizes monoclonal antibodies in a "sandwich" modification of the solid-phase radioimmunoassay, which is capable of reliable quantitative typing of allotypic, isoallotypic, and isotypic immunoglobulin determinants. We show that these highly reproducible, easily disseminated, and essentially inexhaustible reagents can be used for rapid, sensitive, and quantitative Gm typing. Using this system we define two previously unrecognized Gm determinants, one of which, found to date only in Caucasians, is different from all known Gm markers and thus defines previously unrecognized alleles and haplotypes. The other determinant co-segregates with the conventional G3m(b1) marker but is distinct from that marker on serological grounds. The successful preparation of mouse monoclonal antibodies that detect human Gm allotypic differences and the development of an assay system capable of typing isoallotypic as well as allotypic determinants opens the way to further dissection and application of this rich genetic system.

Zelaschi, D; Newby, C; Parsons, M; van West, B; Cavalli-Sforza, L L; Herzenberg, L A; Herzenberg, L A

1983-01-01

328

Strategies for characterizing highly polymorphic markers in human gene mapping.  

PubMed

Before new markers are thoroughly characterized, they are usually screened for high polymorphism on the basis of a small panel of individuals. Four commonly used screening strategies are compared in terms of their power to correctly classify a marker as having heterozygosity of 70% or higher. A small number of typed individuals (10, say) are shown to provide good discrimination power between low- and high-heterozygosity markers when the markers have a small number of alleles. Characterizing markers in more detail requires larger sample sizes (e.g., at least 80-100 individuals) if there is to be a high probability of detecting most or all alleles. For linkage analyses involving highly polymorphic markers, the practice of arbitrarily assuming equal gene frequencies can cause serious trouble. In the presence of untyped individuals, when gene frequencies are unequal but are assumed to be equal in the analysis, recombination-fraction estimates tend to be badly biased, leading to strong false-positive evidence for linkage. PMID:1642229

Ott, J

1992-08-01

329

Combining Markers into Haplotypes Can Improve Population Structure Inference  

PubMed Central

High-throughput genotyping and sequencing technologies can generate dense sets of genetic markers for large numbers of individuals. For most species, these data will contain many markers in linkage disequilibrium (LD). To utilize such data for population structure inference, we investigate the use of haplotypes constructed by combining the alleles at single-nucleotide polymorphisms (SNPs). We introduce a statistic derived from information theory, the gain of informativeness for assignment (GIA), which quantifies the additional information for assigning individuals to populations using haplotype data compared to using individual loci separately. Using a two-loci–two-allele model, we demonstrate that combining markers in linkage equilibrium into haplotypes always leads to nonpositive GIA, suggesting that combining the two markers is not advantageous for ancestry inference. However, for loci in LD, GIA is often positive, suggesting that assignment can be improved by combining markers into haplotypes. Using GIA as a criterion for combining markers into haplotypes, we demonstrate for simulated data a significant improvement of assigning individuals to candidate populations. For the many cases that we investigate, incorrect assignment was reduced between 26% and 97% using haplotype data. For empirical data from French and German individuals, the incorrectly assigned individuals can, for example, be decreased by 73% using haplotypes. Our results can be useful for challenging population structure and assignment problems, in particular for studies where large-scale population–genomic data are available.

Gattepaille, Lucie M.; Jakobsson, Mattias

2012-01-01

330

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

331

Parenting and infant sleep.  

PubMed

Infant sleep undergoes dramatic evolution during the first year of life. This process is driven by underlying biological forces but is highly dependent on environmental cues including parental influences. In this review the links between infant sleep and parental behaviors, cognitions, emotions and relationships as well as psychopathology are examined within the context of a transactional model. Parental behaviors, particularly those related to bedtime interactions and soothing routines, are closely related to infant sleep. Increased parental involvement is associated with more fragmented sleep. Intervention based on modifying parental behaviors and cognitions have direct effect on infant sleep. It appears that parental personality, psychopathology and related cognitions and emotions contribute to parental sleep-related behaviors and ultimately influence infant sleep. However, the links are bidirectional and dynamic so that poor infant sleep may influence parental behaviors and poor infant sleep appears to be a family stressor and a risk factor for maternal depression. PMID:19631566

Sadeh, Avi; Tikotzky, Liat; Scher, Anat

2009-07-23

332

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

333

A worksite parenting program.  

PubMed

With more and more companies offering wellness programs for their employees, it seems reasonable to offer parent training classes to employees as an educational tool and a means of coping with stress. A series of parenting classes was developed using the STAR Parenting Model. The STAR Model teaches parents to stop, think, ask, and respond to their children based on tenets of cognitive behavior management. Classes taught to faculty and staff of the university were well attended and participants indicated that the method positively altered their parenting practices. Parents are challenged by their young children and by their jobs and careers. Parenting education at work may help to ease some employee stress and improve their parenting practices. PMID:2306310

Anderson, R C; Fox, R A

1990-02-01

334

Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus 'Robusta 5' accessions  

PubMed Central

Background Breeding of fire blight resistant scions and rootstocks is a goal of several international apple breeding programs, as options are limited for management of this destructive disease caused by the bacterial pathogen Erwinia amylovora. A broad, large-effect quantitative trait locus (QTL) for fire blight resistance has been reported on linkage group 3 of Malus ‘Robusta 5’. In this study we identified markers derived from putative fire blight resistance genes associated with the QTL by integrating further genetic mapping studies with bioinformatics analysis of transcript profiling data and genome sequence databases. Results When several defined E.amylovora strains were used to inoculate three progenies from international breeding programs, all with ‘Robusta 5’ as a common parent, two distinct QTLs were detected on linkage group 3, where only one had previously been mapped. In the New Zealand ‘Malling 9’ X ‘Robusta 5’ population inoculated with E. amylovora ICMP11176, the proximal QTL co-located with SNP markers derived from a leucine-rich repeat, receptor-like protein ( MxdRLP1) and a closely linked class 3 peroxidase gene. While the QTL detected in the German ‘Idared’ X ‘Robusta 5’ population inoculated with E. amylovora strains Ea222_JKI or ICMP11176 was approximately 6?cM distal to this, directly below a SNP marker derived from a heat shock 90 family protein gene ( HSP90). In the US ‘Otawa3’ X ‘Robusta5’ population inoculated with E. amylovora strains Ea273 or E2002a, the position of the LOD score peak on linkage group 3 was dependent upon the pathogen strains used for inoculation. One of the five MxdRLP1 alleles identified in fire blight resistant and susceptible cultivars was genetically associated with resistance and used to develop a high resolution melting PCR marker. A resistance QTL detected on linkage group 7 of the US population co-located with another HSP90 gene-family member and a WRKY transcription factor previously associated with fire blight resistance. However, this QTL was not observed in the New Zealand or German populations. Conclusions The results suggest that the upper region of ‘Robusta 5’ linkage group 3 contains multiple genes contributing to fire blight resistance and that their contributions to resistance can vary depending upon pathogen virulence and other factors. Mapping markers derived from putative fire blight resistance genes has proved a useful aid in defining these QTLs and developing markers for marker-assisted breeding of fire blight resistance.

2012-01-01

335

Community Engaged Parent Education: Strengthening Civic Engagement among Parents and Parent Educators  

ERIC Educational Resources Information Center

We introduce Community Engaged Parent Education as a model for civic engagement in parent education. In Community Engaged Parent Education, the parent educator weaves the public dimensions of parenting into the everyday practice of group parent education. It is not a curriculum but a community-collaborative way of teaching all parenting topics by…

Doherty, William J.; Jacob, Jenet; Cutting, Beth

2009-01-01

336

New microsatellite markers for assessment of genetic diversity in date palm (Phoenix dactylifera L.).  

PubMed

New primer pairs of genomic DNA microsatellite markers were tested to assess the genetic diversity of eleven date palm genotypes. The results indicated that out of thirty, only seven primers (23.3%) failed to amplify the expected PCR fragments, while thirteen primers (43.3%) amplified monomorphic banding patterns and the remaining ten primers (33.4%) generated polymorphic banding patterns. A total of 77 alleles have been observed with a mean of 7.7 alleles per locus. The average of gene diversity was 0.80 ranging from 0.6 (in marker DP168) to 0.9 (in two markers DP157 and DP175). These new co-dominant markers will be a starting point for researchers making use of the markers for genetic mapping and diversity analysis of date palm. PMID:22582150

Elmeer, Khaled; Sarwath, Hina; Malek, Joel; Baum, Michael; Hamwieh, Aladdin

2011-05-27

337

Ceramic subsurface marker prototypes  

SciTech Connect

The client submitted 5 sets of porcelain and stoneware subsurface (radioactive site) marker prototypes (31 markers each set). The following were determined: compressive strength, thermal shock resistance, thermal crazing resistance, alkali resistance, color retention, and chemical resistance.

Lukens, C.E. [Rockwell International Corp., Richland, WA (United States). Rockwell Hanford Operations

1985-05-02

338

Biologic Markers in Immunotoxicology.  

National Technical Information Service (NTIS)

The report focuses on the human immune system and its response to environmental toxicants. The authoring committee provides direction for continuing development of biologic markers, with strategies for applying markers to immunotoxicity in humans and reco...

1992-01-01

339

Application of a Novel Strategy of Engineering Conditional Alleles to a Single Exon Gene, Sox2  

PubMed Central

Background The Conditional by Inversion (COIN) method for engineering conditional alleles relies on an invertible optimized gene trap-like element, the COIN module, for imparting conditionality. The COIN module contains an optimized 3? splice site-polyadenylation signal pair, but is inserted antisense to the target gene and therefore does not alter transcription, until it is inverted by Cre recombinase. In order to make COIN applicable to all protein-coding genes, the COIN module has been engineered within an artificial intron, enabling insertion into an exon. Methodology/Principal Findings Therefore, theoretically, the COIN method should be applicable to single exon genes, and to test this idea we engineered a COIN allele of Sox2. This single exon gene presents additional design challenges, in that its proximal promoter and coding region are entirely contained within a CpG island, and are also spanned by an overlapping transcript, Sox2Ot, which contains mmu-miR1897. Here, we show that despite disruption of the CpG island by the COIN module intron, the COIN allele of Sox2 (Sox2COIN) is phenotypically wild type, and also does not interfere with expression of Sox2Ot and miR1897. Furthermore, the inverted COIN allele of Sox2, Sox2INV is functionally null, as homozygotes recapitulate the phenotype of Sox2ßgeo/ßgeo mice, a well-characterized Sox2 null. Lastly, the benefit of the eGFP marker embedded in the COIN allele is demonstrated as it mirrors the expression pattern of Sox2. Conclusions/Significance Our results demonstrate the applicability of the COIN technology as a method of choice for targeting single exon genes.

Mandalos, Nikolaos; Saridaki, Marannia; Harper, Jessica Lea; Kotsoni, Anastasia; Yang, Peter; Economides, Aris N.; Remboutsika, Eumorphia

2012-01-01

340

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

341

Assessing Parents and Children.  

ERIC Educational Resources Information Center

|Summarizes a study designed to determine the effectiveness of parental influence on their children. The researcher interviewed nine students from a St. Louis, Missouri Catholic elementary school along with the students' parents and teachers. The author presents findings related to family discipline procedures, parental expectations for children,…

Dixon, Mary

2002-01-01

342

Parents Reviewing Annual Reviews.  

ERIC Educational Resources Information Center

A study examined the perceptions of 12 British parents of children with special needs concerning their involvement in the required annual review process. Analysis of questionnaire and recorded discussions suggested that parents' views might be valued in principle but devalued in practice. Recommendations focus on preparatory meetings for parents

Jones, Phyllis; Swain, John

2001-01-01

343

Black Grandparents as Parents.  

ERIC Educational Resources Information Center

There has been an increase in the number of children being raised by their grandparents. As these grandparents take on the primary parenting responsibilities of their grandchildren, they are being deprived of a wholesome and more typical grandparent-grandchild relationship. Many of these children are born to drug-addicted parents or to parents who…

Poe, Lenora Madison

344

Parenting With Teenagers.  

ERIC Educational Resources Information Center

This paper discusses factors that affect parent-child relationships when children become adolescents. Several factors are seen to be related to the development of reciprocity in parenting behaviors between adolescents and their parents. Factors related to the development of reciprocity are (1) teenagers' physical and intellectual development and…

Wattenberg, William W.

345

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

346

A Parent's Perspective.  

ERIC Educational Resources Information Center

This response to Mahoney et al. (EC 623 392) by a parent of a child with disabilities agrees with the need for parent education in early intervention and offers the author's personal experiences to underscore points such as the importance of collaboration with families and the need to consider parents' limited time and resources. (DB)

Greene, Marci

1999-01-01

347

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

348

Educational Surrogate Parent Manual.  

ERIC Educational Resources Information Center

This manual is intended for individuals who agree to act as educational surrogate parents for children with disabilities in North Dakota. Section 1 provides an overview of the educational surrogate parent service, including surrogate parent qualifications, protections, responsibilities, confidentiality, and the surrogate's partnership with the…

North Dakota State Dept. of Public Instruction, Bismarck.

349

Children of Incarcerated Parents.  

ERIC Educational Resources Information Center

This report summarizes what is known about the children of incarcerated parents in California. The report estimates the number of children in California who have parents in the state's criminal justice system (jail, prison, parole, and probation) and summarizes key findings from the research literature on the impact of parental arrest and…

Simmons, Charlene Wear

2000-01-01

350

Parenting by lying  

Microsoft Academic Search

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 = 127),

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

2009-01-01

351

Categories of Parent Involvement.  

ERIC Educational Resources Information Center

|The growing interest in effective parent involvement has produced several ways to classify or describe ways parents are or should be involved. This article reviews and evaluates Ira Gordon's systems approach, the California-based System Development Corporation's categories, Eugenia H. Berger's parental role categories, Chavkin and Williams'…

Bauch, Jerold P.

1994-01-01

352

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

353

Parenting after Infertility  

ERIC Educational Resources Information Center

|Becoming a parent after experiencing infertility can pose unique challenges to early parenthood. Parents may struggle with the normal anxiety and fatigue, as well as possible depression, that accompany new parenthood, but with added guilt or shame because of how much they wanted a child and how hard they worked to become parents. These feelings…

Olshansky, Ellen

2009-01-01

354

The Teen Parent Academy  

ERIC Educational Resources Information Center

|Pregnant teenagers and young parents often do not receive the quality of education available to other students. Most schools do not have a separate facility or program that deals with their special needs. Pregnant teens and teen parents should not be left behind. The Teen Parent Academy--a unique program in a predominantly Hispanic Texas border…

Baptiste, H. Prentice, Jr.; Walker, Diane

2005-01-01

355

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

356

Sex education for parents  

Microsoft Academic Search

Finds research shows that while parents are potentially an important source of information and support to their children on sexual issues, in practice many parents feel that they lack the skills and confidence to play a direct role in these matters. Presents findings from a pilot project undertaken by Health Promotion Wales and FPA Cymru to enhance parents’ sex education

Virginia Blakey; Jane Frankland

1996-01-01

357

Narcissism and Parenting Styles  

Microsoft Academic Search

Baumrind's authoritative, permissive, and authoritarian parenting styles were analyzed within the context of Kohut's psychology of the self. College student perceptions of their parents were correlated with measures of self-functioning in order to test the hypotheses that perceived parental authoritativeness would be associated with less narcissistic maladjustment, that permissiveness would be associated with immature grandiosity, and that authoritarianism would correlate

P. J. Watson; Tracy Little; Michael D. Biderman

1992-01-01

358

Being a Professional Parent.  

ERIC Educational Resources Information Center

|The parent of a blind child urges other parents of handicapped children to realize their value in relationships with professionals by presenting ideas and information and cooperating with teachers and administrators in problem solving. She emphasizes the importance of parents understanding and communicating their own limits. (CL)|

Patterson, Marilyn

1983-01-01

359

Parent's Journal. [Videotape Series].  

ERIC Educational Resources Information Center

|Parent's Journal is a set of 16 videotapes for parents of prenatal, infant, and toddler-age children, created by the Alaska Native Home Base Video Project of the Tlingit and Haida Head Start Program. This series offers culturally relevant solutions to the challenges of parenting, drawing on the life stories and experiences of capable mothers and…

1999

360

Foster Parent Stress.  

ERIC Educational Resources Information Center

|Research findings regarding foster-parent stress and implications for counselors and counselor educators are discussed. Eleven significant themes are reported from a qualitative and quantitative study of rural foster parents (N=156). Stressful events that affect the well-being of foster parents and their relationships with children and…

Jones, Graham; Morrissette, Patrick J.

1999-01-01

361

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

362

Children of Incarcerated Parents.  

ERIC Educational Resources Information Center

|This report summarizes what is known about the children of incarcerated parents in California. The report estimates the number of children in California who have parents in the state's criminal justice system (jail, prison, parole, and probation) and summarizes key findings from the research literature on the impact of parental arrest and…

Simmons, Charlene Wear

2000-01-01

363

Allele Frequencies at Microsatellite Loci: The Stepwise Mutation Model Revisited  

PubMed Central

We summarize available data on the frequencies of alleles at microsatellite loci in human populations and compare observed distributions of allele frequencies to those generated by a simulation of the stepwise mutation model. We show that observed frequency distributions at 108 loci are consistent with the results of the model under the assumption that mutations cause an increase or decrease in repeat number by one and under the condition that the product Nu, where N is the effective population size and u is the mutation rate, is larger than one. We show that the variance of the distribution of allele sizes is a useful estimator of Nu and performs much better than previously suggested estimators for the stepwise mutation model. In the data, there is no correlation between the mean and variance in allele size at a locus or between the number of alleles and mean allele size, which suggests that the mutation rate at these loci is independent of allele size.

Valdes, A. M.; Slatkin, M.; Freimer, N. B.

1993-01-01

364

Development of simple sequence repeat markers and diversity analysis in alfalfa (Medicago sativa L.).  

PubMed

Efficient and robust molecular markers are essential for molecular breeding in plant. Compared to dominant and bi-allelic markers, multiple alleles of simple sequence repeat (SSR) markers are particularly informative and superior in genetic linkage map and QTL mapping in autotetraploid species like alfalfa. The objective of this study was to enrich SSR markers directly from alfalfa expressed sequence tags (ESTs). A total of 12,371 alfalfa ESTs were retrieved from the National Center for Biotechnology Information. Total 774 SSR-containing ESTs were identified from 716 ESTs. On average, one SSR was found per 7.7 kb of EST sequences. Tri-nucleotide repeats (48.8 %) was the most abundant motif type, followed by di-(26.1 %), tetra-(11.5 %), penta-(9.7 %), and hexanucleotide (3.9 %). One hundred EST-SSR primer pairs were successfully designed and 29 exhibited polymorphism among 28 alfalfa accessions. The allele number per marker ranged from two to 21 with an average of 6.8. The PIC values ranged from 0.195 to 0.896 with an average of 0.608, indicating a high level of polymorphism of the EST-SSR markers. Based on the 29 EST-SSR markers, assessment of genetic diversity was conducted and found that Medicago sativa ssp. sativa was clearly different from the other subspecies. The high transferability of those EST-SSR markers was also found for relative species. PMID:23275197

Wang, Zan; Yan, Hongwei; Fu, Xinnian; Li, Xuehui; Gao, Hongwen

2012-12-29

365

Allele frequencies for 15 autosomal STR loci and admixture estimates in Puerto Rican Americans  

Microsoft Academic Search

Allelic frequencies of 15 short tandem repeats (STR) markers (CSF1PO, FGA, THO1, TPOX, VWA, D3S11358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, D19S433 and D2S1338) were determined using the AmpF? STR® Identifiler™ PCR Amplification Kit in Puerto Rican American individuals (N=205) from Massachusetts. The FGA, D18S51 and D2S1338 loci had a high power of discrimination (PD) with values of 0.967,

J. Zúñiga; M. Ilzarbe; V. Acunha-Alonzo; F. Rosetti; Z. Herbert; V. Romero; I. Almeciga; O. Clavijo; J. N. H. Stern; J. Granados; M. Fridkis-Hareli; P. Morrison; J. Azocar; E. J. Yunis

2006-01-01

366

Allele frequencies of 14 STR loci in the population of Malta  

Microsoft Academic Search

Allele frequencies of 14 STR loci (D13S317, D16S539, D2S1338, vWA, TPOX, D18S51, D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, TH01 and D3S1358) observed in the population of Malta are being reported. Polymerase chain reaction (PCR) amplification using the AmpFl STR® Identifiler kit was performed in a random sample of 157 subjects (314 chromosomes). Markers D2S1338, D18S51 and FGA had the highest

M. Cassar; C. Farrugia; C. Vidal

2008-01-01

367

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

368

Allele-Specific KRT1 Expression Is a Complex Trait  

PubMed Central

The differential expression of alleles occurs commonly in humans and is likely an important genetic factor underlying heritable differences in phenotypic traits. Understanding the molecular basis of allelic expression differences is thus an important challenge. Although many genes have been shown to display differential allelic expression, this is the first study to examine in detail the cumulative effects of multiple cis-regulatory polymorphisms responsible for allele-specific expression differences. We have used a variety of experimental approaches to identify and characterize cis-regulatory polymorphisms responsible for the extreme allele-specific expression differences of keratin-1 (KRT1) in human white blood cells. The combined data from our analyses provide strong evidence that the KRT1 allelic expression differences result from the haplotypic combinations and interactions of five cis-regulatory single nucleotide polymorphisms (SNPs) whose alleles differ in their affinity to bind transcription factors and modulate KRT1 promoter activity. Two of these cis-regulatory SNPs bind transcriptional activators with the alleles on the high-expressing KRT1 haplotype pattern having a higher affinity than the alleles on the low-expressing haplotype pattern. In contrast, the other three cis-regulatory SNPs bind transcriptional inhibitors with the alleles on the low-expressing haplotype pattern having a higher affinity than the alleles on the high-expressing haplotype pattern. Our study provides important new insights into the degree of complexity that the cis-regulatory sequences responsible for allele-specific transcriptional regulation have. These data suggest that allelic expression differences result from the cumulative contribution of multiple DNA sequence polymorphisms, with each having a small effect, and that allele-specific expression can thus be viewed as a complex trait.

Tao, Heng; Cox, David R; Frazer, Kelly A

2006-01-01

369

Relationships among Avena species as revealed by consensus chloroplast simple sequence repeat (ccSSR) markers  

Microsoft Academic Search

Consensus chloroplast simple sequence repeat (ccSSR) makers were used to assess the genetic variation and genetic relationships\\u000a of 80 accessions from 25 taxa of the genus Avena. Fifteen out of 16 ccSSR markers (93.75%) were polymorphic. A total of 51 alleles were detected at the 16 ccSSR loci. The\\u000a number of alleles per locus ranged from 1 to 6, with

Wei-Tao Li; Yuan-Ying Peng; Yu-Ming Wei; Bernard R. Baum; You-Liang Zheng

2009-01-01

370

Genetic characterization of banana cultivars ( Musa spp.) from Brazil using microsatellite markers  

Microsoft Academic Search

Microsatellite markers were used to characterize 35 banana (Musa spp.)genotypes cultivated in Brazil, including triploid cultivars and tetraploid hybrids. A total of 33 Musa-specific primers were tested, and 11 produced clear ,reproducible and discrete bands. The average number of alleles amplified\\u000a per primer was 6.1, ranging from 4 to 8, with a total of 67 alleles identified. Phenetic analysis based

Silvana Creste; Augusto Tulmann Neto; Sebastião de Oliveira Silva; Antonio Figueira

2003-01-01

371

Microsatellite markers reveal high genetic diversity in date palm ( Phoenix dactylifera L.) germplasm from Sudan  

Microsoft Academic Search

Genetic diversity in date palm germplasm from Sudan representing 37 female and 23 male accessions was investigated using 16\\u000a loci of microsatellite (SSR) primers. Eight female accessions from Morocco were included as reference material. The tested\\u000a SSR markers showed a high level of polymorphism. A total of 343 alleles were detected at the 16 loci. The number of alleles\\u000a per

Sakina Elshibli; Helena Korpelainen

2008-01-01

372

Discrimination of Portuguese grapevines based on microsatellite markers.  

PubMed

A set of 46 grapevine denominations was genotyped at 11 microsatellite loci in order to discriminate them. Ninety four alleles with a mean number of 8.55 alleles per locus were observed in a total of 37 detected unique genotypes. Previously assumed synonyms were confirmed and several cases of homonymy resolved. Comparison of the data obtained in this study with data of 32 genotypes previously reported enabled the detection of three parent offspring relationships, and identified other putative parent/progeny relationships. These data allowed understanding the origin of some Portuguese cultivars. The integration of the obtained data with ampelographic data would be very important for the accurate identification of the Portuguese cultivars and can become a significant tool for the certification of quality wines produced in specific regions. PMID:16876897

Lopes, M S; dos Santos, M Rodrigues; Dias, J E Eiras; Mendonça, D; da Câmara Machado, A

2006-06-21

373

Multiple Heterologies Increase Mitotic Double-Strand Break-Induced Allelic Gene Conversion Tract Lengths in Yeast  

Microsoft Academic Search

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 11 frameshift mutation, with flanking markers defining a 3.4-kbp interval. In some crosses, nine additional phenotypically silent RFLP mutations were present at z100-bp intervals. Increasing heterology from 0.2 to 1% in this interval reduced spontane- ous, but

Jac A. Nickoloff; Douglas B. Sweetser; Jennifer A. Clikeman; Guru Jot Khalsa; Sarah L. Wheeler

374

Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato.  

PubMed

Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ? 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ? 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed. PMID:20603706

Li, Li; Paulo, Maria-João; van Eeuwijk, Fred; Gebhardt, Christiane

2010-07-06

375

Statistical epistasis between candidate gene alleles for complex tuber traits in an association mapping population of tetraploid potato  

PubMed Central

Association mapping using DNA-based markers is a novel tool in plant genetics for the analysis of complex traits. Potato tuber yield, starch content, starch yield and chip color are complex traits of agronomic relevance, for which carbohydrate metabolism plays an important role. At the functional level, the genes and biochemical pathways involved in carbohydrate metabolism are among the best studied in plants. Quantitative traits such as tuber starch and sugar content are therefore models for association genetics in potato based on candidate genes. In an association mapping experiment conducted with a population of 243 tetraploid potato varieties and breeding clones, we previously identified associations between individual candidate gene alleles and tuber starch content, starch yield and chip quality. In the present paper, we tested 190 DNA markers at 36 loci scored in the same association mapping population for pairwise statistical epistatic interactions. Fifty marker pairs were associated mainly with tuber starch content and/or starch yield, at a cut-off value of q ? 0.20 for the experiment-wide false discovery rate (FDR). Thirteen marker pairs had an FDR of q ? 0.10. Alleles at loci encoding ribulose-bisphosphate carboxylase/oxygenase activase (Rca), sucrose phosphate synthase (Sps) and vacuolar invertase (Pain1) were most frequently involved in statistical epistatic interactions. The largest effect on tuber starch content and starch yield was observed for the paired alleles Pain1-8c and Rca-1a, explaining 9 and 10% of the total variance, respectively. The combination of these two alleles increased the means of tuber starch content and starch yield. Biological models to explain the observed statistical epistatic interactions are discussed. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1389-3) contains supplementary material, which is available to authorized users.

Li, Li; Paulo, Maria-Joao; van Eeuwijk, Fred

2010-01-01

376

PARENTAL BONDING AND PARENT-CHILD RELATIONSHIP AMONG TERTIARY STUDENTS  

Microsoft Academic Search

Parental bonding is an important predictor that gives a lot of insight into parent-child relationship. Studies have demonstrated the importance of parent child relationship for adjustment, ranging from attachment during infancy, indiscipline style during childhood and adolescence to parenting style during adulthood. This paper aims to investigate the relationship between parental bonding and parent-child relationship among tertiary level students in

TAM CAI LIAN; YEOH SI HAN

377

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

378

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

379

Personality and parenting style in parents of adolescents  

Microsoft Academic Search

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, indulgent, and uninvolved) from scores on the underlying dimensions of support and

Rose M. E. Huver; Roy Otten; Hein de Vries; Rutger C. M. E. Engels

2010-01-01

380

Parental Feeding Practices Predict Authoritative, Authoritarian, and Permissive Parenting Styles  

Microsoft Academic Search

BackgroundOur goal was to identify how parental feeding practices from the nutrition literature link to general parenting styles from the child development literature to understand how to target parenting practices to increase effectiveness of interventions. Stand-alone parental feeding practices could be targeted independently. However, parental feeding practices linked to parenting styles require interventions treating underlying family dynamics as a whole.

Laura Hubbs-Tait; Tay Seacord Kennedy; Melanie C. Page; Glade L. Topham; Amanda W. Harrist

2008-01-01

381

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

382

Variable Microsatellite Markers for Genotyping Tree Shrews, Tupaia, and their Potential Use in Genetic Studies of Fragmented Populations  

Microsoft Academic Search

We describe the sequences of six primer pairs for the PCR amplification of nuclear microsatellite markers in the tree shrews, Tupaia glis and T. belangeri. Multilocus genotyping based on non-destructive DNA sampling of live-trapped animals reveals high allelic variability (A) and heterozygosity (He) at these loci. Such characteristics make these genetic markers ideal for linkage mapping and comparative genomics, and

Sukamol Srikwan; Kristina Hufford; Lori Eggert; David S Woodruff

2002-01-01

383

Linkage Analysis of Quantitative Traits in an Interspecific Cross of Tomato (Lycopersicon esculentum X Lycopersicon pimpinell~olium) by Means of Genetic Markers  

Microsoft Academic Search

Linkage relationships between loci affecting quantitative traits (QTL) and marker loci were examined in an interspecific cross between Lycopersicon esculentum and Lycopersicon pimpinellifolium. Parental lines differed for six morphological markers and for four electrophoretic markers. Almost 1700 F-2 plants were scored with respect to the genetic markers and also with respect to 18 quantitative traits. Major genes affecting the quantitative

J. I. Weller; M. Soller; T. Brody

1988-01-01

384

Schizophrenia susceptibility alleles are enriched for alleles that affect gene expression in adult human brain  

Microsoft Academic Search

It is widely thought that alleles that influence susceptibility to common diseases, including schizophrenia, will frequently do so through effects on gene expression. As only a small proportion of the genetic variance for schizophrenia has been attributed to specific loci, this remains an unproven hypothesis. The International Schizophrenia Consortium (ISC) recently reported a substantial polygenic contribution to that disorder, and

A L Richards; L Jones; V Moskvina; G Kirov; P V Gejman; D F Levinson; A R Sanders; S Purcell; P M Visscher; N Craddock; M J Owen; P Holmans; M C O'Donovan

2012-01-01

385

Ten Novel HLA-DRB1 Alleles and One Novel DRB3 Allele.  

National Technical Information Service (NTIS)

Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the variants are single-nucleotide substitutions, four resulting in an amino acid change (DRB1*1145, *1148, *0828 and *1514) and four with silent substitutions (DRB1*040504, *130103, *160502 ...

A. M. Lazaro J. Ng J. R. Moraes M. E. Moraes N. K. Steiner

2006-01-01

386

Functional association of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive  

Microsoft Academic Search

In mammals, a subset of genes inherit gametic marks that establish parent of origin-dependent expression patterns in the soma ([1] and references therein). The currently most extensively studied examples of this phenomenon, termed genomic imprinting, are the physically linked Igf2 (insulin-like growth factor II) and H19 genes, which are expressed mono-allelically from opposite parental alleles [1,2]. The repressed status of

Chandrasekhar Kanduri; Vinod Pant; Dmitri Loukinov; Elena Pugacheva; Chen-Feng Qi; Alan Wolffe; Rolf Ohlsson; Victor V. Lobanenkov

2000-01-01

387

Excess of transmission of the G allele of the -1438A/G polymorphism of the 5-HT2A receptor gene in patients with schizophrenia responsive to antipsychotics  

PubMed Central

Background The -1438A/G polymorphism of the 5-HT2A gene has been found to be associated with clinical response to clozapine and other second generation antipsychotics. Testing the impact of this marker on response to first generation antipsychotics (which have a lower affinity for the 5-HT2A receptor) provides the opportunity to help disentangling the two different roles that this polymorphism might have. A psychopharmacogenetic role should be detected only for antipsychotics with high affinity to the 5-HT2A receptor (therefore to second generation antipsychotics). An alternative role would imply tagging a subgroup of patients responsive to any antipsychotic, whatever their affinity, meaning that the association is more depending on non pharmacological charaterictics, such as clinical specificities. Methods A family-based sample of 100 Algerian patients with schizophrenia (according to DSM-IV criteria) and their 200 biological parents was recruited, in order to avoid stratification biases. Patients were all treated, or have been treated, by conventional antipsychotics (mainly haloperidol) for at least four weeks, at appropriate dosage. May and Dencker scale was used to distinguish responders and non responders. Results No allele of the -1438A/G polymorphism of the 5-HT2A gene was transmitted in excess (50 transmitted for 38 untransmitted) in the whole sample of patients with schizophrenia (p = .90). In contrast, a significant excess of transmission of the G allele was observed (p = .02) in the subgroup of patients with good treatment response (17 transmitted for 6 untransmitted). Conclusion Using a TDT approach, we showed that the G allele of the -1438A/G polymorphism of the gene coding for the 5-HT2A receptor was associated to schizophrenia with good response to conventional antipsychotics, although this conclusion is based on 88 informative patients only. Because previous data showed the same result with atypical antipsychotics, it can be concluded that the G allele tags a subgroup of schizophrenic patients with greater chance of improvement with antipsychotics of either type.

Benmessaoud, Dalila; Hamdani, Nora; Boni, Claudette; Ramoz, Nicolas; Hamon, Michel; Kacha, Farid; Gorwood, Philip

2008-01-01

388

Maternal transmission of a humanised Igf2r allele results in an Igf2 dependent hypomorphic and non-viable growth phenotype.  

PubMed

The cation independent mannose 6-phosphate/insulin-like growth factor 2 receptor (IGF2R) functions in the transportation and regulation of insulin-like growth factor 2 (IGF2) and mannose 6-phosphate modified proteins. The relative and specific titration of IGF2 by high affinity binding of IGF2R represents a mechanism that supports the parental conflict theory of genomic imprinting. Imprinting of Igf2 (paternal allele expressed) and Igf2r (maternal allele expressed) arose to regulate the relative supply of both proteins. Experiments in the mouse have established that loss of the maternal allele of Igf2r results in disproportionate growth and peri-natal lethality. In order to systematically investigate the consequences of loss of function and of hypomorphic alleles of Igf2r on growth functions, we introduced a conditional human IGF2R exon 3-48 cDNA into the intron 2 region of murine Igf2r. Here we show that the knock-in construct resulted in over-growth when the humanised Igf2r allele was maternally transmitted, a phenotype that was rescued by either paternal transmission of the humanised allele, expression of a wild-type paternal allele or loss of function of Igf2. We also show that expression of IGF2R protein was reduced to less than 50% overall in tissues previously known to be Igf2 growth dependent. This occurred despite the detection of mouse derived peptides, suggesting that trans-splicing of the knock-in human cDNA with the endogenous maternal mouse Igf2r allele. The phenotype following maternal transmission of the humanised allele resulted in overgrowth of the embryo, heart and placenta with partial peri-natal lethality, suggesting that further generation of hypomorphic Igf2r alleles are likely to be at the borderline of maintaining Igf2 dependent viability. PMID:23468951

Hughes, Jennifer; Frago, Susana; Bühnemann, Claudia; Carter, Emma J; Hassan, A Bassim

2013-02-28

389

Maternal Transmission of a Humanised Igf2r Allele Results in an Igf2 Dependent Hypomorphic and Non-Viable Growth Phenotype  

PubMed Central

The cation independent mannose 6-phosphate/insulin-like growth factor 2 receptor (IGF2R) functions in the transportation and regulation of insulin-like growth factor 2 (IGF2) and mannose 6-phosphate modified proteins. The relative and specific titration of IGF2 by high affinity binding of IGF2R represents a mechanism that supports the parental conflict theory of genomic imprinting. Imprinting of Igf2 (paternal allele expressed) and Igf2r (maternal allele expressed) arose to regulate the relative supply of both proteins. Experiments in the mouse have established that loss of the maternal allele of Igf2r results in disproportionate growth and peri-natal lethality. In order to systematically investigate the consequences of loss of function and of hypomorphic alleles of Igf2r on growth functions, we introduced a conditional human IGF2R exon 3–48 cDNA into the intron 2 region of murine Igf2r. Here we show that the knock-in construct resulted in over-growth when the humanised Igf2r allele was maternally transmitted, a phenotype that was rescued by either paternal transmission of the humanised allele, expression of a wild-type paternal allele or loss of function of Igf2. We also show that expression of IGF2R protein was reduced to less than 50% overall in tissues previously known to be Igf2 growth dependent. This occurred despite the detection of mouse derived peptides, suggesting that trans-splicing of the knock-in human cDNA with the endogenous maternal mouse Igf2r allele. The phenotype following maternal transmission of the humanised allele resulted in overgrowth of the embryo, heart and placenta with partial peri-natal lethality, suggesting that further generation of hypomorphic Igf2r alleles are likely to be at the borderline of maintaining Igf2 dependent viability.

Buhnemann, Claudia; Carter, Emma J.; Hassan, A. Bassim

2013-01-01

390

Parenting and Children's Cognitive Development  

Microsoft Academic Search

This study investigated the differences in parenting between the parents of gifted children and the parents of non-gifted children in the context of some parenting dimensions, such as parents' educational values, parent-child interaction, parents' efficacy for their children, independence training, health maintenance, expectation and socialization. An 88-item questionnaire concerning the above parenting dimensions and a corresponding 88-item questionnaire concerning children's

Jing He; Jiannong Shi; Bin Luo

2006-01-01

391

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

392

Allele frequencies of a SNP and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene  

Microsoft Academic Search

Allele frequencies for a SNP (rs17822931) and a 27-bp deletion that are the determinant of earwax type in the ABCC11 gene were investigated in seven Japanese, one Korean, and one German populations. The SNP will be useful as one of ancestry information markers, because it showed marked difference in frequencies between Asian and European populations.

Takashi Kitano; Isao Yuasa; Kentaro Yamazaki; Nori Nakayashiki; Aya Miyoshi; Kyung Sook Park; Kazuo Umetsu

2008-01-01

393

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

394

Inbreeding of Bottlenecked Butterfly Populations: Estimation Using the Likelihood of Changes in Marker Allele Frequencies  

Microsoft Academic Search

Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimen- tally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after found- ing events of 2, 6, 20, or 300 individuals, each bottleneck size being replicated at least four times. Heterozygosity fell more than expected, though not significantly so, but this traditional measure of

Ilik J. Saccheri; Ian J. Wilson; Richard A. Nichols; Michael W. Bruford; Paul M. Brakefield

1999-01-01

395

Microsatellite markers linked to stem rust resistance allele Sr9a in wheat  

Technology Transfer Automated Retrieval System (TEKTRAN)

Stem rust of wheat, caused by Puccinia graminis Pers.: Pers. f.sp. tritici Eriks. & E Henn., is one of the most serious diseases of wheat worldwide. Host resistance is more effective and durable when several stem rust resistance (Sr) genes are pyramided into a single genotype, a process that can be ...

396

Predictors of Depressive Symptoms in Parents of Chronically Ill Children Admitted to the Pediatric Intensive Care Unit  

Microsoft Academic Search

Objective: To identify factors in the pediatric intensive care unit (PICU) patient population that may result in increased risk of depressive symptoms in their parents. Design: Six-month, prospective, observational study in a tertiary-level PICU on parents of chronically ill children admitted to PICU. Parents were assessed by background questionnaire and standardized depression scale. Results: Data was compared to various markers

Karen R. Fauman; Kenneth J. Pituch; Yong Y. Han; Matthew F. Niedner; Janella Reske; Ann Marie LeVine

2011-01-01

397

Use of Allele-Specific FAIRE to Determine Functional Regulatory Polymorphism Using Large-Scale Genotyping Arrays  

PubMed Central

Following the widespread use of genome-wide association studies (GWAS), focus is turning towards identification of causal variants rather than simply genetic markers of diseases and traits. As a step towards a high-throughput method to identify genome-wide, non-coding, functional regulatory variants, we describe the technique of allele-specific FAIRE, utilising large-scale genotyping technology (FAIRE-gen) to determine allelic effects on chromatin accessibility and regulatory potential. FAIRE-gen was explored using lymphoblastoid cells and the 50,000 SNP Illumina CVD BeadChip. The technique identified an allele-specific regulatory polymorphism within NR1H3 (coding for LXR-?), rs7120118, coinciding with a previously GWAS-identified SNP for HDL-C levels. This finding was confirmed using FAIRE-gen with the 200,000 SNP Illumina Metabochip and verified with the established method of TaqMan allelic discrimination. Examination of this SNP in two prospective Caucasian cohorts comprising 15,000 individuals confirmed the association with HDL-C levels (combined beta?=?0.016; p?=?0.0006), and analysis of gene expression identified an allelic association with LXR-? expression in heart tissue. Using increasingly comprehensive genotyping chips and distinct tissues for examination, FAIRE-gen has the potential to aid the identification of many causal SNPs associated with disease from GWAS.

Smith, Andrew J. P.; Howard, Philip; Shah, Sonia; Eriksson, Per; Stender, Stefan; Giambartolomei, Claudia; Folkersen, Lasse; Tybjaerg-Hansen, Anne; Kumari, Meena; Palmen, Jutta; Hingorani, Aroon D.; Talmud, Philippa J.; Humphries, Steve E.

2012-01-01

398

Evaluation of DNA Pooling for the Estimation of Microsatellite Allele Frequencies: A Case Study Using Striped Bass (Morone saxatilis)  

PubMed Central

Using striped bass (Morone saxatilis) and six multiplexed microsatellite markers, we evaluated procedures for estimating allele frequencies by pooling DNA from multiple individuals, a method suggested as cost-effective relative to individual genotyping. Using moment-based estimators, we estimated allele frequencies in experimental DNA pools and found that the three primary laboratory steps, DNA quantitation and pooling, PCR amplification, and electrophoresis, accounted for 23, 48, and 29%, respectively, of the technical variance of estimates in pools containing DNA from 2–24 individuals. Exact allele-frequency estimates could be made for pools of sizes 2–8, depending on the locus, by using an integer-valued estimator. Larger pools of size 12 and 24 tended to yield biased estimates; however, replicates of these estimates detected allele frequency differences among pools with different allelic compositions. We also derive an unbiased estimator of Hardy–Weinberg disequilibrium coefficients that uses multiple DNA pools and analyze the cost-efficiency of DNA pooling. DNA pooling yields the most potential cost savings when a large number of loci are employed using a large number of individuals, a situation becoming increasingly common as microsatellite loci are developed in increasing numbers of taxa.

Skalski, Garrick T.; Couch, Charlene R.; Garber, Amber F.; Weir, Bruce S.; Sullivan, Craig V.

2006-01-01

399

Isolation and characterization of microsatellite markers for the ornamental discus fish Symphysodon discus and cross-species amplification in other Heroini cichlid species  

Microsoft Academic Search

The discus fishes (Symphysodon spp.) are economically important ornamental species. Thirteen microsatellite markers were developed from a CT12- and CA12-enriched whole genomic DNA library of Symphysodon discus. Allelic variability was tested on 44 individuals of two species (S. discus and S. aequifasciatus). Allelic richness ranged from two to 11 alleles per locus and observed heterozygosities from 0.083 to 0.998. All

MANUELLA VILLAR AMADO; TOMAS HRBEK; WALESKA GRAVENA; CLEITON FANTIN; ENEDINA NOGUEIRA DE ASSUNÇÃO; SPARTACO ASTOLFI-FILHO; IZENI P. FARIAS

2008-01-01

400

A series of eIF4E alleles at the Bc-3 locus are associated with recessive resistance to Clover yellow vein virus in common bean.  

PubMed

Clover yellow vein virus (ClYVV) is capable of causing severe damage to common bean (Phaseolus vulgaris L.) production worldwide. The snap bean market class is particularly vulnerable because infection may lead to distortion and necrosis of the fresh green pods and rejection of the harvest. Three putatively independent recessive genes (cyv, desc, bc-3) have been reported to condition resistance to ClYVV; however, their allelic relationships have not been resolved. We identified, evaluated, and characterized the phenotypic and molecular genetic variation present in 21 informative common bean genotypes for resistance to ClYVV. Allelism testing phenotypes from multiple populations provided clear evidence that the three genes were a series of recessive alleles at the Bc-3 locus that condition unique potyvirus strain- and species-specific resistance spectra. Candidate gene analysis revealed complete association between the recessive resistance alleles and unique patterns of predicted amino acid substitutions in P. vulgaris eukaryotic translation initiation factor 4E (PveIF4E). This led to the discovery and characterization of two novel PveIF4E alleles associated with resistance to ClYVV, PveIF4E (3) , and PveIF4E (4) . We developed KASPar allele-specific SNP genotyping assays and demonstrated their ability to accurately detect and differentiate all of the PveIF4E haplotypes present in the germplasm, allelism testing, and in three separate segregating populations. The results contribute to an enhanced understanding and accessibility of the important potyvirus resistance conditioned by recessive alleles at Bc-3. The KASPar assays should be useful to further enable germplasm exploration, allelic discrimination, and marker-assisted introgression of bc-3 alleles in common bean. PMID:23933781

Hart, John P; Griffiths, Phillip D

2013-08-11

401

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

2010-12-09

402

Construction of Bald Eagle (Haliaeetus leucocephalus) Hal01 Locus Allelic Ladder  

Microsoft Academic Search

Allelic ladders contain all the alleles at a given locus and since the components of the allelic ladder and the sample fragments have the same length and sequence, sizing is very accurate when conducted with an allelic ladder. Allelic ladders are therefore very useful in population genetics studies. For this study, an allelic ladder for the Bald Eagle, Haliaeetus leucocephalus,

Manali Patel

2012-01-01

403

Development of EST-based new SSR markers in seabuckthorn  

Microsoft Academic Search

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\\u000a nine primer pairs in H. rhamnoides genotypes and by eleven primer pairs in H. salicifolia genotypes. None of the thirty primer pairs detected polymorphism

Ankit Jain; Rajesh Ghangal; Atul Grover; Saurabh Raghuvanshi; Prakash C. Sharma

2010-01-01

404

Mutations in the arylsulfatase A pseudodeficiency allele causing metachromatic leukodystrophy.  

PubMed Central

We identified a patient suffering from late infantile metachromatic leukodystrophy who genetically seemed to be homozygous for the mutations signifying the arylsulfatase A pseudodeficiency allele. Homozygosity for the pseudodeficiency allele is associated with low arylsulfatase A activity but does not cause a disease. Analysis of the arylsulfatase A gene in this patient revealed a C----T transition in exon 2, causing a Ser 96----Phe substitution in addition to the sequence alterations causing arylsulfatase A pseudodeficiency. Although this mutation was found only in 1 of 78 metachromatic leukodystrophy patients tested, five more patients were identified who seemed hetero- or homozygous for the pseudodeficiency allele. The existence of nonfunctional arylsulfatase A alleles derived from the pseudodeficiency allele calls for caution when the diagnosis of arylsulfatase A pseudodeficiency is based solely on the identification of the mutations characterizing the pseudodeficiency allele. Images Figure 1 Figure 2 Figure 3

Gieselmann, V; Fluharty, A L; T?nnesen, T; Von Figura, K

1991-01-01

405

Parent Stress and Its Relation to Parent Perceptions of Communication following Parent-Coached Language Intervention  

ERIC Educational Resources Information Center

The effects of a parent-coached language intervention on parent stress and its relation to parent perceptions of communication development were examined in 60 parents of toddlers with developmental delays. Results indicated that overall parent stress was not high prior to or following language intervention. Parents' perceptions about the severity…

Smith, Ashlyn L.; Romski, Mary Ann; Sevcik, Rose A.; Adamson, Lauren B.; Bakeman, Roger

2011-01-01

406

Novel tetra-nucleotide microsatellite DNA markers for assessing the evolutionary genetics and demographics of Northern Snakehead ( Channa argus ) invading North America  

Microsoft Academic Search

We document the isolation and characterization of 19 tetra-nucleotide microsatellite DNA markers in northern snakehead (Channa argus) fish that recently colonized Meadow Lake, New York City, New York. These markers displayed moderate levels of allelic diversity\\u000a (averaging 6.8 alleles\\/locus) and heterozygosity (averaging 74.2%). Demographic analyses suggested that the Meadow Lake collection\\u000a has not achieved mutation-drift equilibrium. These results were consistent

T. L. King; R. L. Johnson

2011-01-01

407

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

408

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

Technology Transfer Automated Retrieval System (TEKTRAN)

Microsatellite markers (MS) have traditionally been used for parental verification and are still the international standard in spite of their higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP) -based assays. Despite domestic and international demands fr...

409

Association between ACE D allele and elite short distance swimming  

Microsoft Academic Search

The influence of ACE gene on athletic performance has been widely explored, and most of the published data refers to an I\\/D\\u000a polymorphism leading to the presence (I allele) or absence (D allele) of a 287-bp sequence in intron 16, determining ACE activity\\u000a in serum and tissues. A higher I allele frequency has been reported among elite endurance athletes, while

Aldo Matos Costa; António José Silva; Nuno Domingos Garrido; Hugo Louro; Ricardo Jacó de Oliveira; Luiza Breitenfeld

2009-01-01

410

Parenting Beliefs, Parental Stress, and Social Support Relationships  

Microsoft Academic Search

The present study built on prior research by examining the relationship of parental stress and social support to parenting\\u000a beliefs and behaviors. A sample of 87 parents provided their views concerning the importance of parenting characteristics\\u000a as well as their level of parental stress and perceived social support. These parents completed the Parent Behavior Importance\\u000a Questionnaire-Revised, as well as the

Melissa Respler-Herman; Barbara A. Mowder; Anastasia E. Yasik; Renee Shamah

2009-01-01

411

Power of Daughter and Granddaughter Designs for Determining Linkage Between Marker Loci and Quantitative Trait Loci in Dairy Cattle  

Microsoft Academic Search

ABSTRACT There is considerable interest in bo- vine DNA-level polymorphic marker loci as a means of mapping quantitative trait loci (QTL) of economic,importance in cattle. Progeny of a sire heterozygous for both a marker locus and a linked QTL, which,inherit different alleles for the marker, will have different trait means. Based on this, power to detect QTL, as , grandsire

J. I. Weller; Y. Kashi; M. Soller

1990-01-01

412

Molecular characterization of the SCAR markers tightly linked to the Tm2 locus of the genus Lycopersicon  

Microsoft Academic Search

The Tm-2 gene and its alleles conferring tomato mosaic virus resistance in tomato originate from Lycopersicon peruvianum, a wild relative of tomato. DNA fragments of several RAPD markers tightly linked with the Tm-2 locus in tomato were successfully cloned and sequenced. Subsequently, the 24-mer oligonucleotide primer pairs of the SCAR\\u000a markers corresponding to the RAPD markers were designed based on

Sobir; T. Ohmori; M. Murata; F. Motoyoshi

2000-01-01

413

Toward fully automated genotyping: genotyping microsatellite markers by deconvolution.  

PubMed

Dense genetic linkage maps have been constructed for the human and mouse genomes, with average densities of 2.9 cM and 0.35 cM, respectively. These genetic maps are crucial for mapping both Mendelian and complex traits and are useful in clinical genetic diagnosis. Current maps are largely comprised of abundant, easily assayed, and highly polymorphic PCR-based microsatellite markers, primarily dinucleotide (CA)n repeats. One key limitation of these length polymorphisms is the PCR stutter (or slippage) artifact that introduces a