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At least 1,783 records · Page 99Linked to original sources
PubMed2005

QTLs for enzyme activities and soluble carbohydrates involved in starch accumulation during grain filling in maize.

ADPglucose, the essential substrate for starch synthesis, is synthesized in maize by a pathway involving at least invertases, sucrose synthase, and ADPglucose pyrophosphorylase, as shown by the starch-deficient mutants, mn1, sh1, and bt2 or sh2, respectively. To improve understanding of the relationship between early grain-filling traits and carbohydrate composition in mature grain, QTLs linked to soluble invertase, sucrose synthase, and ADPglucose pyrophosphorylase activities and to starch, sucrose, fructose, and glucose concentrations were investigated. In order to take into account the specific time-course of each enzyme activity during grain filling, sampling was carried out at three periods (15, 25, and 35 d after pollination) on 100 lines from a recombinant inbred family, grown in the field. The MQTL method associated with QTL interaction analysis revealed numerous QTLs for all traits, but only one QTL was consistently observed at the three sampling periods. Some chromosome zones were heavily labelled, forming clusters of QTLs. Numerous possible candidate genes of the starch synthetic pathway co-located with QTLs. Four QTLs were found close to the locus Sh1 (bin 9.01) coding for the sucrose synthase. In order to confirm the importance of this locus, the CAPS polymorphism of the Sh1 gene was analysed in 45 genetically unrelated maize lines from various geographical origins. The DNA polymorphism was significantly associated with phenotypic traits related to grain filling (starch and amylose content, grain matter, and ADPglucose pyrophosphorylase activity at 35 DAP). Thus, the Sh1 locus could provide a physiologically pertinent marker for maize selection.

Carbohydrate Metabolism↗
PubMed2005

A test of the master gene hypothesis for interspersed repetitive DNA sequences.

Many families of interspersed repetitive DNA elements, including human Alu and LINE (Long Interspersed Element) elements, have been proposed to have accumulated through repeated copying from a single source locus: the "master gene." The extent to which a master gene model is applicable has implications for the origin, evolution, and function of such sequences. One repetitive element family for which a convincing case for a master gene has been made is the rodent ID (identifier) elements. Here we devise a new test of the master gene model and use it to show that mouse ID element sequences are not compatible with a strict master gene model. We suggest that a single master gene is rarely, if ever, likely to be responsible for the accumulation of any repeat family.

Alu Elements↗
PubMed2005

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Molecular genetics of natural populations.

Significant progress in evolutionary genetics has been made by studying, on the one hand, patterns of DNA sequence polymorphism and, on the other, genetic architecture of complex adaptive traits. However, connections between nucleotide variants under selection and adaptively relevant phenotypes are missing. Such connections can be established using precise gene replacement. We review the recent successful introduction of this technique to the analysis of two evolutionarily interesting loci--Odysseus and desaturase2. Both genes have subtle phenotypes that nevertheless could be identified using gene replacement, demonstrating that effects of naturally occurring alleles can be measured in the laboratory. This is an important first step in connecting statistical signatures of selection with adaptation in nature. More candidate genes involved in adaptation, for example, through cloning of genes responsible for reproductive isolation, now need to be identified. Molecular genetic manipulation, DNA polymorphism analysis, and field studies then have to be integrated to provide fresh insights into the mechanisms of evolutionary change.

Alleles↗
PubMed2003

GrainGenes, the genome database for small-grain crops.

GrainGenes, http://www.graingenes.org, is the international database for the wheat, barley, rye and oat genomes. For these species it is the primary repository for information about genetic maps, mapping probes and primers, genes, alleles and QTLs. Documentation includes such data as primer sequences, polymorphism descriptions, genotype and trait scoring data, experimental protocols used, and photographs of marker polymorphisms, disease symptoms and mutant phenotypes. These data, curated with the help of many members of the research community, are integrated with sequence and bibliographic records selected from external databases and results of BLAST searches of the ESTs. Records are linked to corresponding records in other important databases, e.g. Gramene's EST homologies to rice BAC/PACs, TIGR's Gene Indices and GenBank. In addition to this information within the GrainGenes database itself, the GrainGenes homepage at http://wheat.pw.usda.gov provides many other community resources including publications (the annual newsletters for wheat, barley and oat, monographs and articles), individual datasets (mapping and QTL studies, polymorphism surveys, variety performance evaluations), specialized databases (Triticeae repeat sequences, EST unigene sets) and pages to facilitate coordination of cooperative research efforts in specific areas such as SNP development, EST-SSRs and taxonomy. The goal is to serve as a central point for obtaining and contributing information about the genetics and biology of these cereal crops.

Alleles↗
PubMed2005

Broiler breeding strategies using indirect carcass measurements.

The objective of the current study was to determine the consequences of using indirect carcass measurements on the genetic response and rate of inbreeding in broiler breeding programs. In the base breeding scheme, selection candidates were evaluated based on direct carcass measurements on relatives. The possibilities of using indirect carcass measurements were investigated in alternative breeding schemes. Three alternative schemes, including indirect and own performance information for carcass traits on selection candidates, were evaluated by deterministic simulation. In the first scheme, indirect carcass traits were measured on male selection candidates. In the second scheme, indirect carcass traits were measured on male selection candidates, and direct carcass traits were measured on relatives. In the third scheme, indirect carcass traits were measured on male and female selection candidates, and direct carcass traits were measured on relatives. In the base scheme, the genetic response for breast muscle percentage (BMP) was 0.3%, and the rate of inbreeding was 0.96% per generation. In the third alternative scheme, the response for BMP increased by 66.2% compared with the base scheme, and the rate of inbreeding decreased to 0.79% per generation. The improved genetic gain resulted from increased accuracy of selection. The use of own performance information for selection candidates reduced the rate of inbreeding in alternative schemes, which is desirable for long-term selection. The accuracy of the indirect carcass measurements had consequences on the response for BMP and the rate of inbreeding. In most cases, an accuracy of 30% was sufficient to result in a higher gain for BMP and a lower rate of inbreeding as compared with the base scheme.

Animals↗
PubMed1990

Cancer models and cancer genetics.

There have been many attempts to develop stochastic multistage models for cancer. The models relate hypothesized biological processes occurring at the cellular level to the occurrence of tumors at the experimental or epidemiologic level of individuals in a population. The existing models fit a variety of data, but none is fully satisfactory and they are in some ways inconsistent with each other. Recently, substantial new data have become available on the nature of cancer-associated mutations observed directly at the cellular level. These data suggest that the number of stages may be greater and more variable among individual tumors of the same organ than has been thought. There may be many pathways to cancer, and the mutations responsible may not constitute a fixed set or sequence. This pattern resembles the genetics of quantitative rather than qualitative traits, and may also be consistent with the variable histology and behavior of tumors of a given organ. Simulations using such models suggest that cancer in the general population may have such heterogeneous etiology, a possibility that has important implications for screening, risk projection, and prevention. Risk-generating processes of a rather generic kind may generate similar hazard functions for diverse chronic diseases in the age ranges often used in epidemiologic studies. This phenomenon raises questions about the purpose and interpretation of statistical epidemiologic models.

Humans↗
PubMed1997

Familial determinants of moderate and intense physical activity: a twin study.

This twin study estimates familial clustering of moderate and intense leisure-time physical activity and investigates quantitatively its genetic and environmental components. Study subjects are 3,344 male twin pairs aged 33-51 yr. Moderate activity levels were assessed with six questions about discretionary walking or stair climbing for exercise. Five questions assessed regular participation in specific, intense athletic activities (running, bicycling, swimming, racquet, and other sports). Familial aggregation is estimated by odds ratio of one twin engaging in an activity when his co-twin does. Monozygotic and dizygotic twin correlations were compared to estimate genetic and nongenetic sources of phenotypic variation. For each activity, the familial aggregation odds ratio was statistically significant with values between 2.9 to 4.6 for intense activities and between 1.4 to 1.9 for all moderate activities but one. Monozygotic twin correlations were higher than dizygotic, suggesting genes play a role in the observed phenotypic variation. For four questions, and a compromise scale of moderate activity, the difference between correlations was statistically significant (P < 0.05). In this cohort, much of the phenotypic variability for both moderate and intense activities is a result of familial effects. Genes may influence regular participation in specific intense exercises more than moderate activity, such as walking for exercise.

Adult↗
PubMed2002

Association study of alcoholism subtypes with a functional promoter polymorphism in the serotonin transporter protein gene.

BACKGROUND: Association studies of a reportedly functional polymorphism in the promoter region (5'-HTTLPR) of the gene encoding the serotonin transporter protein (genetic locus SLC6A4) in alcoholics have yielded conflicting results. The most frequently observed alleles of the 5'-HTTLPR polymorphism are the short and long variants; the short variant is associated with lower transcriptional activity of the SLC6A4 gene than is the long variant. To reduce the heterogeneity that may confound association studies of alcohol dependence, we examined the association of 5'-HTTLPR alleles with three dichotomous typologies of alcoholism based on sex, comorbid drug dependence, or age of onset of alcohol dependence. METHODS: A sample of 471 alcohol-dependent subjects [363 European Americans (EAs) and 108 African Americans (AAs)] and 235 control subjects (192 EAs and 43 AAs) were included in the analyses. Alcohol dependence diagnoses were made using a structured interview. DNA isolated from whole blood was PCR-amplified, and genotypes were assigned on the basis of agarose gel size fractionation. RESULTS: Although allele frequencies differed significantly by population, there was no evidence of differences by diagnosis or as a function of any of the three subtypes. CONCLUSIONS: Variable findings in the literature in relation to the association of 5'-HTTLPR alleles to alcohol dependence seem to be due to factors other than the composition of study samples in terms of univariate typologies based on sex, comorbid drug dependence, or age of onset of alcohol dependence.

Adult↗
PubMed2004

Confirmation and genetic dissection of a major quantitative trait locus for alcohol preference drinking.

OBJECTIVE: In previous work, we created congenic strains that carry the DBA/2IBG (D2) region for alcohol preference on chromosome 2, on an otherwise C57BL/6IBG (B6) background. Here, we report construction and testing of interval-specific congenic recombinant strains (ISCRSs) for the purpose of narrowing the quantitative trait loci (QTL) interval. METHODS: ISCRSs were derived by identifying mice that carry recombination events in the D2 interval, during the backcrossing for congenics. Recombinant mice were backcrossed to B6, and progeny that carry the reduced chromosome 2 region were tested for its effect on the alcohol preference phenotype. RESULTS: We developed multiple ISCR strains, which spanned the QTL interval. Three of these showed the D2 phenotype of reduced alcohol consumption. The overlap of two of these strains reduced the QTL interval from 66.8 to 3.5 Mb. A third positive ISCRS suggests the possibility of a second, linked QTL. CONCLUSIONS: Use of ISCRSs can narrow a QTL region to a few Mb. This reduced interval size will facilitate identification of candidate genes, through bioinformatics, gene expression, and DNA sequencing strategies. Potential difficulties, including reduced power as a result of variable phenotypes or small effect size, are discussed.

Alcohol Drinking↗
PubMed2006

The COX-2 G/C -765 polymorphism may modulate the occurrence of cerebrovascular ischemia.

In the atherosclerotic plaque, cyclooxygenase-2 (COX-2) catalyzes prostaglandin E formation, which acts as a pro-atherogenic factor. A polymorphism, G/C -765, within the COX-2 promoter region modulates gene expression and the risk of cerebrovascular disease. We have evaluated the relation between COX-2 G/C -765 genotypes and the occurrence of cerebrovascular ischemia. We evaluated the COX-2 G/C -765 polymorphism in 110 consecutive patients with a documented history of acute ischemic cerebrovascular disease, in 110 age-matched and sex-matched subjects without such history, and in a general population (n = 324) from the same ethnical background. The frequency of the COX-2 -765C allele in patients [0.21; 95% confidence interval (CI), 0.16-0.26] was similar to those found in controls (0.28; 95% CI, 0.22-0.34) and in the general population (0.26; 95% CI, 0.23-0.29). Carriers of the CC genotype differed between patients (0.02; 95% CI, 0.00-0.05) and controls [0.10 (95% CI, 0.04-0.16), P = 0.019; odds ratio, 0.17 (95% CI, 0.04-0.79)] or the general population [0.08 (95% CI, 0.05-0.11), P = 0.023; odds ratio, 0.22 (95% CI, 0.05-0.95)]. In a multiple logistic regression analysis adjusted for confounding variables, smoking status (P < 0.001), atrial fibrillation (P = 0.004) and COX-2 G/C-765 polymorphism (P = 0.016) independently contributed to cerebrovascular ischemia, with CC carriers exhibiting a lower risk (odds ratio, 0.07; 95% CI, 0.01-0.61). Our data show an association between the COX-2 G/C-765 gene polymorphism and cerebrovascular ischemia, suggesting that the COX-2 gene is a susceptibility locus for the risk of cerebrovascular ischemic disease.

Adult↗
PubMed2003

Automated detection of informative combined effects in genetic association studies of complex traits.

There is a growing body of evidence suggesting that the relationships between gene variability and common disease are more complex than initially thought and require the exploration of the whole polymorphism of candidate genes as well as several genes belonging to biological pathways. When the number of polymorphisms is relatively large and the structure of the relationships among them complex, the use of data mining tools to extract the relevant information is a necessity. Here, we propose an automated method for the detection of informative combined effects (DICE) among several polymorphisms (and nongenetic covariates) within the framework of association studies. The algorithm combines the advantages of the regressive approaches with those of data exploration tools. Importantly, DICE considers the problem of interaction between polymorphisms as an effect of interest and not as a nuisance effect. We illustrate the method with three applications on the relationship between (1). the P-selectin gene and myocardial infarction, (2). the cholesteryl ester transfer protein gene and plasma high-density-lipoprotein cholesterol concentration, and (3). genes of the renin-angiotensin-aldosterone system and myocardial infarction. The applications demonstrated that the method was able to recover results already found using other approaches, but in addition detected biologically sensible effects not previously described.

Algorithms↗
PubMed2006

Informational structure of two closely related eukaryotic genomes.

Attempts to identify a species on the basis of its DNA sequence on purely statistical grounds have been formulated for more than a decade. The most prominent of such genome signatures relies on neighborhood correlations (i.e., dinucleotide frequencies) and, consequently, attributes species identification to mechanisms operating on the dinucleotide level (e.g., neighbor-dependent mutations). For the examples of Mus musculus and Rattus norvegicus we analyze short- and intermediate-range statistical correlations in DNA sequences. These correlation profiles are computed for all chromosomes of the two species. We find that with increasing range of correlations the capacity to distinguish between the species on the basis of this correlation profile is getting better and requires ever shorter sequence segments for obtaining a full species separation. This finding suggests that distinctive traits within the sequence are situated beyond the level of few nucleotides. The large-scale statistical patterning of DNA sequences on which such genome signatures are based is thus substantially determined by mobile elements (e.g., transposons and retrotransposons). The study and interspecies comparison of such correlation profiles can, therefore, reveal features of retrotransposition, segmental duplications, and other processes of genome evolution.

Animals↗
PubMed2006

Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.

Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

Amino Acid Sequence↗
PubMed2005

Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures.

We have examined the phenotype of different KIT genotypes with regard to coat colour and several blood parameters (erythrocyte numbers and measures, total and differential leucocyte numbers, haematocrit and haemoglobin levels and serum components). The effect of two different iron supplement regimes (one or two iron injections) on the blood parameters was also examined. For a total of 184 cross-bred piglets (different combinations of Hampshire, Landrace and Yorkshire) blood parameters were measured four times during their first month of life, and the KIT genotypes of these and 70 additional cross-bred piglets were determined. Eight different KIT genotypes were identified, which confirms the large allelic diversity at the KIT locus in commercial pig populations. The results showed that pigs with different KIT genotypes differ both in coat colour and in haematological parameters. In general, homozygous Dominant white (I/I) piglets had larger erythrocytes with lower haemoglobin concentration, indicating a mild macrocytic anaemia. The effect of two compared with one iron injection was also most pronounced for the I/I piglets.

Animals↗
PubMed2006

Novel integrative genomics strategies to identify genes for complex traits.

Forward genetics is a common approach to dissecting complex traits like common human diseases. The ultimate aim of this approach was the identification of genes that are causal for disease or other phenotypes of interest. However, the forward genetics approach is by definition restricted to the identification of genes that have incurred mutations over the course of evolution or that incurred mutations as a result of chemical mutagenesis, and that as a result lead to disease or to variations in other phenotypes of interest. Genes that harbour no such mutations, but that play key roles in parts of the biological network that lead to disease, are systematically missed by this class of approaches. Recently, a class of novel integrative genomics approaches has been devised to elucidate the complexity of common human diseases by intersecting genotypic, molecular profiling, and clinical data in segregating populations. These novel approaches take a more holistic view of biological systems and leverage the vast network of gene-gene interactions, in combination with DNA variation data, to establish causal relationships among molecular profiling traits and between molecular profiling and disease (or other classic phenotypes). A number of novel genes for disease phenotypes have been identified as a result of these approaches, highlighting the utility of integrating orthogonal sources of data to get at the underlying causes of disease.

Animals↗