These are representative sample records from Science.gov related to your search topic.
For comprehensive and current results, perform a real-time search at Science.gov.
1

Relative predispositional effects (RPEs) of marker alleles with disease: HLA-DR alleles and Graves disease.  

PubMed Central

A method is described to reveal the relative predispositional effects (RPEs) (predisposing, protective, or neutral) of the HLA alleles or of any other marker system that is associated with a disease. When the disease is associated with two or more alleles of a locus, the RPE method identifies the associations sequentially according to their strength; thus the problem that a strong association with one allele can create misleading deviations in the frequencies of other alleles is alleviated. Using this method, we have examined the relative effects of HLA-DR alleles in susceptibility to Graves disease in the Caucasian population. The well-established positive association with DR3 was confirmed as the strongest effect. In addition, a negative association was found between DR5 and Graves disease. The reduced frequency of DR5 among patients is statistically significant and is not a result of the increase in DR3. Finally, when patients were divided according to the presence or absence of eye disease, the latter showed a significant increase in the frequency of DR4. With family data, linkage to HLA of Graves disease was established in both Caucasian and Chinese families by the sib-pair method. PMID:2491013

Payami, H; Joe, S; Farid, N R; Stenszky, V; Chan, S H; Yeo, P P; Cheah, J S; Thomson, G

1989-01-01

2

Development of ?-Carotene Rich Maize Hybrids through Marker-Assisted Introgression of ?-carotene hydroxylase Allele  

PubMed Central

Development of vitamin A-rich cereals can help in alleviating the widespread problem of vitamin A deficiency. We report here significant enhancement of kernel ?-carotene in elite maize genotypes through accelerated marker-assisted backcross breeding. A favourable allele (543 bp) of the ?-carotene hydroxylase (crtRB1) gene was introgressed in the seven elite inbred parents, which were low (1.4 µg/g) in kernel ?-carotene, by using a crtRB1-specific DNA marker for foreground selection. About 90% of the recurrent parent genome was recovered in the selected progenies within two backcross generations. Concentration of ?-carotene among the crtRB1-introgressed inbreds varied from 8.6 to 17.5 µg/g - a maximum increase up to 12.6-fold over recurrent parent. The reconstituted hybrids developed from improved parental inbreds also showed enhanced kernel ?-carotene as high as 21.7 µg/g, compared to 2.6 µg/g in the original hybrid. The reconstituted hybrids evaluated at two locations possessed similar grain yield to that of original hybrids. These ?-carotene enriched high yielding hybrids can be effectively utilized in the maize biofortification programs across the globe. PMID:25486271

Muthusamy, Vignesh; Hossain, Firoz; Thirunavukkarasu, Nepolean; Choudhary, Mukesh; Saha, Supradip; Bhat, Jayant S.; Prasanna, Boddupalli M.; Gupta, Hari S.

2014-01-01

3

Parental allelic variation at COL6A1 and congenital heart defects in trisomy 21  

SciTech Connect

Overt congenital heart defects (CHD) affect over 40% of newborns with Down syndrome. On the hypothesis that genetic variation on chromosome 21 determines this clinical variability, we studied a CHD candidate locus (COL6A1) on 21q22.3. We studied three RFLP loci in COL6A1 in 37 families of known British/Irish population of ancestral origin, and in population-matched controls. Each family had a child with trisomy 21 with or without accompanying congenital heart defect (CHD). Parental and meiotic origin of nondisjunction were determined using peri-centromeric markers. For the analysis, we considered groups of families with trisomic children with and without CHD, and subsets of nondisjoining and disjoining parents. Parental genotypes at nine control RFLP loci on chromosome 21 showed no association with CHD in the trisomic child. By contrast, parental genotypes at all three individual RFLP loci within COL6A1 showed statistically significant association with the trisomic child`s CHD status. Pairwise consideration of these loci in groups of families of trisomic children with and without CHD showed subsets of nondisjoining and disjoining parents to have different linkage disequilibrium patterns at these loci than population-matched controls. This suggests that the COL6A1 alleles of the parents are not representative of the population as a whole. Consideration of all three loci together as haplotypes supports this conclusion. Four results suggest that a functional mutation within, or in linkage disequilibrium with COL6A1 influences CHD outcome in trisomy 21.

Kessling, A.M.; Howard, C.M.; Farrer, M.J. [St. Mary`s Hospital Medical School, London (United Kingdom)] [and others

1994-09-01

4

On coding genotypes for genetic markers with multiple alleles in genetic association study of quantitative traits  

PubMed Central

Background In genetic association study of quantitative traits using F? models, how to code the marker genotypes and interpret the model parameters appropriately is important for constructing hypothesis tests and making statistical inferences. Currently, the coding of marker genotypes in building F? models has mainly focused on the biallelic case. A thorough work on the coding of marker genotypes and interpretation of model parameters for F? models is needed especially for genetic markers with multiple alleles. Results In this study, we will formulate F? genetic models under various regression model frameworks and introduce three genotype coding schemes for genetic markers with multiple alleles. Starting from an allele-based modeling strategy, we first describe a regression framework to model the expected genotypic values at given markers. Then, as extension from the biallelic case, we introduce three coding schemes for constructing fully parameterized one-locus F? models and discuss the relationships between the model parameters and the expected genotypic values. Next, under a simplified modeling framework for the expected genotypic values, we consider several reduced one-locus F? models from the three coding schemes on the estimability and interpretation of their model parameters. Finally, we explore some extensions of the one-locus F? models to two loci. Several fully parameterized as well as reduced two-locus F? models are addressed. Conclusions The genotype coding schemes provide different ways to construct F? models for association testing of multi-allele genetic markers with quantitative traits. Which coding scheme should be applied depends on how convenient it can provide the statistical inferences on the parameters of our research interests. Based on these F? models, the standard regression model fitting tools can be used to estimate and test for various genetic effects through statistical contrasts with the adjustment for environmental factors. PMID:21936918

2011-01-01

5

A combined analysis of D22S278 marker alleles in affected sib-pairs: Support for a susceptibility locus for schizophrenia at chromosome 22q12  

SciTech Connect

Several groups have reported weak evidence for linkage between schizophrenia and genetic markers located on chromosome 22q using the lod score method of analysis. However these findings involved different genetic markers and methods of analysis, and so were not directly comparable. To resolve this issue we have performed a combined analysis of genotypic data from the marker D22S278 in multiply affected schizophrenic families derived from 11 independent research groups worldwide. This marker was chosen because it showed maximum evidence for linkage in three independent datasets. Using the affected sib-pair method as implemented by the program ESPA, the combined dataset showed 252 alleles shared compared with 188 alleles not shared (chi-square 9.31, 1df, P = 0.001) where parental genotype data was completely known. When sib-pairs for whom parental data was assigned according to probability were included the number of alleles shared was 514.1 compared with 437.8 not shared (chi-square 6.12, 1df, P = 0.006). Similar results were obtained when a likelihood ratio method for sib-pair analysis was used. These results indicate that there may be a susceptibility locus for schizophrenia at 22q12. 27 refs., 3 tabs.

Gill, M.; Vallada, H.; Collier, D. [Institute of Psychiatry, London (United Kingdom)] [and others] [Institute of Psychiatry, London (United Kingdom); and others

1996-02-16

6

Parent of origin effect and allelic expression imbalance of the serotonin transporter in bipolar disorder and suicidal behaviour.  

PubMed

Suicide and suicidal behaviour are a major health concern worldwide particularly in patients with mood disorders. Family, adoption and twin studies show that genetics influences suicidal behaviour. The serotonin transporter (5HTT) plays an important role in the pathophysiology of mood disorders and may also be involved in suicidal behaviour since 5HTT binding is decreased in the brain of suicide completers. Because the effect of genomic imprinting in the 5HTT gene on suicidal behaviour has not been investigated, we analysed the parent-of-origin effect (POE) of four 5HTT markers and the differential expression of the 5HTT G2651T (rs1042173) alleles in suicide attempters affected by bipolar disorder. We performed a family based association study and ETDT/QTDT analyses of the rs25531, HTTLPR, VNTR-2 and G2651T polymorphisms in 312 nuclear families with at least one subject affected by bipolar disorder. The main outcomes investigated in this study are bipolar disorder diagnosis, suicide attempts, suicidal behaviour severity and age at onset of bipolar disorder. We also compared the allele-specific mRNA levels in lymphoblastoid cells from 13 bipolar suicide attempters and 8 bipolar non-suicide attempters. Allele 2651T was transmitted significantly more often to bipolar patients (P = 0.042). There was no significant difference between maternal and paternal transmission ratios. Furthermore, there was no significant difference in the ratio of T/G-specific mRNA expression between bipolar attempters and non-attempters. These data do not support a role for differential allelic expression of 5HTT for suicidal behaviour in bipolar disorder. Small sample size and the fact that RNA was obtained from lymphoblastoid cell lines were some of the limitations of this study. PMID:21290142

Pinto, Crystal; Souza, Renan P; Lioult, Diane; Semeralul, Mawahib; Kennedy, James L; Warsh, Jerry J; Wong, Albert H; Luca, Vincenzo De

2011-12-01

7

Development of a codominant PCR-based marker for allelic selection of the pink trait in onions (Allium cepa), based on the insertion mutation in the promoter of the anthocyanidin synthase gene.  

PubMed

Bulb color in onions (Allium cepa) is an important trait and is inherited in a complex manner. However, the mechanism of color inheritance is poorly understood at the molecular level. A previous study showed that pink bulb color in onions is inherited as a single recessive trait. This trait is attributable to a significantly reduced transcription of the anthocyanidin synthase (ANS) gene. In this study, we developed a PCR-based marker for an allelic selection of the ANS gene to avoid the laborious progeny tests traditionally employed. To identify polymorphisms between pink and red alleles of the ANS gene, promoter sequences of both alleles were isolated. There was 97% nucleotide sequence identity between the promoter sequences of the two alleles. A 390-bp insertion was identified 632 bp upstream from the putative transcription start site in the pink allele. A pair of primers was designed on the flanking sequences of the inserted region and utilized as a PCR-based marker for allelic selection of the ANS gene. The reliability of the marker was tested using parents, F1 hybrids, and F3 lines whose genotypes had been identified by progeny tests. The marker was also used to evaluate the distribution of the pink allele in white and yellow breeding lines. The results indicated that a majority of the breeding lines tested were homozygous recessive. PMID:15650815

Kim, Sunggil; Yoo, Kil-Sun; Pike, Leonard M

2005-02-01

8

Development of a co-dominant, PCR-based marker for allelic selection of the pink trait in onions (Allium cepa), based on the insertion mutation in the promoter of the anthocyanidin synthase gene.  

PubMed

Bulb color in onions (Allium cepa) is an important trait and is inherited in a complex manner. However, the mechanism of color inheritance is poorly understood at the molecular level. A previous study showed that pink bulb color in onions is inherited as a single recessive trait. This trait is attributable to a significantly reduced transcription of the anthocyanidin synthase (ANS) gene. In this study, we developed a PCR-based marker for an allelic selection of the ANS gene to avoid the laborious progeny tests traditionally employed. To identify polymorphisms between pink and red alleles of the ANS gene, promoter sequences of both alleles were isolated. There was 97% nucleotide sequence identity between the promoter sequences of the two alleles. A 390-bp insertion was identified 632 bp upstream from the putative transcription start site in the pink allele. A pair of primers was designed on the flanking sequences of the inserted region and utilized as a PCR-based marker for allelic selection of the ANS gene. The reliability of the marker was tested using parents, F1 hybrids, and F3 lines whose genotypes had been identified by progeny tests. The marker was also used to evaluate the distribution of the pink allele in white and yellow breeding lines. The results indicated that a majority of the breeding lines tested were homozygous recessive. PMID:15660238

Kim, Sunggil; Yoo, Kil-Sun; Pike, Leonard M

2005-02-01

9

A and MdMYB1 allele-specific markers controlling apple (Malus x domestica Borkh.) skin color and suitability for marker-assisted selection.  

PubMed

Pre-selection for fruit skin color at the seedling stage would be highly advantageous, with marker-assisted selection offering a potential method for apple pre-selection. A and MdMYB1 alleles are allele-specific DNA markers that are potentially associated with apple skin color, and co-segregate with the Rf and Rni loci, respectively. Here, we assessed the potential application of these 2 alleles for marker-assisted breeding across 30 diverse cultivars and 2 apple seedling progenies. The red skin color phenotype was usually associated with the MdMYB1-1 allele and A(1) allele, respectively, while the 2 molecular markers provided approximately 91% predictability in the 'Fuji' x 'Cripps Pink' and 'Fuji' x 'Gala' progenies. The results obtained from the 30 cultivars and 2 progenies were consistent for the 2 molecular markers. Hence, the results supported that Rf and Rni could be located in a gene cluster, or even correspond to alleles of the same gene. Our results are consistent with the hypothesis that red/yellow dimorphism is controlled by a monogenic system, with the presence of the red anthocyanin pigmentation being dominant. In addition, our results supported that the practical utilization of the 2 function markers to efficiently and accurately select red-skinned apple cultivars in apple scion breeding programs. PMID:25366802

Zhang, X J; Wang, L X; Chen, X X; Liu, Y L; Meng, R; Wang, Y J; Zhao, Z Y

2014-01-01

10

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. PMID:19638216

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

2009-01-01

11

Prediction of hybrid performance in maize using molecular markers and joint analyses of hybrids and parental inbreds.  

PubMed

The identification of superior hybrids is important for the success of a hybrid breeding program. However, field evaluation of all possible crosses among inbred lines requires extremely large resources. Therefore, efforts have been made to predict hybrid performance (HP) by using field data of related genotypes and molecular markers. In the present study, the main objective was to assess the usefulness of pedigree information in combination with the covariance between general combining ability (GCA) and per se performance of parental lines for HP prediction. In addition, we compared the prediction efficiency of AFLP and SSR marker data, estimated marker effects separately for reciprocal allelic configurations (among heterotic groups) of heterozygous marker loci in hybrids, and imputed missing AFLP marker data for marker-based HP prediction. Unbalanced field data of 400 maize dent x flint hybrids from 9 factorials and of 79 inbred parents were subjected to joint analyses with mixed linear models. The inbreds were genotyped with 910 AFLP and 256 SSR markers. Efficiency of prediction (R (2)) was estimated by cross-validation for hybrids having no or one parent evaluated in testcrosses. Best linear unbiased prediction of GCA and specific combining ability resulted in the highest efficiencies for HP prediction for both traits (R (2) = 0.6-0.9), if pedigree and line per se data were used. However, without such data, HP for grain yield was more efficiently predicted using molecular markers. The additional modifications of the marker-based approaches had no clear effect. Our study showed the high potential of joint analyses of hybrids and parental inbred lines for the prediction of performance of untested hybrids. PMID:19916002

Schrag, Tobias A; Möhring, Jens; Melchinger, Albrecht E; Kusterer, Barbara; Dhillon, Baldev S; Piepho, Hans-Peter; Frisch, Matthias

2010-01-01

12

An improved allele-specific PCR primer design method for SNP marker analysis and its application  

PubMed Central

Background Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3’end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge. Results In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3’ end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species. Conclusion The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low- to moderate- throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops. PMID:22920499

2012-01-01

13

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

PubMed

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. PMID:20561550

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

2010-10-01

14

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

15

Inbreeding of bottlenecked butterfly populations. Estimation using the likelihood of changes in marker allele frequencies.  

PubMed Central

Polymorphic enzyme and minisatellite loci were used to estimate the degree of inbreeding in experimentally bottlenecked populations of the butterfly, Bicyclus anynana (Satyridae), three generations after founding 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 the degree of inbreeding did not make full use of the information from genetic markers. It proved more informative to estimate directly the probability distribution of a measure of inbreeding, sigma2, the variance in the number of descendants left per gene. In all bottlenecked lines, sigma2 was significantly larger than in control lines (300 founders). We demonstrate that this excess inbreeding was brought about both by an increase in the variance of reproductive success of individuals, but also by another process. We argue that in bottlenecked lines linkage disequilibrium generated by the small number of haplotypes passing through the bottleneck resulted in hitchhiking of particular marker alleles with those haplotypes favored by selection. In control lines, linkage disequilibrium was minimal. Our result, indicating more inbreeding than expected from demographic parameters, contrasts with the findings of previous (Drosophila) experiments in which the decline in observed heterozygosity was slower than expected and attributed to associative overdominance. The different outcomes may both be explained as a consequence of linkage disequilibrium under different regimes of inbreeding. The likelihood-based method to estimate inbreeding should be of wide applicability. It was, for example, able to resolve small differences in sigma2 among replicate lines within bottleneck-size treatments, which could be related to the observed variation in reproductive viability. PMID:10049922

Saccheri, I J; Wilson, I J; Nichols, R A; Bruford, M W; Brakefield, P M

1999-01-01

16

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.  

PubMed

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P?parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and ?-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition. PMID:25231870

Perry, John R B; Day, Felix; Elks, Cathy E; Sulem, Patrick; Thompson, Deborah J; Ferreira, Teresa; He, Chunyan; Chasman, Daniel I; Esko, Tõnu; Thorleifsson, Gudmar; Albrecht, Eva; Ang, Wei Q; Corre, Tanguy; Cousminer, Diana L; Feenstra, Bjarke; Franceschini, Nora; Ganna, Andrea; Johnson, Andrew D; Kjellqvist, Sanela; Lunetta, Kathryn L; McMahon, George; Nolte, Ilja M; Paternoster, Lavinia; Porcu, Eleonora; Smith, Albert V; Stolk, Lisette; Teumer, Alexander; Tšernikova, Natalia; Tikkanen, Emmi; Ulivi, Sheila; Wagner, Erin K; Amin, Najaf; Bierut, Laura J; Byrne, Enda M; Hottenga, Jouke-Jan; Koller, Daniel L; Mangino, Massimo; Pers, Tune H; Yerges-Armstrong, Laura M; Hua Zhao, Jing; Andrulis, Irene L; Anton-Culver, Hoda; Atsma, Femke; Bandinelli, Stefania; Beckmann, Matthias W; Benitez, Javier; Blomqvist, Carl; Bojesen, Stig E; Bolla, Manjeet K; Bonanni, Bernardo; Brauch, Hiltrud; Brenner, Hermann; Buring, Julie E; Chang-Claude, Jenny; Chanock, Stephen; Chen, Jinhui; Chenevix-Trench, Georgia; Collée, J Margriet; Couch, Fergus J; Couper, David; Coviello, Andrea D; Cox, Angela; Czene, Kamila; D'adamo, Adamo Pio; Davey Smith, George; De Vivo, Immaculata; Demerath, Ellen W; Dennis, Joe; Devilee, Peter; Dieffenbach, Aida K; Dunning, Alison M; Eiriksdottir, Gudny; Eriksson, Johan G; Fasching, Peter A; Ferrucci, Luigi; Flesch-Janys, Dieter; Flyger, Henrik; Foroud, Tatiana; Franke, Lude; Garcia, Melissa E; García-Closas, Montserrat; Geller, Frank; de Geus, Eco E J; Giles, Graham G; Gudbjartsson, Daniel F; Gudnason, Vilmundur; Guénel, Pascal; Guo, Suiqun; Hall, Per; Hamann, Ute; Haring, Robin; Hartman, Catharina A; Heath, Andrew C; Hofman, Albert; Hooning, Maartje J; Hopper, John L; Hu, Frank B; Hunter, David J; Karasik, David; Kiel, Douglas P; Knight, Julia A; Kosma, Veli-Matti; Kutalik, Zoltan; Lai, Sandra; Lambrechts, Diether; Lindblom, Annika; Mägi, Reedik; Magnusson, Patrik K; Mannermaa, Arto; Martin, Nicholas G; Masson, Gisli; McArdle, Patrick F; McArdle, Wendy L; Melbye, Mads; Michailidou, Kyriaki; Mihailov, Evelin; Milani, Lili; Milne, Roger L; Nevanlinna, Heli; Neven, Patrick; Nohr, Ellen A; Oldehinkel, Albertine J; Oostra, Ben A; Palotie, Aarno; Peacock, Munro; Pedersen, Nancy L; Peterlongo, Paolo; Peto, Julian; Pharoah, Paul D P; Postma, Dirkje S; Pouta, Anneli; Pylkäs, Katri; Radice, Paolo; Ring, Susan; Rivadeneira, Fernando; Robino, Antonietta; Rose, Lynda M; Rudolph, Anja; Salomaa, Veikko; Sanna, Serena; Schlessinger, David; Schmidt, Marjanka K; Southey, Mellissa C; Sovio, Ulla; Stampfer, Meir J; Stöckl, Doris; Storniolo, Anna M; Timpson, Nicholas J; Tyrer, Jonathan; Visser, Jenny A; Vollenweider, Peter; Völzke, Henry; Waeber, Gerard; Waldenberger, Melanie; Wallaschofski, Henri; Wang, Qin; Willemsen, Gonneke; Winqvist, Robert; Wolffenbuttel, Bruce H R; Wright, Margaret J; Boomsma, Dorret I; Econs, Michael J; Khaw, Kay-Tee; Loos, Ruth J F; McCarthy, Mark I; Montgomery, Grant W; Rice, John P; Streeten, Elizabeth A; Thorsteinsdottir, Unnur; van Duijn, Cornelia M; Alizadeh, Behrooz Z; Bergmann, Sven; Boerwinkle, Eric; Boyd, Heather A; Crisponi, Laura; Gasparini, Paolo; Gieger, Christian; Harris, Tamara B; Ingelsson, Erik; Järvelin, Marjo-Riitta; Kraft, Peter; Lawlor, Debbie; Metspalu, Andres; Pennell, Craig E; Ridker, Paul M; Snieder, Harold; Sørensen, Thorkild I A; Spector, Tim D; Strachan, David P; Uitterlinden, André G; Wareham, Nicholas J; Widen, Elisabeth; Zygmunt, Marek; Murray, Anna; Easton, Douglas F; Stefansson, Kari; Murabito, Joanne M; Ong, Ken K

2014-10-01

17

Citrus (Rutaceae) SNP markers based on Competitive Allele-Specific PCR; transferability across the Aurantioideae subfamily1  

PubMed Central

• Premise of the study: Single nucleotide polymorphism (SNP) markers based on Competitive Allele-Specific PCR (KASPar) were developed from sequences of three Citrus species. Their transferability was tested in 63 Citrus genotypes and 19 relative genera of the subfamily Aurantioideae to estimate the potential of SNP markers, selected from a limited intrageneric discovery panel, for ongoing broader diversity analysis at the intra- and intergeneric levels and systematic germplasm bank characterization. • Methods and Results: Forty-two SNP markers were developed using KASPar technology. Forty-one were successfully genotyped in all of the Citrus germplasm, where intra- and interspecific polymorphisms were observed. The transferability and diversity decreased with increasing taxonomic distance. • Conclusions: SNP markers based on the KASPar method developed from sequence data of a limited intrageneric discovery panel provide a valuable molecular resource for genetic diversity analysis of germplasm within a genus and should be useful for germplasm fingerprinting at a much broader diversity level. PMID:25202535

Garcia-Lor, Andres; Ancillo, Gema; Navarro, Luis; Ollitrault, Patrick

2013-01-01

18

Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.  

PubMed

Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene. PMID:25320555

Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

2014-09-01

19

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

PubMed Central

Allelic diversity of HMW glutenin loci in several studies revealed that allelic combinations affect dough quality. Dx5 + Dy10 subunits are related to good baking quality and Dx2 + Dy12 are related to undesirable baking quality. One of the most regular methods to evaluate the baking quality is SDS-PAGE which is used to improve baking quality labs. Marker-assisted selection is the method which can recognize the alleles related to baking quality and this method is based on polymerase chain reaction. 10 pairs of specific primers related to Dx2, Dx2.1, Dx5, Dy10, and Dy12 subunits were used for recognizing baking quality of some wheat varieties and some mutant genotypes. Only 5 pairs of them could show the specific bands. All subunits were recognized by the primers except Dx2.1. Some of the primers were extracted from previous studies and the others were designed based on D genome subunits of wheat. SDS-PAGE method accomplished having confidence in these marker's results. To realize the effect of mutation, seed storage proteins were measured. It showed that mutation had effect on the amount of seed storage protein on the mutant seeds (which showed polymorphism). PMID:24883389

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

2014-01-01

20

Genetic mapping, marker assisted selection and allelic relationships for the Pu6 gene conferring rust resistance in sunflower  

PubMed Central

Rust resistance in the sunflower line P386 is controlled by Pu6, a gene which was reported to segregate independently from other rust resistant genes, such as R4. The objectives of this work were to map Pu6, to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu6 and R4. Genetic mapping of Pu6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu6 and R4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the Radv/R4/R11/ R13a/R13b/Pu6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene. PMID:25320555

Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

2014-01-01

21

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

E-print Network

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 ...

Gehring, Mary

22

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

PubMed Central

Background Apparent Amylose Content (AAC), regulated by the Waxy gene, represents the key determinant of rice cooking properties. In occidental countries high AAC rice represents the most requested market class but the availability of molecular markers allowing specific selection of high AAC varieties is limited. Results In this study, the effectiveness of available molecular markers in predicting AAC was evaluated in a collection of 127 rice accessions (125 japonica ssp. and 2 indica ssp.) characterized by AAC values from glutinous to 26%. The analyses highlighted the presence of several different allelic patterns identifiable by a few molecular markers, and two of them, i.e., the SNPs at intron1 and exon 6, were able to explain a maximum of 79.5% of AAC variation. However, the available molecular markers haplotypes did not provide tools for predicting accessions with AAC higher than 24.5%. To identify additional polymorphisms, the re-sequencing of the Waxy gene and 1kbp of the putative upstream regulatory region was performed in 21 genotypes representing all the AAC classes identified. Several previously un-characterized SNPs were identified and four of them were used to develop dCAPS markers. Conclusions The addition of the SNPs newly identified slightly increased the AAC explained variation and allowed the identification of a haplotype almost unequivocally associated to AAC higher than 24.5%. Haplotypes at the waxy locus were also associated to grain length and length/width (L/W) ratio. In particular, the SNP at the first intron, which identifies the Wx a and Wx b alleles, was associated with differences in the width of the grain, the L/W ratio and the length of the kernel, most likely as a result of human selection. PMID:24383761

2014-01-01

23

Fine mapping of leaf rust resistance gene LrZH84 using expressed sequence tag and sequence-tagged site markers, and allelism with other genes on wheat chromosome 1B.  

PubMed

Zhou 8425B, possessing the leaf rust resistance gene LrZH84, is an elite wheat (Triticum aestivum) parental line in the Yellow-Huai Valley region of China. In the present study, 2,086 F(2) plants derived from Zhou 8425B/Chinese Spring were used for fine mapping of LrZH84 with expressed sequence tag (EST) and sequence-tagged site (STS) markers. Seventy inter-simple sequence repeat EST and STS markers on 1BL were used to screen the two parents and resistant and susceptible bulks; those polymorphic were used to analyze the entire F(2) population. Three EST markers (BF474863, BE497107, and CD373538) were closely linked to LrZH84, with genetic distances of 0.7, 0.7, and 1.7 cM, respectively. STS marker Hbsf-1 was developed from the sequences of polymerase chain reaction fragments amplified from EST marker BF474863. LrZH84 was 8.19 cM proximal to Lr44, but may be allelic to LrXi and LrG98 although they showed different reactions with some Puccinia triticina pathotypes. PMID:23113548

Zhou, Yue; Xia, Xianchun; He, Zhonghu; Li, Xing; Li, Zaifeng; Liu, Daqun

2013-02-01

24

New Markers from Sugar Metabolism ESTs: Tagging Positive Alleles from Saccharum spontaneum  

Technology Transfer Automated Retrieval System (TEKTRAN)

Limited genetic gains, obtained from breeding for sugar content in different breeding programs worldwide suggest that a plateau has been reached for this trait. One way to overcome this obstacle would be to identify and introduce into commercial germplasm alternative alleles controlling sugar metab...

25

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

PubMed Central

Allopurinol, a commonly prescribed medication for gout and hyperuricemia, is a frequent cause of severe cutaneous adverse reactions (SCAR), which include the drug hypersensitivity syndrome, Stevens–Johnson syndrome, and toxic epidermal necrolysis. The adverse events are unpredictable and carry significant morbidity and mortality. To identify genetic markers for allopurinol–SCAR, we carried out a case-control association study. We enrolled 51 patients with allopurinol–SCAR and 228 control individuals (135 allopurinol-tolerant subjects and 93 healthy subjects from the general population), and genotyped for 823 SNPs in genes related to drug metabolism and immune response. The initial screen revealed strong association between allopurinol–SCAR and SNPs in the MHC region, including BAT3 (encoding HLA-B associated transcript 3), MSH5 (mutS homolog 5), and MICB (MHC class I polypeptide-related sequence B) (P < 10–7). We then determined the alleles of HLA loci A, B, C, and DRB1. The HLA-B*5801 allele was present in all (100%) 51 patients with allopurinol–SCAR, but only in 20 (15%) of 135 tolerant patients [odds ratio 580.3 (95% confidence interval, 34.4–9780.9); corrected P value = 4.7 × 10–24] and in 19 (20%) of 93 of healthy subjects [393.51 (23.23–6665.26); corrected P value = 8.1 × 10–18]. HLA alleles A*3303, Cw*0302, and DRB1*0301 were in linkage disequilibrium and formed an extended haplotype with HLA-B*5801. Our results indicated that allopurinol–SCAR is strongly associated with a genetic predisposition in Han Chinese. In particular, HLA-B*5801 allele is an important genetic risk factor for this life-threatening condition. PMID:15743917

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

2005-01-01

26

[Applicability of microsatellite DNA markers to the parental identification of Hucho taimen (Pallas)].  

PubMed

Using seven pairs of microsatellite markers we studied the relationship between the size of the the candidate groups and the microsatellite paternity testing accuracy by separate breed or the microsatellite paternity appraisal ability by mixed breed. By computer software analysis, the appraisal ability decreased with the candidate groups increase. For the 81 putative parents the microsatellite paternity testing accuracy was 80% and the microsatellite paternity appraisal ability was 78.9%; for the 9 putative parents, the testing accuracy was 93.3% and the appraisal ability was 92.2%. The results indicated that the microsatellite DNA markers can be used for the parentage determination of Hucho taimen Pallas. PMID:20740701

Zhang, Chun-Lei; Tong, Guang-Xiang; Kuang, You-Yi; Zhang, Chao; Yin, Jia-Sheng

2010-08-01

27

Multiplex PCR identification of wheat HMW glutenin subunit genes by allele-specific markers  

Microsoft Academic Search

Wheat bread-making quality is closely correlated with composition and quantity of gluten proteins, in particular with high-molecular weight (HMW) glutenin subunits encoded by the Glu-1 genes. A multiplex polymerase chain reaction (PCR) method was developed to identify the allele composition of HMW glutenin com- plex Glu-1 loci (Glu-A1, Glu-B1 and Glu-D1) in common wheat genotypes. The study of multiplex PCR

Marcin MOCZULSKI; P. SALMANOWICZ

28

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

ERIC Educational Resources Information Center

This study was conducted to explore the contribution of attentional skills to early language, and the influence of early language markers on the development of attention, simultaneously examining the impact of parent-child interaction factors (reciprocity/synchrony and sensitivity/responsivity), including their potential moderator effects. All…

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

2008-01-01

29

Fractional allele loss is a valuable marker for human lung cancer detection in sputum  

Microsoft Academic Search

Using PCR-based microsatellite DNA analysis with 48 markers we examined sputum and bronchial washing for genetic alterations compared with lymphocyte extracted DNA from 124 lung cancer patients and 36 healthy donors as normal control. Microsatellite alterations (MA) in at least one locus were detected in all cancer patient-derived specimens but only in 22.2% of the healthy donors. Loss of heterozygosity

Demetrios A. Arvanitis; Emmanuel Papadakis; Alexander Zafiropoulos; Demetrios A. Spandidos

2003-01-01

30

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

PubMed

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

da Costa, S R; Santos, C A F

2013-01-01

31

The G protein ?3 subunit 825T allele is a genetic marker for enhanced T cell response  

Microsoft Academic Search

The G protein ?3 subunit (GNB3) 825T allele is predictive of enhanced Gi protein activation. Studying the influence of C825T allele status on cellular in vitro immune responses towards recall antigens and interleukin-2 stimulation we observed a 2–4-fold, significantly increased proliferation in homozygous 825T (TT) vs. C825 allele (CC) carriers. Furthermore, lymphocyte chemotaxis and CD4+ T cell counts of individuals

Monika Lindemann; Sebastian Virchow; Frank Ramann; Vahé Barsegian; Ernst Kreuzfelder; Winfried Siffert; Norbert Müller; Hans Grosse-Wilde

2001-01-01

32

Applicability of major histocompatibility complex DRB1 alleles as markers to detect vertebrate hybridization: a case study from Iberian ibex × domestic goat in southern Spain  

PubMed Central

Background Hybridization between closely related wild and domestic species is of great concern because it can alter the evolutionary integrity of the affected populations. The high allelic variability of Major Histocompatibility Complex (MHC) loci usually excludes them from being used in studies to detect hybridization events. However, if a) the parental species don’t share alleles, and b) one of the parental species possesses an exceptionally low number of alleles (to facilitate analysis), then even MHC loci have the potential to detect hybrids. Results By genotyping the exon2 of the MHC class II DRB1 locus, we were able to detect hybridization between domestic goats (Capra hircus) and free-ranging Iberian ibex (Capra pyrenaica hispanica) by molecular means. Conclusions This is the first documentation of a Capra pyrenaica × Capra hircus hybridization, which presented us the opportunity to test the applicability of MHC loci as new, simple, cost-effective, and time-saving approach to detect hybridization between wild species and their domesticated relatives, thus adding value to MHC genes role in animal conservation and management. PMID:23006678

2012-01-01

33

Using microsatellite DNA markers to determine the genetic identity of parental clones used in the Louisiana sugarcane breeding program  

Technology Transfer Automated Retrieval System (TEKTRAN)

Sugarcane propagates asexually through vegetative cuttings. To validate the genetic identity of sugarcane clones during shipping and handling, we produced molecular fingerprints based on 21 microsatellite (SSR) DNA markers for 116 Louisiana parental clones that were included in the crossing program...

34

Linkage Disequilibrium Inflates Type I Error Rates in Multipoint Linkage Analysis when Parental Genotypes Are Missing  

Microsoft Academic Search

Objectives: Describe the inflation in nonparametric multipoint LOD scores due to inter-marker linkage disequilibrium (LD) across many markers with varied allele frequencies. Method: Using simulated two-generation families with and without parents, we conducted nonparametric multipoint linkage analysis with 2 to 10 markers with minor allele frequencies (MAF) of 0.5 and 0.1. Results: Misspecification of population haplotype frequencies by assuming linkage

Abee L. Boyles; William K. Scott; Eden R. Martin; Silke Schmidt; Yi-Ju Li; Allison Ashley-Koch; Meredyth P. Bass; Michael Schmidt; Margaret A. Pericak-Vance; Marcy C. Speer; Elizabeth R. Hauser

2005-01-01

35

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

36

Two rearranged MET alleles in MNNG-HOS cells reveal the orientation of MET on chromosome 7 to other markers tightly linked to the cystic fibrosis locus.  

PubMed Central

We have found that two alleles of the MET locus are rearranged in the human cell line MNNG-HOS. One allele is the previously characterized TPR-MET oncogene and the other is found on a der(7)t(1;7)(q23;q32) marker chromosome. These data and in situ chromosomal hybridization analysis would indicate that MET and, therefore, the cystic fibrosis locus are located at bands q31-q32 on human chromosome 7. Using somatic cell hybrids, we show that the chromosome containing the TPR-MET oncogene is grossly rearranged and contains both the upstream and downstream portions of the MET protooncogene locus. These results demonstrate that the TPR-MET oncogene rearrangement involving chromosomes 1 and 7 is either due to an insertion of TPR sequences into the MET locus or is more complex. We also show that the upstream MET protooncogene locus is deleted on der(7), while the downstream portion is retained. We cannot exclude that this is due to an interstitial chromosomal deletion or to a more complex rearrangement, but if MET maps at the breakpoint in der(7), then the 3' end of the MET transcription unit should be oriented towards the centromere. We also show that other DNA restriction fragment length polymorphism markers tightly linked with the inheritance of cystic fibrosis are deleted on der(7). Images PMID:3282234

Park, M; Testa, J R; Blair, D G; Parsa, N Z; Vande Woude, G F

1988-01-01

37

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

Microsoft Academic Search

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

J I Weller

1987-01-01

38

Detection and molecular characterization of two FAD3 genes controlling linolenic acid content and development of allele-specific markers in yellow mustard (Sinapis alba).  

PubMed

Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, and low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 and Y1035 with low (3.8%), medium (12.3%) and high (20.8%) linolenic acid (C18?3) content, respectively, in this species. Inheritance studies detected two fatty acid desaturase 3 (FAD3) gene loci controlling the variation of C18?3 content. QTL mapping revealed that the two FAD3 gene loci responsible for 73.0% and 23.4% of the total variation and were located on the linkage groups Sal02 and Sal10, respectively. The FAD3 gene on Sal02 was referred to as SalFAD3.LA1 and that on Sal10 as SalFAD3.LA2. The dominant and recessive alleles were designated as LA1 and la1 for SalFAD3.LA1, and LA2 and la2 for SalFAD3.LA2. Cloning and alignment of the coding and genomic DNA sequences revealed that the SalFAD3.LA1 and SalFAD3.LA2 genes each contained 8 exons and 7 introns. LA1 had a coding DNA sequence (CDS) of 1143 bp encoding a polypeptide of 380 amino acids, whereas la1 was a loss-of-function allele due to an insertion of 584 bp in exon 3. Both LA2 and la2 had a CDS of 1152 bp encoding a polypeptide of 383 amino acids. Allele-specific markers for LA1, la1, LA2 and la2 co-segregated with the C18?3 content in the F2 populations and will be useful for improving fatty acid composition through marker assisted selection in yellow mustard breeding. PMID:24823372

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

2014-01-01

39

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

PubMed Central

Development of yellow mustard (Sinapis alba L.) with superior quality traits (low erucic and linolenic acid contents, and low glucosinolate content) can make this species as a potential oilseed crop. We have recently isolated three inbred lines Y1127, Y514 and Y1035 with low (3.8%), medium (12.3%) and high (20.8%) linolenic acid (C18?3) content, respectively, in this species. Inheritance studies detected two fatty acid desaturase 3 (FAD3) gene loci controlling the variation of C18?3 content. QTL mapping revealed that the two FAD3 gene loci responsible for 73.0% and 23.4% of the total variation and were located on the linkage groups Sal02 and Sal10, respectively. The FAD3 gene on Sal02 was referred to as SalFAD3.LA1 and that on Sal10 as SalFAD3.LA2. The dominant and recessive alleles were designated as LA1 and la1 for SalFAD3.LA1, and LA2 and la2 for SalFAD3.LA2. Cloning and alignment of the coding and genomic DNA sequences revealed that the SalFAD3.LA1 and SalFAD3.LA2 genes each contained 8 exons and 7 introns. LA1 had a coding DNA sequence (CDS) of 1143 bp encoding a polypeptide of 380 amino acids, whereas la1 was a loss-of-function allele due to an insertion of 584 bp in exon 3. Both LA2 and la2 had a CDS of 1152 bp encoding a polypeptide of 383 amino acids. Allele-specific markers for LA1, la1, LA2 and la2 co-segregated with the C18?3 content in the F2 populations and will be useful for improving fatty acid composition through marker assisted selection in yellow mustard breeding. PMID:24823372

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

2014-01-01

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

Parental potentiation of vocalization as a marker for filial bonds in infant animals.  

PubMed

Maternal and paternal potentiation of vocalization are two parts of a promising model of early life social bonds that has been and can be a useful tool in research. Most mammalian infants vocalize when isolated. Interactions with adult females just before isolation have been found to increase vocalizations in several species. Interactions with littermates and other social stimuli do not. In guinea pigs and pigs, the response is specific to the dam. In rats and octagon degus, an unrelated adult female from the colony is sufficient. The presence of an intact adult male in the test chamber with dam-reared pups evokes behavioral inhibition, a fear response. Previous exposure to the male in the home cage, biparental rearing, dramatically transforms the response of the pup. The pup treats the adult male as it does its dam, including potentiation of vocalization during a subsequent isolation. This article outlines the methods, advantages, and disadvantages of parental potentiation as a research tool, as well as a brief review of the evidence supporting its use as a marker for filial attachment. Future research directions are outlined. © 2014 Wiley Periodicals, Inc. Dev Psychobiol 56: 1689-1697, 2014. PMID:24915803

Shair, Harry N

2014-12-01

42

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

PubMed

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

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

2012-08-01

43

nature biotechnology volume 30 number 4 april 2012 333 converted into homozygous parental breeding lines, as desirable allele  

E-print Network

nature biotechnology volume 30 number 4 april 2012 333 converted into homozygous parental breeding. The pol- len was used to generate reverse-breeding haploids from which fertile double haploids were grown the original heterozygous hybrid. A key advantage of this method is the possibility of obtaining breeding lines

Heller, Eric

44

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

USGS Publications Warehouse

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

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

2012-01-01

45

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

USGS Publications Warehouse

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

Landguth, Erin L.; Gedy, Bradley C.; Oyler-McCance, Sara J.; Garey, Andrew L.; Emel, Sarah L.; Mumma, Matthew; Wagner, Helene H.; Fortin, Marie-Josée; Cushman, Samuel A.

2012-01-01

46

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

PubMed Central

Using daily telephone interviews, 82 midlife parents (mean age = 57.4) of children with disabilities (mean age = 29.9) were compared with a closely matched sample of unaffected parents (n = 82) to elucidate the daily experience of nonnormative parenting. In addition, salivary cortisol samples were obtained to examine whether parents of children with disabilities had dysregulated diurnal rhythms and the extent to which the amount of time spent with children was associated with divergent patterns of cortisol expression. We found that parents of children with disabilities had similar patterns of daily time use and similar likelihood of positive daily events as the comparison group, but they had elevated levels of stress, negative affect, and physical symptoms, all reported on a daily basis. In addition, their diurnal rhythm of cortisol expression differed significantly from the comparison group, a pattern that was strongest for parents of children with disabilities on days when they spent more time with their children. PMID:19413131

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

2009-01-01

47

VARIATION OF MICROSATELLITE MARKERS AMONG PARENTAL VARIETIES OF FIVE MAPPING POPULATIONS IN PAPAYA  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated mono- to hexa-nucleotide sequence motifs that frequently differ among the different members of a species. Due to their co-dominant nature, ability to detect high levels of allelic diversity, and ubiquitous distribution, they h...

48

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

49

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

PubMed Central

First, we explore the performance of nonword repetition (NWR) in children with specific language impairment (SLI) and typically developing children (TD) in order to investigate the accuracy of NWR as a clinical marker for SLI in Swedish-speaking school-age children. Second, we examine the relationship between NWR, family aggregation, and parental level of education in children with SLI. A sample of 61 children with SLI, and 86 children with TD, aged 8–12 years, were administered an NWR test. Family aggregation, measured as the prevalence of language and/or literacy problems (LLP) in parents of the children with SLI, was based on family history interviews. The sensitivity and specificity of nonword repetition was analyzed in a binary logistic regression, cut-off values were established with ROC curves, and positive and negative likelihood ratios reported. Results from the present study show that NWR distinguishes well between Swedish-speaking school-children with and without SLI. We found 90.2% sensitivity and 97.7% specificity at a cut-off level of ?2 standard deviations for binary scoring of nonwords. Differences between the SLI and TD groups showed large effect sizes for the two scoring measures binary (d?=?2.11) and percent correct consonants (PCC) (d?=?1.79). The children with SLI were split into two subgroups: those with no parents affected with LLP (n?=?12), and those with one or both parents affected (n?=?49). The subgroup consisting of affected parents had a significantly lower score on NWR binary (p?=?.037), and there was a great difference between the subgroups (d?=?0.7). When compared to the TD group, the difference from the subgroup with affected parents was almost one standard deviation larger (d?=?2.47) than the difference from the TD to the subgroup consisting of non-affected parents (d?=?1.57). Our study calls for further exploration of the complex interaction between family aggregation, language input, and phenotypes of SLI. PMID:24586859

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

2014-01-01

50

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

PubMed Central

DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential for many interactions between cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation was established in the parental germlines or post-fertilization in the embryo is not a determinant in CTCF or cohesin binding. These findings link CTCF and cohesin with the control regions of a subset of imprinted genes, supporting the notion that imprinting control is mechanistically diverse. PMID:23804403

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

2013-01-01

51

Microsatellite (simple sequence repeat) marker-based paternity analysis of a seven-parent sugarcane polycross  

Technology Transfer Automated Retrieval System (TEKTRAN)

It is not feasible to make all possible cross combinations among elite parents used in sugarcane (Saccharum spp.) breeding programs, particularly within a single year. Hence, the polycross approach has been used to maximize the number of cross combinations that can be represented among progeny. Th...

52

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

53

HLA-DRB1 and HLA-DQB1 allele associations in an Albanian patient population with rheumatoid arthritis: correlations with the specific autoantibody markers and inter-population DRB1 allele frequency variability.  

PubMed

The prevalence of rheumatoid arthritis and its specific autoantibodies varies in different populations. This variability depends on the genetic polymorphism of the immune response genes among which the HLA system plays a major role. In this context, we studied the HLA-DRB1 and HLA-DQB1 first-level allele frequencies in 100 Albanian patients with rheumatoid arthritis (RA), and taking into account their rheumatoid factor (RF) and anticitrullinated peptide antibodies (ACPA) serologic subgroups, we compared them with the respective frequencies in a population of 191 Albanian individuals without known pathology. No differences were found between the controls and the RA patient group as a whole, but three statistically significant differences were found: an increase in DRB1*04 among ACPA+, RF+ and ACPA+/RF+ patients, a significant decrease in DRB1*11 among ACPA+/RF+ and also a decrease in DRB1*13 among RF+ patient subgroups. Comparing allele frequencies of putatively associated RA alleles in different European populations revealed a significant negative correlation between the RA predisposing DRB1*04 and protective DRB1*11 allele frequencies. A statistically significant correlation was also found between RA prevalence rates and DRB1*04 as well as DRB1*11 frequencies. The relatively low frequencies of DRB1*04 and high DRB1*11 in the Albanian population might explain the rather low positivity rate of ACPA and RF antibodies among the Albanian RA patients. These specific association patterns suggest that this first study of RA in an Albanian population should be followed up to include second level or higher definition of HLA alleles and to compare RA patterns among European populations. PMID:24381092

Prifti-Kurti, Margarita; Nunes, José Manuel; Shyti, Erkena; Ylli, Zamira; Sanchez-Mazas, Alicia; Sulcebe, Genc

2014-08-01

54

Higher protein diets consumed ad libitum improve cardiovascular risk markers in children of overweight parents from eight European countries.  

PubMed

Dietary strategies to improve early cardiovascular markers in overweight children are needed. We investigated the effect of dietary protein and glycemic index (GI) on cardiovascular markers and metabolic syndrome (MetS) scores in 5- to 18-y-old children of overweight/obese parents from 8 European centers. Families were randomized to 1 of 5 diets consumed ad libitum: high protein (HP) or low protein (LP) combined with high GI (HGI) or low GI (LGI), or a control diet. At 6 centers, families received dietary instruction (instruction centers); at 2 centers, free foods were also provided (supermarket centers). Diet, anthropometry, blood pressure, and serum cardiovascular markers (lipid profile, glucose regulation, and inflammation) were measured in 253 children at baseline, 1 mo, and/or 6 mo. Protein intake was higher in the HP groups (19.9 ± 1.3% energy) than in the LP groups at 6 mo (16.8 ± 1.2% energy) (P = 0.001). The GI was 4.0 points lower (95% CI: 2.1, 6.1) in the LGI compared with the HGI groups (P < 0.001). In the supermarket centers, the HP and LP groups differed more in protein intake than did the groups in the instruction centers (P = 0.009), indicating better compliance. The HP diets evoked a 2.7-cm (95% CI: 0.9, 5.1) smaller waist circumference and a 0.25-mmol/L (95% CI: 0.09, 0.41) lower serum LDL cholesterol compared with the LP diets at 6 mo (P < 0.007). In a separate supermarket center analysis, the HP compared with LP diets reduced waist circumference (P = 0.004), blood pressure (P < 0.01), serum insulin (P = 0.013), and homeostasis model of assessment-insulin resistance (P = 0.016). In the instruction centers, the HP compared with the LP diets reduced LDL cholesterol (P = 0.004). No consistent effect of GI was seen and the MetS scores were not affected. In conclusion, increased protein intake improved cardiovascular markers in high-risk children, particularly in those undergoing most intensive intervention. PMID:23596158

Damsgaard, Camilla T; Papadaki, Angeliki; Jensen, Signe M; Ritz, Christian; Dalskov, Stine-Mathilde; Hlavaty, Petr; Saris, Wim H M; Martinez, J Alfredo; Handjieva-Darlenska, Teodora; Andersen, Malene R; Stender, Steen; Larsen, Thomas M; Astrup, Arne; Mølgaard, Christian; Michaelsen, Kim F

2013-06-01

55

Microsatellite allele dose and configuration establishment (MADCE): an integrated approach for genetic studies in allopolyploids  

PubMed Central

Background Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. Results Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. Conclusions The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids. PMID:22340438

2012-01-01

56

Microsatellite marker development and Mendelian analysis in the Matschie's tree kangaroo (Dendrolagus matschiei).  

PubMed

Matschie's tree kangaroo (Dendrolagus matschiei) is an endangered arboreal macropodid endemic to the Huon Peninsula, Papua New Guinea (PNG). We developed 5 microsatellite markers for D. matschiei, which are the first markers developed for Dendrolagus. We screened 17 additional markers that were developed for other marsupial taxa and identified 3 that were polymorphic in D. matschiei. We estimated allelic and genetic diversity with the set of 8 markers by analyzing 22 D. matschiei from Wasaunon on the Huon Peninsula, PNG. The number of alleles ranged from 2 to 9 and expected heterozygosity ranged from 0.440 to 0.794. We tested for null alleles and Mendelian inheritance by analyzing 19 pairs of D. matschiei parents and offspring from Association of Zoos and Aquariums institutions. Null alleles were not detected and Mendelian inheritance was followed for all 8 markers. We also evaluated the reliability of using the markers to amplify DNA extracted from D. matschiei fecal samples and the ability of the markers to amplify DNA samples from Goodfellow's tree kangaroo (Dendrolagus goodfellowi ssp.), Doria's tree kangaroo (Dendrolagus dorianus ssp.), and Grizzled tree kangaroo (Dendrolagus inustus ssp.). Microsatellite markers can be used to inform management decisions to conserve D. matschiei in captivity and the wild. PMID:19783838

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2010-01-01

57

Combined use of maternal, paternal and bi-parental genetic markers for the identification of wolf–dog hybrids  

Microsoft Academic Search

The identification of hybrids is often a subject of primary concern for the development of conservation and management strategies, but can be difficult when the hybridizing species are closely related and do not possess diagnostic genetic markers. However, the combined use of mitochondrial DNA (mtDNA), autosomal and Y chromosome genetic markers may allow the identification of hybrids and of the

C Vilà; C Walker; A-K Sundqvist; Ø Flagstad; Z Andersone; A Casulli; I Kojola; H Valdmann; J Halverson; H Ellegren

2003-01-01

58

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

59

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

60

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. PMID:22931243

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

2012-01-01

61

[Forensic DNA typing using AmpliType PM (Amp-PM) kit--allele frequency distributions of the five marker loci in Japanese population, and evaluation of Amp-PM markers for typing of saliva stain and hair].  

PubMed

Population study was carried out on the Japanese from Toyama district using the AmpliType PM PCR amplification and typing kit (Perkin Elmer) system, and then application of the kit system to forensic materials was evaluated. Using the kit system, 2 alleles could be identified for every locus of low density lipoprotein receptor (LDLR), glycophorin A (GYPA), hemoglobin G gammaglobin (HBGG), D7S8, and 3 alleles for group specific component (GC) in a sample size of 100 unrelated individuals. Allele frequency distributions of the sample were 0.18 for A, 0.82 for B in LDLR; 0.61 for A, 0.39 for B in GYPA; 0.27 for A, 0.73 for B, 0 for C in HBGG; 0.61 for A, 0.39 for B in D7S8 and 0.31 for A, 0.48 for B, 0.21 for C in GC. Deviations from Hardy-Weinberg equilibrium could not be observed in LDLR, GYPA, D7S8 and GC loci, except in HBGG locus (p < 0.05). All genotypes of the 5 loci could be detected from every saliva stains from 12 donors, but the genotypes estimated from 3 saliva samples unexpectedly did not correspond to those on the blood from same donors. Identification of the genotype from a hair root in telophase was available only in 3 individual samples out of 12 donors. The present experiment show that further improvement should be made on the application of the kit system to saliva stain. PMID:7674560

Yamaguchi, H; Takizawa, H; Shimasaki, C

1995-06-01

62

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.].  

PubMed

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F(2) population, i.e. "B100" of cultivated S. italica and "A10" of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces' grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together. PMID:19139840

Jia, Xiaoping; Zhang, Zhongbao; Liu, Yinghui; Zhang, Chengwei; Shi, Yunsu; Song, Yanchun; Wang, Tianyu; Li, Yu

2009-02-01

63

Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon.  

PubMed Central

Wild species are valued as a unique source of genetic variation, but they have rarely been used for the genetic improvement of quantitative traits. To identify trait-improving quantitative trait loci (QTL) alleles from exotic species, an accession of Oryza rufipogon, a relative of cultivated rice, was chosen on the basis of a genetic diversity study. An interspecific BC2 testcross population (V20A/O. rufipogon//V20B///V20B////Ce64) consisting of 300 families was evaluated for 12 agronomically important quantitative traits. The O. rufipogon accession was phenotypically inferior for all 12 traits. However, transgressive segregants that outperformed the original elite hybrid variety, V20A/Ce64, were observed for all traits examined. A set of 122 RFLP and microsatellite markers was used to identify QTL. A total of 68 significant QTL were identified, and of these, 35 (51%) had beneficial alleles derived from the phenotypically inferior O. rufipogon parent. Nineteen (54%) of these beneficial QTL alleles were free of deleterious effects on other characters. O. rufipogon alleles at two QTL on chromosomes 1 and 2 were associated with an 18 and 17% increase in grain yield per plant, respectively, without delaying maturity or increasing plant height. This discovery suggests that the innovative use of molecular maps and markers can alter the way geneticists utilize wild and exotic germplasm. PMID:9755218

Xiao, J; Li, J; Grandillo, S; Ahn, S N; Yuan, L; Tanksley, S D; McCouch, S R

1998-01-01

64

Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression  

PubMed Central

Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele-workbench. Additionally, all software is ready for immediate use from an Atmosphere Virtual Machine Image available from the iPlant Collaborative (www.iplantcollaborative.org). PMID:25541944

Soderlund, Carol A.; Nelson, William M.; Goff, Stephen A.

2014-01-01

65

Allele workbench: transcriptome pipeline and interactive graphics for allele-specific expression.  

PubMed

Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele-workbench. Additionally, all software is ready for immediate use from an Atmosphere Virtual Machine Image available from the iPlant Collaborative (www.iplantcollaborative.org). PMID:25541944

Soderlund, Carol A; Nelson, William M; Goff, Stephen A

2014-01-01

66

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. PMID:18192281

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

67

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. 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.

2013-01-01

68

NUMBER OF SEX ALLELES IN A SAMPLE OF HONEYBEE COLONIES Jean-Marie CORNUET Franck ARIES  

E-print Network

NUMBER OF SEX ALLELES IN A SAMPLE OF HONEYBEE COLONIES Jean-Marie CORNUET Franck ARIES Station of bree- ding work, this paper gives the theoretical distribution of the number of sex alleles in a sample the factors interfering with this trait, there is the possible identity of sex alleles of the workers' parents

Paris-Sud XI, Université de

69

Counting Alleles with Rarefaction: Private Alleles and Hierarchical Sampling Designs  

Microsoft Academic Search

The number of alleles (allelic richness) in a population is a fundamental measure of genetic variation, and a useful statistic for identifying populations for conservation. Estimating allelic richness is complicated by the effects of sample size: large samples are expected to have more alleles. Rarefaction solves this problem. This communication extends the rarefaction procedure to count private alleles and to

Steven T. Kalinowski

2004-01-01

70

DRD2 A1 allele and P300 abnormalities in obesity  

SciTech Connect

Obesity is a heterogeneous and prevalent disorder having both inheritable and environmental components. The role of the dopamine system in P300 has been implicated. We genotyped 193 neuropsychiatrically ill patients with and without comorbid drug and alcohol/abuse/dependence and obesity for the prevalence of the A1 allele of the DRD2 gene. We found a significant linear trend ({chi}{sup 2} = 40.4, df=1, p<0.00001) where the percent prevalence of the A1 increased with increasing polysubstance abuse. Where the A1 allele was found in 44% of 40 obese subjects, the A1 allele prevalence was found in as much as 91% of 11 obese subjects with comorbid polysubstance abuse. 53 obese subjects having a mean body weight (BMI) of 34.6{+-}8.2 were mapped for brain electrical activity and compared with 15 controls with a BMI of 22.3{+-}3.0 (P<.001). The P3 amplitude was significantly different (two tailed; t=3.24, df=16.2, P = 0.005), whereas P3 latency was not significant. Preliminarily, we found a significant decreased P3 amplitude correlated with parental polysubstance abuse (p=0.4) with prolongation of P3 latency correlated with the three risk factors of parental substance abuse, chemical dependency and carbohydrate bingeing (P<0.02). Finally, in a small sample, the A1 allele was present in 25% of probands having 0 risk compared to 66% in those obese subjects with any risk. This work represents the first electrophysiological data to implicate P3 abnormalities in a subset of obesity and further confirms an association of the DRD2 gene and a electrophysiological marker previously indicated to have predictive value in vulnerability to addictive behaviors.

Blum, K. [Univ. of Texas Health Science Center, San Antonio, TX (United States)]|[PATH Foundation, Princeton, NJ (United States); Wood, R.; Sheridan, L.P.J. [Univ. of Texas Health Science Center, San Antonio, TX (United States)] [and others

1994-09-01

71

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

72

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

PubMed Central

Background Polyploidy is a major component of eukaryote evolution. Estimation of allele copy numbers for molecular markers has long been considered a challenge for polyploid species, while this process is essential for most genetic research. With the increasing availability and whole-genome coverage of single nucleotide polymorphism (SNP) markers, it is essential to implement a versatile SNP genotyping method to assign allelic configuration efficiently in polyploids. Scope This work evaluates the usefulness of the KASPar method, based on competitive allele-specific PCR, for the assignment of SNP allelic configuration. Citrus was chosen as a model because of its economic importance, the ongoing worldwide polyploidy manipulation projects for cultivar and rootstock breeding, and the increasing availability of SNP markers. Conclusions Fifteen SNP markers were successfully designed that produced clear allele signals that were in agreement with previous genotyping results at the diploid level. The analysis of DNA mixes between two haploid lines (Clementine and pummelo) at 13 different ratios revealed a very high correlation (average = 0·9796; s.d. = 0·0094) between the allele ratio and two parameters [? angle = tan?1 (y/x) and y? = y/(x + y)] derived from the two normalized allele signals (x and y) provided by KASPar. Separated cluster analysis and analysis of variance (ANOVA) from mixed DNA simulating triploid and tetraploid hybrids provided 99·71 % correct allelic configuration. Moreover, triploid populations arising from 2n gametes and interploid crosses were easily genotyped and provided useful genetic information. This work demonstrates that the KASPar SNP genotyping technique is an efficient way to assign heterozygous allelic configurations within polyploid populations. This method is accurate, simple and cost-effective. Moreover, it may be useful for quantitative studies, such as relative allele-specific expression analysis and bulk segregant analysis. PMID:23422023

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

2013-01-01

73

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. 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

2012-01-01

74

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

75

Identification of RAPD markers linked to a Rhynchosporium secalis resistance locus in barley using near-isogenic lines and bulked segregant analysis.  

PubMed

Three hundred random sequence 10-mer primers were used to screen a pair of near-isogenic lines of barley and their donor parent for markers linked to genes conferring resistance to Rhynchosporium secalis. One primer was identified which reproducibly generated a product, SC10-65-H400, from the donor parent and the Rhynchosporium-resistant near-isogenic line but not from the recurrent parent. Segregation analysis on a barley doubled haploid population and examination of a further three near-isogenic lines, their donor and recurrent parents confirmed that this marker was linked to the Rhynchosporium resistance locus (Rh) on chromosome 3L. The presence or absence of SC10-65-H400 was subsequently used along with the resistance phenotype to identify two groups of individuals in the doubled haploid population which possessed alternative alleles at both loci and defined a genetic interval between these two markers. Based on that information two bulked DNA samples were constructed by combining equal amounts of DNA from five individuals from each group. The two bulks and doubled haploid parental lines were screened with 700 10-mer primers. Seven products were identified which were present in the 'resistant' bulk and parent and were absent in the susceptible samples. Segregation analysis established their association with Rh. In addition co-segregation of the linked markers with a set of chromosome arm specific RFLPs confirmed the location of the Rh locus on the long arm of barley chromosome 3. PMID:8376177

Barua, U M; Chalmers, K J; Hackett, C A; Thomas, W T; Powell, W; Waugh, R

1993-08-01

76

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  

Microsoft Academic Search

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

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

1998-01-01

77

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

78

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

SciTech Connect

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

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

2007-07-06

79

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. PMID:22574143

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

2012-01-01

80

Multiple mating and reproductive skew in parental and introgressed females of the live-bearing fish xiphophorus birchmanni.  

PubMed

Just as mating patterns can promote speciation or hybridization, the presence of hybridization can shape mating patterns within a population. In this study, we characterized patterns of multiple mating and reproductive skew in a naturally hybridizing swordtail fish species, Xiphophorus birchmanni. We quantified multiple mating using microsatellite markers to genotype embryos from 43 females collected from 2 wild populations. We also used a suite of single-nucleotide polymorphism markers to categorize females and their inferred mates as either parental X. birchmanni or as introgressed individuals, which carried alleles from a sister species, X. malinche. We found that parental and introgressed X. birchmanni females mated multiply with both parental and introgressed males. We found no difference in mating patterns or reproductive skew between parental and introgressed X. birchmanni females. However, nonintrogressed X. birchmanni males mated more often with large, fecund females. These females also had the greatest levels of skew in fertilization success of males. Thus, our results show that X. birchmanni has a polygynandrous mating system and that introgression of X. malinche alleles has only subtle effects on mating patterns in this species. PMID:25433083

Paczolt, Kimberly A; Passow, Courtney N; Delclos, Pablo J; Kindsvater, Holly K; Jones, Adam G; Rosenthal, Gil G

2015-01-01

81

Trans allele methylation and paramutation-like effects in mice  

PubMed Central

In mammals, imprinted genes have parent-of-origin–specific patterns of DNA methylation that cause allele-specific expression. At Rasgrf1 (encoding RAS protein-specific guanine nucleotide-releasing factor 1), a repeated DNA element is needed to establish methylation and expression of the active paternal allele1. At Igf2r (encoding insulin-like growth factor 2 receptor), a sequence called region 2 is needed for methylation of the active maternal allele2,3. Here we show that replacing the Rasgrf1 repeats on the paternal allele with region 2 allows both methylation and expression of the paternal copy of Rasgrf1, indicating that sequences that control methylation can function ectopically. Paternal transmission of the mutated allele also induced methylation and expression in trans of the normally unmethylated and silent wild-type maternal allele. Once activated, the wild-type maternal Rasgrf1 allele maintained its activated state in the next generation independently of the paternal allele. These results recapitulate in mice several features in common with paramutation described in plants4. PMID:12740578

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

2009-01-01

82

Detection of Parent-of-Origin Effects Based on Complete and Incomplete Nuclear Families with Multiple Affected Children  

PubMed Central

Parent-of-origin effects are important in studying genetic traits. More than 1% of all mammalian genes are believed to show parent-of-origin effects. Some statistical methods may be ineffective or fail to detect linkage or association for a gene with parent-of-origin effects. Based on case-parents trios, the parental-asymmetry test (PAT) is simple and powerful in detecting parent-of-origin effects. However, it is common in practice to collect nuclear families with both parents as well as nuclear families with only one parent. In this paper, when only one parent is available for each family with an arbitrary number of affected children, we firstly develop a new test statistic 1-PAT to test for parent-of-origin effects in the presence of association between an allele at the marker locus under study and a disease gene. Then we extend the PAT to accommodate complete nuclear families each with one or more affected children. Combining families with both parents and families with only one parent, the C-PAT is proposed to detect parent-of-origin effects. The validity of the test statistics is verified by simulation in various scenarios of parameter values. A power study shows that using the additional information from incomplete nuclear families in the analysis greatly improves the power of the tests, compared to that based on only complete nuclear families. Also, utilizing all affected children in each family, the proposed tests have a higher power than when only one affected child from each family is selected. Additional power comparison also demonstrates that the C-PAT is more powerful than a number of other tests for detecting parent-of-origin effects. PMID:18931505

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

2008-01-01

83

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. PMID:23341750

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

2012-01-01

84

Development of 11 polymorphic microsatellite markers for the blackberry rust fungus Phragmidium violaceum  

Technology Transfer Automated Retrieval System (TEKTRAN)

Eleven polymorphic microsatellite markers were developed for the Uredinales fungus Phragmidium violaceum, which causes leaf rust on European blackberry (Rubus fruticosus L. aggregate). Allele frequency ranged between two and seventeen alleles per locus with no evidence of linkage disequilibrium amon...

85

Gestational Diabetes Mellitus Worsens the Profile of Cardiometabolic Risk Markers and Decrease Indexes of Beta-Cell Function Independently of Insulin Resistance in Nondiabetic Women with a Parental History of Type 2 Diabetes  

PubMed Central

Background. Women with a history of both parental type 2 diabetes (pt2DM) and previous gestational diabetes (pGDM) represent a group at high risk of cardiovascular events. We hypothesized that pGDM changes cardiometabolic risk markers levels as well as theirs associations with glucose indices in nondiabetic pt2DM women. Methods. Anthropometric parameters, glucose regulation (OGTT), insulin resistance (HOMA-IR), beta-cell function, lipid levels, parameters of endothelial dysfunction, and inflammation were evaluated in 55 women with pt2DM, 40 with both pt2DM and pGDM 2–24 months postpartum, and 35 controls. Results. Prediabetes was diagnosed more frequently in women with both pt2DM and pGDM in comparison with women with only pt2DM (10 versus 8, P = 0.04). The pGDM group had higher LDL-cholesterol, sICAM-1, tPa Ag, fibrinogen, and lower beta-cell function after adjustment for HOMA-IR, in comparison with pt2DM group. In pt2DM group postchallenge glucose correlated independently with hsCRP and in pGDM group fasting glucose with HOMA-IR. Conclusions. pGDM exerts a combined effect on cardiometabolic risk markers in women with pt2DM. In these women higher LDL-cholesterol, fibrinogen, sICAM-1, tPa Ag levels and decreased beta cell function are associated with pGDM independently of HOMA-IR index value. Fasting glucose is an important cardiometabolic risk marker and is independently associated with HOMA-IR. PMID:25097861

Sokup, Alina; Ruszkowska-Ciastek, Barbara; Walentowicz-Sad?ecka, Ma?gorzata; Grabiec, Marek; Ro??, Danuta

2014-01-01

86

Launching Parent to Parent Schemes.  

ERIC Educational Resources Information Center

"Parent to Parent" is a telephone-contact self-help group for families of special needs children. Support parents are recruited and trained to provide counseling to other parents. Professionals lead the training course, which focuses on listening, understanding, and action planning. Parents carry out the support group's administrative tasks via…

Hornby, Garry

1988-01-01

87

Distinguishing species of European sturgeons Acipenser spp. using microsatellite allele sequences.  

PubMed

Five microsatellite markers were analysed and their alleles were sequenced for the three sturgeon species that lived in western Europe: the European sturgeon Acipenser sturio, the Atlantic sturgeon Acipenser oxyrinchus and the Adriatic sturgeon Acipenser naccarii. A total of 94 different allele sequences were obtained. Fixed mutations in the flanking regions or in the core repeat of microsatellites provided a clear distinction between the different species. Comparison of allele sequences also provided some insights into microsatellites and the evolution of Acipenser species. These nuclear markers can be used to solve species determination problems, and combined with mitochondrial markers, will be useful to identify introgression and hybridization among the three species. Moreover, because they are short and with a limited allele size range, they are particularly suited for analysis of museum specimens or archaeological remains. PMID:21235556

Chassaing, O; Hänni, C; Berrebi, P

2011-01-01

88

Parental origin of sequence variants associated with complex diseases  

Microsoft Academic Search

Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined.

Valgerdur Steinthorsdottir; Gisli Masson; Gudmar Thorleifsson; Patrick Sulem; Soren Besenbacher; Aslaug Jonasdottir; Asgeir Sigurdsson; Kari Th. Kristinsson; Adalbjorg Jonasdottir; Michael L. Frigge; Arnaldur Gylfason; Pall I. Olason; Sigurjon A. Gudjonsson; Sverrir Sverrisson; Simon N. Stacey; Bardur Sigurgeirsson; Kristrun R. Benediktsdottir; Helgi Sigurdsson; Thorvaldur Jonsson; Rafn Benediktsson; Jon H. Olafsson; Oskar Th. Johannsson; Astradur B. Hreidarsson; Gunnar Sigurdsson; Benjamin F. Voight; Laura J. Scott; Christian Dina; Eleftheria Zeggini; Cornelia Huth; Yurii S. Aulchenko; Ryan P. Welch; Laura J. McCulloch; Teresa Ferreira; Harald Grallert; Najaf Amin; Guanming Wu; Cristen J. Willer; Soumya Raychaudhuri; Shaun Purcell; Steve A. McCarroll; Claudia Langenberg; Oliver M. Hoffmann; Josée Dupuis; Lu Qi; Ayellet V. Segrè; Mandy van Hoek; Pau Navarro; Kristin Ardlie; Beverley Balkau; Amanda J. Bennett; Roza Blagieva; Eric Boerwinkle; Lori L. Bonnycastle; Kristina Bengtsson Boström; Bert Bravenboer; Suzannah Bumpstead; Noël P. Burtt; Guillaume Charpentier; Peter S. Chines; Marilyn Cornelis; David J. Couper; Gabe Crawford; Alex S. F. Doney; Katherine S. Elliott; Amanda L. Elliott; Michael R. Erdos; Caroline S. Fox; Christopher S. Franklin; Martha Ganser; Christian Gieger; Niels Grarup; Todd Green; Simon Griffin; Christopher J. Groves; Candace Guiducci; Samy Hadjadj; Neelam Hassanali; Christian Herder; Bo Isomaa; Anne U. Jackson; Paul R. V. Johnson; Torben Jørgensen; Wen H. L. Kao; Norman Klopp; Peter Kraft; Johanna Kuusisto; Torsten Lauritzen; Man Li; Alouisius Lieverse; Cecilia M. Lindgren; Valeriya Lyssenko; Michel Marre; Thomas Meitinger; Kristian Midthjell; Mario A Morken; Narisu Narisu; Peter Nilsson; Katharine R. Owen; Felicity Payne; John R. B. Perry; Ann-Kristin Petersen; Carl Platou; Christine Proença; Inga Prokopenko; Wolfgang Rathmann; N. William Rayner; Neil R. Robertson; Ghislain Rocheleau; Michael Roden; Michael J. Sampson; Richa Saxena; Beverley M. Shields; Peter Shrader; Nicholas Smith; Thomas Sparsø; Klaus Strassburger; Heather M. Stringham; Qi Sun; Amy J. Swift; Barbara Thorand; Jean Tichet; Tiinamaija Tuomi; Rob van Dam; Thijs van Herpt; G. Bragi Walters; Michael N. Weedon; Jacqueline Witteman; Richard N. Bergman; Stephane Cauchi; Francis S. Collins; Anna L. Gloyn; Ulf Gyllensten; Torben Hansen; Winston A. Hide; Graham A. Hitman; Albert Hofman; David Hunter; Kristian Hveem; Markku Laakso; Karen L. Mohlke; Andrew D. Morris; Colin N. A. Palmer; Peter P. Pramstaller; Igor Rudan; Eric Sijbrands; Lincoln D. Stein; Jaakko Tuomilehto; Andre Uitterlinden; Mark Walker; Nicholas J. Wareham; Richard M. Watanabe; Goncalo R. Abecasis; Inês Barroso; Bernhard O. Boehm; Harry Campbell; Mark J. Daly; Jose C. Florez; Timothy M. Frayling; Leif Groop; Andrew T. Hattersley; Frank B. Hu; James B. Meigs; Andrew P. Morris; James S. Pankow; Oluf Pedersen; Rob Sladek; Unnur Thorsteinsdottir; H.-Erich Wichmann; James F. Wilson; Thomas Illig; Philippe Froguel; Cornelia M. van Duijn; David Altshuler; Michael Boehnke; Anne C. Ferguson-Smith; Daniel F. Gudbjartsson; Augustine Kong; Kari Stefansson

2009-01-01

89

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. 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.

2013-01-01

90

Mapping QTL for popping expansion volume in popcorn with simple sequence repeat markers.  

PubMed

Popping expansion volume is the most important quality trait in popcorn ( Zea mays L.), but its genetics is not well understood. The objectives of this study were to map quantitative trait loci (QTLs) responsible for popping expansion volume in a popcorn x dent corn cross, and to compare the predicted efficiencies of phenotypic selection, marker-based selection, and marker-assisted selection for popping expansion volume. Of 259 simple sequence repeat (SSR) primer pairs screened, 83 pairs were polymorphic between the H123 (dent corn) and AG19 (popcorn) parental inbreds. Popping test data were obtained for 160 S(1) families developed from the [AG19(H123 x AG19)] BC(1) population. The heritability ( h(2)) for popping expansion volume on an S(1) family mean basis was 0.73. The presence of the gametophyte factor Ga1(s) in popcorn complicates the analysis of popcorn x dent corn crosses. But, from a practical perspective, the linkage between a favorable QTL allele and Ga1(s) in popcorn will lead to selection for the favorable QTL allele. Four QTLs, on chromosomes 1S, 3S, 5S and 5L, jointly explained 45% of the phenotypic variation. Marker-based selection for popping expansion volume would require less time and work than phenotypic selection. But due to the high h(2) of popping expansion volume, marker-based selection was predicted to be only 92% as efficient as phenotypic selection. Marker-assisted selection, which comprises index selection on phenotypic and marker scores, was predicted to be 106% as efficient as phenotypic selection. Overall, our results suggest that phenotypic selection will remain the preferred method for selection in popcorn x dent corn crosses. PMID:12589541

Lu, H-J; Bernardo, R; Ohm, H W

2003-02-01

91

Identification of parental line specific effects of MLF2 on resistance to coccidiosis in chickens  

PubMed Central

Background MLF2 was the candidate gene associated with coccidiosis resistance in chickens. Although single marker analysis supported the association between MLF2 and coccidiosis resistance, causative mutation relevant to coccidiosis was not identified yet. Thus, this study suggested segregation analysis of MLF2 haplotype and the association test of the other candidate genes using improved data transformation. Results A haplotype probably originated from one parental line was found out of 4 major haplotypes of MLF2. Frequency of this haplotype was 0.2 in parental chickens and its offspring in 12 families. Allele substitution effect of the MLF2 haplotype originated from a specific line was associated with increased body weight and fecal egg count explaining coccidiosis resistance. Nevertheless Box-Cox transformation was able to improve normality; association test did not produce obvious different results compared with analysis with log transformed phenotype. Conclusion Allele substitution effect analysis and classification of MLF2 haplotype identified the segregation of haplotype associated with coccidiosis resistance. The haplotype originated from a specific parental line was associated with improving disease resistance. Estimating effect of MLF2 haplotype on coccidiosis resistance will provide useful information for selecting animals or lines for future study. PMID:21645301

2011-01-01

92

Genetic Diversity Among Wheat Cultivars Using Molecular Markers  

Microsoft Academic Search

The objective of this study was to compare amplified fragment length polymorphism (AFLP), random amplified polymorphic DNA (RAPD), and DNA amplification fingerprinting (DAF) marker systems for estimating genetic diversity among 13 Iranian wheat (Triticum aestivum L.) cultivars through average expected heterozygosity (Hav), sum of effective number of alleles (SENA), and marker index (MI). The AFLP markers had the highest values

Babak Abdollahi Mandoulakani; Ali-Akbar Shahnejat-Bushehri; Badredin Ebrahim Sayed Tabatabaei; Sepideh Torabi; Alireza Mohammadi Hajiabad

2010-01-01

93

Parent Support.  

ERIC Educational Resources Information Center

The push for parent involvement shows up at the federal, state, and district level. Without a plan that includes a definition, specific goals, and research-based practices, the result can be parent interference--not parent involvement. Lists publications, organizations, and Web sites that address parent involvement in education. (MLF)

Black, Susan

1998-01-01

94

Epigenetic Regulation of Monoallelic Rearrangement (Allelic Exclusion) of Antigen Receptor Genes  

PubMed Central

While most genes in the mammalian genome are transcribed from both parental chromosomes in cells where they are expressed, approximately 10% of genes are expressed monoallelically, so that any given cell will express either the paternal or maternal allele, but not both. The antigen receptor genes in B and T cells are well-studied examples of a gene family, which is expressed in a monoallelic manner, in a process coined “allelic exclusion.” During lymphocyte development, only one allele of each antigen receptor undergoes V(D)J rearrangement at a time, and once productive rearrangement is sensed, rearrangement of the second allele is prevented. In this mini review, we discuss the epigenetic processes, including asynchronous replication, nuclear localization, chromatin condensation, histone modifications, and DNA methylation, which appear to regulate the primary rearrangement of a single allele, while blocking the rearrangement of the second allele. PMID:25538709

Levin-Klein, Rena; Bergman, Yehudit

2014-01-01

95

Use of short sequence repeat DNA polymorphisms after PCR amplification to detect the parental origin of the additional chromosome 21 in Down syndrome.  

PubMed Central

The origin of nondisjunction in trisomy 21 has so far been studied using cytogenetic heteromorphisms and DNA polymorphisms using Southern blot analysis. Short sequence repeats have recently been described as an abundant class of DNA polymorphisms in the human genome, which can be typed using the polymerase chain reaction (PCR) amplification. We describe the usage of such markers on chromosome 21 in the study of parental origin of the additional chromosome 21 in 87 cases of Down syndrome. The polymorphisms studied were (a) two (GT)n repeats and a poly(A) tract of an Alu sequence within the HMG14 gene and (b) a (GT)n repeat of locus D21S156. The parental origin was determined in 68 cases by studying the segregation of polymorphic alleles in the nuclear families (either by scoring three different alleles in the proband or by dosage comparison of two different alleles in the proband). Our results demonstrate the usefulness of highly informative PCR markers for the study of nondisjunction in Down syndrome. Images Figure 1 Figure 2 PMID:1824668

Petersen, M B; Schinzel, A A; Binkert, F; Tranebjaerg, L; Mikkelsen, M; Collins, F A; Economou, E P; Antonarakis, S E

1991-01-01

96

Marker development  

SciTech Connect

This report is to discuss the marker development for radioactive waste disposal sites. The markers must be designed to last 10,000 years, and place no undue burdens on the future generations. Barriers cannot be constructed that preclude human intrusion. Design specifications for surface markers will be discussed, also marker pictograms will also be covered.

Adams, M.R.

1987-05-01

97

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. PMID:23103470

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

98

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

99

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

100

Mapping a disease locus by allelic?association  

PubMed Central

Allelic association provides a means to map disease genes that, in a dense map of polymorphic markers, has considerably higher resolution than linkage methods. We describe here a composite likelihood estimate of location for a disease gene against a high-resolution marker map by using allele frequencies at linked loci. Data may be family-based, as in the transmission disequilibrium test, or from a case-control study. ?2 tests, logarithm of odds, standard errors, and information weights are provided. The method is illustrated by analysis of published cystic fibrosis haplotypes, in which ?F508 is more accurately localized than by other association studies. This differs from current approaches by adopting a more general Malecot model for isolation by distance, where distance here is between marker and disease locus, allowance for errors in the map and model, and freedom from assumptions about demography, systematic pressures, and the ratio of physical to genetic distance. When these assumptions are introduced the number of generations since the original mutation may be estimated, but this is not required to determine location and its standard error, so that evidence from allelic association may be efficiently combined with linkage evidence to identify a region for positional cloning of a disease gene. PMID:9465087

Collins, A.; Morton, N. E.

1998-01-01

101

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. PMID:22737155

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

2012-01-01

102

Linkage mapping in tetraploid willows: segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba x Salix fragilis interspecific hybrids.  

PubMed

Salix alba-Salix fragilis complex includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of these willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Since nothing is known about their genomic constitution, tetraploidy (2n=4x=76) in willow species makes basic and applied genetic studies difficult. We have used a two-way pseudotestcross strategy and single-dose markers (SDMs) to construct the first linkage maps for both pistillate and staminate willows. A total of 242 amplified fragment length polymorphisms (AFLPs) and 50 selective amplifications of microsatellite polymorphic loci (SAMPL) markers, which showed 1:1 segregation in the F(1) mapping populations, were used in linkage analysis. In S. alba, 73 maternal and 48 paternal SDMs were mapped to 19 and 16 linkage groups covering 708 and 339 cM, respectively. In S. fragilis, 13 maternal and 33 paternal SDMs were mapped in six and 14 linkage groups covering 98 and 321 cM, respectively. For most cosegregation groups, a comparable number of markers linked in coupling and repulsion was identified. This finding suggests that most of chromosomes pair preferentially as occurs in allotetraploid species exhibiting disomic inheritance. The detection of 10 pairs of marker alleles from single parents showing codominant inheritance strengthens this hypothesis. The fact that, of the 1122 marker loci identified in the two male and female parents, the vast majority (77.5%) were polymorphic and as few as 22.5% were shared between parental species highlight that S. alba and S. fragilis genotypes are differentiated. The highly difference between S. alba- and S. fragilis-specific markers found in both parental combinations (on average, 65.3 vs 34.7%, respectively) supports the (phylogenetic) hypothesis that S. fragilis is derived from S. alba-like progenitors. PMID:12634824

Barcaccia, G; Meneghetti, S; Albertini, E; Triest, L; Lucchin, M

2003-02-01

103

Parenting Multiples  

MedlinePLUS

... for parents of multiples can help, as can marriage counselors or clergy. It's important that you do ... and from early on it's apparent that their relationship is special. Parenting multiples has its ... reviewed: October 2013 Back

104

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

105

AGG interruptions and maternal age affect FMR1 CGG repeat allele stability during transmission  

PubMed Central

Background The presence of AGG interruptions in the CGG repeat locus of the fragile X mental retardation 1 (FMR1) gene decreases the instability of the allele during transmission from parent to child, and decreases the risk of expansion of a premutation allele to a full mutation allele (the predominant cause of fragile X syndrome) during maternal transmission. Methods To strengthen recent findings on the utility of AGG interruptions in predicting instability or expansion to a full mutation of FMR1 CGG repeat alleles, we assessed the outcomes of 108 intermediate (also named gray zone) and 710 premutation alleles that were transmitted from parent to child, and collected from four international clinical sites. We have used the results to revise our initial model that predicted the risk of a maternal premutation allele expanding to a full mutation during transmission and to test the effect of AGG interruptions on the magnitude of expanded allele instability of intermediate or premutation alleles that did not expand to a full mutation. Results Consistent with previous studies, the number of AGG triplets that interrupts the CGG repeat locus was found to influence the risk of allele instability, including expansion to a full mutation. The total length of the CGG repeat allele remains the best predictor of instability or expansion to a full mutation, but the number of AGG interruptions and, to a much lesser degree, maternal age are also factors when considering the risk of transmission of the premutation allele to a full mutation. Conclusions Our findings demonstrate that a model with total CGG length, number of AGG interruptions, and maternal age is recommended for calculating the risk of expansion to a full mutation during maternal transmission. Taken together, the results of this study provide relevant information for the genetic counseling of female premutation carriers, and improve the current predictive models which calculate risk of expansion to a full mutation using only total CGG repeat length. PMID:25110527

2014-01-01

106

Applicability of bovine microsatellite markers for population genetic studies on African buffalo (Syncerus caffer)  

Microsoft Academic Search

The applicability of bovine autosomal micro- satellite markers for population genetic studies on African buffalo was investigated. A total of 168 microsatellite markers were tested for PCR amplification on a test panel of seven African buffalo. Amplification was observed for 139 markers (83%), and 101 markers were studied further with 91 (90%) being polymorphic. The mean number of alleles per

Hooft van W. F; O. Hanotte; P. W. Wenink; A. F. Groen; Y. Sugimoto; H. H. T. Prins; A. Teale

1999-01-01

107

Assessing genetic diversity of wheat ( Triticum aestivum L.) germplasm using microsatellite markers  

Microsoft Academic Search

A set of 24 wheat microsatellite markers, representing at least one marker from each chromosome, was used for the assessment of genetic diversity in 998 accessions of hexaploid bread wheat (Triticum aestivum L.) which originated from 68 countries of five continents. A total of 470 alleles were detected with an average allele number of 18.1 per locus. The highest number

X. Q. Huang; A. Börner; M. S. Röder; M. W. Ganal

2002-01-01

108

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

109

Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa).  

PubMed

The oriental melon (Cucumis melo var. makuwa), called 'chamoe' in Korean, is a popular fruit crop cultivated mainly in Asia and a high-market value crop in Korea. To provide molecular breeding resources for chamoe, we developed and characterized genomic SSR markers from the preliminary Illumina read assemblies of Gotgam chamoe (one of the major landraces; KM) and SW3 (the breeding parent). Mononucleotide motifs were the most abundant type of markers, followed by di-, tri-, tetra-, and pentanucleotide motifs. The most abundant dinucleotide was AT, followed by AG and AC, and AAT was the most abundant trinucleotide motif in both assemblies. Following our SSR-marker development strategy, we designed a total of 370 primer sets. Of these, 236 primer sets were tested, exhibiting 93 % polymorphism between KM and SW3. Those polymorphic SSRs were successfully amplified in the netted and Kirkagac melons, which respectively exhibited 81 and 76 % polymorphism relative to KM, and 32 and 38 % polymorphism relative to SW3. Seven selected SSR markers with a total of 17 alleles (2-3 alleles per locus) were used to distinguish between KM, SW3, and four chamoe cultivars. Our results represent the first attempt to provide genomic resources for Korean landraces for the purposes of chamoe breeding, as well as to discover a set of SSR markers capable of discriminating chamoe varieties from Korea and the rest of Asia, which possess little genetic diversity. This study establishes a highly efficient strategy for developing SSR markers from preliminary Illumina assemblies of AT-rich genomes. PMID:24096890

Park, Inkyu; Kim, Jungeun; Lee, Jeongyeo; Kim, Sewon; Cho, Okhee; Yang, Kyungbong; Ahn, Jongmoon; Nahm, Seokhyeon; Kim, Hyeran

2013-12-01

110

Development of AFLP and RAPD markers linked to a locus associated with twisted growth in corkscrew willow (Salix matsudana 'Tortuosa').  

PubMed

Salix matsudana Koidz. cultivar 'Tortuosa' (corkscrew willow) is characterized by extensive stem bending and curling of leaves. To investigate the genetic basis of this trait, controlled crosses were made between a corkscrew female (S. matsudana 'Tortuosa') and a straight-stemmed, wild-type male (Salix alba L. Clone 99010). Seventy-seven seedlings from this family (ID 99270) were grown in the field for phenotypic observation. Among the progeny, 39 had straight stems and leaves and 38 had bent stems and curled leaves, suggesting that a dominant allele at a single locus controls this phenotype. As a first step in characterizing the locus, we searched for amplified fragment length polymorphism (AFLP) and randomly amplified polymorphic DNA (RAPD) markers linked to the tortuosa allele using bulked segregant analysis. Samples of DNA from 10 corkscrew individuals were combined to produce a corkscrew pool, and DNA from 10 straight progeny was combined to make a wild-type pool. Sixty-four AFLP primer combinations and 640 RAPD primers were screened to identify marker bands amplified from the corkscrew parent and progeny pool, but not from the wild-type parent or progeny pool. An AFLP marker and a RAPD marker linked to and flanking the tortuosa locus were placed on a preliminary linkage map constructed based on segregation among the 77 progeny. Sectioning and analysis of shoot tips revealed that the corkscrew phenotype is associated with vascular cell collapse, smaller cell size in regions near the cambium and less developed phloem fibers than in wild-type progeny. Identification of a gene associated with this trait could lead to greater understanding of the control of normal stem development in woody plants. PMID:17669747

Lin, Juan; Gunter, Lee E; Harding, Scott A; Kopp, Richard F; McCord, Rachel P; Tsai, Chung-Jui; Tuskan, Gerald A; Smart, Lawrence B

2007-11-01

111

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

PubMed

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

Ghaffari, Parvin; Talebi, Reza; Keshavarzi, Fatemeh

2014-04-01

112

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

PubMed

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

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

2011-05-01

113

The role of double-strand break-induced allelic homologous recombination in somatic plant cells.  

PubMed

During meiosis, homologous recombination occurs between allelic sequences. To evaluate the biological significance of such a pathway in somatic cells, we used transgenic tobacco plants with a restriction site for the rare cutting endonuclease I-SceI within a negative selectable marker gene. These plants were crossed with two tobacco lines containing, in allelic position, either a deletion or an insertion within the marker gene that rendered both marker gene and restriction site inactive. After the double-strand break induction, we selected for repair events resulting in a loss of marker gene function. This loss was mostly due to deletions. We were also able to detect double strand break-induced allelic recombination in which the break was repaired by a faithful copying process from the homologue carrying the shortened transgene. The estimated frequency indicates that homologous recombination in somatic cells between allelic sites appears to occur at the same order of magnitude as between ectopic sites, and is thus far too infrequent to act as major repair pathway. As somatic changes can be transferred to the germ line, the prevalence of intrachromatid rearrangements over allelic recombination might be an indirect prerequisite for the enhanced genome plasticity postulated for plants. PMID:12410807

Gisler, Brigitte; Salomon, Siegfried; Puchta, Holger

2002-11-01

114

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

2013-05-01

115

Investigation of Japanese-specific alleles: Most are of Jomon lineage.  

PubMed

Japanese-specific alleles are expected to be powerful markers for the differentiation of the Japanese from other people. In this study, three single nucleotide polymorphisms (SNPs) in the GALNT11, H19, and PLA2G12A genes were analyzed in 2396 DNA samples from 25 global populations, and the derived alleles suggested that Japanese-specific alleles exist on autosomes. To identify new Japanese-specific alleles, candidate SNPs obtained from the HapMap database were investigated using 875 DNA samples from nine populations. A total of 67 (nearly) Japanese-specific derived alleles were observed. Of them, 57 showed higher frequencies in the Ryukyuans, living in the southernmost part of the Japanese Archipelago, than in the Wajins living in mainland Japan, and 43 were also present in Koreans at low frequencies. Jomon skeletons excavated from Hokkaido, the northernmost island of Japan, showed higher frequencies of the three derived alleles in the GALNT11, H19, and PLA2G12A genes than the Ryukyuans, suggesting that most of the 57 derived alleles observed at the high frequencies in the Ryukyuans originated from the Jomon lineage. These novel markers will be useful in the field of forensics. PMID:25239165

Yuasa, Isao; Umetsu, Kazuo; Adachi, Noboru; Matsusue, Aya; Nakayashiki, Nori; Fujihara, Junko; Akane, Atsushi; Harihara, Shinji; Jin, Feng; Ishikawa, Takaki

2015-01-01

116

Genetic diversity analysis among collected purslane (Portulaca oleracea L.) accessions using ISSR markers.  

PubMed

Genetic diversity and relationships among 45 collected purslane accessions were evaluated using ISSR markers. The 28 primers gave a total of 167 bands, among which 163 were polymorphic (97.6%). The genetic diversity as estimated by Shannon's information index was 0.513, revealing a quite high level of genetic diversity in the germplasm. The average number of observed allele, effective allele, expected heterozygosity, polymorphic information content (PIC) and Nei's index were 5.96, 1.59, 0.43, 0.35 and 0.35, respectively. The UPGMA dendrogram based on Nei's genetic distance grouped the whole germplasm into 7 distinct clusters. The analysis of molecular variance (AMOVA) revealed that 89% of total variation occurred within population, while 11% were found among populations. Based on the constructed dendrogram using ISSR markers those accessions that are far from each other by virtue of genetic origin and diversity index (like Ac1 and Ac42; Ac19 and Ac45; Ac9 and Ac23; Ac18 and A25; Ac24 and Ac18) are strongly recommended to select as parent for future breeding program to develop high yielding and stress tolerant purslane variety in contribution to global food security. PMID:25468001

Alam, M Amirul; Juraimi, Abdul Shukor; Rafii, Mohd Yusop; Hamid, Azizah Abdul; Arolu, Ibrahim Wasiu; Abdul Latif, M

2015-01-01

117

Haptoglobin genotyping of Vietnamese: Global distribution of HP(del), complete deletion allele of the HP gene.  

PubMed

The haptoglobin (HP) gene deletion allele (HP(del)) is responsible for anhaptoglobinemia and a genetic risk factor for anaphylaxis reaction after transfusion due to production of the anti-HP antibody. The distribution of this allele has been explored by several groups including ours. Here, we studied the frequency of HP(del) in addition to the distribution of common HP genotypes in 293 Vietnamese. The HP(del) was encountered with the frequency of 0.020. The present result suggested that this deletion allele is restricted to East and Southeast Asians. Thus, this allele seems to be a potential ancestry informative marker for these populations. PMID:25212669

Soejima, Mikiko; Agusa, Tetsuro; Iwata, Hisato; Fujihara, Junko; Kunito, Takashi; Takeshita, Haruo; Lan, Vi Thi Mai; Minh, Tu Binh; Takahashi, Shin; Trang, Pham Thi Kim; Viet, Pham Hung; Tanabe, Shinsuke; Koda, Yoshiro

2015-01-01

118

Null allele, allelic dropouts or rare sex detection in clonal organisms: simulations and application to real data sets of pathogenic microbes  

PubMed Central

Background Pathogens and their vectors are organisms whose ecology is often only accessible through population genetics tools based on spatio-temporal variability of molecular markers. However, molecular tools may present technical difficulties due to the masking of some alleles (allelic dropouts and/or null alleles), which tends to bias the estimation of heterozygosity and thus the inferences concerning the breeding system of the organism under study. This is especially critical in clonal organisms in which deviation from panmixia, as measured by Wright’s FIS, can, in principle, be used to infer both the extent of clonality and structure in a given population. In particular, null alleles and allelic dropouts are locus specific and likely produce high variance of Wright’s FIS across loci, as rare sex is expected to do. In this paper we propose a tool enabling to discriminate between consequences of these technical problems and those of rare sex. Methods We have performed various simulations of clonal and partially clonal populations. We introduce allelic dropouts and null alleles in clonal data sets and compare the results with those that exhibit increasing rates of sexual recombination. We use the narrow relationship that links Wright’s FIS to genetic diversity in purely clonal populations as assessment criterion, since this relationship disappears faster with sexual recombination than with amplification problems of certain alleles. Results We show that the relevance of our criterion for detecting poorly amplified alleles depends partly on the population structure, the level of homoplasy and/or mutation rate. However, the interpretation of data becomes difficult when the number of poorly amplified alleles is above 50%. The application of this method to reinterpret published data sets of pathogenic clonal microbes (yeast and trypanosomes) confirms its usefulness and allows refining previous estimates concerning important pathogenic agents. Conclusion Our criterion of superimposing between the FIS expected under clonality and the observed FIS, is effective when amplification difficulties occur in low to moderate frequencies (20-30%). PMID:25027508

2014-01-01

119

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. PMID:21251263

2011-01-01

120

Parent's Notebook.  

ERIC Educational Resources Information Center

This parent resource manual was developed for use in home-based preschool programs and is part of a learning package which instructs prospective family workers, family worker trainers, and parents in the entry level skills, knowledge, and orientations needed to provide children from birth through 8 years of age with school oriented learning…

Gotts, Edward E., Ed.

121

Valuing Parents  

ERIC Educational Resources Information Center

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

Gerdes, Eugenia Proctor

2004-01-01

122

Parenting Conflicts  

MedlinePLUS

... life, and you are not going to let differences undermine your common goals. Each of you needs to demonstrate some flexibility. As you form ground rules for the family, identify the areas in which each parent excels. That parent should then exert leadership in the areas of his or her strength, ...

123

Perspectives on Parenting  

E-print Network

Parents' Perspectives on Parenting Styles and Disciplining Children The National Children's Strategy Research Series #12;#12;Parents' Perspectives on Parenting Styles and Disciplining Children 2010 Intergenerational transmission of discipline strategies 3 Parenting styles 3 Parental attitudes to physical

O'Mahony, Donal E.

124

Intra-population genetic diversity of cultivated carrot (Daucus carota L.) assessed by analysis of microsatellite markers.  

PubMed

Intra-population variation of 18 cultivated carrot (Daucus carota L. ssp. sativus) populations of diverse origins was evaluated using codominant microsatellite (SSR) markers. Using 27 genomic and EST-derived SSR markers, 253 alleles were identified with a mean 9.4 alleles per marker. Most of the alleles (60.5%) were rare i.e., with the frequency ? 0.05 while only 3.95% of alleles occurred with frequency > 0.6. EST-derived SSR markers were less polymorphic than genomic SSR markers. Differences in allele occurrence allowed 16 out of 18 populations to be assigned to either the Western or Asian carrot gene pools with high probability. Populations could be also discriminated due to the presence of private alleles (25.3% of all alleles). Most populations had excess of alleles in the homozygous state indicating their inbreeding, although heterozygous loci were common in F1 hybrids. Genetic diversity was due to allelic variation among plants within populations (62% of total variation) and between populations (38%). Accessions originating from continental Asia and Europe had more allelic variants and higher diversity than those from Japan and USA. Also, allelic richness and variability in landraces was higher than in F1 hybrids and open-pollinated cultivars. PMID:24432327

Maksylewicz, Anna; Baranski, Rafal

2013-01-01

125

Genetic analysis and molecular characterization of Chinese sesame (Sesamum indicum L.) cultivars using Insertion-Deletion (InDel) and Simple Sequence Repeat (SSR) markers  

PubMed Central

Background Sesame is an important and ancient oil crop in tropical and subtropical areas. China is one of the most important sesame producing countries with many germplasm accessions and excellent cultivars. Domestication and modern plant breeding have presumably narrowed the genetic basis of cultivated sesame. Several modern sesame cultivars were bred with a limited number of landrace cultivars in their pedigree. The genetic variation was subsequently reduced by genetic drift and selection. Characterization of genetic diversity of these cultivars by molecular markers is of great value to assist parental line selection and breeding strategy design. Results Three hundred and forty nine simple sequence repeat (SSR) and 79 insertion-deletion (InDel) markers were developed from cDNA library and reduced-representation sequencing of a sesame cultivar Zhongzhi 14, respectively. Combined with previously published SSR markers, 88 polymorphic markers were used to assess the genetic diversity, phylogenetic relationships, population structure, and allele distribution among 130 Chinese sesame accessions including 82 cultivars, 44 landraces and 4 wild germplasm accessions. A total of 325 alleles were detected, with the average gene diversity of 0.432. Model-based structure analysis revealed the presence of five subgroups belonging to two main groups, which were consistent with the results from principal coordinate analysis (PCA), phylogenetic clustering and analysis of molecular variance (AMOVA). Several missing or unique alleles were identified from particular types, subgroups or families, even though they share one or both parental/progenitor lines. Conclusions This report presented a by far most comprehensive characterization of the molecular and genetic diversity of sesame cultivars in China. InDels are more polymorphic than SSRs, but their ability for deciphering genetic diversity compared to the later. Improved sesame cultivars have narrower genetic basis than landraces, reflecting the effect of genetic drift or selection during breeding processes. Comparative analysis of allele distribution revealed genetic divergence between improved cultivars and landraces, as well as between cultivars released in different years. These results will be useful for assessing cultivars and for marker-assisted breeding in sesame. PMID:24641723

2014-01-01

126

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

127

Genetic backgrounds of the Plasmodium falciparum chloroquine resistant transporter (pfcrt) alleles in Pakistan.  

PubMed

Chloroquine (CQ) resistance in Plasmodium falciparum has been associated with point mutations in the P. falciparum CQ resistance transporter gene (pfcrt). Previous studies have shown 4-5 independent origins for CQ resistant pfcrt alleles globally, two in South America, one each in Southeast Asia, Papua New Guinea (PNG) and Philippines. In Asia, at least two different alleles corresponding to amino acids 72-76 (CVIET and SVMNT) have been found. The CVIET allele originated in Southeast Asia and then spread to Asia and Africa as well. The SVMNT allele, originating from PNG, has been found in India. This study was undertaken to investigate the genetic background of the CQ resistant pfcrt haplotypes in Pakistan. We genotyped microsatellite markers surrounding the pfcrt gene (six different markers at -12.3, -4.8, -1, 1.5, 3.9, 18.8 kb) in 114 clinical isolates of P. falciparum collected from different regions in Pakistan. Microsatellite analysis showed a significant reduction in genetic variation among the mutant SVMNT pfcrt alleles when compared to wild type alleles. The predominant SVMNT haplotype found in this study shared the same microsatellite haplotype found in both PNG and India. Two isolates with CVIET haplotypes showed similar microsatellite background to those found in Africa and Asia. In conclusion, this study suggests that CQ resistant SVMNT haplotypes in India and Pakistan have a common ancestral origin similar to that of Papua New Guinean isolates. PMID:22138496

Rawasia, Wasiq Faraz; Sridaran, Sankar; Patel, Jaymin C; Abdallah, Joseph; Ghanchi, Najia Karim; Barnwell, John W; Escalante, Ananias A; Udhayakumar, Venkatachalam; Beg, Mohammad Asim

2012-03-01

128

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

Microsoft Academic Search

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

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

1998-01-01

129

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...

130

Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis.  

PubMed

Exploitation of heterosis is one of the most important applications of genetics in agriculture. However, the genetic mechanisms of heterosis are only partly understood, and a global view of heterosis from a representative number of hybrid combinations is lacking. Here we develop an integrated genomic approach to construct a genome map for 1,495 elite hybrid rice varieties and their inbred parental lines. We investigate 38 agronomic traits and identify 130 associated loci. In-depth analyses of the effects of heterozygous genotypes reveal that there are only a few loci with strong overdominance effects in hybrids, but a strong correlation is observed between the yield and the number of superior alleles. While most parental inbred lines have only a small number of superior alleles, high-yielding hybrid varieties have several. We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. PMID:25651972

Huang, Xuehui; Yang, Shihua; Gong, Junyi; Zhao, Yan; Feng, Qi; Gong, Hao; Li, Wenjun; Zhan, Qilin; Cheng, Benyi; Xia, Junhui; Chen, Neng; Hao, Zhongna; Liu, Kunyan; Zhu, Chuanrang; Huang, Tao; Zhao, Qiang; Zhang, Lei; Fan, Danlin; Zhou, Congcong; Lu, Yiqi; Weng, Qijun; Wang, Zi-Xuan; Li, Jiayang; Han, Bin

2015-01-01

131

Total parenting.  

PubMed

In this essay, Richard Smith observes that being a parent, like so much else in our late-modern world, is required to become ever more efficient and effective, and is increasingly monitored by the agencies of the state, often with good reason given the many recorded instances of child abuse and cruelty. However, Smith goes on to argue, this begins to cast being a parent as a matter of "parenting," a technological deployment of skills and techniques, with the loss of older, more spontaneous and intuitive relations between parents and children. Smith examines this phenomenon further through a discussion of how it is captured to some extent in Hannah Arendt's notion of "natality" and how it is illuminated by Charles Dickens in his classic novel, Dombey and Son. PMID:20662172

Smith, Richard

2010-01-01

132

Working Parents  

MedlinePLUS

... Go for a walk or go to the gym. Do some recreational reading. While family time is ... Every Parent Needs to Know Family Life Health Management - Medical Home Family Dynamics Media Work & Play Getting ...

133

Parents' talk : multiple schemas and parenting practice  

E-print Network

relationships, parenting styles, and child behavior.style on parenting practices and affect in interactions with their children;parenting behaviors and affects are twofold: Parents’ attachment style has profound effects on the child’

Sarda, Zoltan G.

2012-01-01

134

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

Technology Transfer Automated Retrieval System (TEKTRAN)

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,...

135

SNP-specific array-based allele-specific expression analysis  

PubMed Central

We have developed an optimized array-based approach for customizable allele-specific gene expression (ASE) analysis. The central features of the approach are the ability to select SNPs at will for detection, and the absence of need to PCR amplify the target. A surprisingly long probe length (39–49 nt) was needed for allelic discrimination. Reconstitution experiments demonstrate linearity of ASE over a broad range. Using this approach, we have discovered at least two novel imprinted genes, NLRP2, which encodes a member of the inflammasome, and OSBPL1A, which encodes a presumed oxysterol-binding protein, were both preferentially expressed from the maternal allele. In contrast, ERAP2, which encodes an aminopeptidase, did not show preferential parent-of-origin expression, but rather, cis-acting nonimprinted differential allelic control. The approach is scalable to the whole genome and can be used for discovery of functional epigenetic modifications in patient samples. PMID:18369178

Bjornsson, Hans T.; Albert, Thomas J.; Ladd-Acosta, Christine M.; Green, Roland D.; Rongione, Michael A.; Middle, Christina M.; Irizarry, Rafael A.; Broman, Karl W.; Feinberg, Andrew P.

2008-01-01

136

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

Microsoft Academic Search

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

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

1987-01-01

137

Multiple null alleles at a polymorphic SSR-locus in a large-scale population study: Structure and geographic distribution in chum salmon  

Technology Transfer Automated Retrieval System (TEKTRAN)

Polymorphic DNA markers, e.g. mini- or microsatellite (SSR) loci, are often removed from data analyses if an excess of homozygosity, presumably an indication of null alleles, is observed. However, exclusion of such loci can reduce available information if multiple loci carry null alleles. Because nu...

138

Analyses of a multi-parent population derived from two diverse alfalfa germplasms: testcross evaluations and phenotype-DNA associations.  

PubMed

In a previous study, we showed that the genetic variation present in the Medicago sativa subsp. sativa Peruvian and M. sativa subsp. falcata WISFAL germplasms could be used to improve forage yields when favorable alleles were recombined and used in hybrid combination with cultivated alfalfa. In this paper, we present testcross forage yield and fall growth data for two seasons of a C0 population generated after intermating the Peruvian x WISFAL population for several generations. In addition, we conducted marker-trait association analysis as an attempt to identify Peruvian and WISFAL genomics regions affecting the targeted traits. Five and seven genomic regions were found significantly associated with forage yield and fall growth, respectively. In the case of fall growth, alleles from both accessions were positively associated with plant height. However, more alleles from WISFAL were positively associated with forage yield than from Peruvian. WISFAL is known for its winter hardiness and genomic regions with large effects on winter survival may have masked the effect of forage yield from Peruvian. The fact that most of the genomic regions discovered in this study have been previously associated with traits involved in winter hardiness validates our findings and suggests that associations between DNA fragments and agronomic traits can be detected without the necessity of developing bi-parental mapping populations. PMID:17676305

Maureira-Butler, I J; Udall, J A; Osborn, T C

2007-10-01

139

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

PubMed Central

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF are made up of coenocytic networks of hyphae through which nuclei and organelles can freely migrate. In this study, we investigated the possibility of a genetic bottleneck and segregation of allelic variation at sporulation for a low-copy Polymerase1-like gene, PLS. Specifically, our objectives were (1) to estimate what allelic diversity is passed on to a single spore (2) to determine whether this diversity is less than the total amount of variation found in all spores (3) to investigate whether there is any differential segregation of allelic variation. We inoculated three tomato plants with a single spore of Glomus etunicatum each and after six months sampled between two and three daughter spores per tomato plant. Pyrosequencing PLS amplicons in eight spores revealed high levels of allelic diversity; between 43 and 152 alleles per spore. We corroborated the spore pyrosequencing results with Sanger- and pyrosequenced allele distributions from the original parent isolate. Both sequencing methods retrieved the most abundant alleles from the offspring spore allele distributions. Our results indicate that individual spores contain only a subset of the total allelic variation from the pooled spores and parent isolate. Patterns of allele diversity between spores suggest the possibility for segregation of PLS alleles among spores. We conclude that a genetic bottleneck could potentially occur during sporulation in AMF, with resulting differences in genetic variation among sister spores. We suggest that the effects of this bottleneck may be countered by anastomosis (hyphal fusion) between related hyphae. PMID:24386173

St-Arnaud, Marc; Hijri, Mohamed

2013-01-01

140

Body for Parents (Girls)  

MedlinePLUS

... Illness & disability Drugs, alcohol & smoking Your feelings Relationships Bullying Safety Your future Environmental health Skip section navigation ( ... parents Girls' feelings for parents Relationships for parents Bullying for parents Safety for parents The future for ...

141

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. PMID:22808236

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

2012-01-01

142

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

143

Identification of a rare off-ladder allele of the D13S325 locus during paternity testing.  

PubMed

This study demonstrates an unusual rare allele of D13S325 that was falsely categorized as an allele of D12S391 under the STRtyper™-10F/G system. The parentage cases with these rare alleles were analyzed using the Sinofiler™ system and singleplex amplification system, and the alleles of D13S325 extracted from the electrophoresis gel were sequenced. 5 Cases with the rare alleles misread as allele 20 of D12S391 were identified in total 2618 cases (including 3200 unrelated parents). This rare allele was designated as allele 5.1 of D13S325 based on its DNA sequence. Its frequency in the Chinese population was 1.6×10(-3). Because the rare allele 5.1 of D13S325 locus tends to be incorrectly labeled in the STRtyper™-10F/G system, particular attention should be paid when the system is used in paternity testing, personal identification, and DNA database comparisons. PMID:24144442

Chen, Wenjing; Cheng, Jianding; Tong, Dayue; Liu, Sujuan; Zhang, Yinming; Sun, Hongyu

2014-01-01

144

Genetic diversity and population structure among pea (Pisum sativum L.) cultivars as revealed by simple sequence repeat and novel genic markers.  

PubMed

Field pea (Pisum sativum L.) is an important cool season legume crop widely grown around the world. This research provides a basis for selection of pea germplasm across geographical regions in current and future breeding and genetic mapping efforts for pea improvement. Eleven novel genic markers were developed from pea expressed sequence tag (EST) sequences having significant similarity with gene calls from Medicago truncatula spanning at least one intron. In this study, 96 cultivars widely grown or used in breeding programs in the USA and Canada were analyzed for genetic diversity using 31 microsatellite or simple sequence repeat (SSR) and 11 novel EST-derived genic markers. The polymorphic information content varied from 0.01-0.56 among SSR markers and 0.04-0.43 among genic markers. The results showed that SSR and EST-derived genic markers displayed one or more highly reproducible, multi-allelic, and easy to score loci ranging from 200 to 700 bp in size. Genetic diversity was assessed through unweighted neighbor-joining method, and 96 varieties were grouped into three main clusters based on the dissimilarity matrix. Four subpopulations were determined through STRUCTURE analysis with no significant geographic separation of the subpopulations. The findings of the present study can be used to select diverse genotypes to be used as parents of crosses aimed for breeding improved pea cultivars. PMID:24894738

Jain, Shalu; Kumar, Ajay; Mamidi, Sujan; McPhee, Kevin

2014-10-01

145

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

Microsoft Academic Search

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

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

1998-01-01

146

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. PMID:23324082

2013-01-01

147

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

148

Total Parenting  

ERIC Educational Resources Information Center

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

Smith, Richard

2010-01-01

149

HLA-DRB1*13:01 allele in the genetic susceptibility to colorectal carcinoma.  

PubMed

Increasing evidence suggests that HLA-DRB1 alleles reduce or increase the risk of developing ulcerative colitis-associated colorectal carcinoma (CRC) tumors. However, the role of HLA-DRB1 locus on the susceptibility to develop CRC tumor, in the absence of a history of inflammatory bowel diseases (IBDs), is unclear. The aim of our study was to determine whether HLA-DRB1 alleles are associated with IBD-independent CRC tumor. HLA-DRB1 allele polymorphisms were identified by sequence-based typing method in 53 CRC patients and 57 sex- and age-matched healthy Caucasian controls. Pearson's chi-squared analysis with Yate's correction or Fisher's exact test with Bonferroni's correction, as appropriate, were used to compare the allele frequency (AF) differences of HLA-DRB1 in patients and controls. A total of 29 HLA-DRB1 alleles were recognized. A detailed study of these alleles allowed to identify DRB1*13:01 and DRB1*11:01 alleles that were significantly associated with an increased and reduced risk to develop CRC tumor, respectively. AF of DRB1*13:01, in CRC patients, was significantly higher than that of healthy controls, even following Bonferroni's correction (p?=?0.029). In contrast, the presence of the DRB1*11:01 allele was negatively associated with CRC tumor as evidenced by the significantly lower AF in CRC patients than that of healthy controls (p?=?0.005). However, following Bonferroni's correction, the AF of DRB*11:01 lost its statistical significance. These results suggest that HLA-DRB1*13:01 allele could be a potential marker for predicting genetic susceptibility to CRC tumor. In contrast, the protective role of DRB1*11:01 remains unclear. PMID:25346274

Aureli, Anna; Canossi, Angelica; Del Beato, Tiziana; Franceschilli, Luana; Buonomo, Oreste; Papola, Franco; De Sanctis, Flavio; Lanzilli, Giulia; Sileri, Pierpaolo; Coppola, Andrea; Caratelli, Sara; Arriga, Roberto; Orlandi, Augusto; Lauro, Davide; Rossi, Piero; Sconocchia, Giuseppe

2014-10-23

150

Immunogenetic study of a new HLA allele, B*2723.  

PubMed

A novel HLA-B*27 allele (B*2723) detected by irregular serological and PCR-SSP typing results was identified by nucleotide sequencing of exons 2 and 3. B*2723 differs from B*27052 by nine nucleotides which encode seven amino acid changes at positions 63 (Glu to Asn), 67 (Cys to Phe), 69 (Ala to Thr), 70 (Lys to Asn), 71 (Ala to Thr), 74 (Asp to Tyr) and 77 (Asp to Ser) in the alpha1 helix. All these substitutions are possessed by B*35 alleles suggesting that B*2723 was created by a gene conversion-like event involving B*27052 and a B*35 allele. Using the HLA-A*26 and DRB1*12 alleles of the B*2723-bearing haplotype as 'markers', two further examples of B*2723 were found in 29,851 blood donors. Therefore, B*2723 has a 'minimum' gene frequency of 0.000034 (phenotype frequency 0.0067%) in blood donors resident in Wales. In all three families, B*2723 was present on a haplotype with: A*26; Cw*0202; DRB1*1201/6/7; DRB3*02; DQA1*05; DQB1*0301. The B*2723 product failed to react with HLA-B27 antisera and reacted weakly or not at all with Bw4 antisera. Lack of the ECAKA motif at amino acid positions 63, 67, 69-71 probably accounts for lack of the B27 specificity while the amino acid combination 74Y, 77S, 80T, 81L may cause aberrant Bw4 reactivity. PMID:12492816

Darke, C; Street, J; Hammond, L; Downing, J; Thompson, J

2002-11-01

151

ALLELE-SPECIFIC EXPRESSION OF APC IN ADENOMATOUS POLYPOSIS FAMILIES  

PubMed Central

Backgound & Aims Germline mutations of the APC gene are the pathogenic cause of most cases of familial adenomatous polyposis (FAP) and a lesser proportion of attenuated FAP (AFAP). Systematic analysis of APC at the RNA level may provide insight into the pathogenicity of identified mutations and uncover the molecular basis of FAP/AFAP in families without identifiable mutations. Here, we analyzed the prevalence of imbalances in the allelic expression of APC in polyposis families with germline mutations in the gene and without detectable mutations in APC or and MUTYH. Methods Allele-specific expression (ASE) was determined by single nucleotide primer extension using an exon 11 polymorphism as an allele-specific marker. In total, 52 APC-mutation-positive (36 families) and 24 APC/MUTYH-mutation-negative (23 families) informative patients were analyzed. Seventy-six controls were also included. Results Of the APC-mutation-positive families, most of those in which the mutation was located before the last exon of the gene (12 of 14) showed ASE imbalance, which is consistent with a mechanism of nonsense-mediated decay (NMD). Of the APC/MUTYH mutation-negative families, two (9%) showed ASE imbalance as a hallmark of the putative pathogenic cause of the disease. Normal allele expression was restored after treatment of short-term cultured lymphocytes with puromycin, supporting the NMD hypothesis. Conclusions ASE analysis may be an indicator of pathogenicity for some cases of FAP and AFAP in which APC mutations are not found. ASE might also be useful for prioritizing the order in which different areas of APC should be tested. Our results underline the importance of RNA-level studies in molecular diagnosis of FAP. PMID:20434453

Castellsagué, Ester; González, Sara; Guinó, Elisabet; Stevens, Kristen N.; Borràs, Ester; Raymond, Victoria M.; Lázaro, Conxi; Blanco, Ignacio; Gruber, Stephen B.; Capellá, Gabriel

2010-01-01

152

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

153

Parental Power and Adolescents' Parental Identification.  

ERIC Educational Resources Information Center

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

Acock, Alan C.; Yang, Wen Shan

1984-01-01

154

A novel measurement of allele discrimination for assessment of allele-specific silencing by RNA interference.  

PubMed

Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs. PMID:25037272

Takahashi, Masaki; Hohjoh, Hirohiko

2014-11-01

155

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

PubMed Central

Assessing allele-specific gene expression (ASE) on a large scale continues to be a technically challenging problem. Certain biological phenomena, such as X chromosome inactivation and parental imprinting, affect ASE most drastically by completely shutting down the expression of a whole set of alleles. Other more subtle effects on ASE are likely to be much more complex and dependent on the genetic environment and are perhaps more important to understand since they may be responsible for a significant amount of biological diversity. Tools to assess ASE in a diploid biological system are becoming more reliable. Non-diploid systems are, however, not uncommon. In humans full or partial polyploid states are regularly found in both healthy (meiotic cells, polynucleated cell types) and diseased tissues (trisomies, non-disjunction events, cancerous tissues). In this work we have studied ASE in the medaka fish model system. We have developed a method for determining ASE in polyploid organisms from RNAseq data and we have implemented this method in a software tool set. As a biological model system we have used nuclear transplantation to experimentally produce artificial triploid medaka composed of three different haplomes. We measured ASE in RNA isolated from the livers of two adult, triploid medaka fish that showed a high degree of similarity. The majority of genes examined (82%) shared expression more or less evenly among the three alleles in both triploids. The rest of the genes (18%) displayed a wide range of ASE levels. Interestingly the majority of genes (78%) displayed generally consistent ASE levels in both triploid individuals. A large contingent of these genes had the same allele entirely suppressed in both triploids. When viewed in a chromosomal context, it is revealed that these genes are from large sections of 4 chromosomes and may be indicative of some broad scale suppression of gene expression. PMID:24945156

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

2014-01-01

156

Parent Academic Overview Student-Parent Orientation  

E-print Network

their academic, personal, and professional goals by providing high quality academic advisingParent Academic Overview Student-Parent Orientation Program University of California, Irvine #12;Purpose of Parent Academic Overview 1.Provide the Mission Statement of the UCI

Rose, Michael R.

157

Assessment of genetic diversity in broomcorn millet ( Panicum miliaceum L.) using SSR markers  

Microsoft Academic Search

The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, wasanalyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles werefound, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91.

Xingyu Hu; Jianfei Wang; Ping Lu; Hongsheng Zhang

2009-01-01

158

Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses  

PubMed Central

Prediction of heterosis has a long history with mixed success, partly due to low numbers of genetic markers and/or small data sets. We investigated the prediction of heterosis for egg number, egg weight and survival days in domestic white Leghorns, using ?400?000 individuals from 47 crosses and allele frequencies on ?53?000 genome-wide single nucleotide polymorphisms (SNPs). When heterosis is due to dominance, and dominance effects are independent of allele frequencies, heterosis is proportional to the squared difference in allele frequency (SDAF) between parental pure lines (not necessarily homozygous). Under these assumptions, a linear model including regression on SDAF partitions crossbred phenotypes into pure-line values and heterosis, even without pure-line phenotypes. We therefore used models where phenotypes of crossbreds were regressed on the SDAF between parental lines. Accuracy of prediction was determined using leave-one-out cross-validation. SDAF predicted heterosis for egg number and weight with an accuracy of ?0.5, but did not predict heterosis for survival days. Heterosis predictions allowed preselection of pure lines before field-testing, saving ?50% of field-testing cost with only 4% loss in heterosis. Accuracies from cross-validation were lower than from the model-fit, suggesting that accuracies previously reported in literature are overestimated. Cross-validation also indicated that dominance cannot fully explain heterosis. Nevertheless, the dominance model had considerable accuracy, clearly greater than that of a general/specific combining ability model. This work also showed that heterosis can be modelled even when pure-line phenotypes are unavailable. We concluded that SDAF is a useful predictor of heterosis in commercial layer breeding. PMID:24105438

Amuzu-Aweh, E N; Bijma, P; Kinghorn, B P; Vereijken, A; Visscher, J; van Arendonk, J AM; Bovenhuis, H

2013-01-01

159

Parental stress, parenting behavior and observed parent-child interaction  

Microsoft Academic Search

This study investigated the relationship between parental stress, social support, and directly observed parenting behavior and dyadic interaction in a non-clinical sample of 26 parent-child dyads, in which the child was age five or younger. This study also explored the differential impact of various types of stress on parenting behavior and dyadic interaction, including life stress as measured by the

Katrina L Adams

2006-01-01

160

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

PubMed Central

Background Extensive studies on heterosis in plants using transcriptome analysis have identified differentially expressed genes (DEGs) in F1 hybrids. However, it is not clear why yield in heterozygotes is superior to that of the homozygous parents or how DEGs are produced. Global allele-specific expression analysis in hybrid rice has the potential to answer these questions. Results We report a genome-wide allele-specific expression analysis using RNA-sequencing technology of 3,637–3,824 genes from three rice F1 hybrids. Of the expressed genes, 3.7% exhibited an unexpected type of monoallelic expression and 23.8% showed preferential allelic expression that was genotype-dependent in reciprocal crosses. Those genes exhibiting allele-specific expression comprised 42.4% of the genes differentially expressed between F1 hybrids and their parents. Allele-specific expression accounted for 79.8% of the genes displaying more than a 10-fold expression level difference between an F1 and its parents, and almost all (97.3%) of the genes expressed in F1, but non-expressed in one parent. Significant allelic complementary effects were detected in the F1 hybrids of rice. Conclusions Analysis of the allelic expression profiles of genes at the critical stage for highest biomass production from the leaves of three different rice F1 hybrids identified genotype-dependent allele-specific expression genes. A cis-regulatory mechanism was identified that contributes to allele-specific expression, leading to differential gene expression and allelic complementary effects in F1 hybrids. PMID:24358981

2013-01-01

161

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

162

Limited efficacy of hydroxyurea in lowering of the JAK2 V617F allele burden.  

PubMed

Besides being an invaluable marker of clonal disease in chronic myeloproliferative disorders (CMPDs), the JAK2 V617F mutation and the mutated allele burden have an impact on disease phenotype and may provide information on prognosis. Recently, hydroxyurea (HU) has been shown to induce a rapid decline in the JAK2 V617F allele burden. The aim of the present study was to assess the dynamics of the JAK2 V617F allele burden during long-term treatment with HU in a series of patients with CMPDs. The JAK2 V617F allele burden was determined by quantitative PCR in 24 patients of whom 17 received HU, four received anagrelide and three were followed without any cytoreductive therapy. During a median follow-up of 24.2 months, no significant reductions in the JAK2 V617F allele burden were seen in patients treated with HU. We conclude that HU has only a limited effect on the JAK2 V617F allele burden in CMPD. PMID:19154659

Larsen, Thomas Stauffer; Pallisgaard, Niels; de Stricker, Karin; Møller, Michael Boe; Hasselbalch, Hans Carl

2009-02-01

163

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

164

Parentage and kinship studies in an obligate brood parasitic bird, the brown-headed cowbird (Molothrus ater), using microsatellite DNA markers.  

PubMed

Recent studies suggest that single-locus microsatellite DNA markers have the potential to unambiguously resolve parentage among individuals in natural populations where maternity is known. However, their power for determining parentage when neither parent is known is unclear. Here we investigate the usefulness of microsatellite DNA markers to determine parentage in a brood parasitic bird, the brown-headed cowbird (Molothrus ater), where, for a given offspring, no a priori knowledge of either parent is available. Seven polymorphic microsatellite DNA markers isolated from brown-headed cowbirds and yellow warblers (Dendroica petechia) were used to genetically characterize an individually marked breeding population of male and female cowbirds at Delta Marsh, Manitoba. Forty-four males, 21 females, and 61 cowbird chicks were genotyped at seven loci using DNA amplified from blood and tissue samples. The mean exclusion probabilities pooled across all seven loci were 0.9964 for males and 0.9948 for females. Two null (non-amplifying) alleles at one locus were discovered and accounted for by constructing alternate nonoverlapping primer sets. Exclusion analyses performed using all individuals determined both paternity and maternity for 43 chicks and paternity only for 4 chicks. Another microsatellite locus was then used to determine paternity for three additional chicks. Relatedness analyses placed 12 of the 18 remaining chicks not assigned both maternity and paternity into four unique full sibling groups. Overall, 90.16% (55 of 61) of all offspring examined were placed into distinct parent/sibling groups, demonstrating that this marker set is extremely useful for parentage studies in this species. PMID:9987928

Alderson, G W; Gibbs, H L; Sealy, S G

1999-01-01

165

SCN5A allelic expression imbalance in African-Americans heterozygous for the common variant p.Ser1103Tyr  

PubMed Central

Background Heterozygous and homozygous carriers of SCN5A-p.Ser1103Tyr, a common genetic variant with functional effects among African-Americans, have an increased risk of sudden death. We hypothesized that some heterozygous carriers may have unequal expression of wild-type and variant alleles and secondarily that predominance of the variant gene copy could further increase risk for sudden death in this population. Methods We quantified allele-specific expression of SCN5A-p.Ser1103Tyr by real-time reverse-transcription polymerase chain reaction (RT-PCR) in heart tissue from heterozygous African-American infants, who died from sudden infant death syndrome (SIDS) or from other causes, to test for allelic expression imbalance. Results We observed significant allelic expression imbalance in 13 of 26 (50%) African-American infant hearts heterozygous for SCN5A-p.Ser1103Tyr, and a significant (p < 0.0001) bimodal distribution of log2 allelic expression ratios. However, there were no significant differences in the mean log2 allelic expression ratios in hearts of infants dying from SIDS as compared to infants dying from other causes and no significant difference in the proportion of cases with greater expression of the variant allele. Conclusions Our data provide evidence that SCN5A allelic expression imbalance occurs in African-Americans heterozygous for p.Ser1103Tyr, but this phenomenon alone does not appear to be a marker for risk of SIDS. PMID:20470418

2010-01-01

166

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. PMID:19630983

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

2009-01-01

167

Molecular genetics of MHC class II alleles in Chinese patients with IgA nephropathy.  

PubMed

We have studied the restriction fragment length polymorphism (RFLP) of the major histocompatibility complex (MHC) class II DQ and DR regions of 79 Chinese patients with IgA nephropathy (IgAN) and compared it with 104 normal Chinese controls. The DR and DQ alleles were confirmed by polymerase chain reaction using sequence specific primers. There was a significantly higher frequency of homozygous DQ beta 3b (DQ7) in patients with IgAN (16.4%) compared with controls (5.7%). Seventy-one IgAN patients had their renal biopsies graded according to histopathological severity: grades I, II or III. There was no statistical difference in the DR and DQ alleles among the three grades. Seventy-three patients were classified into group A with normal and stable renal function (serum creatinine < or = 150 mumol/liter) and group B with chronic renal failure (serum creatinine > 150 mumol/liter). There was a significant increase in frequency of DQA2 U (DX alpha U) allele in group B (66.9%) compared with group A (26.9%). Also, there was an increased frequency of DQ alpha 2 allele in the group A (40.4%) compared with group B (14.3%). Out of the 24 patients carrying the DQ alpha 2 allele, 17 were DQA2 U allele-negative and they all had normal renal function, suggesting that DQA2 U allele is associated with a poor prognostic factor in IgAN. The study shows that DQ alleles are probably the important genetic loci or are close markers for the disease susceptibility and prognostic index for IgAN in Chinese people. PMID:7933837

Li, P K; Poon, A S; Lai, K N

1994-07-01

168

Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: a review.  

PubMed

Sequencing of rice genome has facilitated the understanding of rice evolution and has been utilized extensively for mining of DNA markers to facilitate marker-assisted breeding. Simple sequence repeat (SSR) markers that are tandemly repeated nucleotide sequence motifs flanked by unique sequences are presently the maker of choice in rice improvement due to their abundance, co-dominant inheritance, high levels of allelic diversity, and simple reproducible assay. The current level of genome coverage by SSR markers in rice is sufficient to employ them for genotype identification and marker-assisted selection in breeding for mapping of genes and quantitative trait loci analysis. This review provides comprehensive information on the mapping and applications of SSR markers in investigation of rice cultivars to study their genetic divergence and marker-assisted selection of important agronomic traits. PMID:24915404

Kaur, Shubhneet; Panesar, Parmjit S; Bera, Manab B; Kaur, Varinder

2015-01-01

169

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. PMID:23170872

2012-01-01

170

Optimal Design for Marker-assisted Gene Pyramiding in Cross Population  

PubMed Central

Marker-assisted gene pyramiding aims to produce individuals with superior economic traits according to the optimal breeding scheme which involves selecting a series of favorite target alleles after cross of base populations and pyramiding them into a single genotype. Inspired by the science of evolutionary computation, we used the metaphor of hill-climbing to model the dynamic behavior of gene pyramiding. In consideration of the traditional cross program of animals along with the features of animal segregating populations, four types of cross programs and two types of selection strategies for gene pyramiding are performed from a practical perspective. Two population cross for pyramiding two genes (denoted II), three population cascading cross for pyramiding three genes(denoted III), four population symmetry (denoted IIII-S) and cascading cross for pyramiding four genes (denoted IIII-C), and various schemes (denoted cross program-A–E) are designed for each cross program given different levels of initial favorite allele frequencies, base population sizes and trait heritabilities. The process of gene pyramiding breeding for various schemes are simulated and compared based on the population hamming distance, average superior genotype frequencies and average phenotypic values. By simulation, the results show that the larger base population size and the higher the initial favorite allele frequency the higher the efficiency of gene pyramiding. Parents cross order is shown to be the most important factor in a cascading cross, but has no significant influence on the symmetric cross. The results also show that genotypic selection strategy is superior to phenotypic selection in accelerating gene pyramiding. Moreover, the method and corresponding software was used to compare different cross schemes and selection strategies. PMID:25049625

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

2012-01-01

171

PARENT'S GUIDE Tips for Parents & Families  

E-print Network

Irvine parent, you play a unique role. Your involvement with the university and the support you pro- videPARENT'S GUIDE Tips for Parents & Families Seeing your child leave for college, whether, 2013 Dear UCI Parents, Welcome to the UC Irvine Family! The UC Irvine Student Housing staff is looking

Rose, Michael R.

172

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

PubMed

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

Waldbieser, G C; Bosworth, B G

2013-08-01

173

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

174

Exploring the distribution of genetic markers of pharmacogenomics relevance in Brazilian and Mexican populations.  

PubMed

Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701

Bonifaz-Peña, Vania; Contreras, Alejandra V; Struchiner, Claudio Jose; Roela, Rosimeire A; Furuya-Mazzotti, Tatiane K; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L; Hidalgo-Miranda, Alfredo; Parra, Esteban J; Fernández-López, Juan Carlos; Suarez-Kurtz, Guilherme

2014-01-01

175

Exploring the Distribution of Genetic Markers of Pharmacogenomics Relevance in Brazilian and Mexican Populations  

PubMed Central

Studies of pharmacogenomics-related traits are increasingly being performed to identify loci that affect either drug response or susceptibility to adverse drug reactions. However, the effect of the polymorphisms can differ in magnitude or be absent depending on the population being assessed. We used the Affymetrix Drug Metabolizing Enzymes and Transporters (DMET) Plus array to characterize the distribution of polymorphisms of pharmacogenetics and pharmacogenomics (PGx) relevance in two samples from the most populous Latin American countries, Brazil and Mexico. The sample from Brazil included 268 individuals from the southeastern state of Rio de Janeiro, and was stratified into census categories. The sample from Mexico comprised 45 Native American Zapotecas and 224 self-identified Mestizo individuals from 5 states located in geographically distant regions in Mexico. We evaluated the admixture proportions in the Brazilian and Mexican samples using a panel of Ancestry Informative Markers extracted from the DMET array, which was validated with genome-wide data. A substantial variation in ancestral proportions across census categories in Brazil, and geographic regions in Mexico was identified. We evaluated the extent of genetic differentiation (measured as FST values) of the genetic markers of the DMET Plus array between the relevant parental populations. Although the average levels of genetic differentiation are low, there is a long tail of markers showing large frequency differences, including markers located in genes belonging to the Cytochrome P450, Solute Carrier (SLC) and UDP-glucuronyltransferase (UGT) families as well as other genes of PGx relevance such as ABCC8, ADH1A, CHST3, PON1, PPARD, PPARG, and VKORC1. We show how differences in admixture history may have an important impact in the distribution of allele and genotype frequencies at the population level. PMID:25419701

Bonifaz-Peña, Vania; Contreras, Alejandra V.; Struchiner, Claudio Jose; Roela, Rosimeire A.; Furuya-Mazzotti, Tatiane K.; Chammas, Roger; Rangel-Escareño, Claudia; Uribe-Figueroa, Laura; Gómez-Vázquez, María José; McLeod, Howard L.; Hidalgo-Miranda, Alfredo

2014-01-01

176

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

177

Characterization of the treefrog null allele, 1991  

SciTech Connect

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 found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

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

1992-04-01

178

Microsatellite markers for Russian olive (Elaeagnus angustifolia; Elaeagnaceae)1  

PubMed Central

• Premise of the study: Microsatellite markers were developed for the plant species Elaeagnus angustifolia to assist in future investigations of genetic variability in its native and invasive ranges and the precise origins of the United States/Canada invasion. • Methods and Results: Eleven polymorphic microsatellite markers were developed. The number of alleles observed for each locus ranged from three to 11. • Conclusions: These microsatellites have sufficient potential variability to define population structure and origins of the Russian olive invasion. PMID:25202584

Gaskin, John F.; Hufbauer, Ruth A.; Bogdanowicz, Steven M.

2013-01-01

179

Descriptors: Elementary School Parents  

E-print Network

The purpose of this study was to analyze parental or guardian attitudes, general education behavior of parents and homework assistance behavior. The amount of time spent on assisting students with homework will also be studied. The objectives of this study was to (1) analyze parental involvement attitudes in relationship to grade level of the child, parent’s gender, parent’s age, educational level of the parent, employment status of the parent and child’s grades, (2) analyze parental behaviors in relationship to grade level of the child, parent’s gender, parent’s age, educational level of the parent, employment status of the parent and child’s grades, and (3) analyze the relationship of parent’s help with schoolwork and the child’s grades. The population of this study consisted of parents or guardians from Area Three of the Chicago Public School System to respond to the questionnaire designed by the i researcher to question the relationships between parent attitudes, parent behaviors, and the child’s grades and parents help with schoolwork. The research instrument for this study was divided into three parts. Part I contains demographic information. Part II consists of 26 attitude questions ranked on a

Veronica Mcdaniel

180

High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces.  

PubMed

Current genome editing techniques available for Saccharomyces yeast species rely on auxotrophic markers, limiting their use in wild and industrial strains and species. Taking advantage of the ancient loss of thymidine kinase in the fungal kingdom, we have developed the herpes simplex virus thymidine kinase gene as a selectable and counterselectable marker that forms the core of novel genome engineering tools called the H: aploid E: ngineering and R: eplacement P: rotocol (HERP) cassettes. Here we show that these cassettes allow a researcher to rapidly generate heterogeneous populations of cells with thousands of independent chromosomal allele replacements using mixed PCR products. We further show that the high efficiency of this approach enables the simultaneous replacement of both alleles in diploid cells. Using these new techniques, many of the most powerful yeast genetic manipulation strategies are now available in wild, industrial, and other prototrophic strains from across the diverse Saccharomyces genus. PMID:25209147

Alexander, William G; Doering, Drew T; Hittinger, Chris Todd

2014-11-01

181

Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping.  

PubMed

Allele-specific (AS) assessment of chromatin has the potential to elucidate specific cis-regulatory mechanisms, which are predicted to underlie the majority of the known genetic associations to complex disease. However, development of chromatin landscapes at allelic resolution has been challenging since sites of variable signal strength require substantial read depths not commonly applied in sequencing based approaches. In this study, we addressed this by performing parallel analyses of input DNA and chromatin immunoprecipitates (ChIP) on high-density Illumina genotyping arrays. Allele-specificity for the histone modifications H3K4me1, H3K4me3, H3K27ac, H3K27me3, and H3K36me3 was assessed using ChIP samples generated from 14 lymphoblast and 6 fibroblast cell lines. AS-ChIP SNPs were combined into domains and validated using high-confidence ChIP-seq sites. We observed characteristic patterns of allelic-imbalance for each histone-modification around allele-specifically expressed transcripts. Notably, we found H3K4me1 to be significantly anti-correlated with allelic expression (AE) at transcription start sites, indicating H3K4me1 allelic imbalance as a marker of AE. We also found that allelic chromatin domains exhibit population and cell-type specificity as well as heritability within trios. Finally, we observed that a subset of allelic chromatin domains is regulated by DNase I-sensitive quantitative trait loci and that these domains are significantly enriched for genome-wide association studies hits, with autoimmune disease associated SNPs specifically enriched in lymphoblasts. This study provides the first genome-wide maps of allelic-imbalance for five histone marks. Our results provide new insights into the role of chromatin in cis-regulation and highlight the need for high-depth sequencing in ChIP-seq studies along with the need to improve allele-specificity of ChIP-enrichment. PMID:25055051

Light, Nicholas; Adoue, Véronique; Ge, Bing; Chen, Shu-Huang; Kwan, Tony; Pastinen, Tomi

2014-09-01

182

Allelic relationships of genes controlling number of flowers per axis in chickpea  

Microsoft Academic Search

Genetic variation for number of flowers per axis in chickpea (Cicer arietinum L.) includes single-flower, double-flower, triple-flower and multi-flower traits. A double-flowered (DF) line ICC 4929, a triple-flowered (TF) line IPC 99-18 and a multi-flowered (MF) line JGM 7 were intercrossed in all possible combinations and flowering behavior of parents, F1s and F2s was studied to establish allelic relationships, penetrance

S. Srinivasan; P. M. Gaur; S. K. Chaturvedi; B. V. Rao

2006-01-01

183

Derivative Alleles of the Arabidopsis Gibberellin-Insensitive (gai) Mutation Confer a Wild-Type Phenotype.  

PubMed Central

The gai mutation of Arabidopsis confers a dwarf phenotype resembling that of mutants defective in gibberellin (GA) biosynthesis. However, gai mutant plants differ from GA biosynthesis mutants because they fail to respond to exogenous GAs and accumulate endogenous GA species to higher (rather than lower) levels than found in wild-type controls. The gai mutation, therefore, identifies a gene that modulates the response of plant cells to GA. We have mapped gai with respect to visible and restriction fragment length polymorphism (RFLP) markers from chromosome 1. To observe the phenotype exhibited by individuals potentially lacking wild-type (GAI) function, we have also isolated novel irradiation-induced derivative alleles of gai. When homozygous, these alleles confer a revertant phenotype that is indistinguishable from the wild type. gai is a semidominant mutation that exerts its effects either because it is a gain-of-function mutation or because it is a loss-of-function or reduced-function mutation. The genetic and physiological properties of the derivative alleles are considered with reference to these alternative modes of dominance of gai. Because these alleles are potential deletion or rearrangement mutations, together with the closely linked RFLP markers identified in the linkage mapping experiments, they provide useful resources for the isolation of the gai locus via a map-based cloning approach. PMID:12271067

Peng, J; Harberd, NP

1993-01-01

184

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea  

PubMed Central

Characterization of natural allelic diversity and understanding the genetic structure and linkage disequilibrium (LD) pattern in wild germplasm accessions by large-scale genotyping of informative microsatellite and single nucleotide polymorphism (SNP) markers is requisite to facilitate chickpea genetic improvement. Large-scale validation and high-throughput genotyping of genome-wide physically mapped 478 genic and genomic microsatellite markers and 380 transcription factor gene-derived SNP markers using gel-based assay, fluorescent dye-labelled automated fragment analyser and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass array have been performed. Outcome revealed their high genotyping success rate (97.5%) and existence of a high level of natural allelic diversity among 94 wild and cultivated Cicer accessions. High intra- and inter-specific polymorphic potential and wider molecular diversity (11–94%) along with a broader genetic base (13–78%) specifically in the functional genic regions of wild accessions was assayed by mapped markers. It suggested their utility in monitoring introgression and transferring target trait-specific genomic (gene) regions from wild to cultivated gene pool for the genetic enhancement. Distinct species/gene pool-wise differentiation, admixed domestication pattern, and differential genome-wide recombination and LD estimates/decay observed in a six structured population of wild and cultivated accessions using mapped markers further signifies their usefulness in chickpea genetics, genomics and breeding. PMID:25222488

Kujur, Alice; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

2014-01-01

185

Multiple target sites of allelic imbalance on chromosome 17 in Barrett's oesophageal cancer  

Microsoft Academic Search

Twelve Barrett's adenocarcinomas have been analysed for the occurrence of allelic imbalance (LOH) on chromosome 17 using 41 microsatellite markers. This study provides evidence for 13 minimal regions of LOH, six on 17p and seven on 17q. Four of these centre in the vicinity of the known tumour suppressor genes (TSGs) TP53 (17p13.1), NF1 (17q11.2), BRCA1 (17q21.1), and a putative

J Dunn; J Garde; K Dolan; J R Gosney; R Sutton; S J Meltzer; J K Field

1999-01-01

186

Typing for brown trout LDH-C1* alleles together with microsatellites by automated sequencing  

Microsoft Academic Search

The eye-specific lactate dehydrogenase (LDH-C1) locus is a genetic marker of evolutionary and ecological interests for brown\\u000a trout. We developed a new protocol to genotype the point mutation responsible for this polymorphism by automated sequencing.\\u000a To that end, we designed and employed two primer pairs in a single polymerase chain reaction, each pair including one allele-specific\\u000a primer. This new method

Joëlle Chat; Aurélie Manicki; Nacira Merchermek

2008-01-01

187

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

188

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

Microsoft Academic Search

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

Ryan C Garrick; Paul Sunnucks; Rodney J Dyer

2010-01-01

189

Seed fates in crop–wild hybrid sunflower: crop allele and maternal effects  

PubMed Central

Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank.

Pace, Brian A; Alexander, Helen M; Emry, Jason D; Mercer, Kristin L

2015-01-01

190

Seed fates in crop-wild hybrid sunflower: crop allele and maternal effects.  

PubMed

Domestication has resulted in selection upon seed traits found in wild populations, yet crop-wild hybrids retain some aspects of both parental phenotypes. Seed fates of germination, dormancy, and mortality can influence the success of crop allele introgression in crop-wild hybrid zones, especially if crop alleles or crop-imparted seed coverings result in out-of-season germination. We performed a seed burial experiment using crop, wild, and diverse hybrid sunflower (Helianthus annuus) cross types to test how a cross type's maternal parent and nuclear genetic composition might affect its fate under field conditions. We observed higher maladaptive fall germination in the crop- and F1- produced seeds than wild-produced seeds and, due to an interaction with percent crop alleles, fall germination was higher for cross types with more crop-like nuclear genetics. By spring, crop-produced cross types had the highest overwintering mortality, primarily due to higher fall germination. Early spring germination was identical across maternal types, but germination continued for F1-produced seeds. In conclusion, the more wild-like the maternal parent or the less proportion of the cross type's genome contributed by the crop, the greater likelihood a seed will remain ungerminated than die. Wild-like dormancy may facilitate introgression through future recruitment from the soil seed bank. PMID:25685189

Pace, Brian A; Alexander, Helen M; Emry, Jason D; Mercer, Kristin L

2015-02-01

191

ON RECOMBINATION BETWEEN CLOSE AND DISTANT MARKERS IN PHAGE LAMBDA  

Microsoft Academic Search

The contribution of parental DNA to progeny phages genetically recomb- inant for close markers, distant markers, or both simultaneously was studied in biparental and triparental replication-blocked crosses. The data are compatible with the previously proposed view that heterozygous overlaps at the sites of crossing over are sometimes about as long as the lambda chromosome. However, about half of the close

FRANKLIN W. STAI-IL; MARY M. STAHL

192

Positive selection vectors for allelic exchange  

Microsoft Academic Search

We describe here the development and use of two new allelic exchange vectors, pKAS32 and pKAS46. These vectors can be used for allelic exchange in a wide variety of bacterial species because their R6K origin of replication functions only in bacteria engineered to produce the replication protein n. In addition, these vectors express the Escherichia coli rpsL gene, encoding ribosomal

Karen Skorupski; Ronald K. Taylor

1996-01-01

193

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. PMID:22443094

2012-01-01

194

Most parsimonious haplotype allele sharing determination  

PubMed Central

Background The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, the power of the association study methods are still low, in particular on quantitative traits, and the description of the full allelic spectrum is deemed still far from reach. Given increasing density of single nucleotide polymorphisms available and suggested by the block-like structure of the human genome, a popular and prosperous strategy is to use haplotypes to try to capture the correlation structure of SNPs in regions of little recombination. The key to the success of this strategy is thus the ability to unambiguously determine the haplotype allele sharing status among the members. The association studies based on haplotype sharing status would have significantly reduced degrees of freedom and be able to capture the combined effects of tightly linked causal variants. Results For pedigree genotype datasets of medium density of SNPs, we present two methods for haplotype allele sharing status determination among the pedigree members. Extensive simulation study showed that both methods performed nearly perfectly on breakpoint discovery, mutation haplotype allele discovery, and shared chromosomal region discovery. Conclusion For pedigree genotype datasets, the haplotype allele sharing status among the members can be deterministically, efficiently, and accurately determined, even for very small pedigrees. Given their excellent performance, the presented haplotype allele sharing status determination programs can be useful in many downstream applications including haplotype based association studies. PMID:19379528

Cai, Zhipeng; Sabaa, Hadi; Wang, Yining; Goebel, Randy; Wang, Zhiquan; Xu, Jiaofen; Stothard, Paul; Lin, Guohui

2009-01-01

195

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

196

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

PubMed

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

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

2012-11-01

197

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. PMID:16826532

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

2006-01-01

198

Allele-Specific Deletions in Mouse Tumors Identify Fbxw7 as Germline Modifier of Tumor Susceptibility  

PubMed Central

Genome-wide association studies (GWAS) have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs) and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5–10%). There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p?=?0.001), but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility. PMID:22348067

Perez-Losada, Jesus; Wu, Di; DelRosario, Reyno; Balmain, Allan; Mao, Jian-Hua

2012-01-01

199

VARIATION OF MICROSATELLITE MARKERS AMONG SELECTED PAPAYA VARIETIES  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microsatellites, or simple sequence repeats (SSRs), are simple, tandemly repeated mono- to hexa-nucleotide sequence motifs. Due to their co-dominant nature, ability to detect high levels of allelic diversity, and ubiquitous distribution, they have been widely used as genetic markers. Genomic researc...

200

Genetic variation (protein markers and microsatellites) in endangered Catalonian donkeys  

Microsoft Academic Search

Genetic variation of the endangered Catalonian donkey breed (Equus asinus) has been analysed at 19 loci including seven protein loci and 12 microsatellite loci isolated from the domestic horse, in 98 individuals of both sexes. Only four protein markers and three microsatellites were polymorphic. Allele frequencies of the analysed loci showed close agreement with Hardy–Weinberg proportions, with the exception of

J. Jordana; P. Folch; A. Sanchez

1999-01-01

201

Discipline: Parents' and  

E-print Network

Parenting Styles and Discipline: Parents' and Children's Perspectives SUMMARY REPORT The National Children's Strategy Research Series #12;#12;Parenting Styles and Discipline: Parents' Perspectives SUMMARY national survey of parenting styles and discipline in Ireland. A large body of research literature

O'Mahony, Donal E.

202

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

203

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

PubMed

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 small 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, we 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. PMID:8290589

Pena, S D; de Souza, K T; de Andrade, M; Chakraborty, R

1994-01-18

204

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

205

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. PMID:12737656

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

2003-01-01

206

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

PubMed

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

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

2013-07-01

207

Composition and functional analysis of low-molecular-weight glutenin alleles with Aroona near-isogenic lines of bread wheat  

PubMed Central

Background Low-molecular-weight glutenin subunits (LMW-GS) strongly influence the bread-making quality of bread wheat. These proteins are encoded by a multi-gene family located at the Glu-A3, Glu-B3 and Glu-D3 loci on the short arms of homoeologous group 1 chromosomes, and show high allelic variation. To characterize the genetic and protein compositions of LMW-GS alleles, we investigated 16 Aroona near-isogenic lines (NILs) using SDS-PAGE, 2D-PAGE and the LMW-GS gene marker system. Moreover, the composition of glutenin macro-polymers, dough properties and pan bread quality parameters were determined for functional analysis of LMW-GS alleles in the NILs. Results Using the LMW-GS gene marker system, 14–20 LMW-GS genes were identified in individual NILs. At the Glu-A3 locus, two m-type and 2–4 i-type genes were identified and their allelic variants showed high polymorphisms in length and nucleotide sequences. The Glu-A3d allele possessed three active genes, the highest number among Glu-A3 alleles. At the Glu-B3 locus, 2–3?m-type and 1–3?s-type genes were identified from individual NILs. Based on the different compositions of s-type genes, Glu-B3 alleles were divided into two groups, one containing Glu-B3a, B3b, B3f and B3g, and the other comprising Glu-B3c, B3d, B3h and B3i. Eight conserved genes were identified among Glu-D3 alleles, except for Glu-D3f. The protein products of the unique active genes in each NIL were detected using protein electrophoresis. Among Glu-3 alleles, the Glu-A3e genotype without i-type LMW-GS performed worst in almost all quality properties. Glu-B3b, B3g and B3i showed better quality parameters than the other Glu-B3 alleles, whereas the Glu-B3c allele containing s-type genes with low expression levels had an inferior effect on bread-making quality. Due to the conserved genes at Glu-D3 locus, Glu-D3 alleles showed no significant differences in effects on all quality parameters. Conclusions This work provided new insights into the composition and function of 18 LMW-GS alleles in bread wheat. The variation of i-type genes mainly contributed to the high diversity of Glu-A3 alleles, and the differences among Glu-B3 alleles were mainly derived from the high polymorphism of s-type genes. Among LMW-GS alleles, Glu-A3e and Glu-B3c represented inferior alleles for bread-making quality, whereas Glu-A3d, Glu-B3b, Glu-B3g and Glu-B3i were correlated with superior bread-making quality. Glu-D3 alleles played minor roles in determining quality variation in bread wheat. Thus, LMW-GS alleles not only affect dough extensibility but greatly contribute to the dough resistance, glutenin macro-polymers and bread quality. PMID:23259617

2012-01-01

208

Factors Influencing Ascertainment Bias of Microsatellite Allele Sizes: Impact on Estimates of Mutation Rates  

PubMed Central

Microsatellite loci play an important role as markers for identification, disease gene mapping, and evolutionary studies. Mutation rate, which is of fundamental importance, can be obtained from interspecies comparisons, which, however, are subject to ascertainment bias. This bias arises, for example, when a locus is selected on the basis of its large allele size in one species (cognate species 1), in which it is first discovered. This bias is reflected in average allele length in any noncognate species 2 being smaller than that in species 1. This phenomenon was observed in various pairs of species, including comparisons of allele sizes in human and chimpanzee. Various mechanisms were proposed to explain observed differences in mean allele lengths between two species. Here, we examine the framework of a single-step asymmetric and unrestricted stepwise mutation model with genetic drift. Analysis is based on coalescent theory. Analytical results are confirmed by simulations using the simuPOP software. The mechanism of ascertainment bias in this model is a tighter correlation of allele sizes within a cognate species 1 than of allele sizes in two different species 1 and 2. We present computations of the expected average allele size difference, given the mutation rate, population sizes of species 1 and 2, time of separation of species 1 and 2, and the age of the allele. We show that when the past demographic histories of the cognate and noncognate taxa are different, the rate and directionality of mutations affect the allele sizes in the two taxa differently from the simple effect of ascertainment bias. This effect may exaggerate or reverse the effect of difference in mutation rates. We reanalyze literature data, which indicate that despite the bias, the microsatellite mutation rate estimate in the ancestral population is consistently greater than that in either human or chimpanzee and the mutation rate estimate in human exceeds or equals that in chimpanzee with the rate of allele length expansion in human being greater than that in chimpanzee. We also demonstrate that population bottlenecks and expansions in the recent human history have little impact on our conclusions. PMID:23525076

Li, Biao; Kimmel, Marek

2013-01-01

209

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

210

Questions about Biological Parents  

MedlinePLUS

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

211

Parental Involvement to Parental Engagement: A Continuum  

ERIC Educational Resources Information Center

Based on the literature of the field, this article traces a continuum between parental involvement with schools, and parental engagement with children's learning. The article seeks to shed light on an area of confusion; previous research has shown that different stakeholder groups understand "parental engagement" in different ways.…

Goodall, Janet; Montgomery, Caroline

2014-01-01

212

Resilient Parenting: Overcoming Poor Parental Bonding  

ERIC Educational Resources Information Center

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

Travis, Wendy J.; Combs-Orme, Terri

2007-01-01

213

FINDbase: a worldwide database for genetic variation allele frequencies updated  

PubMed Central

Frequency of INherited Disorders database (FIND base; http://www.findbase.org) records frequencies of causative genetic variations worldwide. Database records include the population and ethnic group or geographical region, the disorder name and the related gene, accompanied by links to any related external resources and the genetic variation together with its frequency in that population. In addition to the regular data content updates, we report the following significant advances: (i) the systematic collection and thorough documentation of population/ethnic group-specific pharmacogenomic markers allele frequencies for 144 markers in 14 genes of pharmacogenomic interest from different classes of drug-metabolizing enzymes and transporters, representing 150 populations and ethnic groups worldwide; (ii) the development of new data querying and visualization tools in the expanded FINDbase data collection, built around Microsoft’s PivotViewer software (http://www.getpivot.com), based on Microsoft Silverlight technology (http://www.silverlight.net) that facilitates querying of large data sets and visualizing the results; and (iii) the establishment of the first database journal, by affiliating FINDbase with Human Genomics and Proteomics, a new open-access scientific journal, which would serve as a prime example of a non-profit model for sustainable database funding. PMID:21113021

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

2011-01-01

214

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

215

Imputation of microsatellite allele from dense SNP genotypes for parentage verification  

Technology Transfer Automated Retrieval System (TEKTRAN)

Microsatellite (MS) markers have recently been used for parental verification and are still the international standard despite higher cost, error rate, and turnaround time compared with Single Nucleotide Polymorphisms (SNP)-based assays. Despite domestic and international interest from producers an...

216

HLA allele detection using molecular techniques.  

PubMed

There are now many molecular biological techniques available to define HLA class I and class II alleles. Some of these are also applicable to other human polymorphic genes, in particular to those non-HLA genes encoded within the Mhc. The range of techniques available allows laboratories to choose those most suited to their purpose. The routine laboratory supporting solid organ transplants will need to type large numbers of potential recipients over a period of time, probably using PCR-SSOP while donors will be typed singly and rapidly using PCR-SSP with HLA allele compatibility determined by heteroduplex analysis. Laboratories supporting bone marrow transplantation, where time is less pressing, can choose from the whole range of techniques to determine accurately donor recipient Mhc compatibility. For disease studies, techniques defining precise HLA allele sequence polymorphisms are needed and high sample numbers have to be accommodated. When an association is established allele sequencing has to be used. In the near future, the precise role of HLA alleles in transplantation and disease susceptibility is likely to be established unambiguously. PMID:8112019

Dyer, P A; Jawaheer, D; Ollier, B; Poulton, K; Sinnott, P; Thomson, W

1993-11-01

217

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. PMID:21798064

2011-01-01

218

Marker-Assisted Introgression in Backcross Breeding Programs  

PubMed Central

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10-20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ~10-20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations. PMID:8978075

Visscher, P. M.; Haley, C. S.; Thompson, R.

1996-01-01

219

Effortful Control and Parenting: Associations with HPA Axis Reactivity in Early Childhood  

ERIC Educational Resources Information Center

While activation of the hypothalamic-pituitary-adrenal (HPA) axis is an adaptive response to stress, excessive HPA axis reactivity may be an important marker of childhood vulnerability to psychopathology. Parenting, including parent affect during parent-child interactions, may play an important role in shaping the developing HPA system; however,…

Kryski, Katie R.; Dougherty, Lea R.; Dyson, Margaret W.; Olino, Thomas M.; Laptook, Rebecca S.; Klein, Daniel N.; Hayden, Elizabeth P.

2013-01-01

220

Highly Informative Single-Copy Nuclear Microsatellite DNA Markers Developed Using an AFLP-SSR Approach in Black Spruce (Picea mariana) and Red Spruce (P. rubens)  

PubMed Central

Background Microsatellites or simple sequence repeats (SSRs) are highly informative molecular markers for various biological studies in plants. In spruce (Picea) and other conifers, the development of single-copy polymorphic genomic microsatellite markers is quite difficult, owing primarily to the large genome size and predominance of repetitive DNA sequences throughout the genome. We have developed highly informative single-locus genomic microsatellite markers in black spruce (Picea mariana) and red spruce (Picea rubens) using a simple but efficient method based on a combination of AFLP and microsatellite technologies. Principal Findings A microsatellite-enriched library was constructed from genomic AFLP DNA fragments of black spruce. Sequencing of the 108 putative SSR-containing clones provided 94 unique sequences with microsatellites. Twenty-two of the designed 34 primer pairs yielded scorable amplicons, with single-locus patterns. Fourteen of these microsatellite markers were characterized in 30 black spruce and 30 red spruce individuals drawn from many populations. The number of alleles at a polymorphic locus ranged from 2 to 18, with a mean of 9.3 in black spruce, and from 3 to 15, with a mean of 6.2 alleles in red spruce. The polymorphic information content or expected heterozygosity ranged from 0.340 to 0.909 (mean?=?0.67) in black spruce and from 0.161 to 0.851 (mean?=?0.62) in red spruce. Ten SSR markers showing inter-parental polymorphism inherited in a single-locus Mendelian mode, with two cases of distorted segregation. Primer pairs for almost all polymorphic SSR loci resolved microsatellites of comparable size in Picea glauca, P. engelmannii, P. sitchensis, and P. abies. Significance The AFLP-based microsatellite-enriched library appears to be a rapid, cost-effective approach for isolating and developing single-locus informative genomic microsatellite markers in black spruce. The markers developed should be useful in black spruce, red spruce and other Picea species for various genetics, genomics, breeding, forensics, conservation studies and applications. PMID:25126846

Shi, Yong-Zhong; Forneris, Natascha; Rajora, Om P.

2014-01-01

221

Estimating African American admixture proportions by use of population-specific alleles.  

PubMed Central

We analyzed the European genetic contribution to 10 populations of African descent in the United States (Maywood, Illinois; Detroit; New York; Philadelphia; Pittsburgh; Baltimore; Charleston, South Carolina; New Orleans; and Houston) and in Jamaica, using nine autosomal DNA markers. These markers either are population-specific or show frequency differences >45% between the parental populations and are thus especially informative for admixture. European genetic ancestry ranged from 6.8% (Jamaica) to 22.5% (New Orleans). The unique utility of these markers is reflected in the low variance associated with these admixture estimates (SEM 1.3%-2.7%). We also estimated the male and female European contribution to African Americans, on the basis of informative mtDNA (haplogroups H and L) and Y Alu polymorphic markers. Results indicate a sex-biased gene flow from Europeans, the male contribution being substantially greater than the female contribution. mtDNA haplogroups analysis shows no evidence of a significant maternal Amerindian contribution to any of the 10 populations. We detected significant nonrandom association between two markers located 22 cM apart (FY-null and AT3), most likely due to admixture linkage disequilibrium created in the interbreeding of the two parental populations. The strength of this association and the substantial genetic distance between FY and AT3 emphasize the importance of admixed populations as a useful resource for mapping traits with different prevalence in two parental populations. PMID:9837836

Parra, E J; Marcini, A; Akey, J; Martinson, J; Batzer, M A; Cooper, R; Forrester, T; Allison, D B; Deka, R; Ferrell, R E; Shriver, M D

1998-01-01

222

Marker Removal in Staphylococci via Cre Recombinase and Different lox Sites  

Microsoft Academic Search

Allelic replacement in staphylococci is frequently aided by antibiotic resistance markers that replace the gene(s) of interest. In multiply modified strains, the number of mutated genes usually correlates with the number of selection markers in the strain's chromosome. Site-specific recombination systems are capable of eliminating such markers, if they are flanked by recombinase recognition sites. In this study, a Cre-lox

Martina Leibig; Bernhard Krismer; Martina Kolb; Alexandra Friede; Friedrich Gotz; Ralph Bertram

2008-01-01

223

Mapping 245 SSR markers on the Vitis vinifera genome: a tool for grape genetics  

Microsoft Academic Search

The aim of the present work was to develop a microsatellite marker-based map of the Vitis vinifera genome ( n=19), useful for genetic studies in this perennial heterozygous species, as SSR markers are highly transferable co-dominant markers. A total of 346 primer pairs were tested on the two parents (Syrah and Grenache) of a full sib population of 96 individuals

A.-F. Adam-Blondon; C. Roux; D. Claux; G. Butterlin; D. Merdinoglu; P. This

2004-01-01

224

DRD4 gene variants and sustained attention in attention deficit hyperactivity disorder (ADHD): effects of associated alleles at the VNTR and -521 SNP.  

PubMed

Associations between attention deficit hyperactivity disorder (ADHD) and genetic variants within the dopamine D4 receptor gene have been much reported. Variants investigated include the 7-repeat allele of a VNTR within the third exon, and two SNPs (-521 and -616) located with the promoter region. We investigated the relationship between the VNTR, -521, and -616 SNPs and sustained attention performance in 54 ADHD probands, relative to a non-genotyped control group. Participants performed the Sustained Attention to Response Task (SART) in which the response to an unpredictably occurring target digit must be inhibited. This task, therefore, challenged sustained attention and included a response inhibition component. Consistent with previous reports, ADHD participants possessing the 7-repeat allele of the VNTR outperformed those children not possessing this allele, both in terms of errors and response variability. In family based analyses, better performance on the SART tended to predict biased transmission of the 7-repeat allele from heterozygous parents. For the -521 SNP, A allele homozygotes showed greater impairment than heterozygotes or those not possessing this allele, both in terms of total errors and response variability. Family based analysis showed that higher total errors on the SART predicted transmission of the A allele from heterozygous parents. There were no effects of the -616 SNP. Our results suggest dissociable effects of the "associated alleles" of DRD4 gene variants on sustained attention: while the 7-repeat allele of the VNTR is associated with relatively better performance, the A allele of the -521 SNP is associated with poorer performance. PMID:15909295

Bellgrove, Mark A; Hawi, Ziarih; Lowe, Naomi; Kirley, Aiveen; Robertson, Ian H; Gill, Michael

2005-07-01

225

Cryptic virulence and avirulence alleles revealed by controlled sexual recombination in pea aphids.  

PubMed

Although aphids are worldwide crop pests, little is known about aphid effector genes underlying virulence and avirulence. Here we show that controlling the genetics of both aphid and host can reveal novel recombinant genotypes with previously undetected allelic variation in both virulence and avirulence functions. Clonal F1 progeny populations were derived from reciprocal crosses and self-matings between two parental genotypes of pea aphid (Acyrthosiphon pisum) differing in virulence on a Medicago truncatula host carrying the RAP1 and RAP2 resistance genes. These populations showed Mendelian segregation consistent with aphid performance being controlled largely by a dominant virulence allele derived from only one parent. Altered segregation ratios on near-isogenic host genotypes differing in the region carrying RAP1 were indicative of additional heritable functions likely related to avirulence genes originating from both parents. Unexpectedly, some virulent F1 progeny were recovered from selfing of an avirulent parent, suggesting a reservoir of cryptic alleles. Host chlorosis was associated with virulence, whereas necrotic hypersensitive-like response was not. No maternal inheritance was found for any of these characteristics, ruling out sex-linked, cytoplasmic, and endosymbiotic factors. Our results demonstrate the tractability of dissecting the genetic basis of pest-host resistance mechanisms and indicate that the annual sexual cycle in aphids may lead to frequent novel genotypes with both increased and decreased virulence. Availability of genomes for both pest and host can facilitate definition of cognate gene-for-gene relationships, potentially leading to selection of crop genotypes with multiple resistance traits. PMID:25519896

Kanvil, Sadia; Collins, C Matilda; Powell, Glen; Turnbull, Colin G N

2015-02-01

226

Genetic Exchange of Fimbrial Alleles Exemplifies the Adaptive Virulence Strategy of Porphyromonas gingivalis  

PubMed Central

Porphyromonas gingivalis is a gram–negative anaerobic bacterium, a member of the human oral microbiome, and a proposed “keystone” pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions. PMID:24626479

Kerr, Jennifer E.; Abramian, Jared R.; Dao, Doan-Hieu V.; Rigney, Todd W.; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D.

2014-01-01

227

Genetic exchange of fimbrial alleles exemplifies the adaptive virulence strategy of Porphyromonas gingivalis.  

PubMed

Porphyromonas gingivalis is a gram-negative anaerobic bacterium, a member of the human oral microbiome, and a proposed "keystone" pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions. PMID:24626479

Kerr, Jennifer E; Abramian, Jared R; Dao, Doan-Hieu V; Rigney, Todd W; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D

2014-01-01

228

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 coalition…

IDRA Newsletter, 1994

1994-01-01

229

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

230

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

231

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

232

Involving Latino Parents.  

ERIC Educational Resources Information Center

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

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

2003-01-01

233

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

234

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

235

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

236

Correlates of Adolescent Parenting.  

ERIC Educational Resources Information Center

Studied correlates of teenage parenting in self-selected sample of 177 teenage parents. Parental race, punitive attitudes toward child rearing, and parental age were statistically significant predictors of total Home Observation for Measurement of the Environment scores. Older, white adolescent mothers with less punitive attitudes toward child…

Reis, Janet S.; Herz, Elicia J.

1987-01-01

237

Reconceptualizing Parent Involvement: Parent as Accomplice or Parent as Partner?  

ERIC Educational Resources Information Center

Policy statements of the last two decades have directed schools to enter into partnerships with parents to enhance the social, emotional, and academic growth of their children. However, in practice and scholarship, parental involvement has been constructed as attendance to school-based activities and needs. This article draws on data from an…

Stitt, Nichole M.; Brooks, Nancy J.

2014-01-01

238

Marker-assisted selection to improve drought adaptation in maize: the backcross approach, perspectives, limitations, and alternatives.  

PubMed

A number of different marker-assisted selection (MAS) approaches do exist for the improvement of polygenic traits. Results of a marker-assisted backcross (MABC) selection experiment aimed at improving grain yield under drought conditions in tropical maize are presented and compared with alternative MAS strategies. The introgression of favourable alleles at five target regions involved in the expression of yield components and flowering traits increased grain yield and reduced the asynchrony between male and female flowering under water-limited conditions. Eighty-five per cent of the recurrent parent's genotype at non-target loci was recovered in only four generations of MABC by screening large segregating populations (2200 individuals) for three of the four generations. Selected MABC-derived BC(2)F(3) families were crossed with two testers and evaluated under different water regimes. Mean grain yield of MABC-derived hybrids was consistently higher than that of control hybrids (crosses from the recurrent parent to the same two testers as the MABC-derived families) under severe water stress conditions. Under those conditions, the best five MABC-derived hybrids yielded, on average, at least 50% more than control hybrids. Under mild water stress, defined as resulting in <50% yield reduction, no difference was observed between MABC-derived hybrids and the control plants, thus confirming that the genetic regulation for drought tolerance is dependent on stress intensity. MABC conversions involving several target regions are likely to result in partial rather than complete line conversion. Simulations were conducted to assess the utility of such partial conversions, i.e. containing favourable donor alleles at non-target regions, for subsequent phenotypic selection. The results clearly showed that selecting several genotypes (10-20) at each MABC cycle was most efficient. In the light of these results, alternative approaches to MABC are discussed, including recurrent selection, illustrated by an example of improving the adaptation of maize to low temperatures. Given the current approaches for MAS and the choices of marker technologies available now and potential for future developments, the use of MAS techniques in further improving grain yield under abiotic stresses in maize appears very promising. PMID:17158111

Ribaut, Jean-Marcel; Ragot, Michel

2007-01-01

239

Non-random Allelic Variation Natural Selection  

E-print Network

Non-random Allelic Variation AKA Natural Selection #12;Adaptation!Adaptation! #12;#12;Venus comb or ­ a feature that is maintained because of natural selection for its function preadaptation ­ a trait history #12;Natural Selection Evolution evolution is a two step process 1) origin of genetic variation 2

Houde, Peter

240

Tetrasomic segregation for multiple alleles in alfalfa.  

PubMed

Evidence of tetrasomic inheritance in alfalfa, Medicago sativa L. and M. falcata L., for multiple codominant alleles at three isozymic loci is reported in this study. The locus Prx-1 governing anodal peroxidase and the loci Lap-1 and Lap-2 governing anodal leucine-aminopeptidase were studied by starch gel electrophoresis in seedling root tissue or seeds. The progenies from several di-, tri- or tetra-allelic plants belong to the species M. sativa and M. falcata and their hybrids were studied for the segregation of the three genes. In all cases, tetrasomic inheritance of chromosomal-type segregation was observed. In another progeny resulting from the crossing of two plants involving four different alleles at locus Lap-2, tetrasomic segregation with the possible occurrence of double reduction was observed. This study presents direct evidence of autotetraploidy and the existence of tetra-allelic loci in alfalfa. It also supports the concept that the species M. sativa and M. falcata are genetically close enough to be considered biotypes of a common species. PMID:17246077

Quiros, C F

1982-05-01

241

Original article Latitudinal clines of allelic frequencies  

E-print Network

of Ceratitis capitata (Wiedemann) A Kourti P Hatzopoulos2 1 Agricultural University of Athens, Laboratory October 1994) Summary - Collections of Ceratitis capitata from 6 different areas from 4 Mediterranean.00 to 0.63) is observed in the axis of the north-south transect. Ceratitis capitata/ allelic frequency

Paris-Sud XI, Université de

242

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. PMID:21443335

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

2011-01-01

243

Synchronous allelic expression at the glucosephosphate isomerase A and B loci in interspecific sunfish hybrids.  

PubMed

Allelic isozymes of glucosephosphate isomerase at the Gpi-A and -B loci were separated by starch gel electrophoresis in the warmouth (Lepomis gulosus) and green sunfish (L. cyanellus). The specific tissue distributions and developmental expressions of the GPI-A2, -AB, and -B2 isozymes were not different between these two species. The synchrony of allelic expression in normal intraspecific sunfish crosses was demonstrated by means of an electrophoretic variant at the Gpi-B locus. In embryos formed from warmouth x green sunfish hybrid crosses, the paternal GPI-A2 isozymes were first expressed at the same time in both reciprocal hybrids, at 21-25 hr after fertilization. The maternal and paternal GPI-B subunits were synchronously expressed in reciprocal hybrids just for prior to hatching. The parental allelic isozymes at both loci shoed codominant expression in all tissues of the mature F1 hybrids. These results are consistent with the absence of allelic asynchrony and inhibition in interspecific hybrids formed from more evolutionarily related species. PMID:1008802

Champion, M J; Whitt, G S

1976-10-01

244

Allelic variation for a candidate gene for GS7, responsible for grain shape in rice.  

PubMed

Grain shape is an important component of end-use quality in rice. The genomic location of the grain shape QTL GS7 was narrowed to lie within a 4.8-kb segment on chromosome 7. The homologous region in cv. Nipponbare contains no annotated genes, while two open reading frames were predicted, one of which (ORF2) represented a likely candidate for GS7 gene on the basis of correlation between sequence variation and phenotype. Semi-quantitative and quantitative RT-PCR analysis of ORF2 transcription showed that the gene was active in both the leaf and panicle when the cv. D50 allele was present, but not in the presence of the cv. HB277 allele. A microsatellite-based phylogeny and a re-sequencing analysis of ORF2 among a set of 52 diverse rice accessions suggested that the cv. D50 GS7 allele may have originated from the tropical japonica genepool. The effect on grain length of the alternative alleles at GS7and GS3 showed that combination type 3/A was associated with longer grains than type 1/A. An Indel marker developed within the ORF2 sequence was informative for predicting grain length. PMID:22772587

Shao, Gaoneng; Wei, Xiangjin; Chen, Mingliang; Tang, Shaoqing; Luo, Ju; Jiao, Guiai; Xie, Lihong; Hu, Peisong

2012-10-01

245

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. PMID:22471693

2012-01-01

246

Allele frequency of resistance to Bacillus thuringiensis Cry1ab corn in Louisiana populations of sugarcane borer (Lepidoptera: Crambidae).  

PubMed

Transgenic Bacillus thuringiensis (Bt) corn, Zea mays L., has been widely used to manage a corn borer complex in the mid-southern region of the United States. The sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), has become a dominant cornstalk boring species in some areas of this region, especially in Louisiana. Therefore, management of sugarcane borer resistance to Bt corn is critical to ensure the long-term sustainability of Bt corn for the region. This study screened 280 two-parent family-lines of sugarcane borer from four geographical populations in Louisiana during 2005 to determine whether Bt resistance allele frequency in sugarcane borer is sufficiently low to meet the rare resistance assumption of the current "high dose/refuge" resistance management strategy for Bt corn. These sugarcane borer family-lines were examined for Bt resistance by using novel F2 screening procedures. No major Bt resistance alleles were detected in these four populations. The estimated frequency of major Bt resistance alleles was < 0.0027, with a 95% probability and a detection power of 94%. The estimated minor resistance allele frequency was 0.0063, with a 95% CI of 0.0025-0.0117. During a previous study, a major Bt resistance allele was detected in one individual from 213 family-lines of another Louisiana population of sugarcane borer. Combining these data with the current screen, the frequency of major Bt resistance alleles across the five populations was 0.001, with a 95% credibility interval of 0.0001-0.0028 and a detection power of 95%. Major Bt resistance allele frequencies in Louisiana sugarcane borer populations seem to be low, and they should support the rare resistance allele requirement of the high dose/refuge strategy. PMID:18459416

Huang, Fangneng; Leonard, B Rogers; Moore, Steven H; Cook, Donald R; Baldwin, Jack; Tindall, Kelly V; Lee, Donna R

2008-04-01

247

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

2013-03-01

248

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

ERIC Educational Resources Information Center

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

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

2014-01-01

249

Exploration of presence/absence variation and corresponding polymorphic markers in soybean genome.  

PubMed

This study was designed to reveal the genome-wide distribution of presence/absence variation (PAV) and to establish a database of polymorphic PAV markers in soybean. The 33 soybean whole-genome sequences were compared to each other with that of Williams 82 as a reference genome. A total of 33,127 PAVs were detected and 28,912 PAV markers with their primer sequences were designed as the database NJAUSoyPAV_1.0. The PAVs scattered on whole genome while only 518 (1.8%) overlapped with simple sequence repeats (SSRs) in BARCSOYSSR_1.0 database. In a random sample of 800 PAVs, 713 (89.13%) showed polymorphism among the 12 differential genotypes. Using 126 PAVs and 108 SSRs to test a Chinese soybean germplasm collection composed of 828 Glycine soja Sieb. et Zucc. and Glycine max (L.) Merr. accessions, the per locus allele number and its variation appeared less in PAVs than in SSRs. The distinctness among alleles/bands of PCR (polymerase chain reaction) products showed better in PAVs than in SSRs, potential in accurate marker-assisted allele selection. The association mapping results showed SSR?+?PAV was more powerful than any single marker systems. The NJAUSoyPAV_1.0 database has enriched the source of PCR markers, and may fit the materials with a range of per locus allele numbers, if jointly used with SSR markers. PMID:24751174

Wang, Yufeng; Lu, Jiangjie; Chen, Shouyi; Shu, Liping; Palmer, Reid G; Xing, Guangnan; Li, Yan; Yang, Shouping; Yu, Deyue; Zhao, Tuanjie; Gai, Junyi

2014-10-01

250

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

251

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

252

When Parents Argue  

MedlinePLUS

... you. But your parents' arguments are never your fault. Parents are responsible for their own actions and ... feels better and life can get back to normal. Being part of a family means everyone pitches ...

253

Sexual Orientation (For Parents)  

MedlinePLUS

... being gay is caused by early childhood experiences, parenting styles, or the way someone is raised. Efforts to ... 3 For Teens For Kids For Parents ... and Answers About Sex Teaching Your Child Tolerance Transgender People Am I in a Healthy ...

254

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

255

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. PMID:21768136

Ramchiary, Nirala; Nguyen, Van Dan; Li, Xiaonan; Hong, Chang Pyo; Dhandapani, Vignesh; Choi, Su Ryun; Yu, Ge; Piao, Zhong Yun; Lim, Yong Pyo

2011-01-01

256

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

257

Mutant maize variety containing the glt1-1 allele  

DOEpatents

A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

Nelson, Oliver E. (Cross Plains, WI); Pan, David (Madison, WI)

1994-01-01

258

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

259

Quantification of the paternal allele bias for new germline mutations in the retinoblastoma gene  

SciTech Connect

New germline mutations in the human retinoblastoma gene preferentially arise on a paternally derived allele. In nonhereditary retinoblastoma, the initial somatic mutation seems to have no such bias. The few previous reports of these phenomena included relatively few cases (less than a dozen new germline or initial somatic mutations), so that the magnitude of the paternal allele bias for new germline mutations is not known. Knowledge of the magnitude of the bias is valuable for genetic counseling, since, for example, patients with new germline mutations who reproduce transmit risk for retinoblastoma according to the risk that the transmitted allele has a germline mutation. We sought to quantitate the paternal allele bias and to determine whether paternal age is a factor possibly accounting for it. We studied 311 families with retinoblastoma (261 simplex, 50 multiplex) that underwent clinical genetic testing and 5 informative families recruited from earlier research. Using RFLPs and polymorphic microsatellites in the retinoblastoma gene, we could determine the parental origin of 45 new germline mutations and 44 probable initial somatic mutations. Thirty-seven of the 45 new germline mutations, or 82%, arose on a paternal allele while only 24 of the 44 initial somatic mutations (55%) did so. Increased paternal age does not appear to account for the excess of new paternal germline mutations, since the average age of fathers of children with new germline mutations (29.4 years, n=26, incomplete records on 11) was not significantly different from the average age of fathers of children with maternal germline mutations or somatic initial mutations (29.8 years, n=35, incomplete records on 17).

Morrow, J.F.; Rapaport, J.M.; Dryia, T.P. [Massachusetts Eye & Ear Infirmary, Boston, MA (United States)

1994-09-01

260

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

261

Single Parent Adoption.  

ERIC Educational Resources Information Center

Presenting two views of the single-parent family, this pamphlet includes an article by two researchers (William Feigelman and Arnold R. Silverman) and a short statement by a single adoptive parent (Amanda Richards). The first paper summarizes earlier research on single-parent adoptions and discusses the results of a nationwide survey of 713…

Administration for Children, Youth, and Families (DHHS), Washington, DC.

262

A Parent Communication Group  

ERIC Educational Resources Information Center

The purpose of this communication group is to train parents in the skills of active listening and conflict resolution. The model borrows extensively from Gordon's Parent Effectiveness Training. The parents learn to use communication skills and problem-solving techniques. (Author/PC)

McWhirter, J. Jeffries; Kahn, Sharon E.

1974-01-01

263

The Parent Loan Trap  

ERIC Educational Resources Information Center

As the cost of college has spiraled ever upward and median family income has fallen, the loan program, called Parent PLUS, has become indispensable for increasing numbers of parents desperate to make their children's college plans work. Last year the government disbursed $10.6-billion in Parent PLUS loans to just under a million families. Even…

Wang, Marian; Supiano, Beckie; Fuller, Andrea

2012-01-01

264

Perspectives on Parenting Styles  

E-print Network

Children's Perspectives on Parenting Styles and Discipline: A Developmental Approach The National Children's Strategy Research Series #12;#12;Children's Perspectives on Parenting Styles and Discipline Aims of the study 9 Approach to the research 10 2. liTerATure review 11 Effects of parents on children

O'Mahony, Donal E.

265

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

266

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. PMID:23029233

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

2012-01-01

267

Child ?-Opioid Receptor Gene Variant Influences Parent–Child Relations  

PubMed Central

Variation in the ?-opioid receptor gene has been associated with early social behavior in mice and rhesus macaques. The current study tested whether the functional OPRM1 A118G predicted various indices of social relations in children. The sample included 226 subjects of self-reported European ancestry (44% female; mean age 13.6, SD=2.2) who were part of a larger representative study of children aged 9–17 years in rural North Carolina. Multiple aspects of recent (past 3 months) parent–child relationship were assessed using the Child and Adolescent Psychiatric Assessment. Parent problems were coded based upon a lifetime history of mental health problems, substance abuse, or criminality. Child genotype interacted with parent behavior such that there were no genotype differences for those with low levels of parent problems; however, when a history of parent problems was reported, the G allele carriers had more enjoyment of parent–child interactions (mean ratio (MR)=3.5, 95% CI=1.6, 8.0) and fewer arguments (MR=3.1, 95% CI=1.1, 8.9). These findings suggest a role for the OPRM1 gene in the genetic architecture of social relations in humans. In summary, a variant in the ?-opioid receptor gene (118G) was associated with improved parent–child relations, but only in the context of a significant disruption in parental functioning. PMID:21326192

Copeland, William E; Sun, Hui; Costello, E Jane; Angold, Adrian; Heilig, Markus A; Barr, Christina S

2011-01-01

268

KRAS mutant allele-specific imbalance in lung adenocarcinoma.  

PubMed

The significance of KRAS mutant allele-specific imbalance (MASI) in lung adenocarcinomas is unknown. KRAS MASI was defined as predominance of the mutant allele over the wild-type allele. We assessed the frequency of KRAS MASI by comparing peak heights of mutant and wild-type alleles on sequencing electropherograms and by KRAS fluorescence in situ hybridization (FISH). A review of sequencing electropherograms of 207 KRAS-mutated lung adenocarcinomas demonstrated 23 (11%) cases with the mutant allele peak higher than the wild-type allele peak and 15 (7%) cases with the mutant allele peak equal to the wild-type allele peak. Of 17 cases with the mutant allele peak higher or equal to the wild-type allele peak, 8 (47%) showed KRAS amplification by FISH. KRAS FISH analysis of 36 KRAS-mutated lung adenocarcinomas with the mutant allele peak lower than the wild-type allele peak, 21 KRAS and EGFR wild-type and 16 EGFR-mutated adenocarcinomas showed no KRAS amplification. KRAS MASI was associated with selective amplification of the KRAS mutant allele (P<0.001). Patients with KRAS MASI showed worse overall survival. The cumulative proportion surviving at 17 months for KRAS MASI group was 35% compared with 84.1% for patients with KRAS mutant allele peak lower than wild-type allele peak (P=0.012). The adverse prognostic significance of KRAS MASI was independent of clinical stage and was maintained among stage I patients. The detection of KRAS MASI in lung adenocarcinomas by sequencing electropherograms may identify patients with more aggressive disease. PMID:21743433

Chiosea, Simion I; Sherer, Carol K; Jelic, Tomislav; Dacic, Sanja

2011-12-01

269

Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting—peak ratios) method  

Microsoft Academic Search

Polysomic inheritance frequently results in the simultaneous occurrence of several microsatellite DNA alleles on a single locus. The MAC-PR (microsatellite DNA allele counting—peak ratios) method was recently developed for the analysis of polyploid plants and makes use of the quantitative values for microsatellite allele peak areas. To date, this approach has only been used in plants with known genetic relationships.

G. D. Esselink; H. Nybom; B. J. Vosman

2004-01-01

270

Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database.  

PubMed

Interindividual variability in xenobiotic metabolism and drug response is extensive and genetic factors play an important role in this variation. A majority of clinically used drugs are substrates for the cytochrome P450 (CYP) enzyme system and interindividual variability in expression and function of these enzymes is a major factor for explaining individual susceptibility for adverse drug reactions and drug response. Because of the existence of many polymorphic CYP genes, for many of which the number of allelic variants is continually increasing, a universal and official nomenclature system is important. Since 1999, all functionally relevant polymorphic CYP alleles are named and published on the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Web site (http://www.cypalleles.ki.se). Currently, the database covers nomenclature of more than 660 alleles in a total of 30 genes that includes 29 CYPs as well as the cytochrome P450 oxidoreductase (POR) gene. On the CYP-allele Web site, each gene has its own Webpage, which lists the alleles with their nucleotide changes, their functional consequences, and links to publications identifying or characterizing the alleles. CYP2D6, CYP2C9, CYP2C19, and CYP3A4 are the most important CYPs in terms of drug metabolism, which is also reflected in their corresponding highest number of Webpage hits at the CYP-allele Web site.The main advantage of the CYP-allele database is that it offers a rapid online publication of CYP-alleles and their effects and provides an overview of peer-reviewed data to the scientific community. Here, we provide an update of the CYP-allele database and the associated nomenclature. PMID:23475683

Sim, Sarah C; Ingelman-Sundberg, Magnus

2013-01-01

271

Development and characterization of novel microsatellite markers in Hyptis pectinata (Lamiaceae).  

PubMed

A microsatellite-enriched library was constructed and a set of 19 SSR markers were developed to characterize a germplasm collection of Hyptis pectinata (L.) Poit., maintained at the Universidade Federal de Sergipe (UFS). Fifteen markers of 19 ranged from moderately to highly polymorphic. A total of 113 alleles were identified, with a mean of 7.52 alleles per locus. The mean HO and HE were 0.582 and 0.657, respectively. The primers developed were efficient tools for accessing the genetic diversity of the germplasm collection analyzed and may also be useful for other studies involving this species and other species in the genus Hyptis. PMID:25501228

Blank, A F; Jesus, A S; Santos, C P; Grando, C; Pinheiro, J B; Zucchi, M I; Arrigoni-Blank, M F

2014-01-01

272

Isolation of 21 polymorphic microsatellite markers for the Virginia opossum (Didelphis virginiana).  

PubMed

Twenty-one polymorphic microsatellite markers were developed for the Virginia opossum (Didelphis virginiana). The number of alleles ranged from two to 13 and observed heterozygosities ranged from 0.464 to 0.964. Significant heterozygote deficiencies were observed at three loci and null alleles were detected at five loci. Evidence for gametic disequilibrium was observed between three sets of paired loci after a sequential Bonferroni correction was applied. These markers will enable us to investigate the mating tactics, movement behaviour and social structure of Virginia opossum populations inhabiting fragmented agricultural landscapes. PMID:21564875

Fike, Jennifer A; Beasley, James C; Rhodes, Olin E

2009-07-01

273

Complex hybridization dynamics between golden-winged and blue-winged warblers (Vermivora chrysoptera and Vermivora pinus) revealed by AFLP, microsatellite, intron and mtDNA markers.  

PubMed

Blue-winged (Vermivora pinus) and golden-winged warblers (Vermivora chrysoptera) have an extensive mosaic hybrid zone in eastern North America. Over the past century, the general trajectory has been a rapid replacement of chrysoptera by pinus in a broad, northwardly moving area of contact. Previous mtDNA-based studies on these species' hybridization dynamics have yielded variable results: asymmetric and rapid introgression from pinus into chrysoptera in some areas and bidirectional maternal gene flow in others. To further explore the hybridization genetics of this otherwise well-studied complex, we surveyed variation in three nuclear DNA marker types--microsatellites, introns, and a panel of amplified fragment length polymorphisms (AFLPs)--with the goal of generating a multilocus assay of hybrid introgression. All markers were first tested on birds from phenotypically and mitochondrially pure parental-type populations from outside the hybrid zone. Searches for private alleles and assignment test approaches found no combination of microsatellite or intron markers that could separate the parental populations, but seven AFLP characters exhibited significant frequency differences among them. We then used the AFLP markers to examine the extent and pattern of introgression in a population where pinus-phenotype individuals have recently invaded a region that previously supported only a chrysoptera-phenotype population. Despite the low frequency of phenotypic hybrids at this location, the AFLP data suggest that almost a third of the phenotypically pure chrysoptera have introgressed genotypes, indicating the presence of substantial cryptic hybridization in the history of this species. The evidence for extensive cryptic introgression, combined with the lack of differentiation at other nuclear loci, cautions against hybrid assessments based on single markers or on phenotypic traits that are likely to be determined by a small number of loci. Considered in concert, these results from four classes of molecular markers indicate that pinus and chrysoptera are surprisingly weakly differentiated and that far fewer genetically 'pure' populations of chrysoptera may exist than previously assumed, two findings with broad implications for the conservation of this rapidly declining taxon. PMID:17498229

Vallender, R; Robertson, R J; Friesen, V L; Lovette, I J

2007-05-01

274

Single Nucleotide Polymorphism Array Analysis of Flow-Sorted Epithelial Cells from Frozen Versus Fixed Tissues for Whole Genome Analysis of Allelic Loss in Breast Cancer  

Microsoft Academic Search

Analysis of allelic loss in archival tumor specimens is constrained by quality and quantity of tissue and by technical limitations on the number of chromosomal sites that can be efficiently evaluated in conventional analyses using polymorphic microsatellite markers. Newly developed array-based assays have the poten- tial to yield genome-wide data from small amounts of tissue but have not been validated

Elizabeth L. Schubert; Li Hsu; Laura A. Cousens; Jeri Glogovac; Steve Self; Brian J. Reid; Peter S. Rabinovitch; Peggy L. Porter

2002-01-01

275

Development of microsatellite markers for Pythium helicoides.  

PubMed

A strategy combining dual-suppression PCR and thermal asymmetric interlaced PCR was used to determine sequences flanking microsatellite regions in Pythium helicoides. The primer pairs were designed to amplify loci containing (AC)n, (GA)n, (AGC)n, (CAC)n(CAA)n, (TCA)n and (CTTT)n repeats from the P. helicoides nuclear genome. The PCR products of each primer pair, amplified from three representative isolates collected from different hosts and locations, were cloned and sequenced. Different degrees of polymorphism were detected among these microsatellite markers. The numbers of alleles were 6, 2, 4, 11, 4 and 4 in YL-AC, YL-AGC, YL-CAA, YL-CTTT, YL-GA and YL-TCA, respectively. Allele analysis of 30 P. helicoides isolates showed length polymorphisms in all loci, except for YL-AC, using capillary electrophoresis. Thus, we have developed a simple method for designing PCR primers to amplify microsatellite markers from P. helicoides. PMID:19278526

Yin-Ling; Zhou, Wei; Motohashi, Keiichi; Suga, Haruhisa; Fukui, Hirokazu; Kageyama, Koji

2009-04-01

276

Evaluation of a Blog Based Parent Involvement Approach by Parents  

ERIC Educational Resources Information Center

Despite the well-known benefits of parent involvement in children's education, research clearly shows that it is difficult to effectively involve parents. This study aims to capture parents' views of a Blog Based Parent Involvement Approach (BPIA) designed to secure parent involvement in education by strengthening school-parent communication. Data…

Ozcinar, Zehra; Ekizoglu, Nihat

2013-01-01

277

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. PMID:19531560

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

278

Development of EST-based new SSR markers in seabuckthorn.  

PubMed

EST-based SSR markers were developed by screening a collection of 1584 clustered ESTs of seabuckthorn (Hippophae rhamnoides). PCR primers were designed for the amplification of 30 microsatellite loci. Two to five allelic bands were displayed by nine primer pairs in H. rhamnoides genotypes and by eleven primer pairs in H. salicifolia genotypes. None of the thirty primer pairs detected polymorphism in H. tibetana genotypes. Considering the high polymorphism detected in the tested genotypes and their direct origin from the genic regions, these EST-SSR markers hold immense promise in seabuckthorn genome analysis, molecular breeding and population genetics. PMID:23572988

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

2010-12-01

279

A Novel Class of Simple PCR Markers with SNP-Level Sensitivity for Mapping and Haplotype Characterization in Solanum Species  

Microsoft Academic Search

The RB gene from wild potato Solanum bulbocastanum imparts broad-spectrum late blight resistance to cultivated potato. To explore marker associations and haplotype frequencies\\u000a near RB, we developed, optimized, validated, and employed a set of markers specific to the haplotype associated with the RB resistance allele. Our markers, developed using a mismatch amplification mutation assay (MAMA)-PCR approach, have single\\u000a nucleotide polymorphism-level

Ryan L. Syverson; James M. Bradeen

2011-01-01

280

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. PMID:9799270

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

1998-01-01

281

Aberrant allele-switch imprinting of a novel IGF1R intragenic antisense non-coding RNA in breast cancers.  

PubMed

The insulin-like growth factor type I receptor (IGF1R) is frequently dysregulated in breast cancers, yet the molecular mechanisms are unknown. A novel intragenic long non-coding RNA (lncRNA) IRAIN within the IGF1R locus has been recently identified in haematopoietic malignancies using RNA-guided chromatin conformation capture (R3C). In breast cancer tissues, we found that IRAIN lncRNA was transcribed from an intronic promoter in an antisense direction as compared to the IGF1R coding mRNA. Unlike the IGF1R coding RNA, this non-coding RNA was imprinted, with monoallelic expression from the paternal allele. In breast cancer tissues that were informative for single nucleotide polymorphism (SNP) rs8034564, there was an imbalanced expression of the two parental alleles, where the 'G' genotype was favorably imprinted over the 'A' genotype. In breast cancer patients, IRAIN was aberrantly imprinted in both tumours and peripheral blood leucocytes, exhibiting a pattern of allele-switch: the allele expressed in normal tissues was inactivated and the normally imprinted allele was expressed. Epigenetic analysis revealed that there was extensive DNA demethylation of CpG islands in the gene promoter. These data identify IRAIN lncRNA as a novel imprinted gene that is aberrantly regulated in breast cancer. PMID:25465188

Kang, Lihua; Sun, Jingnan; Wen, Xue; Cui, Jiuwei; Wang, Guanjun; Hoffman, Andrew R; Hu, Ji-Fan; Li, Wei

2015-01-01

282

Inheritance of Mutator Activity in ZEA MAYS as Assayed by Somatic Instability of the bz2-mu1 Allele  

PubMed Central

Mutator lines of maize were originally defined by their high forward mutation rate, now known to be caused by the transposition of numerous Mu elements. A high frequency of somatic instability, seen as a fine purple spotting pattern on the aleurone tissue, is characteristic of Mu-induced mutable alleles of genes of the anthocyanin pathway. Loss of such somatic instability has been correlated with the de novo, specific modification of Mu element DNA. In this report the presence or loss of somatic instability at the bz2-mu1 allele has been monitored to investigate the inheritance of the Mutator phenomenon. The active state is labile and may become weakly active (low fraction of spotted kernel progeny) or totally inactive (no spotted kernel progeny) during either outcrossing to non-Mutator lines or on self-pollination. In contrast, the inactive state is relatively permanent with rare reactivation in subsequent crosses to non-Mutator lines. Cryptic bz2-mu1 alleles in weakly active lines can be efficiently reactivated to somatic instability when crossed with an active line. However, in reciprocal crosses of active and totally inactive individuals, strong maternal effects were observed on the inactivation of a somatically unstable bz2-mu1 allele and on the reactivation of cryptic bz2-mu1 alleles. In general, the activity state of the female parent determines the mutability of the progeny. PMID:3803916

Walbot, Virginia

1986-01-01

283

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

2013-11-01

284

The loss-of-allele assay for ES cell screening and mouse genotyping.  

PubMed

Targeting vectors used to create directed mutations in mouse embryonic stem (ES) cells consist, in their simplest form, of a gene for drug selection flanked by mouse genomic sequences, the so-called homology arms that promote site-directed homologous recombination between the vector and the target gene. The VelociGene method for the creation of targeted mutations in ES cells employs targeting vectors, called BACVecs, that are based on bacterial artificial chromosomes. Compared with conventional short targeting vectors, BacVecs provide two major advantages: (1) their much larger homology arms promote high targeting efficiencies without the need for isogenicity or negative selection strategies; and (2) they enable deletions and insertions of up to 100kb in a single targeting event, making possible gene-ablating definitive null alleles and other large-scale genomic modifications. Because of their large arm sizes, however, BACVecs do not permit screening by conventional assays, such as long-range PCR or Southern blotting, that link the inserted targeting vector to the targeted locus. To exploit the advantages of BACVecs for gene targeting, we inverted the conventional screening logic in developing the loss-of-allele (LOA) assay, which quantifies the number of copies of the native locus to which the mutation was directed. In a correctly targeted ES cell clone, the LOA assay detects one of the two native alleles (for genes not on the X or Y chromosome), the other allele being disrupted by the targeted modification. We apply the same principle in reverse as a gain-of-allele assay to quantify the copy number of the inserted targeting vector. The LOA assay reveals a correctly targeted clone as having lost one copy of the native target gene and gained one copy of the drug resistance gene or other inserted marker. The combination of these quantitative assays makes LOA genotyping unequivocal and amenable to automated scoring. We use the quantitative polymerase chain reaction (qPCR) as our method of allele quantification, but any method that can reliably distinguish the difference between one and two copies of the target gene can be used to develop an LOA assay. We have designed qPCR LOA assays for deletions, insertions, point mutations, domain swaps, conditional, and humanized alleles and have used the insert assays to quantify the copy number of random insertion BAC transgenics. Because of its quantitative precision, specificity, and compatibility with high throughput robotic operations, the LOA assay eliminates bottlenecks in ES cell screening and mouse genotyping and facilitates maximal speed and throughput for knockout mouse production. PMID:20691873

Frendewey, David; Chernomorsky, Rostislav; Esau, Lakeisha; Om, Jinsop; Xue, Yingzi; Murphy, Andrew J; Yancopoulos, George D; Valenzuela, David M

2010-01-01

285

Maternal Personality, Parenting Cognitions, and Parenting Practices  

Microsoft Academic Search

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 5-factor model

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

2011-01-01

286

Genographic: Permanent Markers  

NSDL National Science Digital Library

In this lesson, the second in a set of lessons exploring migration, genetic markers, markers in context, and the Genographic Project (a five-year study of human origins and migration based on genetic markers), students will review background information about the basics of DNA and chromosomal structure. They will then explore the Genographic Project and the work of lead scientist Dr. Spencer Wells. Using a hands-on simulation activity, they will learn how genetic markers are passed from generation to generation and haplogroups are formed. Finally, they will use the Atlas of the Human Journey to track one genetic marker over time.

287

Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males.  

PubMed

The genotypes of 36 Y-chromosomal short tandem repeat (Y-STR) marker units were analysed in a Dutch population sample of 2085 males. Profiling results were compared for several partially overlapping kits, i.e. PowerPlex Y, Yfiler, PowerPlex Y23, and two in-house designed multiplexes with rapidly mutating Y-STRs. Nineteen Y-STR marker units, of which two are rapidly mutating, reside in at least two of these multiplexes, and for these markers concordance testing was performed. Two samples showed discordant genotyping results and the probable causative base change was revealed by Sanger sequencing. In addition, we encountered concordant, but aberrant genotyping results including one allele with low peak height and several null alleles. For 12 samples, this involved a null allele in two adjacent loci suggesting a large and recurrent deletion as the samples represent three distinct haplogroups. For each marker unit, the allele counts and frequencies are presented, as are the haplotype counts and haplotype diversities for several combinations of markers. PMID:25450789

Westen, Antoinette A; Kraaijenbrink, Thirsa; Clarisse, Lindy; Grol, Laurens J W; Willemse, Patricia; Zuniga, Sofia B; Robles de Medina, Elizaveta A; Schouten, Ron; van der Gaag, Kristiaan J; Weiler, Natalie E C; Kal, Arnoud J; Kayser, Manfred; Sijen, Titia; de Knijff, Peter

2015-01-01

288

Determination of knockdown resistance allele frequencies in global human head louse populations using the serial invasive signal amplification reaction  

PubMed Central

BACKGROUND Pediculosis is the most prevalent parasitic infestation of humans. Resistance to pyrethrin- and pyrethroid-based pediculicides is due to knockdown (kdr)-type point mutations in the voltage-sensitive sodium channel ?-subunit gene. Early detection of resistance is crucial for the selection of effective management strategies. RESULTS Kdr allele frequencies of lice from 14 countries were determined using serial invasive signal amplification reaction. Lice collected from Uruguay, UK and Australia had kdr allele frequencies of 100% while lice from Ecuador, Papua New Guinea, South Korea and Thailand had kdr allele frequencies of 0%. The remaining 7 countries investigated, including seven US populations, two Argentina, Brazil, Denmark, Czech Republic, Egypt and Israel, displayed variable kdr allele frequencies, ranging from 11% to 97%. CONCLUSION The newly developed and validated SISAR method is suitable for accurate monitoring of kdr allele frequencies in head lice. Proactive management is needed where kdr-type resistance is not yet saturated. Based on sodium channel insensitivity and its occurrence in louse populations resistant to pyrethrin- and pyrethroid-based pediculicides, the T917I mutation appears a key marker for resistance. Results from the Egyptian population, however, indicate that phenotypic resistance of lice with single or double mutations (M815I and/or L920F) should also be determined. PMID:20564731

Hodgdon, Hilliary E.; Yoon, Kyong Sup; Previte, Domenic J.; Kim, Hyo Jeong; Aboelghar, Gamal E.; Lee, Si Hyeock; Clark, J. Marshall

2010-01-01

289

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. PMID:16789827

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

2006-01-01

290

Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast.  

PubMed

Twenty-one X-chromosomal short tandem repeat (STR) loci, including the six clusters of linked markers DXS10148-DXS10135-DXS8378 (Xp22), DXS7132-DXS10079-DXS10074 (Xq12), DXS6801-DXS6809-DXS6789 (Xq21), DXS7424-DXS101 (Xq22), DXS10103-HPRTB-DXS10101 (Xq26), DXS8377-DXS10146-DXS10134-DXS7423 (Xq28) and the loci DXS6800, GATA172D05 and DXS10011 were typed in a population sample from Ivory Coast (n=125; 51 men and 74 women). Allele and haplotype frequencies as well as linkage disequilibrium data for kinship calculations are provided. On the whole, no significant differences in the genetic variability of X-STR markers were observed between Ivorians and other sub-Saharan African populations belonging to the Niger-Kordofanian linguistic group. PMID:21717153

Pasino, Serena; Caratti, Stefano; Del Pero, Massimiliano; Santovito, Alfredo; Torre, Carlo; Robino, Carlo

2011-09-01

291

Genetic polymorphism of major histocompatibility complex class IIB alleles and pathogen resistance in the giant spiny frog Quasipaa spinosa.  

PubMed

Major histocompatibility complex (MHC) genes are candidates for determining disease susceptibility due to their pivotal role in both innate and adaptive immune responses. Accordingly, the association between the genetic variation of MHC genes and the pathogen resistance has been investigated in numerous vertebrates. To date, however, little is reported in amphibians. In this study, we investigate the genetic variation at the MHC class IIB gene in the giant spiny frog Quasipaa spinosa, which has high commercial value in China. The full length of MHC class IIB cDNA was cloned from Q. spinosa by homology cloning and rapid amplification of cDNA end-polymerase chain reaction (RACE-PCR). Two MHC class IIB loci were identified in Q. spinosa. We also developed PCR primers for a portion of the second exon of the MHC class IIB gene. A total of 26 MHC class IIB alleles were identified. The dN rate was significantly higher than the dS rate in the putative peptide-binding region, thereby proving the positive selection hypothesis. In addition, individuals intraperitoneally injected with Aeromonas hydrophila were used to study the association between MHC class IIB alleles and pathogen resistance/susceptibility, to explore the specific alleles in balancing selection. Eighty frogs were used after exposure to A. hydrophila infection. Nine alleles were used to study the association between the alleles and disease resistance. Two alleles, namely, Pasa-DAB(?)1301 and Pasa-DAB(?)0901, were significantly associated with resistance against A. hydrophila. This study provides valuable information on the structure of the MHC class IIB gene and confirms the association between MHC class IIB gene alleles and disease resistance to bacterial infection in Q. spinosa. Moreover, pathogen resistance-related MHC markers can be used for the selective breeding of the giant spiny frog. PMID:25269786

Yu, Xiaoyun; Zheng, Rongquan; Zhang, Jiayong; Shen, Bing; Dong, Baojuan

2014-12-01

292

A comparison of single nucleotide polymorphism and microsatellite markers for analysis of parentage and kinship in a cooperatively breeding bird.  

PubMed

The development of genetic markers has revolutionized molecular studies within and among populations. Although poly-allelic microsatellites are the most commonly used genetic marker for within-population studies of free-living animals, biallelic single nucleotide polymorphisms, or SNPs, have also emerged as a viable option for use in nonmodel systems. We describe a robust method of SNP discovery from the transcriptome of a nonmodel organism that resulted in more than 99% of the markers working successfully during genotyping. We then compare the use of 102 novel SNPs with 15 previously developed microsatellites for studies of parentage and kinship in cooperatively breeding superb starlings (Lamprotornis superbus) that live in highly kin-structured groups. For 95% of the offspring surveyed, SNPs and microsatellites identified the same genetic father, but only when behavioural information about the likely parents at a nest was included to aid in assignment. Moreover, when such behavioural information was available, the number of SNPs necessary for successful parentage assignment was reduced by half. However, in a few cases where candidate fathers were highly related, SNPs did a better job at assigning fathers than microsatellites. Despite high variation between individual pairwise relatedness values, microsatellites and SNPs performed equally well in kinship analyses. This study is the first to compare SNPs and microsatellites for analyses of parentage and relatedness in a species that lives in groups with a complex social and kin structure. It should also prove informative for those interested in developing SNP loci from transcriptome data when published genomes are unavailable. PMID:25224810

Weinman, Lucia R; Solomon, Joseph W; Rubenstein, Dustin R

2014-09-15

293

Preschool Parent's Questionnaire: An Analysis.  

ERIC Educational Resources Information Center

The Preschool Parent's Questionnaire (PPQ) was administered, in English and Spanish, to 120 parents (95 Black, 25 Mexican) of preschool children enrolled in child care programs, to ascertain the parents' attitudes regarding four basic issues: (1) parent's relationship to the child care program, (2) parent's attitudes toward teachers, (3) parent's…

Smith, Rutha L.

294

Mitochondrial microsatellite markers for the Australian ectomycorrhizal fungus Laccaria sp. A (Hydnangiaceae)1  

PubMed Central

• Premise of the study: Microsatellite loci were developed for the ectomycorrhizal fungus Laccaria sp. A to investigate the population genetic structure of this fungal symbiont across its fragmented distribution in southeastern Australia. • Methods and Results: A partial genome sequence from an individual collection of Laccaria sp. A was obtained by 454 genome sequencing. Eight microsatellite markers were selected from 66 loci identified in the genome. The selected markers were highly polymorphic (4–19 alleles per locus, average 13 alleles) and amplified reproducibly from collections made across the distribution of this species. Five of these markers also amplified reproducibly in the sister species Laccaria sp. E (1). All eight of the selected microsatellite loci were from the mitochondrial genome. • Conclusions: The highly polymorphic markers described here will enable population structure of Laccaria sp. A to be determined, contributing to research on mycorrhizal fungi from a novel distribution. PMID:25202611

Sheedy, Elizabeth M.; Van de Wouw, Angela P.; Howlett, Barbara J.; May, Tom W.

2014-01-01

295

Microsatellite DNA markers for delineating population structure and kinship among the endangered Kirtland's warbler (Dendroica kirtlandii)  

USGS Publications Warehouse

We document the isolation and characterization of 23 microsatellite DNA markers for the endangered Kirtland's warbler (Dendroica kirtlandii), a Nearctic/Neotropical migrant passerine. This suite of markers revealed moderate to high levels of allelic diversity (averaging 7.7 alleles per locus) and heterozygosity (averaging 72%). Genotypic frequencies at 22 of 23 (95%) markers conformed to Hardy-Weinberg equilibrium expectations, and no linkage disequilibrium was observed in blood samples taken from 14 warblers found on the wintering grounds in the Bahamas archipelago. Multilocus genotypes resulting from this suite of markers should reduce the amount of resources required for initiating new genetic studies assessing breeding structure, parentage, demographics, and individual-level ecological interactions for D. kirtlandii. ?? 2005 Blackwell Publishing Ltd.

King, T.L.; Eackles, M.S.; Henderson, A.P.; Bocetti, C.I.; Currie, D.; Wunderle, J.M., Jr.

2005-01-01

296

Sophora microphylla (Fabaceae) microsatellite markers and their utility across the genus1  

PubMed Central

• Premise of the study: Genus-specific microsatellite markers were developed for Sophora for population genetic and systematic studies of the group in New Zealand, and potentially elsewhere in the geographic range. • Methods and Results: From sequencing a total genomic DNA library (using Roche 454), we identified and developed 29 polymorphic microsatellite markers for S. microphylla and S. chathamica. We tested 12 of these markers on 14 S. chathamica individuals and four S. microphylla populations. All loci amplified in both species and species-specific alleles occurred at seven loci. In S. microphylla populations, the observed and expected heterozygosities ranged from 0.000–0.960 and 0.000–0.908, respectively, with alleles per locus ranging from seven to 23. • Conclusions: The developed markers will be valuable in studies of phylogenetics, population structure, mating system, and selection of provenances for restoration projects. PMID:25202609

Van Etten, Megan L.; Houliston, Gary J.; Mitchell, Caroline M.; Heenan, Peter B.; Robertson, Alastair W.; Tate, Jennifer A.

2014-01-01

297

Allele-specific deposition of macroH2A1 in Imprinting Control Regions  

SciTech Connect

In the current study, we analyzed the deposition patterns of macroH2A1 at a number of different genomic loci located in X chromosome and autosomes. MacroH2A1 is preferentially deposited at methylated CpG CpG-rich regions located close to promoters. The macroH2A1 deposition patterns at the methylated CpG islands of several imprinted domains, including the Imprinting Control Regions (ICRs) of Xist, Peg3, H19/Igf2 Igf2, Gtl2/Dlk1, and Gnas domains, show consistent allele-specificity towards inactive, methylated alleles. The macroH2A1 deposition levels at the ICRs and other Differentially Methylated Regions (DMRs) of these domains are also either higher or comparable to those observed at the inactive X chromosome of female mammals. Overall, our results indicate that besides DNA methylation macroH2A1 is another epigenetic component in the chromatin of ICRs displaying differential association with two parental alleles.

Choo, J H; Kim, J D; Chung, J H; Stubbs, L; Kim, J

2006-01-13

298

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

299

Demography can favour female-advantageous alleles.  

PubMed

When female fecundity is relatively independent of male abundance, while male reproduction is proportional to female abundance, females have a larger effect on population dynamics than males (i.e. female demographic dominance). This population dynamic phenomenon might not appear to influence evolution, because male and female genomes still contribute equally much to the next generation. However, here we examine two evolutionary scenarios to provide a proof of principle that spatial structure can make female demographic dominance matter. Our two simulation models combine dispersal evolution with local adaptation subjected to intralocus sexual conflict and environmentally driven sex ratio biases, respectively. Both models have equilibria where one environment (without being intrinsically poorer) has so few reproductive females that trait evolution becomes disproportionately determined by those environments where females survive better (intralocus sexual conflict model), or where daughters are overproduced (environmental sex determination model). Surprisingly, however, the two facts that selection favours alleles that benefit females, and population growth is improved when female fitness is high, together do not imply that all measures of population performance are improved. The sex-specificity of the source-sink dynamics predicts that populations can evolve to fail to persist in habitats where alleles do poorly when expressed in females. PMID:25056617

Harts, Anna M F; Schwanz, Lisa E; Kokko, Hanna

2014-09-01

300

Plasminogen Alleles Influence Susceptibility to Invasive Aspergillosis  

PubMed Central

Invasive aspergillosis (IA) is a common and life-threatening infection in immunocompromised individuals. A number of environmental and epidemiologic risk factors for developing IA have been identified. However, genetic factors that affect risk for developing IA have not been clearly identified. We report that host genetic differences influence outcome following establishment of pulmonary aspergillosis in an exogenously immune suppressed mouse model. Computational haplotype-based genetic analysis indicated that genetic variation within the biologically plausible positional candidate gene plasminogen (Plg; Gene ID 18855) correlated with murine outcome. There was a single nonsynonymous coding change (Gly110Ser) where the minor allele was found in all of the susceptible strains, but not in the resistant strains. A nonsynonymous single nucleotide polymorphism (Asp472Asn) was also identified in the human homolog (PLG; Gene ID 5340). An association study within a cohort of 236 allogeneic hematopoietic stem cell transplant (HSCT) recipients revealed that alleles at this SNP significantly affected the risk of developing IA after HSCT. Furthermore, we demonstrated that plasminogen directly binds to Aspergillus fumigatus. We propose that genetic variation within the plasminogen pathway influences the pathogenesis of this invasive fungal infection. PMID:18566672

Zaas, Aimee K.; Liao, Guochun; Chien, Jason W.; Weinberg, Clarice; Shore, David; Giles, Steven S.; Marr, Kieren A.; Usuka, Jonathan; Burch, Lauranell H.; Perera, Lalith; Perfect, John R.; Peltz, Gary; Schwartz, David A.

2008-01-01

301

Analysis of paternal alleles in nucleated red blood cells enriched from maternal blood.  

PubMed

The purpose of our study was to identify paternal alleles in NRBC enriched from maternal peripheral blood for detection of the presence of foetal cells in the maternal circulation and to establish a reliable non-invasive method which should allow following genetic testing. For enrichment of foetal cells from peripheral maternal blood we combined Ficoll-Paque density gradient centrifugation and MACS. Maternal leukocytes were firstly depleted using anti-CD14 and anti-CD45 microbeads. NRBC were sorted from the CD14-/CD45- fraction by positive selection using CD71 microbeads. Paternal alleles in the CD14-/CD45-/CD71+ fraction were indicated by the PCR method using HLA (DRB1, DQB1, DQA1) and Polymarker System (LDLR, GYPA, HBGG, D7S8, GC) as genetic markers. Different paternal alleles of studied 8 loci were detected in 13 out of 19 samples of cells enriched from maternal peripheral blood between the 13th and 36th week of gestation. Our results demonstrate that foetal cells enriched from maternal peripheral blood may be used as a source of foetal DNA for prenatal diagnosis, paternity testing and other application. PMID:11232868

Hromadníková, I; Bendukidze, N; Mrstinová, M; Ivasková, E

2001-01-01

302

Combination of two mutant alpha spectrin alleles underlies a severe spherocytic hemolytic anemia.  

PubMed Central

We studied a patient with a severe spherocytic hemolytic anemia without family history of spherocytosis. Analysis of patient's erythrocyte membrane proteins revealed spectrin deficiency and a truncated alpha spectrin protein. We determined that the patient is a compound heterozygote with two mutations in alpha spectrin gene. Mutation in the paternal allele, designated alpha spectrin(PRAGUE), is a transition A to G in the penultimate position of intron 36 that leads to skipping of exon 37, frameshift, and production of the truncated alpha spectrin protein. The maternal allele, designated alpha spectrin(LEPRA), contains transition C-->T in position -99 of intron 30. This mutation enhances an alternative acceptor splice site 70 nucleotides upstream from the regular site. The alternative splicing causes a frameshift and premature termination of translation leading to a significant decrease in alpha spectrin production. The alpha(LEPRA) mutation is linked to a spectrin alphaIIa marker that was found to be associated with recessive or nondominant spectrin-deficient hereditary spherocytosis in approximately 50% of studied families. We conclude that the alpha(LEPRA) mutation combined in trans with the alpha(PRAGUE) mutation underlie the severe hemolytic anemia in the proband. We suggest that allele alpha spectrin(LEPRA) may be frequently involved in pathogenesis of recessive or nondominant spectrin-deficient hereditary spherocytosis. PMID:8941647

Wichterle, H; Hanspal, M; Palek, J; Jarolim, P

1996-01-01

303

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. PMID:20930948

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

2010-01-01

304

Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium  

Microsoft Academic Search

Microsatellite markers were developed in Acacia mangium Willd. to provide highly variable co-dominant markers for linkage mapping and studies of the breeding system. After an enrichment\\u000a procedure 40% of colonies contained microsatellites in contrast with less than 1% from a non-enriched library. The majority\\u000a of microsatellite sequences were AC repeats. Co-dominant segregation of alleles in two full-sib crosses of A.

P. A. Butcher; S. Decroocq; Y. Gray; G. F. Moran

2000-01-01

305

Comparison of marker-based pairwise relatedness estimators on a pedigreed plant population  

Microsoft Academic Search

Several estimators have been proposed that use molecular marker data to infer the degree of relatedness for pairs of individuals.\\u000a The objective of this study was to evaluate the performance of seven estimators when applied to marker data of a set of 33\\u000a key individuals from a large complex apple pedigree. The evaluation considered different scenarios of allele frequencies and

Marco C. A. M. Bink; Amy D. Anderson; W. Eric van de Weg; Elizabeth A. Thompson

2008-01-01

306

Characterization of 29 polymorphic artiodactyl microsatellite markers for the mountain goat (Oreamnos americanus)  

Microsoft Academic Search

We report the results of a cross-species amplification test of 156 bovine, ovine and cervid micro- satellite markers in a wild population of mountain goats, Oreamnos americanus , inhabiting Caw Ridge, Alberta, Canada. Twenty-nine markers were found to be low to moderately poly- morphic with between two to nine alleles per locus. Observed heterozygosity ranged from 0.14 to 0.85 for

JULIEN MAINGUY; AMY S. LLEWELLYN; KIRSTY WORLEY; STEEVE D. COTE; DAVID W. COLTMAN

2005-01-01

307

Genetic Analysis and Linkage Mapping in a Resource Pig Population Using Microsatellite Markers  

Microsoft Academic Search

The use of markers and linkage map construction are important for QTL mapping in pigs. In this article, the genetic characteristics were studied and the linkage map was constructed in a pig resource population including 214 individuals by typing 39 microsatellite marker loci on Sus scrofa chromosomes, SSC4, SSC6, SSC7, SSC8, and SSC13. Results indicated that the average allele number,

Jinghu Zhang; Yuanzhu Xiong; Bo Zuo; Minggang Lei; Siwen Jiang; Feng'e Li; Rong Zheng; Jialian Li

2007-01-01

308

Parent Abuse: A Review  

Microsoft Academic Search

A recent focus of research and clinical practice has been on the issue of abuse of parents by their children (parent abuse).\\u000a This paper reviews the literature on this phenomenon. While parent abuse falls under the umbrella of family violence, it appears\\u000a to be qualitatively different from other forms of intra-family abuse. Research has primarily focused on prevalence rates and

Nicola Kennair; David Mellor

2007-01-01

309

Schooling and Parental Death  

Microsoft Academic Search

Loss of a parent is one of the most traumatic events a child can face. If loss of a parent reduces investments in children, it can also have long-lasting implications. This study uses parametric and seminonpara-metric matching techniques to estimate how one human capital investment, school enrollment, is affected by a parent's recent death. We analyze data from 600,000 households

Paul Gertler; David I. Levine; Minnie Ames

2004-01-01

310

Schooling and Parental Death  

Microsoft Academic Search

Loss of a parent is one of the most traumatic events a child can face. If loss of a parent reduces investments in children, it can also have long-lasting implications. This study uses parametric and semi-nonparametric matching techniques to estimate how one human capital investment, school enrollment, is affected by a parent's recent death. We analyze data from 600,000 households

Paul Gertler; David I. Levine; Minnie Ames

2002-01-01

311

Maternal inheritance and chromosome 18 allele sharing in unilineal bipolar illness pedigrees  

SciTech Connect

We have replicated the observation that there is excess maternal transmission of illness in a series of previously described unilineal Bipolar manic-depressive illness extended pedigrees. ({open_quotes}Transmission{close_quotes} is defined for any ill person in a pedigree when father or mother has a personal or immediate family history of major affective disorder.) We divided our pedigrees into exclusively maternal transmission (Mat) and mixed maternal-paternal transmission (in different pedigree branches) (Pat). Using affected sib-pair-analysis, linkage to a series of markers on chromosome 18p-cen was observed in the Pat but not the Mat pedigrees, with significantly greater identity by descent (IBD) at these markers in the Pat pedigrees. As compared with the pedigree series as a whole, the proportion of alleles IBD in the linkage region is much increased in the Pat pedigrees. As the sharing proportion of alleles in affected relative pairs increases, the number of such pairs needed to resolve the linkage region to a 1 cM interval becomes smaller. Genetic subdivision of an illness by clinical or pedigree configuration criteria may thus play an important role in discovery of disease susceptibility mutations. 10 refs., 2 figs., 3 tabs.

Gershon, E.S.; Badner, J.A.; Detera-Wadleigh, S.D. [National Inst. of Mental Health, Bethesda, MD (United States)] [and others] [National Inst. of Mental Health, Bethesda, MD (United States); and others

1996-04-09

312

Homeostatic Maintenance of Allele-Specific p16 Methylation in Cancer Cells Accompanied by Dynamic Focal Methylation and Hydroxymethylation  

PubMed Central

Aim p16 Methylation frequently occurs in carcinogenesis. While it has been hypothesized that the p16 methylation states are dynamically maintained in cancer cells, direct evidence supporting this hypothesis has not been available until now. Methods A fusion cell model was established which reprogrammed the native DNA methylation pattern of the cells. The methylation status of the p16 alleles was then repeatedly quantitatively analyzed in the fusion monoclonal, parental cancer cell lines (p16-completely methylated-AGS and unmethylated-MGC803), and HCT116 non-fusion cell using DHPLC and bisulfite sequencing. Histone methylation was analyzed using chromatin immuno-precipitation (ChIP)-PCR. P16 expression status was determined using immuno-staining and RT-PCR. Results The methylation status for the majority of the p16 alleles was stably maintained in the fusion monoclonal cells after up to 60 passages. Most importantly, focal de novo methylation, demethylation, and hydroxymethylation were consistently observed within about 27% of the p16 alleles in the fusion monoclones, but not the homozygously methylated or unmethylated parental cells. Furthermore, subclones of the monoclones consistently maintained the same p16 methylation pattern. A similar phenomenon was also observed using the p16 hemi-methylated HCT116 non-fusion cancer cell line. Interestingly, transcription was not observed in p16 alleles that were hydroxymethylated with an antisense-strand-specific pattern. Also, the levels of H3K9 and H3K4 trimethylation in the fusion cells were found to be slightly lower than the parental AGS and MGC803 cells, respectively. Conclusion The present study provides the first direct evidence confirming that the methylation states of p16 CpG islands is not only homeostatically maintained, but also accompanied by a dynamic process of transient focal methylation, demethylation, and hydroxymethylation in cancer cells. PMID:24828678

Qin, Sisi; Li, Qiang; Zhou, Jing; Liu, Zhao-jun; Su, Na; Wilson, James; Lu, Zhe-ming; Deng, Dajun

2014-01-01

313

Allele-Specific Amplification in Cancer Revealed by SNP Array Analysis  

PubMed Central

Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer. In recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. Similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. We have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (SNP) array data to arrive at allele-specific copy number across the genome. Our approach applies an expectation-maximization algorithm to a model derived from a novel classification of SNP array probes. This method is the first to our knowledge that is able to (a) determine the generalized genotype of aberrant samples at each SNP site (e.g., CCCCT at an amplified site), and (b) infer the copy number of each parental chromosome across the genome. With this method, we are able to determine not just where amplifications and deletions occur, but also the haplotype of the region being amplified or deleted. The merit of our model and general approach is demonstrated by very precise genotyping of normal samples, and our allele-specific copy number inferences are validated using PCR experiments. Applying our method to a collection of lung cancer samples, we are able to conclude that amplification is essentially monoallelic, as would be expected under the mechanisms currently believed responsible for gene amplification. This suggests that a specific parental chromosome may be targeted for amplification, whether because of germ line or somatic variation. An R software package containing the methods described in this paper is freely available at http://genome.dfci.harvard.edu/~tlaframb/PLASQ. PMID:16322765

2005-01-01

314

Inheritance and interactions of incompatibility alleles in the tetraploid sour cherry.  

PubMed

Three progenies of sour cherry (Prunus cerasus) were analysed to correlate self-(in)compatibility status with S-RNase phenotype in this allotetraploid hybrid of sweet and ground cherry. Self-(in)compatibility was assessed in the field and by monitoring pollen tube growth after selfing. The S-RNase phenotypes were determined by isoelectric focusing of stylar proteins and staining for RNase activity and, for the parents, confirmed by PCR. Seedling phenotypes were generally consistent with disomic segregation of S-RNase alleles. The genetic arrangements of the parents were deduced to be 'Köröser' (self-incompatible) S1S4.S(B) S(D), 'Schattenmorelle' (self-compatible) S6S13.S(B)S(B), and clone 43.87 (self-compatible) S4S13.S(B)S(B), where "." separates the two homologous genomes. The presence of S4 and S6 alleles at the same locus led to self-incompatibility, whereas S13 and S(B) at homologous loci led to self-compatibility. The failure of certain heteroallelic genotypes in the three crosses or in the self-incompatible seedlings indicates that S4 and S6 are dominant to S(B). However, the success of S13S(B) pollen on styles expressing corresponding S-RNases indicates competitive interaction or lack of pollen-S components. In general, the universal compatibility of S13S(B) pollen may explain the frequent occurrence of S13 and S(B) together in sour cherry cultivars. Alleles S(B) and S(D), that are presumed to derive from ground cherry, and S13, presumably from sweet cherry, were sequenced. Our findings contribute to an understanding of inheritance of self-(in)compatibility, facilitate screening of progenies for self-compatibility and provide a basis for studying molecular interactions in heteroallelic pollen. PMID:16307228

Boskovi?, R I; Wolfram, B; Tobutt, K R; Cerovi?, R; Sonneveld, T

2006-01-01

315

Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection.  

PubMed

We experimentally investigated more than 1,200 entries in dbSNP that would change amino-acids (nsSNPs), using various subsets of DNA samples drawn from 18 global populations (approximately 1,000 subjects in total). First, we mined the data for any SNP features that correlated with a high validation rate. Useful predictors of valid SNPs included multiple submissions to dbSNP, having a dbSNP validation statement, and being present in a low number of ESTs. Together, these features improved validation rates by almost 10-fold. Higher-abundance SNPs (e.g., T/C variants) also validated more frequently. Second, we considered derived alleles and noted a considerably (approximately 10%) increased average derived allele frequency (DAF) in Europeans vs. Africans, plus a further increase in some other populations. This was not primarily due to an SNP ascertainment bias, nor to the effects of natural selection. Instead, it can be explained as a drift-based, progressive increase in DAF that occurs over many generations and becomes exaggerated during population bottlenecks. This observation could be used as the basis for novel DAF-based tests for comparing demographic histories. Finally, we considered individual marker patterns and identified 37 SNPs with allele frequency variance or FST values consistent with the effects of population-specific natural selection. Four particularly striking clusters of these markers were apparent, and three of these coincide with genes/regions from among only several dozen such domains previously suggested by others to carry signatures of selection. PMID:16429399

Fredman, David; Sawyer, Sarah L; Strömqvist, Linda; Mottagui-Tabar, Salim; Kidd, Kenneth K; Wahlestedt, Claes; Chanock, Stephen J; Brookes, Anthony J

2006-02-01

316

Favorable QTL Alleles for Yield and Its Components Identified by Association Mapping in Chinese Upland Cotton Cultivars  

PubMed Central

Linkage disequilibrium based association mapping is a powerful tool for dissecting the genetic basis underlying complex traits. In this study, an association mapping panel consisting of 356 representative Upland cotton cultivars was constructed, evaluated in three environments and genotyped using 381 SSRs to detect molecular markers associated with lint yield and its components. The results showed that abundant phenotypic and moderate genetic diversities existed within this germplasm panel. The population could be divided into two subpopulations, and weak relatedness was detected between pair-wise accessions. LD decayed to the background (r2?=?0.1182, P?0.01), r2?=?0.1 and r2?=?0.2 level within 12–13 cM, 17–18 cM and 3–4 cM, respectively, providing the potential for association mapping of agronomically important traits in Chinese Upland cotton. A total of 55 marker-trait associations were detected between 26 SSRs and seven lint yield traits, based on a mixed linear model (MLM) and Bonferroni correction (P?0.05/145, ?log10P?3.46). Of which 41 could be detected in more than one environment and 17 markers were simultaneously associated with two or more traits. Many associations were consistent with QTLs identified by linkage mapping in previous reports. Phenotypic values of alleles of each loci in 41 stably detected associations were compared, and 23 favorable alleles were identified. Population frequency of each favorable allele in historically released cultivar groups was also evaluated. The QTLs detected in this study will be helpful in further understanding the genetic basis of lint yield and its components, and the favorable alleles may facilitate future high-yield breeding by genomic selection in Upland cotton. PMID:24386089

Mei, Hongxian; Zhu, Xiefei; Zhang, Tianzhen

2013-01-01

317

Genetic Anthropology of the Colorectal Cancer–Susceptibility Allele APC I1307K: Evidence of Genetic Drift within the Ashkenazim  

PubMed Central

The adenomatous polyposis coli (APC) I1307K allele is found in 6% of the Ashkenazi Jewish population and in 1%–2% of Sephardi Jews; it confers a relative risk of 1.5–2.0 for colorectal cancer (CRC) on all carriers. Within the Ashkenazim, the existence of numerous high-prevalence mutations, including I1307K, has sparked controversy over whether genetic drift or selection is the underlying cause. For the present population-based case-control study of CRC in Israel, we tested whether selection has operated at I1307K. We also estimated the age of the I1307K allele, to understand its origin in the context of the Jewish diasporas and subsequent founder events. We genotyped 83 matched pairs, in which one or both members of the pair carried I1307K, at three microsatellites and two SNPs. Haplotypes were statistically constructed using PHASE software. Single-marker age estimates for I1307K were calculated using the approach described by Risch et al. A common progenitor haplotype spanned across APC I1307K from the centromeric marker D5S135 to the telomeric marker D5S346 and was observed in individuals of Ashkenazi, Sephardi, and Arab descent. The ancestor of modern I1307K alleles existed 87.9–118 generations ago (?2,200–2,950 years ago). This age estimate indicates that I1307K existed at about the time of the beginning of the Jewish diaspora, explaining its presence in non-Ashkenazi populations. Our data do not indicate that selection operated at I1307K (D5S346, P=.114; D5S135, P=.373), providing compelling evidence that the high frequency of disease-susceptibility alleles in the Ashkenazim is due to genetic drift, not selection. This research underscores the importance of the migratory patterns of ancestral populations in the ethnic and geographic distribution of APC I1307K. PMID:14624392

Niell, Bethany L.; Long, Jeffrey C.; Rennert, Gad; Gruber, Stephen B.

2003-01-01

318

Parental origin of the extra chromosome in Down's syndrome  

Microsoft Academic Search

Chromosome 21 fluorescent heteromorphisms were studied in 42 patients with Down's syndrome, their parents and their siblings. Included in this number are two instances of an aunt and niece affected with trisomy 21, and one of affected siblings. One case has a de novo 21\\/21 translocation. Blood group, red cell and serum protein markers were also studied for linkage, gene

R. E. Magenis; K. M. Overton; J. Chamberlin; T. Brady; E. Lovrien

1977-01-01

319

Parental origin of sequence variants associated with complex diseases.  

PubMed

Effects of susceptibility variants may depend on from which parent they are inherited. Although many associations between sequence variants and human traits have been discovered through genome-wide associations, the impact of parental origin has largely been ignored. Here we show that for 38,167 Icelanders genotyped using single nucleotide polymorphism (SNP) chips, the parental origin of most alleles can be determined. For this we used a combination of genealogy and long-range phasing. We then focused on SNPs that associate with diseases and are within 500 kilobases of known imprinted genes. Seven independent SNP associations were examined. Five-one with breast cancer, one with basal-cell carcinoma and three with type 2 diabetes-have parental-origin-specific associations. These variants are located in two genomic regions, 11p15 and 7q32, each harbouring a cluster of imprinted genes. Furthermore, we observed a novel association between the SNP rs2334499 at 11p15 and type 2 diabetes. Here the allele that confers risk when paternally inherited is protective when maternally transmitted. We identified a differentially methylated CTCF-binding site at 11p15 and demonstrated correlation of rs2334499 with decreased methylation of that site. PMID:20016592

Kong, Augustine; Steinthorsdottir, Valgerdur; Masson, Gisli; Thorleifsson, Gudmar; Sulem, Patrick; Besenbacher, Soren; Jonasdottir, Aslaug; Sigurdsson, Asgeir; Kristinsson, Kari Th; Jonasdottir, Adalbjorg; Frigge, Michael L; Gylfason, Arnaldur; Olason, Pall I; Gudjonsson, Sigurjon A; Sverrisson, Sverrir; Stacey, Simon N; Sigurgeirsson, Bardur; Benediktsdottir, Kristrun R; Sigurdsson, Helgi; Jonsson, Thorvaldur; Benediktsson, Rafn; Olafsson, Jon H; Johannsson, Oskar Th; Hreidarsson, Astradur B; Sigurdsson, Gunnar; Ferguson-Smith, Anne C; Gudbjartsson, Daniel F; Thorsteinsdottir, Unnur; Stefansson, Kari

2009-12-17

320

MAPPING PHYSIOLOGICAL TRAITS IN CARICA PAPAYA USING MICROSATELLITE MARKERS  

Technology Transfer Automated Retrieval System (TEKTRAN)

Different varieties of papaya (Carica papaya L.) vary in the phenotypic expression of agronomically important traits. Genetic loci responsible for these differences can be mapped using DNA markers to genotype a segregating progeny population derived from a controlled cross between parents having dif...

321

INTRODUCTION Parental care demands an investment of parental resources, and  

E-print Network

of behavioral diversification, including several independent transitions in parental care strategy (Goodwin et3269 INTRODUCTION Parental care demands an investment of parental resources, and represents a trade of parental care but, despite this, males and females frequently differ in the amount and nature of parental

Renn, Susan C.P.

322

Parenting behaviour among parents of children with autism spectrum disorder  

Microsoft Academic Search

Contrary to the extensive amount of empirical findings about parental perceptions, parenting cognitions, and coping in families with a child with autism spectrum disorder (ASD), research about parenting itself is very scarce. A first goal of this study was to examine the factor structure and internal consistency of two scales to measure parenting behaviour: the Parental Behaviour Scale-short version (PBS,

Greet Lambrechts; Karla Van Leeuwen; Hannah Boonen; Bea Maes; Ilse Noens

2011-01-01

323

Parenting Styles and Conceptions of Parental Authority during Adolescence.  

ERIC Educational Resources Information Center

Reports of parenting styles were assessed in 100 mostly white, middle-class, 6th, 8th, and 10th graders and their parents. Adolescents viewed their parents as more permissive and more authoritarian than parents viewed themselves, whereas parents viewed themselves as more authoritative than did adolescents. Differences were primarily over the…

Smetana, Judith G.

1995-01-01

324

Handbook of Parenting. Volume 1: Children and Parenting.  

ERIC Educational Resources Information Center

Concerned with different types of parents and the forces that shape parenting, this volume, the first of four volumes on parenting deals specifically with parent-child relationships throughout the lifespan and the parenting of children of different physical, behavioral, and intellectual needs. The volume consists of 12 chapters as follows: (1)…

Bornstein, Marc H., Ed.

325

Dismay and Disappointment: Parental Involvement of Latino Immigrant Parents  

Microsoft Academic Search

Parental involvement in schools has become more popular over the past decade due to Goals 2000 and research suggesting that student academic success increases when parents are included in the education of their children. Although researchers have examined the issue of parents and schools, limited research on parental involvement has been conducted within immigrant communities. Latino immigrant parents within a

A. Y. Fred Ramirez

2003-01-01

326

Handbook of Parenting. Volume 1: Children and Parenting. Second Edition.  

ERIC Educational Resources Information Center

Concerned with different types of parents and the forces that shape parenting, this volume, the first of five volumes on parenting, deals specifically with parent-child relationships throughout the lifespan and the parenting of children of different physical, behavioral, and intellectual needs. The volume consists of the following 14 chapters: (1)…

Bornstein, Marc H., Ed.

327

Allele-specific disparity in breast cancer  

PubMed Central

Background In a cancer cell the number of copies of a locus may vary due to amplification and deletion and these variations are denoted as copy number alterations (CNAs). We focus on the disparity of CNAs in tumour samples, which were compared to those in blood in order to identify the directional loss of heterozygosity. Methods We propose a numerical algorithm and apply it to data from the Illumina 109K-SNP array on 112 samples from breast cancer patients. B-allele frequency (BAF) and log R ratio (LRR) of Illumina were used to estimate Euclidian distances. For each locus, we compared genotypes in blood and tumour for subset of samples being heterozygous in blood. We identified loci showing preferential disparity from heterozygous toward either the A/B-allele homozygous (allelic disparity). The chi-squared and Cochran-Armitage trend tests were used to examine whether there is an association between high levels of disparity in single nucleotide polymorphisms (SNPs) and molecular, clinical and tumour-related parameters. To identify pathways and network functions over-represented within the resulting gene sets, we used Ingenuity Pathway Analysis (IPA). Results To identify loci with a high level of disparity, we selected SNPs 1) with a substantial degree of disparity and 2) with substantial frequency (at least 50% of the samples heterozygous for the respective locus). We report the overall difference in disparity in high-grade tumours compared to low-grade tumours (p-value < 0.001) and significant associations between disparity in multiple single loci and clinical parameters. The most significantly associated network functions within the genes represented in the loci of disparity were identified, including lipid metabolism, small-molecule biochemistry, and nervous system development and function. No evidence for over-representation of directional disparity in a list of stem cell genes was obtained, however genes appeared to be more often altered by deletion than by amplification. Conclusions Our data suggest that directional loss and amplification exist in breast cancer. These are highly associated with grade, which may indicate that they are enforced with increasing number of cell divisions. Whether there is selective pressure for some loci to be preferentially amplified or deleted remains to be confirmed. PMID:22188678

2011-01-01

328

Applying SNP marker technology in the cacao breeding program at the Cocoa Research Institute of Ghana  

Technology Transfer Automated Retrieval System (TEKTRAN)

In this investigation 45 parental cacao plants and five progeny derived from the parental stock studied were genotyped using six SNP markers to determine off-types or mislabeled clones and to authenticate crosses made in the Cocoa Research Institute of Ghana (CRIG) breeding program. Investigation wa...

329

Intrafamilial segregation analysis of the p.E148Q MEFV allele in familial Mediterranean fever  

PubMed Central

Background Familial Mediterranean fever (FMF) is the most frequent of the recurrent inherited fevers. This autosomal recessive disorder is characterised by periodic episodes of fever and serositis that commonly affect the people of Arab, Armenian, Sephardic Jewish and Turkish origin. Most of the described MEFV gene anomalies responsible for the disease are missense mutations. In the absence of any functional test, epidemiological studies or pedigree analyses are the only means of proving the deleterious character of these sequence variations. Evidence was provided by our recent study using a population?based approach, that the p.E148Q allele is probably a benign polymorphism and not a disease?causing mutation. Its implication in FMF remains, however, controversial. Objective To evaluate the segregation of the p.E148Q MEFV allele with FMF disease by using pedigree analysis. Participants 21 patients and 48 unaffected relatives belonging to 18 independent families with FMF. Results Segregation analysis of the p.E148Q allele was compatible with a Mendelian autosomal recessive transmission of the disease phenotype in only three families. In 15 of 18 families, segregation was partly or completely defective. The p.E148Q allele was not transmitted to 14 of 19 (74%) affected children. Conclusions No evidence of preferential transmission of p.E148Q from heterozygous parents to their affected offspring was observed. MEFV is not associated with the clinical manifestations of several patients carrying this variant. Considering p.E148Q to be a benign polymorphism should reduce the possibility of false?positive diagnoses, while highlighting genetic heterogeneity in FMF. PMID:16439437

Tchernitchko, D O; Gérard?Blanluet, M; Legendre, M; Cazeneuve, C; Grateau, G; Amselem, S

2006-01-01

330

Association of isozyme marker-genes on chromosome 6 with resistance to MDMV in maize  

E-print Network

Association of isozyme marker-genes on chromosome 6 with resistance to MDMV in maize D Ignjatovi&jadnr; D Ivanovi&jadnr;, B Tadi&jadnr; Maize Research Institute, Zemun Polje, Belgrade-Zemun, Serbia of Mdm1 on the maize chromosome map, isozymes of the chromosome 6 were used as genetic markers. Parental

Boyer, Edmond

331

Molecular markers closely linked to fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5  

Microsoft Academic Search

A population of 131 recombinant inbred lines from a wide cross between chickpea ( Cicer arietinum L., resistant parent) and Cicer reticulatum (susceptible parent) segregating for the closely linked resistances against Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on

A.-M. Benko-Iseppon; P. Winter; B. Huettel; C. Staginnus; F. J. Muehlbauer; G. Kahl

2003-01-01

332

Nomenclature for human CYP2D6 alleles.  

PubMed

To standardize CYP2D6 allele nomenclature, and to conform with international human gene nomenclature guidelines, an alternative to the current arbitrary system is described. Based on recommendations for human genome nomenclature, we propose that alleles be designated by CYP2D6 followed by an asterisk and a combination of roman letters and arabic numerals distinct for each allele with the number specifying the key mutation and, where appropriate, a letter specifying additional mutations. Criteria for classification as a separate allele and protein nomenclature are also presented. PMID:8807658

Daly, A K; Brockmöller, J; Broly, F; Eichelbaum, M; Evans, W E; Gonzalez, F J; Huang, J D; Idle, J R; Ingelman-Sundberg, M; Ishizaki, T; Jacqz-Aigrain, E; Meyer, U A; Nebert, D W; Steen, V M; Wolf, C R; Zanger, U M

1996-06-01

333

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys.  

PubMed

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

2015-01-01

334

Developing genome-wide microsatellite markers of bamboo and their applications on molecular marker assisted taxonomy for accessions in the genus Phyllostachys  

PubMed Central

Morphology-based taxonomy via exiguously reproductive organ has severely limitation on bamboo taxonomy, mainly owing to infrequent and unpredictable flowering events of bamboo. Here, we present the first genome-wide analysis and application of microsatellites based on the genome of moso bamboo (Phyllostachys edulis) to assist bamboo taxonomy. Of identified 127,593 microsatellite repeat-motifs, the primers of 1,451 microsatellites were designed and 1,098 markers were physically mapped on the genome of moso bamboo. A total of 917 markers were successfully validated in 9 accessions with ~39.8% polymorphic potential. Retrieved from validated microsatellite markers, 23 markers were selected for polymorphic analysis among 78 accessions and 64 alleles were detected with an average of 2.78 alleles per primers. The cluster result indicated the majority of the accessions were consistent with their current taxonomic classification, confirming the suitability and effectiveness of the developed microsatellite markers. The variations of microsatellite marker in different species were confirmed by sequencing and in silico comparative genome mapping were investigated. Lastly, a bamboo microsatellites database (http://www.bamboogdb.org/ssr) was implemented to browse and search large information of bamboo microsatellites. Consequently, our results of microsatellite marker development are valuable for assisting bamboo taxonomy and investigating genomic studies in bamboo and related grass species. PMID:25620112

Zhao, Hansheng; Yang, Li; Peng, Zhenhua; Sun, Huayu; Yue, Xianghua; Lou, Yongfeng; Dong, Lili; Wang, Lili; Gao, Zhimin

2015-01-01

335

Parent News Offline, 2001.  

ERIC Educational Resources Information Center

This document is comprised of the two issues in volume 3 of "Parent News Offline," a publication of the National Parent Information Network (NPIN) designed to introduce those without Internet access to the activities and information available through NPIN. The Spring 2001 issue contains the following articles: (1) "What To Consider in Starting a…

Robertson, Anne S., Ed.

2001-01-01

336

Rh Incompatibility (For Parents)  

MedlinePLUS

KidsHealth from Nemours for Parents for Kids for Teens Parents Home General Health Growth & Development Infections Diseases & Conditions Pregnancy & Baby Nutrition & Fitness Emotions & Behavior School & Family Life First Aid & Safety Doctors & Hospitals Q&A Recipes En Español Teachers - ...

337

Pneumocystis Pneumonia (For Parents)  

MedlinePLUS

KidsHealth from Nemours for Parents for Kids for Teens Parents Home General Health Growth & Development Infections Diseases & Conditions Pregnancy & Baby Nutrition & Fitness Emotions & Behavior School & Family Life First Aid & Safety Doctors & Hospitals Q&A Recipes En Español Teachers - ...

338

Parents and Nutrition.  

ERIC Educational Resources Information Center

Parents and the extended family are the most influential factors in the child's lifelong eating habits, general health and development, and brain power. Convincing parents of diet components that insure adequate nutrition is of prime importance; if the home does not support the content of the school's nutritional curriculum, the child may feel…

Boehnlein, Mary Maher

339

Parental Involvement in Education.  

ERIC Educational Resources Information Center

Initially, public education came into being in this country as a direct result of the efforts of parents. However, affluence in the 1950s resulted in less need for parental assistance in the schools. Since the 1950s, the erosion of the relationship between school and home has continued. The publication "A Nation at Risk: The Imperative for…

Kimmel, Carol

340

Parent Resources Inventory.  

ERIC Educational Resources Information Center

This resource guide provides an annotated bibliography of 101 articles and newsletters of interest to parents and teachers of children in preschool through grade 3. The bibliography contains the titles and short descriptions of materials, selected with the assistance of parents and teachers from across Alberta (Canada), on a wide range of topics…

Alberta Education Response Centre, Edmonton.

341

Parent Resources Inventory.  

ERIC Educational Resources Information Center

This resource inventory is for the use of parent groups and others who are concerned with parent education and support services. The inventory contains the titles of articles, copies of which are available through the Alberta Education Response Centre. The articles and publications listed cover a wide range of topics related to child development…

Alberta Education Response Centre, Edmonton.

342

Handling "Helicopter Parents"  

ERIC Educational Resources Information Center

Once upon a time, parents would help their children move into dorm rooms and apartments, then wave good-bye for the semester. Not anymore. Baby boomers have arguably been more involved in their children's educations--and their lives in general--than any preceding generation of parents, university observers say. And boomers see no reason why that…

Lum, Lydia

2006-01-01

343

Understanding the Parent's Perspective  

ERIC Educational Resources Information Center

Sally Smith's contribution to the world of children with learning disabilities is well documented, particularly by the other contributors to this journal. An area deserving attention, but one usually overlooked, is Smith's understanding of the parent's perspective--the challenges of parenting a child with learning disabilities. It was a priceless…

Tilley, Kim

2010-01-01

344

Parents, Peers and Pot.  

ERIC Educational Resources Information Center

This book looks at the problem of drug abuse, particularly the use of marihuana by children ages 9 to 14, and describes one strategy parents can use to prevent drug use by their children. On the premise that nonmedical drug use is not acceptable for children, parents need to provide guidance and exercise discipline with respect to drug use among…

Manatt, Marsha

345

Parents' Views on Leadership.  

ERIC Educational Resources Information Center

A survey of 73 parents, most having gifted children, examined perceptions of the development of leadership abilities. Parents identified: leader characteristics; their children's strongest and weakest areas of leadership skills; methods for encouraging leadership development; school opportunities for leadership experiences; the role of teachers,…

Meriweather, Suzanne; Karnes, Frances A.

1989-01-01

346

Pinterest for Parent Education  

ERIC Educational Resources Information Center

As more parents are using the Internet to answer their questions, Extension needs to provide practical, research-based resources in an accessible format. Pinterest is a platform that can be used by Extension educators to provide continued education and make reputable resources more discoverable for parents. Based on Knowles adult learning theory…

Routh, Brianna; Langworthy, Sara; Jastram, Hannah

2014-01-01

347

Exceptional Parent, 1993.  

ERIC Educational Resources Information Center

This document consists of the nine issues of the journal "Exceptional Parent" published during 1993. This journal contains articles particularly aimed at parents of children with disabilities. Major articles published during this period are the following: "Annual Guide to Products and Services"; "Coping with Incontinence" (Katherine F. Jeter);…

Klein, Stanley D., Ed.

1993-01-01

348

Partnering with Latino Parents  

ERIC Educational Resources Information Center

A growing body of research confirms that parents have a profound impact on their children's educational attainment, particularly in the secondary grades. Yet many Latino parents, particularly those of first-generation college students, lack information and knowledge about what their children need to prepare for college and are less likely to help…

Clark, Amy Aparicio; Dorris, Amanda

2007-01-01

349

Parent News Offline, 1999.  

ERIC Educational Resources Information Center

This document is comprised of the two issues published in volume 1 (1999) of "Parent News Offline," a newsletter of the National Parent Information Network (NPIN), designed to introduce those without Internet access to the activities and information available through NPIN. The spring 1999 issue contains the following articles: (1) "Child Care: How…

Robertson, Anne S., Ed.

1999-01-01

350

Popular Primers for Parents  

ERIC Educational Resources Information Center

The extent and characteristics of the parental audience for practical child care manuals are discussed. Information is integrated from four studies: a survey of child care publications; a questionnaire about sources of child care advice; a questionnaire distributed to readers of parenting books through the public library; and interviews with…

Clarke-Stewart, K. Alison

1978-01-01

351

Pointers for Parenting.  

ERIC Educational Resources Information Center

Presented are 11 brief articles designed to help parents enhance their children's school performance and generally improve the home environment. Included is information on the following topics: the role of the social worker in parent education, home activities to improve a child's reading skills, developing listening skill through instructional…

Bessant, Helen P., Ed.

352

Exceptional Parent, 1996.  

ERIC Educational Resources Information Center

Twelve 1996 issues of "Exceptional Parent" magazine provide a variety of articles and resources on parenting the child or young adult with a disability. The January issue is a resource guide, with directories of national organizations, associations, products, and services. The February issue focuses on early childhood, including articles on…

Klein, Stanley, Ed.

1996-01-01

353

Case-control study of allele frequencies of 15 short tandem repeat loci in males with impulsive violent behavior  

PubMed Central

Background Analysis of genetic polymorphisms in short tandem repeats (STRs) is an accepted method for detecting associations between genotype and phenotype but it has not previously been used in the study of the genetics of impulsive violent behavior. Objective Compare the prevalence of different polymorphisms in 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) between men with a history of impulsive violence and male control subjects without a history of impulsive violence. Methods The distributions of the alleles of the 15 STR loci were compared between 407 cases with impulsive violent behavior and 415 controls using AmpFlSTR® Identifiler™ kits. Results Compared to controls, the average frequencies of the following alleles were significantly lower in individuals with a history of violent behavior: allele 10 of TH01 (OR=0.29, 95%CI=0.16-0.52, p<0.0001,), allele 8 of TPOX (OR=0.71, 95%CI=0.58-0.86, p=0.0005), allele 9 of TPOX (OR=0.65, 95%CI=0.47-0.89, p=0.0072) and allele 14 of CSF1PO (OR=0.27, 95%CI=0.11-0.68, p=0.0035). One allele was significantly higher in cases than controls: allele 11 of TPOX (OR=1.79, 95%CI=1.45-2.22, p<0.0001). Conclusions To the best of our knowledge, this is the first behavioral genetic study that clearly demonstrates a close relationship between specific genetic markers and impulsive aggression in non-psychiatric offenders. Further prospective work will be needed to determine whether or not the alleles identified can be considered risk factors for impulsive aggression and, if so, the underlying mechanisms that result in this relationship. PMID:24991178

Yang, Chun; Ba, Huajie; Gao, Zhiqin; Zhao, Hanqing; Yu, Haiying; Guo, Wei

2013-01-01

354

Identification of 24 polymorphic microsatellite markers for the double-crested cormorant ( Phalacrocorax auritus )  

Microsoft Academic Search

Twenty-four polymorphic microsatellite markers were developed for the double-crested cormorant (Phalacrocorax auritus). The number of alleles ranged from two to 13 and observed heterozygosities ranged from 0.032 to 0.871. The use of these loci should enable researchers and biologists to learn more about the population structure and ecology of this species.

JENNIFER A. FIKE; TRAVIS L. DEVAULT; OLIN E. RHODES

2009-01-01

355

Identification of 24 polymorphic microsatellite markers for the double-crested cormorant (Phalacrocorax auritus).  

PubMed

Twenty-four polymorphic microsatellite markers were developed for the double-crested cormorant (Phalacrocorax auritus). The number of alleles ranged from two to 13 and observed heterozygosities ranged from 0.032 to 0.871. The use of these loci should enable researchers and biologists to learn more about the population structure and ecology of this species. PMID:21564869

Fike, Jennifer A; Devault, Travis L; Rhodes, Olin E

2009-07-01

356

Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii  

Microsoft Academic Search

Breeding for scab-resistant apple cultivars by pyramiding several resistance genes in the same genetic background is a promising way to control apple scab caused by the fungus Venturia inaequalis. To achieve this goal, DNA markers linked to the genes of interest are required in order to select seedlings with the desired resistance allele combinations. For several apple scab resistance genes,

M Gygax; L Gianfranceschi; M Kellerhals; C Gessler; A Patocchi

2004-01-01

357

A Study of Conservation Genetics in Cupressus chengiana , an Endangered Endemic of China, Using ISSR Markers  

Microsoft Academic Search

ISSR markers were used to analyze the genetic diversity and genetic structure of eight natural populations of Cupressus chengiana in China. ISSR analysis using 10 primers was carried out on 92 different samples. At the species level, 136 polymorphic loci were detected. The percentage of polymorphic bands (PPB) was 99%. Genetic diversity (H e) was 0.3120, effective number of alleles

Bingqing Hao; Wang Li; Mu Linchun; Yao Li; Zhang Rui; Tang Mingxia; Bao Weikai

2006-01-01

358

Characterization of twelve microsatellite markers for the native redbud tree (Cercis canadensis)  

Technology Transfer Automated Retrieval System (TEKTRAN)

Eight microsatellite DNA markers were developed for studies of gene flow in the redbud tree (Cercis canadensis), which is native to North America. The loci were unlinked and polymorphic in a sample of 22 individuals collected from a single population in Oak Ridge, Tennessee. Allele number ranged fr...

359

Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Genetic diversity of thirty five Psidium guajava accessions maintained at the USDA, National Plants Germplasm System, Hilo, HI, was characterized using 20 simple sequence repeat (SSR) markers. Diversity analysis detected a total of 178 alleles ranging from four to 16. The observed mean heterozygosit...

360

Development and characterization of twenty-five new polymorphic microsatellite markers in proso millet ( Panicum miliaceum L .)  

Microsoft Academic Search

Millets such as proso millet have excellent nutritional properties and could become a basic resource for crop breeding programs\\u000a and food diversification. In this study, 25 polymorphic microsatellite markers were developed and characterized through construction\\u000a of an SSR-enriched library from genomic DNA of proso millet (Panicum miliaceum L.). In total, 110 alleles were detected, with an average of 4.4 alleles

Young-Il Cho; Jong-Wook Chung; Gi-An Lee; Kyung-Ho Ma; Anupam Dixit; Jae-Gyun Gwag; Yong-Jin Park

2010-01-01

361

Imprinted chromosomal domains revealed by allele-specific replication timing of the GABRB3 and GABRA5 genes  

SciTech Connect

The GABRB3 and GABRA5 genes are organized as a cluster in chromosome 15q11-q13. The genes are separated by around 100 kb and arranged in opposite transcriptional orientations. The GABA{sub A} receptor cluster lies near the Angelman and Prader-Willi loci and displays asynchronous DNA replication, suggesting that this region is subject to parental imprinting. In order to further study the association between DNA replication and imprinting, allele-specific replication was assayed by fluorescence in situ hybridization with {lambda}-phage probes from the GABRB3/A5 region and a D15Z1 satellite probe to identify the parental origin of each chromosome. The replication kinetics of each allele was determined by using a flow sorter to fractionate mitogen-stimulated lymphocytes on the basis of cell cycle progression prior to FISH analysis. These kinetic studies reveal a 50-150 kb chromosomal domain extending from the middle of the GABRB3/A5 intergenic region into the GABRA5 5{prime}-UTR which displays maternal replication in early S with paternal replication delayed until the end of S. In contrast, genomic regions on either side of this maternal early replication domain exhibit the opposite pattern with paternal before maternal replication and both alleles replicating in the latter half of S. These results indicate that the GABRB3/A5 region is divided into domains in which replication timing is determined by parental origin. In addition to a loss of asynchronous replication, organization into replication timing domains is also lost in lymphocytes from maternal and paternal uniparental disomy 15 patients suggesting that a chromosome contribution from both parents is required for the establishment of the imprinted replication domains.

LaSalle, J.; Flint, A.; Lalande, M. [Harvard Medical School, Boston, MA (United States)] [and others

1994-09-01

362

IMMUNOLOGY AND MOLECULAR BIOLOGY Microsatellite Markers Linked to Salmonella enterica Serovar Enteritidis Vaccine Response in Young F1 Broiler-Cross Chicks1  

Microsoft Academic Search

Reduction in Salmonella enteritidis (SE) con- tamination is of importance for poultry production as well as for food safety. The objectives of this study were to identify potential genetic markers of antibody response to SE vaccine in young broiler chicks and then to confirm this linkage in broiler-cross offspring, as well as to explore interactions of marker alleles with dam

M. G. Kaiser; N. Deeb; S. J. Lamont

363

Selection, trans-species polymorphism, and locus identification of major histocompatibility complex class II?? alleles of New World ranid frogs  

USGS Publications Warehouse

Genes encoded by the major histocompatibility complex (MHC) play key roles in the vertebrate immune system. However, our understanding of the evolutionary processes and underlying genetic mechanisms shaping these genes is limited in many taxa, including amphibians, a group currently impacted by emerging infectious diseases. To further elucidate the evolution of the MHC in frogs (anurans) and develop tools for population genetics, we surveyed allelic diversity of the MHC class II ??1 domain in both genomic and complementary DNA of seven New World species in the genus Rana (Lithobates). To assign locus affiliation to our alleles, we used a "gene walking" technique to obtain intron 2 sequences that flanked MHC class II?? exon 2. Two distinct intron sequences were recovered, suggesting the presence of at least two class II?? loci in Rana. We designed a primer pair that successfully amplified an orthologous locus from all seven Rana species. In total, we recovered 13 alleles and documented trans-species polymorphism for four of the alleles. We also found quantitative evidence of selection acting on amino acid residues that are putatively involved in peptide binding and structural stability of the ??1 domain of anurans. Our results indicated that primer mismatch can result in polymerase chain reaction (PCR) bias, which influences the number of alleles that are recovered. Using a single locus may minimize PCR bias caused by primer mismatch, and the gene walking technique was an effective approach for generating single-copy orthologous markers necessary for future studies of MHC allelic variation in natural amphibian populations. ?? 2010 Springer-Verlag.

Kiemnec-Tyburczy, K. M.; Richmond, J.Q.; Savage, A.E.; Zamudio, K.R.

2010-01-01

364

Cell Surface Markers Group  

Cancer.gov

Posted: September 22, 2014 Posted: September 22, 2014 Cell Surface Markers Group Dr. Gordon Whiteley, Cell Surface Markers Group Lead Contact Dr. Gordon Whiteley301-228-4347whiteleg@mail.nih.gov Current Work Protein drugs (such as antibodies) are

365

Orientation Booklet for Parents Enrolled in Parent Education Cooperative Groups. Columbia Basin College Parent Education Program.  

ERIC Educational Resources Information Center

This booklet provides parents with information to help them get the most from their enrollment in parent education cooperative groups. Orientation information is presented for both the Parent Walkabout/Parent Toddler Programs and the Parent Cooperative Preschool Programs at Columbia Basin College (CBC), Washington. Informative material on the…

Debban, Barbara, Comp.; And Others

366

Fostered and left behind alleles in peanut: interspecific QTL mapping reveals footprints of domestication and useful natural variation for breeding  

PubMed Central

Background Polyploidy can result in genetic bottlenecks, especially for species of monophyletic origin. Cultivated peanut is an allotetraploid harbouring limited genetic diversity, likely resulting from the combined effects of its single origin and domestication. Peanut wild relatives represent an important source of novel alleles that could be used to broaden the genetic basis of the cultigen. Using an advanced backcross population developed with a synthetic amphidiploid as donor of wild alleles, under two water regimes, we conducted a detailed QTL study for several traits involved in peanut productivity and adaptation as well as domestication. Results A total of 95 QTLs were mapped in the two water treatments. About half of the QTL positive effects were associated with alleles of the wild parent and several QTLs involved in yield components were specific to the water-limited treatment. QTLs detected for the same trait mapped to non-homeologous genomic regions, suggesting differential control in subgenomes as a consequence of polyploidization. The noteworthy clustering of QTLs for traits involved in seed and pod size and in plant and pod morphology suggests, as in many crops, that a small number of loci have contributed to peanut domestication. Conclusion In our study, we have identified QTLs that differentiated cultivated peanut from its wild relatives as well as wild alleles that contributed positive variation to several traits involved in peanut productivity and adaptation. These findings offer novel opportunities for peanut improvement using wild relatives. PMID:22340522

2012-01-01

367

Development of microsatellite markers in Caryophyllaeus laticeps (Cestoda: Caryophyllidea), monozoic fish tapeworm, using next-generation sequencing approach.  

PubMed

Caryophyllaeus laticeps (Pallas 1781) (Cestoda: Caryophyllidea) is a monozoic tapeworm of cyprinid fishes with a distribution area that includes Europe, most of the Palaearctic Asia and northern Africa. Broad geographic distribution, wide range of definitive fish hosts and recently revealed high morphological plasticity of the parasite, which is not in an agreement with molecular findings, make this species to be an interesting model for population biology studies. Microsatellites (short tandem repeat (STR) markers), as predominant markers for population genetics, were designed for C. laticeps using a next-generation sequencing (NGS) approach. Out of 165 marker candidates, 61 yielded PCR products of the expected size and in 25 of the candidates a declared repetitive motif was confirmed by Sanger sequencing. After the fragment analysis, six loci were proved to be polymorphic and tested for heterozygosity, Hardy-Weinberg equilibrium and the presence of null alleles on 59 individuals coming from three geographically widely separated populations (Slovakia, Russia and UK). The number of alleles in particular loci and populations ranged from two to five. Significant deficit of heterozygotes and the presence of null alleles were found in one locus in all three populations. Other loci showed deviations from Hardy-Weinberg equilibrium and the presence of null alleles only in some populations. In spite of relatively low polymorphism and the potential presence of null alleles, newly developed microsatellites may be applied as suitable markers in population genetic studies of C. laticeps. PMID:25482859

Králová-Hromadová, Ivica; Minárik, Gabriel; Bazsalovicsová, Eva; Mikulí?ek, Peter; Oravcová, Alexandra; Pálková, Lenka; Hanzelová, Vladimíra

2014-12-01

368

INVESTIGATION Evidence for a Natural Allelic Series at the Maize  

E-print Network

INVESTIGATION Evidence for a Natural Allelic Series at the Maize Domestication Locus teosinte architecture and ear morphology between domesticated maize and teosinte; however, the effect of tb1 on trait teosinte alleles of tb1 that were introgressed into an isogenic maize inbred background. Our results

Doebley, John

369

Biased allelic expression in human primary fibroblast single cells.  

PubMed

The study of gene expression in mammalian single cells via genomic technologies now provides the possibility to investigate the patterns of allelic gene expression. We used single-cell RNA sequencing to detect the allele-specific mRNA level in 203 single human primary fibroblasts over 133,633 unique heterozygous single-nucleotide variants (hetSNVs). We observed that at the snapshot of analyses, each cell contained mostly transcripts from one allele from the majority of genes; indeed, 76.4% of the hetSNVs displayed stochastic monoallelic expression in single cells. Remarkably, adjacent hetSNVs exhibited a haplotype-consistent allelic ratio; in contrast, distant sites located in two different genes were independent of the haplotype structure. Moreover, the allele-specific expression in single cells correlated with the abundance of the cellular transcript. We observed that genes expressing both alleles in the majority of the single cells at a given time point were rare and enriched with highly expressed genes. The relative abundance of each allele in a cell was controlled by some regulatory mechanisms given that we observed related single-cell allelic profiles according to genes. Overall, these results have direct implications in cellular phenotypic variability. PMID:25557783

Borel, Christelle; Ferreira, Pedro G; Santoni, Federico; Delaneau, Olivier; Fort, Alexandre; Popadin, Konstantin Y; Garieri, Marco; Falconnet, Emilie; Ribaux, Pascale; Guipponi, Michel; Padioleau, Ismael; Carninci, Piero; Dermitzakis, Emmanouil T; Antonarakis, Stylianos E

2015-01-01

370

Tests and Estimates of Allelic Association in Complex Inheritance  

Microsoft Academic Search

Family-based procedures such as the transmission disequilibrium test (TDT) were motivated by concern that sample-based methods to map disease genes by allelic association are not robust to population stratification, migration, and admixture. Other factors to consider in designing a study of allelic association are specification of gene action in a weakly parametric model, efficiency, diagnostic reliability for hypernormal individuals, interest

N. E. Morton; A. Collins

1998-01-01

371

Observations Suggesting Allelism of the Achondroplasia and Hypochondroplasia Genes  

Microsoft Academic Search

It is argued that there are at least two alleles at the achondroplasia locus: one responsible for classic achondroplasia and one responsible for hypochondroplasia. Homozygosity for the achondroplasia gene produces a lethal skeletal dysplasia; homozygosity for hypochondroplasia has not been described. We report here a child considered to be a genetic compound for the achondroplasia and hypochondroplasia alleles.

Victor A. McKusick; Thaddeus E. Kelly; John P. Dorst

1973-01-01

372

Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat  

E-print Network

Tyrosinase and Tyrosinase Related Protein 1 Alleles Specify Domestic Cat Coat Color Phenotypes in domestic cat coat color, we determined the complete nucleotide coding sequence of the domestic cat genes microsatellite, previously found to be fixed in a cat breed selected for the chocolate (b) allele of the B locus

Eizirik, Eduardo

373

Effect of Glu-B3 Allelic Variation on Sodium Dodecyl Sulfate Sedimentation Volume in Common Wheat (Triticum aestivum L.)  

PubMed Central

Sodium dodecyl sulfate (SDS) sedimentation volume has long been used to characterize wheat flours and meals with the aim of predicting processing and end-product qualities. In order to survey the influence of low-molecular-weight glutenin subunits (LMW-GSs) at Glu-B3 locus on wheat SDS sedimentation volume, a total of 283 wheat (Triticum aestivum L.) varieties including landraces and improved and introduced cultivars were analyzed using 10 allele-specific PCR markers at the Glu-B3 locus. The highest allele frequency observed in the tested varieties was Glu-B3i with 21.9% in all varieties, 21.1% in landraces, 25.5% in improved cultivars, and 12% in introduced cultivars. Glu-B3 locus represented 8.6% of the variance in wheat SDS sedimentation volume, and Glu-B3b, Glu-B3g, and Glu-B3h significantly heightened the SDS sedimentation volume, but Glu-B3a, Glu-B3c, and Glu-B3j significantly lowered the SDS sedimentation volume. For the bread-making quality, the most desirable alleles Glu-B3b and Glu-B3g become more and more popular and the least desirable alleles Glu-B3a and Glu-B3c got less and less in modern improved cultivars, suggesting that wheat grain quality in China has been significantly improved through breeding effort. PMID:23861659

Zhao, Manli; He, Fuxia; Ma, Chuanxi

2013-01-01

374

Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus  

PubMed Central

With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ? 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ? 0.95) and monomorphic (0.95 ? 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

1980-01-01

375

A Set of Novel Microsatellite Markers Developed for Luculia yunnanensis (Rubiaceae), an Endangered Plant Endemic to Yunnan, China  

PubMed Central

The genus Luculia Sweet contains about five species of small trees or shrubs and is a member of the family Rubiaceae (tribe Cinchoneae). Luculia yunnanensis is an endangered ornamental shrub endemic to southwest China. Only two natural populations of L. yunnanensis exist in the wild according to our field investigation. It can be inferred that L. yunnanensis is facing a very high risk of extinction in the wild and an urgent conservation strategy is required. By using a modified biotin-sterptavidin capture method, 24 primer sets were identified in two wild populations. Of these primers, 11 displayed polymorphisms and 13 were monomorphic. The number of alleles per locus ranged from two to four, values for observed and expected heterozygosities ranged from 0.000 to 0.833 and from 0.431 to 0.771, with averages of 0.389 and 0.614, respectively. These markers will be useful for further investigation of conservation of resources, selecting parental types in cross-breeding, evolution of this species at the molecular level and related research in Luculia species. PMID:22312269

Ma, Hong; Wang, Lan; Wan, Youming; Li, Hongzhe; Li, Zhenghong; Liu, Xiuxian; Liang, Ning; Li, Wenjuan

2012-01-01

376

An association mapping approach to identify favourable alleles for tomato fruit quality breeding.  

PubMed

BackgroundGenome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits. In parallel, genotyping was carried out by using the Illumina Infinium SolCAP array, which allows data to be collected from 7,720 single nucleotide polymorphism (SNP) markers.ResultsThe Mixed Linear Model used to detect associations between markers and traits allowed population structure and relatedness to be evidenced within our collection, which have been taken into consideration for association analysis. GWAS identified 20 SNPs that were significantly associated with seven out of ten traits considered. In particular, our analysis revealed two markers associated with phenolic compounds, three with ascorbic acid, ß-carotene and trans-lycopene, six with titratable acidity, and only one with pH and fresh weight. Co-localization of a group of associated loci with candidate genes/QTLs previously reported in other studies validated the approach. Moreover, 19 putative genes in linkage disequilibrium with markers were found. These genes might be involved in the biosynthetic pathways of the traits analyzed or might be implied in their transcriptional regulation. Finally, favourable allelic combinations between associated loci were identified that could be pyramided to obtain new improved genotypes.ConclusionsOur results led to the identification of promising candidate loci controlling fruit quality that, in the future, might be transferred into tomato genotypes by Marker Assisted Selection or genetic engineering, and highlighted that intraspecific variability might be still exploited for enhancing tomato fruit quality. PMID:25465385

Ruggieri, Valentino; Francese, Gianluca; Sacco, Adriana; D Alessandro, Antonietta; Rigano, Maria; Parisi, Mario; Milone, Marco; Cardi, Teodoro; Mennella, Giuseppe; Barone, Amalia

2014-12-01

377

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria  

NASA Astrophysics Data System (ADS)

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain (`K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread.

Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O.; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M.; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

2014-01-01

378

A molecular marker of artemisinin-resistant Plasmodium falciparum malaria.  

PubMed

Plasmodium falciparum resistance to artemisinin derivatives in southeast Asia threatens malaria control and elimination activities worldwide. To monitor the spread of artemisinin resistance, a molecular marker is urgently needed. Here, using whole-genome sequencing of an artemisinin-resistant parasite line from Africa and clinical parasite isolates from Cambodia, we associate mutations in the PF3D7_1343700 kelch propeller domain ('K13-propeller') with artemisinin resistance in vitro and in vivo. Mutant K13-propeller alleles cluster in Cambodian provinces where resistance is prevalent, and the increasing frequency of a dominant mutant K13-propeller allele correlates with the recent spread of resistance in western Cambodia. Strong correlations between the presence of a mutant allele, in vitro parasite survival rates and in vivo parasite clearance rates indicate that K13-propeller mutations are important determinants of artemisinin resistance. K13-propeller polymorphism constitutes a useful molecular marker for large-scale surveillance efforts to contain artemisinin resistance in the Greater Mekong Subregion and prevent its global spread. PMID:24352242

Ariey, Frédéric; Witkowski, Benoit; Amaratunga, Chanaki; Beghain, Johann; Langlois, Anne-Claire; Khim, Nimol; Kim, Saorin; Duru, Valentine; Bouchier, Christiane; Ma, Laurence; Lim, Pharath; Leang, Rithea; Duong, Socheat; Sreng, Sokunthea; Suon, Seila; Chuor, Char Meng; Bout, Denis Mey; Ménard, Sandie; Rogers, William O; Genton, Blaise; Fandeur, Thierry; Miotto, Olivo; Ringwald, Pascal; Le Bras, Jacques; Berry, Antoine; Barale, Jean-Christophe; Fairhurst, Rick M; Benoit-Vical, Françoise; Mercereau-Puijalon, Odile; Ménard, Didier

2014-01-01

379

Identification and characterization of high-molecular-weight glutenin genes in Polish triticale cultivars by PCR-based DNA markers  

Microsoft Academic Search

Molecular markers were used to identify the allele\\/gene composition of complex lociGlu-A1 andGlu-B1 of high-molecular-weight (HMW) glutenin subunits in triticale cultivars. Forty-six Polish cultivars of both winter and spring\\u000a triticale were analysed with 7 PCR-based markers. Amplified DNA fragments of HMW gluteninGlu-1 genes were separated by agarose slab-gel electrophoresis. Differences between all 3 alleles at the locusGlu-A1 [Glu-A1a (encoding Ax1),1b

Boles?aw P. Salmanowicz; Monika Dylewicz

2007-01-01

380

Microsatellite markers for linkage and association studies.  

PubMed

During the 1990s and the first several years of this century, microsatellites or short tandem repeats were the workhorse genetic markers for hypothesis-independent studies in human genetics, facilitating genome-wide linkage studies and allelic imbalance studies. However, the rise of higher throughput and cost-effective single-nucleotide polymorphism (SNP) platforms led to the era of the SNP for genome scans. Nevertheless, it is important to note that microsatellites remain highly informative and useful measures of genomic variation for linkage and association studies. Their continued advantage in complementing SNPs lies in their greater allelic diversity than biallelic SNPs as well as in their population history, in which single-step expansion or contraction of the tandem repeat on the background of ancestral SNP haplotypes can break up common haplotypes, leading to greater haplotype diversity within the linkage disequilibrium block of interest. In fact, microsatellites have starred in association studies leading to widely replicated discoveries of type 2 diabetes (TCF7L2) and prostate cancer genes (the 8q21 region). At the end of the day, it will be important to catalog all variation, including SNPs, microsatellites, copy number variations, and polymorphic inversions in human genetic studies. This article describes the utilities of microsatellites and experimental approaches in their use. PMID:22474656

Gulcher, Jeffrey

2012-04-01

381

Sleepwalking (For Parents)  

MedlinePLUS

... pauses in breathing while sleeping) bedwetting (enuresis) night terrors Back Continue Is Sleepwalking Harmful? Sleepwalking itself is ... Kids For Parents MORE ON THIS TOPIC Night Terrors Nightmares Sleep Problems in Teens What Causes Night ...

382

Alpha Thalassemia (For Parents)  

MedlinePLUS

... of alpha thalassemia trait may want to seek genetic counseling if they're considering having children. If your ... For Parents MORE ON THIS TOPIC Genetic Testing Genetic Counseling All About Genetics Blood Blood Test: Hemoglobin Electrophoresis ...

383

Gay and Lesbian Parents  

MedlinePLUS

... in a civil union. The AAP supports civil marriage for all same sex parents who wish to ... of legal and economic security as does Civil Marriage. Children are interested in and affected by their ...

384

Single Parent Families  

MedlinePLUS

... be a more desirable circumstance than the tumultuous marriage that preceded it. Many single parents describe the ... having put the tension and dissension of their marriage behind them, and in making a new life ...

385

Enterovirus (For Parents)  

MedlinePLUS

... spread beyond the digestive tract can cause hand, foot, and mouth disease , hemorrhagic conjunctivitis (an infection of the eye), ... Parents MORE ON THIS TOPIC Coxsackievirus Infections Hand, Foot, and Mouth Disease Pinkeye (Conjunctivitis) What Are Germs? Why Is ...

386

Lactose Intolerance (For Parents)  

MedlinePLUS

... to Know Lactose Intolerance KidsHealth > Parents > Diseases & Conditions > Digestive System > Lactose Intolerance Print A A A Text Size ... Child Inflammatory Bowel Disease Irritable Bowel Syndrome (IBS) Digestive System About Recipes for Kids With Lactose Intolerance Lactose ...

387

Understanding Depression (For Parents)  

MedlinePLUS

... Word! Depression Bipolar Disorder Talking to Parents About Depression Stress & Coping Center Seasonal Affective Disorder Going to a Therapist Finding Low-Cost Mental Health Care 5 Ways to Fight Depression Posttraumatic Stress Disorder Cutting Death and Grief Depression ...

388

Gun Safety (For Parents)  

MedlinePLUS

... For Kids For Parents MORE ON THIS TOPIC School Violence and the News Childproofing and Preventing Household Accidents ... Your Child Gun Safety Should You Worry About School Violence? Someone at School Has a Weapon. What Should ...

389

Meningococcal Vaccine (For Parents)  

MedlinePLUS

... to Expect Ebola: What to Know Your Child's Immunizations: Meningococcal Vaccine KidsHealth > Parents > General Health > Your Kid's ... bacterial infection that can lead to bacterial meningitis . Immunization Schedule Vaccination is recommended: when kids are 11 ...

390

EMG (Electromyography) (For Parents)  

MedlinePLUS

... Checkups: What to Expect Ebola: What to Know EMG (Electromyogram) KidsHealth > Parents > General Health > Sick Kids > EMG ( ... muscular dystrophy and nerve disorders. How Is an EMG Done? Muscles are stimulated by signals from nerve ...

391

Parental Socialization of Emotion  

PubMed Central

Recently, there has been a resurgence of research on emotion, including the socialization of emotion. In this article, a heuristic model of factors contributing to the socialization of emotion is presented. Then literature relevant to the socialization of children’s emotion and emotion-related behavior by parents is reviewed, including (a) parental reactions to children’s emotions, (b) socializers’ discussion of emotion, and (c) socializers’ expression of emotion. The relevant literature is not conclusive and most of the research is correlational. However, the existing body of data provides initial support for the view that parental socialization practices have effects on children’s emotional and social competence and that the socialization process is bidirectional. In particular, parental negative emotionality and negative reactions to children’s expression of emotion are associated with children’s negative emotionality and low social competence. In addition, possible moderators of effects such as level of emotional arousal are discussed. PMID:16865170

Cumberland, Amanda; Spinrad, Tracy L.

2006-01-01

392

Living Now: For Parents  

MedlinePLUS

... most parents and kids are ready for the NG tube.” —Becky Manes, RN, MSN, CPON, BMT Coordinator, Vanderbilt ... more often, it could indicate that a nasogastric (NG) tube might be needed. An NG tube is a ...

393

Dinosaur Reproduction and Parenting  

NASA Astrophysics Data System (ADS)

Non-avian dinosaur reproductive and parenting behaviors were mostly similar to those of extant archosaurs. Non-avian dinosaurs were probably sexually dimorphic and some may have engaged in hierarchical rituals. Non-avian coelurosaurs (e.g. Troodontidae, Oviraptorosauria) had two active oviducts, each of which produced single eggs on a daily or greater time scale. The eggs of non-coelurosaurian dinosaurs (e.g. Ornithischia, Sauropoda) were incubated in soils, whereas the eggs of non-avian coelurosaurs (e.g. Troodon, Oviraptor) were incubated with a combination of soil and direct parental contact. Parental attention to the young was variable, ranging from protection from predators to possible parental feeding of nest-bound hatchlings. Semi-altricial hadrosaur hatchlings exited their respective nests near the time of their first linear doubling. Some reproductive behaviors, once thought exclusive to Aves, arose first in non-avian dinosaurs. The success of the Dinosauria may be related to reproductive strategies.

Horner, John R.

394

Diabetes Movie (For Parents)  

MedlinePLUS Videos and Cool Tools

... Crisp Choosing Safe Toys Checkups: What to Expect Ebola: What to Know Diabetes Movie KidsHealth > Parents > Diabetes ... purposes only. For specific medical advice, diagnoses, and treatment, consult your doctor. © 1995- The Nemours Foundation. All ...

395

Absence of the human CYP2C8*3 allele in Ugandan children exposed to Plasmodium falciparum malaria.  

PubMed

Study of host pharmacogenetics can improve our knowledge of mechanisms of drug resistance selection and spread. This issue has recently been addressed with respect to chloroquine and amodiaquine in malaria endemic areas of West and East Africa. Here we report, from surveys performed in two different areas of Uganda, that the human CYP2C8*3 allele, which had been reported to be strongly associated with parasite drug resistance in Zanzibar, is absent, being a marker of genetic admixture of the Zanzibari population with a Caucasoid component. Moreover, a retrospective analysis of CYP2C8*2 and the Plasmodium falciparum drug resistant pfmdr1 86Y allele does not show any association, which may be related to the high level of drug resistance. PMID:25183026

Paganotti, Giacomo Maria; Cosentino, Valentina; Russo, Gianluca; Tabacchi, Francesca; Gramolelli, Silvia; Coluzzi, Mario; Romano, Rita

2014-10-01

396

Foster Parent College: Interactive Multimedia Training for Foster Parents  

ERIC Educational Resources Information Center

Foster Parent College was recently developed through Northwest Media, Inc. as an interactive multimedia training venue for foster parents. Users can take brief parenting courses, either online (http://www.FosterParentCollege.com) or on DVD, on a variety of topics dealing with serious child behavior problems. Currently, these problems include…

Pacifici, Caesar; Delaney, Richard; White, Lee; Cummings, Kelli; Nelson, Carol

2005-01-01

397

Real Parents, Real Children: Parenting the Adopted Child.  

ERIC Educational Resources Information Center

Parenting an adopted child is, for the most part, the same as parenting any other child, but is different in some unique and critical ways related to the child's separation from birth parents and genetic roots. Understanding how a child interprets, understands, and feels about adoption, and why, can help the parent guide the adopted child…

van Gulden, Holly; Bartels-Rabb, Lisa M.

398

Stages of Parental Engagement in a Universal Parent Training Program  

ERIC Educational Resources Information Center

This paper reports findings on parental engagement in a community-based parent training intervention. As part of a randomized trial, 821 parents were offered group-based Triple P as a parenting skills prevention program. Program implementation was conducted by practitioners. The intervention was implemented between Waves 1 and 2 of a longitudinal…

Eisner, Manuel; Meidert, Ursula

2011-01-01

399

Implications of antisocial parents.  

PubMed

Antisocial behavior is a socially maladaptive and harmful trait to possess. This can be especially injurious for a child who is raised by a parent with this personality structure. The pathology of antisocial behavior implies traits such as deceitfulness, irresponsibility, unreliability, and an incapability to feel guilt, remorse, or even love. This is damaging to a child's emotional, cognitive, and social development. Parents with this personality makeup can leave a child traumatized, empty, and incapable of forming meaningful personal relationships. Both genetic and environmental factors influence the development of antisocial behavior. Moreover, the child with a genetic predisposition to antisocial behavior who is raised with a parental style that triggers the genetic liability is at high risk for developing the same personality structure. Antisocial individuals are impulsive, irritable, and often have no concerns over their purported responsibilities. As a parent, this can lead to erratic discipline, neglectful parenting, and can undermine effective care giving. This paper will focus on the implications of parents with antisocial behavior and the impact that this behavior has on attachment as well as on the development of antisocial traits in children. PMID:21293928

Torry, Zachary D; Billick, Stephen B

2011-12-01

400

Development of STS and CAPS markers for identification of three tall larkspurs (Delphinium spp.).  

PubMed

One cleaved amplified polymorphic sequence (CAPS) and nine sequence tagged site (STS) markers were developed for identifying tall larkspur (Delphinium spp.) plants in three species based on the DNA sequence of known species-specific RAPD markers. Four STS markers were used for identification of Delphinium occidentale, three STS markers for Delphinium barbeyi, and one CAPS and two STS markers for Delphinium glaucum. One hundred sixty-six individual plants collected at 19 locations in the western U.S.A. were tested using the STS and CAPS markers. Over 95% of the D. occidentale plants contained all four D. occidentale specific STS markers, whereas the remaining plants contained three of the four STS markers. Approximately 97% of D. barbeyi plants contained all three D. barbeyi specific STS markers, and the rest had two of the three STS markers. A small percentage of D. barbeyi plants contained one D. occidentale specific STS marker. Hybrid populations were characterized as having more D. occidentale specific than D. barbeyi specific STS markers, suggesting that the three hybrid populations are composed not of F1 hybrid plants of the parental species but of segregating offspring of different generations from original hybrids. This set of STS and CAPS markers for larkspur species should be useful in classification of unknown plant materials and the identification of hybrid populations. PMID:11962619

Li, Xiaomei; Gardner, Dale R; Ralphs, Michael H; Wang, Richard R C

2002-04-01

401

Parental Substance Use Impairment, Parenting and Substance Use Disorder Risk  

PubMed Central

Using data from a nationally representative sample, this study investigated substance use disorder (SUD) among respondents ages 15-54 as a function of their parents’ substance-related impairment and parents’ treatment history. Additionally, associations among maternal and paternal substance-related impairment, specific parenting behaviors, and the risk for SUD in the proband were examined. As expected, parental substance-related impairment was associated with SUD. Paternal treatment history was associated with a decreased risk for SUD in the proband, but did not appear to be associated with positive parenting practices. Results of post-hoc analyses suggested that parenting behaviors might operate differently to influence SUD risk in children where parents are affected by substance use problems compared to non-affected families. Future research is warranted to better understand the complex relationships among parental substance use, treatment, parenting behaviors, and SUD risk in offspring. Opportunities might exist within treatment settings to improve parenting skills. PMID:22112506

Arria, Amelia M.; Mericle, Amy A.; Meyers, Kathleen; Winters, Ken C.

2011-01-01

402

A Risk Allele for Nicotine Dependence in CHRNA5 Is a Protective Allele for Cocaine Dependence  

PubMed Central

Background A non-synonymous coding polymorphism, rs16969968, of the CHRNA5 gene which encodes the alpha-5 subunit of the nicotinic acetylcholine receptor (nAChR) has been found to be associated with nicotine dependence (20). The goal of the present study is to examine the association of this variant with cocaine dependence. Methods Genetic association analysis in two, independent samples of unrelated cases and controls; 1.) 504 European-American participating in the Family Study on Cocaine Dependence (FSCD); 2.) 814 European Americans participating in the Collaborative Study on the Genetics of Alcoholsim (COGA). Results In the FSCD, there was a significant association between the CHRNA5 variant and cocaine dependence (OR = 0.67 per allele, p = 0.0045, assuming an additive genetic model), but in the reverse direction compared to that previously observed for nicotine dependence. In multivariate analyses that controlled for the effects of nicotine dependence, both the protective effect for cocaine dependence and the previously documented risk effect for nicotine dependence were statistically significant. The protective effect for cocaine dependence was replicated in the COGA sample. In COGA, effect sizes for habitual smoking, a proxy phenotype for nicotine dependence, were consistent with those observed in FSCD. Conclusion The minor (A) allele of rs16969968, relative to the major G allele, appears to be both a risk factor for nicotine dependence and a protective factor for cocaine dependence. The biological plausibility of such a bidirectional association stems from the involvement of nAChRs with both excitatory and inhibitory modulation of dopamine-mediated reward pathways. PMID:18519132

Grucza, Richard A; Wang, Jen C.; Stitzel, Jerry A.; Hinrichs, Anthony L.; Saccone, Scott F.; Saccone, Nancy L.; Bucholz, Kathleen K.; Cloninger, C. Robert; Neuman, Rosalind J.; Budde, John P.; Fox, Louis; Bertelsen, Sarah; Kramer, John; Hesselbrock, Victor; Tischfield, Jay; Nurnberger, John. I.; Almasy, Laura; Porjesz, Bernice; Kuperman, Samuel; Schuckit, Marc A.; Edenberg, Howard J.; Rice, John P.; Goate, Alison M.; Bierut, Laura J.

2008-01-01

403

Parental origin of transcription from the human GNAS1 gene.  

PubMed Central

Variation in the phenotypic expression of Albright's hereditary osteodystrophy (AHO) determined by the parent of transmission, suggests that the human Gs alpha gene (GNAS1), in which mutations occur in AHO, may be under imprinted control. GNAS1 is also known to map to a chromosomal region (20q13.11) showing syntenic homology with the imprinted mouse region 2E1-2H3. To establish if GNAS1 is indeed imprinted, we have examined the parental origin of GNAS1 transcription in human fetal tissues. Of 75 fetuses genotyped, at gestational ages ranging from 6 to 13 weeks, 13 heterozygous for a FokI polymorphism in exon 5 of GNAS1 were identified whose mothers were homozygous for one or other allele. RNA from up to 10 different tissues from each fetus was analysed by RT-PCR. In all cases expression from both parental alleles was shown by FokI digestion of RT-PCR products and quantification of the resulting fragments. No tissue specific pattern of expression was discerned in these experiments. If genomic imprinting regulates the expression of the human GNAS1 gene, our data suggest that the effect must either be subtle and quantitative, or be confined to a small subset of specialised hormone responsive cells within the target tissues. Images PMID:7815417

Campbell, R; Gosden, C M; Bonthron, D T

1994-01-01

404

Generation of a Conditional Null Allele of Jumonji  

PubMed Central

Summary: The jumonji (jmj) gene plays important roles in multiple organ development in mouse, including cardiovascular development. Since JMJ is expressed widely during mouse development, it is essential that conditional knockout approaches be employed to ablate JMJ in a tissue-specific manner to identify the cell lineage specific roles of JMJ. In this report, we describe the establishment of a jmj conditional null allele in mice by generating a loxP-flanked (floxed) jmj allele, which allows the in vivo ablation of jmj via Cre recombinase-mediated deletion. Gene targeting was used to introduce loxP sites flanking exon 3 of the jmj allele to mouse embryonic stem cells. Our results indicate that the jmj floxed allele converts to a null allele in a heart-specific manner when embryos homozygous for the floxed jmj allele and carrying the ?-myosin heavy chain promoter-Cre transgene were analyzed by Southern and Northern blot analyses. Therefore, this mouse line harboring the conditional jmj null allele will provide a valuable tool for deciphering the tissue and cell lineage specific roles of JMJ. PMID:16900512

Mysliwiec, Matthew R.; Chen, Junqin; Powers, Patricia A.; Bartley, Christopher R.; Schneider, Michael D.; Lee, Youngsook

2007-01-01

405

Parenting Practices, Parenting Style, and Children’s School Achievement  

Microsoft Academic Search

This study, drawing on data from the 2002 Survey of Approaches to Educational Planning (SAEP), examined the predictive effects\\u000a of parenting practices and parenting style on children’s school achievement, and the predictive effects of parental expectations\\u000a and parental beliefs on parenting style for 6,626 respondents with children aged 5–18 years in Canada. Hierarchical multiple\\u000a regression analyses, after controlling for family socioeconomic

Shaljan Areepattamannil

2010-01-01

406

Allelic sequence heterozygosity in single Giardia parasites  

PubMed Central

Background Genetic heterogeneity has become a major inconvenience in the genotyping and molecular epidemiology of the intestinal protozoan parasite Giardia intestinalis, in particular for the major human infecting genotype, assemblage B. Sequence-based genotyping of assemblage B Giardia from patient fecal samples, where one or several of the commonly used genotyping loci (beta-giardin, triosephosphate isomerase and glutamate dehydrogenase) are implemented, is often hampered due to the presence of sequence heterogeneity in the sequencing chromatograms. This can be due to allelic sequence heterozygosity (ASH) and /or co-infections with parasites of different assemblage B sub-genotypes. Thus, two important questions have arisen; i) does ASH occur at the single cell level, and/or ii) do multiple sub-genotype infections commonly occur in patients infected with assemblage B, G. intestinalis isolates? Results We used micromanipulation in order to isolate single Giardia intestinalis, assemblage B trophozoites (GS isolate) and cysts from human patients. Molecular analysis at the tpi loci of trophozoites from the GS lineage indicated that ASH is present at the single cell level. Analyses of assemblage B Giardia cysts from clinical samples at the bg and tpi loci also indicated ASH at the single cell level. Additionally, alignment of sequence data from several different cysts that originated from the same patient yielded different sequence patterns, thus suggesting the presence of multiple sub-assemblage infections in congruence with ASH within the same patient. Conclusions Our results conclusively show that ASH does occur at the single cell level in assemblage B Giardia. Furthermore, sequence heterogeneity generated during sequence-based genotyping of assemblage B isolates may possess the complexity of single cell ASH in concurrence with co-infections of different assemblage B sub-genotypes. These findings explain the high abundance of sequence heterogeneity commonly found when performing sequence based genotyping of assemblage B Giardia, and illuminates the necessity of developing new G. intestinalis genotyping tools. PMID:22554281

2012-01-01

407

Active Parenting Now: Program Kit.  

ERIC Educational Resources Information Center

Based largely on the theories of Alfred Adler and Rudolf Dreikurs, this parent education curriculum is a video-based interactive learning experience that teaches a comprehensive model of parenting to parents of children ages 5 to 12 years. The kit provides parents with the skills needed to help their children develop courage, responsibility, and…

Popkin, Michael H.

408

Parents, Teens, and Online Privacy  

ERIC Educational Resources Information Center

Most parents of teenagers are concerned about what their teenage children do online and how their behavior could be monitored by others. Some parents are taking steps to observe, discuss, and check up on their children's digital footprints. A new survey of 802 parents and their teens shows that: (1) 81% of parents of online teens say they are…

Madden, Mary; Cortesi, Sandra; Gasser, Urs; Lenhart, Amanda; Duggan, Maeve

2012-01-01

409

Parent Perceptions of Children's Fears.  

ERIC Educational Resources Information Center

Examined fears of fifth grade students and ways in which their parents perceived the fears. Responses from 66 students and 47 parents suggest that children have more fears than parents think they have. Children reported concerns over accidents, nuclear war, and death, while parents expected children to have more fears about scary movies, the dark,…

Jones, Elizabeth A.; Borgers, Sherry

1988-01-01

410

Isolation and Characterization of 13 New Polymorphic Microsatellite Markers in the Phaseolus vulgaris L. (Common Bean) Genome  

PubMed Central

In this study, 13 polymorphic microsatellite markers were isolated from the Phaseolus vulgaris L. (common bean) by using the Fast Isolation by AFLP of Sequence COntaining Repeats (FIASCO) protocol. These markers revealed two to seven alleles, with an average of 3.64 alleles per locus. The polymorphic information content (PIC) values ranged from 0.055 to 0.721 over 13 loci, with a mean value of 0.492, and 7 loci having PIC greater than 0.5. The expected heterozygosity (HE) and observed heterozygosity (HO) levels ranged from 0.057 to 0.814 and from 0.026 to 0.531, respectively. Cross-species amplification of the 13 prime pairs was performed in its related specie of Vigna unguiculata L. Seven out of all these markers showed cross-species transferability. These markers will be useful for future genetic diversity and population genetics studies for this agricultural specie and its related species. PMID:23109846

Wang, Aihua; Ding, Yi; Hu, Zhenhua; Lin, Chufa; Wang, Shuzhen; Wang, Bingcai; Zhang, Hongyuan; Zhou, Guolin

2012-01-01

411

Characterization of microsatellite markers for the vulnerable grassland forb Senecio macrocarpus (Asteraceae)1  

PubMed Central

• Premise of the study: Development of microsatellite markers for the vulnerable forb Senecio macrocarpus was performed to begin an assessment of its population structure and breeding method to aid in the conservation of the species in Victoria, Australia. • Methods and Results: Fifteen microsatellite markers were developed for S. macrocarpus from 454 pyrosequencing. The markers were tested on 104 individuals from four populations. The markers produced between two and seven alleles per locus while the expected heterozygosity ranged from 0.20 to 0.67 and the observed heterozygosity ranged from 0.00 to 1.00. The observed heterozygosity is suggestive that the populations may be apomictic. • Conclusions: The microsatellite markers developed for S. macrocarpus are intended to be used on future studies that aim to assess the population genetics and local breeding dynamics of the species with an emphasis on conservation. PMID:25202496

Ahrens, Collin W.; James, Elizabeth A.

2013-01-01

412

The Use of Multiple Markers in a Bayesian Method for Mapping Quantitative Trait Loci  

PubMed Central

Information on multiple linked genetic markers was used in a Bayesian method for the statistical mapping of quantitative trait loci (QTL). Bayesian parameter estimation and hypothesis testing were implemented via Markov chain Monte Carlo algorithms. Variables sampled were the augmented data (marker-QTL genotypes, polygenic effects), an indicator variable for linkage or nonlinkage, and the parameters. The parameter vector included allele frequencies at the markers and the QTL, map distances of the markers and the QTL, QTL substitution effect, and polygenic and residual variances. The criterion for QTL detection was the marginal posterior probability of a QTL being located on the chromosome carrying the markers. The method was evaluated empirically by analyzing simulated granddaughter designs consisting of 2000 sons, 20 related sires, and their ancestors. PMID:8844168

Uimari, P.; Thaller, G.; Hoeschele, I.

1996-01-01

413

Rapid detection of autosomal aneuploidy using microsatellite markers  

SciTech Connect

Trisomy occurs in at least 4% of all clinically recognized pregnancies, making it the most common type of chromosome abnormality in humans. The most commonly occurring trisomies are those of chromosomes 13, 18, 21 and aneuploidy of X and Y, accounting for about 0.3% of all newborns and a much higher percentage of conceptuses. In Canada, prenatal chromosome analysis by amniocentesis is offered to those women {ge} 35 years of age at the time of delivery or equivalent risk by maternal serum screen. We are developing a rapid molecular diagnostic test to detect the most common autosomal aneuploidies in prenatal and neonatal samples. The tests makes use of highly polymorphic short tandem repeat markers labeled with fluorescent tags which allow analysis on a GENESCANNER automated fragment analyzer (ABI). Multiple polymorphic markers have been selected on each of chromosomes 13, 18 and 21. At a given locus, trisomic fetuses/neonates will have either three alleles or two alleles with one allele having twice the intensity of the other. Unaffected individuals have two equal intensity alleles. We are conducting a blind study that will compare the detection efficiencies of FISH analysis on uncultured cells and the molecular method on confirmation amniotic fluid samples collected at the time of termination of affected fetuses. Results on cultured amniocytes from one such patient confirmed that trisomy 21 can be detected. FISH was not done on this sample. In addition, detection efficiency of the molecular method in whole blood samples from affected neonates is also being studied. To date, two such samples have been tested, one with trisomy 13 and one with trisomy 18, and both samples were diagnosed correctly. Preliminary results suggest that this method may provide a valuable tool for the rapid diagnosis of aneuploidy.

Ray, P.N.; Teshima, I.E. [Hospital for Sick Children, Ontario (Canada); Winsor, E.J.T. [Toronto Hospital, Ontario (Canada)] [and others

1994-09-01

414

Phenotypic Diversity among Alleles at the PER-1 Locus of NEUROSPORA CRASSA  

PubMed Central

Comparison of 11 perithecial color mutants suggested that all were alleles at the per-1 locus but nonetheless separable into two groups because of phenotypic differences. Three of the mutant strains produced orange perithecia and black ascospores, and eight produced paler, yellow perithecia and white ascospores. Perithecial phenotype was dependent upon the genotype of the protoperithecial parent; ascospore phenotype, upon the genotype of the individual ascospore. No evidence was found that the white ascospores were due to chromosomal rearrangements. No separation of the perithecial and ascospore phenotypes by recombination was observed in a cross between one of the mutants and a per-1+ strain. However, apparent low levels of recombination in crosses between some of the mutants indicated possible genetic complexity at the per-1 locus. The phase specificity of the per-1 mutations and the possible nature and mode of expression of the orange and yellow perithecial pigments are discussed. PMID:131733

Howe, H. Branch; Johnson, T. E.

1976-01-01

415

HLA allele and haplotype frequencies in the Albanian population and their relationship with the other European populations.  

PubMed

Human leucocyte antigen (HLA) alleles are very interesting markers in identifying population relationships. Moreover, their frequency distribution data are important in the implementation of donor-recipient registry programs for transplantation purposes and also in determining the genetic predisposition for many diseases. For these reasons, we studied the HLA class I and II allele and haplotype frequencies in 160 healthy, unrelated Albanian individuals originating from all regions of the country. The HLA genotyping was performed through a 2-digit resolution SSOP method. The data were analysed with Arlequin and Phylip programs. No deviation was found from the Hardy-Weinberg equilibrium. A total of 17 A*, 30 B*, 12 Cw*, 13 DRB1* and 5 DQB1* alleles were identified. The six most frequent HLA-A-B-DRB1 haplotypes were A*02-B*18-DRB1*11 (5.60%), A*02-B*51-DRB1*16 (4.74%), A*01-B*08-DRB1*03 (3.48%), A*24-B*35-DRB1*11 (2.77%), A*02-B*51-DRB1*13 (2.21%), A*24-B*35-DRB1*14 (1.89%). Interestingly, 12 HLA-A-B-Cw-DRB1-DQB1 haplotypes occurred at a frequency >1%. When compared with the other populations, a close relationship was found with North Greek, Bulgarian, Macedonian, Romanian, Turkish, Cretan, Serbian, Croatian and Italian populations. A higher differentiation in allele frequency level was found with Western Europe populations. These data are the first report of HLA allele and haplotype distribution in an Albanian population inside this country. When compared with other populations, their distribution frequencies show close similarities with neighbouring populations of the entire Balkan area. PMID:19703234

Sulcebe, G; Sanchez-Mazas, A; Tiercy, J-M; Shyti, E; Mone, I; Ylli, Z; Kardhashi, V

2009-12-01

416

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

PubMed Central

Background A widely-used approach for screening nuclear DNA markers is to obtain sequence data and use bioinformatic algorithms to estimate which two alleles are present in heterozygous individuals. It is common practice to omit unresolved genotypes from downstream analyses, but the implications of this have not been investigated. We evaluated the haplotype reconstruction method implemented by PHASE in the context of phylogeographic applications. Empirical sequence datasets from five non-coding nuclear loci with gametic phase ascribed by molecular approaches were coupled with simulated datasets to investigate three key issues: (1) haplotype reconstruction error rates and the nature of inference errors, (2) dataset features and genotypic configurations that drive haplotype reconstruction uncertainty, and (3) impacts of omitting unresolved genotypes on levels of observed phylogenetic diversity and the accuracy of downstream phylogeographic analyses. Results We found that PHASE usually had very low false-positives (i.e., a low rate of confidently inferring haplotype pairs that were incorrect). The majority of genotypes that could not be resolved with high confidence included an allele occurring only once in a dataset, and genotypic configurations involving two low-frequency alleles were disproportionately represented in the pool of unresolved genotypes. The standard practice of omitting unresolved genotypes from downstream analyses can lead to considerable reductions in overall phylogenetic diversity that is skewed towards the loss of alleles with larger-than-average pairwise sequence divergences, and in turn, this causes systematic bias in estimates of important population genetic parameters. Conclusions A combination of experimental and computational approaches for resolving phase of segregating sites in phylogeographic applications is essential. We outline practical approaches to mitigating potential impacts of computational haplotype reconstruction on phylogeographic inferences. With targeted application of laboratory procedures that enable unambiguous phase determination via physical isolation of alleles from diploid PCR products, relatively little investment of time and effort is needed to overcome the observed biases. PMID:20429950

2010-01-01

417

‘Overgrowth’ mutants in barley and wheat: new alleles and phenotypes of the ‘Green Revolution’ Della gene  

PubMed Central

A suppressor screen using dwarf mutants of barley (Hordeum vulgare L.) led to the isolation of ‘overgrowth’ derivatives, which retained the original dwarfing gene but grew at a faster rate because of a new mutation. The new mutations were in the Slender1 (Sln1) gene (11/13 cases), which encodes the DELLA protein central to gibberellin (GA) signalling, showed 100% genetic linkage to Sln1 (1/13), or were in the Spindly1 (Spy1) gene (1/13), which encodes another protein involved in GA signalling. The overgrowth mutants were characterized by increased GA signalling, although the extent still depended on the background GA biosynthesis capacity, GA receptor function, and DELLA activity. A comparison between two GA responses, ?-amylase production and leaf growth rate, revealed degrees of specificity for both the overgrowth allele and the GA response under consideration. Many overgrowth mutants were also isolated in a dwarf line of bread wheat (Triticum aestivum L.) and 19 new alleles were identified in the Rht-B1 gene, one of the ‘Green Revolution’ semi-dwarfing genes and the orthologue of Sln1. The sites of amino acid substitutions in the DELLA proteins of both species provide insight into DELLA function, and included examples where identical but independent substitutions were observed. In both species, the starting lines were too dwarfed to be directly useful in breeding programmes, but new overgrowth derivatives with semidwarf heights have now been characterized. The variation they exhibit in GA-influenced traits identifies novel alleles with perfect markers that are of potential use in breeding. PMID:23382550

Chandler, Peter Michael

2013-01-01

418

Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions.  

PubMed

Influences of allelic variations in starch synthesis-related genes (SSRGs) on rice grain quality were examined. A total of 187 nonglutinous Korean rice varieties, consisting of 170 Japonica and 17 Tongil-type varieties, were grown in the field and in two greenhouse conditions. The percentages of head rice and chalky grains, amylose content, alkali digestion value, and rapid visco-analysis characteristics were evaluated in the three different environments. Among the 10 previously reported SSRG markers used in this study, seven were polymorphic, and four of those showed subspecies-specific allele distributions. Six out of the seven polymorphic SSRG markers were significantly associated with at least one grain quality trait (R (2) > 0.1) across the three different environments. However, the association level and significance were markedly lower when the analysis was repeated using only the 170 Japonica varieties. Similarly, the significant associations between SSRG allelic variations and changes in grain quality traits under increased temperature were largely attributable to the biased allele frequency between the two subpopulations. Our results suggest that within Korean Japonica varieties, these 10 major SSRG loci have been highly fixed during breeding history and variations in grain quality traits might be influenced by other genetic factors. PMID:24987303

Mo, Young-Jun; Jeung, Ji-Ung; Shin, Woon-Chul; Kim, Ki-Young; Ye, Changrong; Redoña, Edilberto D; Kim, Bo-Kyeong

2014-06-01

419

Effects of allelic variations in starch synthesis-related genes on grain quality traits of Korean nonglutinous rice varieties under different temperature conditions  

PubMed Central

Influences of allelic variations in starch synthesis-related genes (SSRGs) on rice grain quality were examined. A total of 187 nonglutinous Korean rice varieties, consisting of 170 Japonica and 17 Tongil-type varieties, were grown in the field and in two greenhouse conditions. The percentages of head rice and chalky grains, amylose content, alkali digestion value, and rapid visco-analysis characteristics were evaluated in the three different environments. Among the 10 previously reported SSRG markers used in this study, seven were polymorphic, and four of those showed subspecies-specific allele distributions. Six out of the seven polymorphic SSRG markers were significantly associated with at least one grain quality trait (R2 > 0.1) across the three different environments. However, the association level and significance were markedly lower when the analysis was repeated using only the 170 Japonica varieties. Similarly, the significant associations between SSRG allelic variations and changes in grain quality traits under increased temperature were largely attributable to the biased allele frequency between the two subpopulations. Our results suggest that within Korean Japonica varieties, these 10 major SSRG loci have been highly fixed during breeding history and variations in grain quality traits might be influenced by other genetic factors. PMID:24987303

Mo, Young-Jun; Jeung, Ji-Ung; Shin, Woon-Chul; Kim, Ki-Young; Ye, Changrong; Redoña, Edilberto D.; Kim, Bo-Kyeong

2014-01-01

420

LDLR, GYPA, HBGG, D7S8 and GC allele and genotype frequencies in the northwest Italian population.  

PubMed

Allele and genotype frequencies for five PCR-based DNA markers (LDLR, GYPA, HBGG, D7S8 and GC) were determined in 100 unrelated individuals from Piedmont (Northwest Italy). All five Ioci met Hardy-Weinberg expectations in the sampled population. The combined PD and CE were, respectively, 0.995 and 0.697. Frequencies obtained were compared with other previously published data on Caucasian populations with no significant differences. The genetic data from this study, in addition to those already collected by other groups, contribute to the expansion of the Italian DNA database suitable for forensic casework and paternity testing. PMID:9987883

Gino, S; Robino, C; Torre, C; Iorio, M; Peruccio, D

1999-01-01