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PubMed2006

Identification of QTL and association of a phytoene synthase gene with endosperm colour in durum wheat.

The yellow colour of durum wheat (Triticum turgidum L. var durum) semolina is due in part to the presence of carotenoid pigments found in the endosperm and is an important end-use quality trait. We hypothesized that variation in the genes coding for phytoene synthase (Psy), a critical enzyme in carotenoid biosynthesis, may partially explain the phenotypic variation in endosperm colour observed among durum cultivars. Using rice sequence information, primers were designed to PCR clone and sequence the Psy genes from Kofa (high colour) and W9262-260D3 (medium colour) durum cultivars. Sequencing confirmed the presence of four Psy genes in each parent, corresponding to a two member gene family designated as Psy1-1, Psy1-2 and Psy2-1 and Psy2-2. A genetic map was constructed using 155 F1-derived doubled haploid lines from the cross W9262-260D3/Kofa with 194 simple sequence repeat and DArT markers. Using Psy1-1 and Psy2-1 allele-specific markers and chromosome mapping, the Psy1 and Psy2 genes were located to the group 7 and 5 chromosomes, respectively. Four quantitative trait loci (QTL) underlying phenotypic variation in endosperm colour were identified on chromosomes 2A, 4B, 6B, and 7B. The Psy1-1 locus co-segregated with the 7B QTL, demonstrating an association of this gene with phenotypic variation for endosperm colour. This work is the first report of mapping Psy genes and supports the role of Psy1-1 in elevated levels of endosperm colour in durum wheat. This gene is a target for the further development of a molecular marker to enhance selection for endosperm colour in durum wheat breeding programs.

Alkyl and Aryl Transferases↗
PubMed2005

Quantitative trait nucleotide analysis using Bayesian model selection.

Although much attention has been given to statistical genetic methods for the initial localization and fine mapping of quantitative trait loci (QTLs), little methodological work has been done to date on the problem of statistically identifying the most likely functional polymorphisms using sequence data. In this paper we provide a general statistical genetic framework, called Bayesian quantitative trait nucleotide (BQTN) analysis, for assessing the likely functional status of genetic variants. The approach requires the initial enumeration of all genetic variants in a set of resequenced individuals. These polymorphisms are then typed in a large number of individuals (potentially in families), and marker variation is related to quantitative phenotypic variation using Bayesian model selection and averaging. For each sequence variant a posterior probability of effect is obtained and can be used to prioritize additional molecular functional experiments. An example of this quantitative nucleotide analysis is provided using the GAW12 simulated data. The results show that the BQTN method may be useful for choosing the most likely functional variants within a gene (or set of genes). We also include instructions on how to use our computer program, SOLAR, for association analysis and BQTN analysis.

Bayes Theorem↗
PubMed2000

Application of genetic algorithms for the design of ozone control strategies.

Designing air quality management strategies is complicated by the difficulty in simultaneously considering large amounts of relevant data, sophisticated air quality models, competing design objectives, and unquantifiable issues. For many problems, mathematical optimization can be used to simplify the design process by identifying cost-effective solutions. Optimization applications for controlling nonlinearly reactive pollutants such as tropospheric ozone, however, have been lacking because of the difficulty in representing nonlinear chemistry in mathematical programming models. We discuss the use of genetic algorithms (GAs) as an alternative optimization approach for developing ozone control strategies. A GA formulation is described and demonstrated for an urban-scale ozone control problem in which controls are considered for thousands of pollutant sources simultaneously. A simple air quality model is integrated into the GA to represent ozone transport and chemistry. Variations of the GA formulation for multiobjective and chance-constrained optimization are also presented. The paper concludes with a discussion of the practically of using more sophisticated, regulatory-scale air quality models with the GA. We anticipate that such an approach will be practical in the near term for supporting regulatory decision-making.

Air Pollution↗
PubMed2001

Identification of a microsatellite on chromosome 7B showing a strong linkage with yellow pigment in durum wheat (Triticum turgidum L. var. durum).

The objective of this study is to identify QTLs linked to yellow pigment content in durum wheat. A durum-dicoccoides genetic linkage map was constructed using 124 microsatellites, 149 amplified fragment length polymorphism (AFLPs), and six seed storage proteins (SSP) in a population of 114 recombinant inbred lines (F8). The population has been obtained from a cross between a durum cultivar Omrabi5 and Triticum dicoccoides600545 and backcrossed to Omrabi5. The map consists of 14-durum chromosomes plus an unknown group; and shows a good synteny to the previously published wheat maps. Yellow pigment was measured in the population in three different locations during 3 seasons. Analysis of QTLs was based on simple and simplified composite interval mapping (SIM and sCIM). Three QTLs for yellow pigment were detected on the chromosomal group 7 (7AL and 7BL telomeres) explaining 62% of the total variation. On 7BL, a major microsatellite (Xgwm344) explained by itself 53%, whereas on 7AL, the other two QTLs have contributed 13 and 6%. All determined QTLs showed a strong genetic effect and a weak QTL x E effect. The QTLs effect was consistent across all environments and showed a large effect. Consequently, promising QTLs will be used in the marker assisted breeding program to enhance the selection efficiency for yellow pigment.

Chromosomes↗
PubMed1997

Random amplified polymorphic DNA (RAPD) markers for determination of genetic variation in wild populations of the black tiger prawn (Penaeus monodon) in Thailand.

Random amplified polymorphic DNA (RAPD) analysis was used to amplify the genome of black tiger prawns (Penaeus monodon) to detect DNA markers and assess the utility of the RAPD method for investigating genetic variation in wild P. monodon in Thailand. A total of 200 ten-base primers were screened, and 84 primers yielded amplification products. Six positive primers that gave highly reproducible RAPD patterns were selected for the analysis of three geographically different samples of Thai P. monodon. A total of 70 reproducible RAPD fragments ranging in size from 200 to 2000 bp were scored, and 40 fragments (57%) were polymorphic. The RAPD analysis of broodstocks from three different locales, Satun-Trang, Trat, and Angsila, revealed different levels of genetic variability among the samples. The percentages of polymorphic bands were 48% and 45% in Satun-Trang and Trat, respectively, suggesting a high genetic variability of the two samples to be used in selective breeding programs. Only 25% polymorphic bands were found in the Angsila sample, indicating the lowest polymorphic level among the three samples examined. Primer 428 detected a RAPD marker that was found only in P. monodon originating from Satun-Trang, suggesting the potential use of this marker as a population-specific marker in this species.

Animals↗
PubMed1994

A secondary structure model of the integrin alpha subunit N-terminal domain based on analysis of multiple alignments.

The integrins are alpha/beta heterodimeric proteins which mediate cell-matrix and cell-cell interactions. Current data indicate that the N-terminal moiety of the alpha subunit is involved in ligand binding. This region of the receptor is made up of a seven-fold repeated sequence of unknown structure which contains EF-hand-like putative divalent cation-binding sites. Recent studies have shown that multiple sequence alignments can be analysed to yield secondary structure predictions. Therefore, to obtain a model structure for the integrin alpha subunit N-terminal domain repeat, a large alignment of the seven repeats from sixteen integrin sequences was generated. Two methods of analysis were used: First, Chou and Fasman and Garnier, Osguthorpe and Robson predictions were carried out for individual sequences and the consensus predictions derived. Consensus hydrophobicity and chain flexibility data were also used to provide additional data. Second, sites of conservation and variation were analysed by a computer program STAMA (STructure After Multiple Alignment) to yield a secondary structure prediction. The two analyses gave essentially the same predicted structure: undefined region, loop, alpha-helix, beta-strand, divalent cation-binding loop, beta-strand, putative turn, loop, beta-strand. This is the first model structure to be presented for an integrin domain. Its implications for integrin function are discussed.

Amino Acid Sequence↗
PubMed2005

Beta-fibrinogen haplotypes and the risk for cardiovascular disease in a dialysis cohort.

BACKGROUND: Elevated plasma fibrinogen levels are common in dialysis patients and may be related to an elevated risk for cardiovascular disease (CVD). We tested the hypothesis that genetic variation in the beta-fibrinogen ( FGB ) gene, shown to explain 1% to 5% of fibrinogen level variation in the general population, has an important role in elevated fibrinogen levels and excess CVD risk in dialysis patients. METHODS: Plasma fibrinogen was measured in 735 dialysis patients a median of 3 months from the start of dialysis therapy by using an automated clot-rate assay. Seven polymorphisms of the FGB gene were determined. Haplotype analysis was conducted using the Phase program to estimate haplotypes, with stratification for race. CVD events were ascertained from medical records. RESULTS: During a median follow-up of 2.1 years, 279 CVD events occurred. Genotype frequencies were in Hardy-Weinberg equilibrium. Four common haplotypes identified were not associated with fibrinogen levels or CVD risk in the entire cohort or after stratification by race. The -455A allele, known to increase gene expression in vitro, was marginally associated with fibrinogen levels only in patients without diabetes (regression coefficient [beta], 20 mg/dL [for +1 copy of the A allele; P = 0.06]), adjusted for age, sex, race, smoking, baseline dialysis modality, comorbidity, and history of diabetes and CVD. Post hoc analysis showed that -249C-->T (defining haplotype 3) was associated with greater fibrinogen levels and CVD risk among patients without diabetes and current smokers. CONCLUSION: The FGB gene likely does not have an important role in determining the variation in elevated plasma fibrinogen levels or excess CVD risk in dialysis patients.

Adult↗
PubMed2005

Exploring the evolution of Wolbachia compatibility types: a simulation approach.

Wolbachia-induced cytoplasmic incompatibility (CI) is observed when males bearing the bacterium mate with uninfected females or with females bearing a different Wolbachia variant; in such crosses, paternal chromosomes are lost at the first embryonic mitosis, most often resulting in developmental arrest. The molecular basis of CI is currently unknown, but it is useful to distinguish conceptually the male and female sides of this phenomenon: in males, Wolbachia must do something, before it is shed from maturing sperm, that will disrupt paternal chromosomes functionality [this is usually termed "the modification (mod) function"]; in females, Wolbachia must somehow restore embryonic viability, through what is usually called "the rescue (resc) function." The occurrence of CI in crosses between males and females bearing different Wolbachia variants demonstrates that the mod and resc functions interact in a specific manner: different mod resc pairs make different compatibility types. We are interested in the evolutionary process allowing the diversification of compatibility types. In an earlier model, based on the main assumption that the mod and resc functions can mutate independently, we have shown that compatibility types can evolve through a two-step process, the first involving drift on mod variations and the second involving selection on resc variations. This previous study has highlighted the need for simulation-based models that would include the effects of nondeterministic evolutionary forces. This study is based on a simulation program fulfilling this condition, allowing us to follow the evolution of compatibility types under mutation, drift, and selection. Most importantly, simulations suggest that in the frame of our model, the evolution of compatibility types is likely to be a gradual process, with new compatibility types remaining partially compatible with ancestral ones.

Animals↗
PubMed1993

Genetic diversity among Borrelia burgdorferi isolates: more than three genospecies?

In order to assess the genetic relationships among isolates of Borrelia burgdorferi, we have determined chromosomal DNA restriction fragment length polymorphisms (RFLP) of 27 isolates. Using five restriction enzymes and seven DNA probes, we recorded 246 different hybridizing bands. The resulting matrix was subjected to factorial correspondence analysis and to phylogenetic analysis using a parsimony program. These analyses demonstrate two closely related genospecies and three individual strains. RFLP variations among these three strains are much more pronounced than among the members of the other two genospecies. This may indicate the existence of more than three genospecies. Plasmid analysis did not contribute significantly to the genotypic differentiation.

Borrelia burgdorferi Group↗
PubMed2004

Design and analysis of admixture mapping studies.

Admixture between populations originating on different continents can be exploited to detect disease susceptibility loci at which risk alleles are distributed differentially between these populations. We first examine the statistical power and mapping resolution of this approach in the limiting situation in which gamete admixture and locus ancestry are measured without uncertainty. We show that, for a rare disease, the most efficient design is to study affected individuals only. In a typical African American population (two-way admixture proportions 0.8/0.2, ancestry crossover rate 2 per 100 cM), a study of 800 affected individuals has 90% power to detect at P values <10(-5) a locus that generates a risk ratio of 2 between populations, with an expected mapping resolution (size of 95% confidence region for the position of the locus) of 4 cM. In practice, to infer locus ancestry from marker data requires Bayesian computationally intensive methods, as implemented in the program ADMIXMAP. Affected-only study designs require strong prior information on the frequencies of each allele given locus ancestry. We show how data from unadmixed and admixed populations can be combined to estimate these ancestry-specific allele frequencies within the admixed population under study, allowing for variation between allele frequencies in unadmixed and admixed populations. Using simulated data based on the genetic structure of the African American population, we show that 60% of information can be extracted in a test for linkage using markers with an ancestry information content of 36% at 3-cM spacing. As in classic linkage studies, the most efficient strategy is to use markers at a moderate density for an initial genome search and then to saturate regions of putative linkage with additional markers, to extract nearly all information about locus ancestry.

Black People↗
PubMed2004

Selecting appropriate animal models and experimental designs for endocrine disruptor research and testing studies.

Evidence that chemicals in the environment may cause developmental and reproductive abnormalities in fish and wildlife by disrupting normal endocrine functions has increased concern about potential adverse human health effects from such chemicals. US laws have now been enacted that require the US Environmental Protection Agency (EPA) to develop and validate a screening program to identify chemicals in food and water with potential endocrine-disrupting activity. EPA subsequently proposed an Endocrine Disruptor Screening Program that uses in vitro and in vivo test systems to identify chemicals that may adversely affect humans and ecologically important animal species. However, the endocrine system can be readily modulated by many experimental factors, including diet and the genetic background of the selected animal strain or stock. It is therefore desirable to minimize or avoid factors that cause or contribute to experimental variation in endocrine disruptor research and testing studies. Standard laboratory animal diets contain high and variable levels of phytoestrogens, which can modulate physiologic and behavioral responses similar to both endogenous estrogen as well as exogenous estrogenic chemicals. Other studies have determined that some commonly used outbred mice and rats are less responsive to estrogenic substances than certain inbred mouse and rat strains for various estrogen-sensitive endpoints. It is therefore critical to select appropriate biological models and diets for endocrine disruptor studies that provide optimal sensitivity and specificity to accomplish the research or testing objectives. An introduction is provided to 11 other papers in this issue that review these and other important laboratory animal experimental design considerations in greater detail, and that review laboratory animal and in vitro models currently being used or evaluated for endocrine disruptor research and testing. Selection of appropriate animal models and experimental design parameters for endocrine disruptor research and testing will minimize confounding experimental variables, increase the likelihood of replicable experimental results, and contribute to more reliable and relevant test systems.

Animals↗
PubMed2004

Admixture and diversity in West African cattle populations.

We present a population genetic analysis of microsatellite variation in 16 West African cattle populations. West Africa represents a unique juxtaposition of different climatic and ecological zones in a relatively small geographical area. While more humid coastal regions are inhabited by the tsetse fly, a vector which spreads trypanosomiasis among cattle, the disease is not transmitted in the drier areas outside this zone. This is the most thorough study of genetic diversity in cattle within this area, which contains genetically important trypanotolerant Bos taurus breeds. Genetic relationships among the many breeds are examined and levels of diversity are assessed. Admixture levels were determined using a variety of methods. Ancestry informative or population-associated alleles (PAAs) were selected using populations from India, the Near East and Europe. Multivariate analysis, the admix program and model-based Bayesian admixture analysis approaches were also employed. These analyses reveal the direct impact of ecological factors and the profound effect of admixture on the cattle of this region. They also highlight the importance of efforts to prevent further dilution of African taurine breeds by B. indicus cattle.

Africa↗
PubMed1992

Evidence for immune selection of hepatitis C virus (HCV) putative envelope glycoprotein variants: potential role in chronic HCV infections.

E2/nonstructural protein 1, the putative envelope glycoprotein (gp72) of HCV, possesses an N-terminal hypervariable (E2 HV) domain from amino acids 384 to 414 of unknown significance. The high degree of amino acid sequence variation in the E2 HV domain appears to be comparable to that observed in the human immunodeficiency virus type 1 gp120 V3 domain. This observation and the observation that the HCV E2 HV domain lacks conserved secondary structure imply that, like the V3 loop of human immunodeficiency virus 1 gp120, the N-terminal E2 region may encode protective epitopes that are subject to immune selection. Antibody-epitope binding studies revealed five isolate-specific linear epitopes located in the E2 HV region. These results suggest that the E2 HV domain is a target for the human immune response and that, in addition to the three major groups of HCV, defined by nucleotide and amino acid sequence identity among HCV isolates, E2 HV-specific subgroups also exist. Analysis of the partial or complete E2 sequences of two individuals indicated that E2 HV variants can either coexist simultaneously in a single individual or that a particular variant may predominate during different episodes of disease. In the latter situation, we found one individual who developed antibodies to a subregion of the E2 HV domain (amino acids 396-407) specific to a variant that was predominant during one major episode of hepatitis but who lacked detectable antibodies to the corresponding region of a second variant that was predominant during a later episode of disease. The data suggest that the variability in the E2 HV domain may result from immune selection. The findings of this report could impact vaccine strategies and drug therapy programs designed to control and eliminate HCV.

Amino Acid Sequence↗
PubMedDate not supplied

Do early-life events permanently alter behavioral and hormonal responses to stressors?

Early-life stimulation (e.g., brief handling) attenuates the behavioral and neuroendocrine responses to stressors encountered in adulthood, particularly with respect to activation of hypothalamic-pituitary-adrenal (HPA) activity. In contrast, if neonates were subjected to a more severe stressor, such as protracted separation from the dam or exposure to an endotoxin, then the adult response to a stressor was exaggerated. These early-life experiences program HPA functioning, including negative feedback derived from stimulation of hippocampal glucocorticoid receptors, and corticotropin-releasing hormone (CRH) and arginine vasopressin (AVP) coexpression in PVN neurons, to modify the response to subsequent stressor experiences. The persistent variations of HPA activity observed in handled/stimulated animals may stem from alterations in dam-pup interactions (e.g. increased arched-back feeding, licking, grooming). In addition genetic makeup is critical in determining stress reactivity. For instance, BALB/cByJ mice are more reactive to stressors than C57BL/6ByJ mice, exhibiting greater HPA hormonal alterations and behavioral disturbances. BALB/cByJ also fail to acquire a spatial learning response in a Morris water-maze paradigm, which has been shown to be correlated with hippocampal cell loss associated with aging. Early-life handling of BALB/cByJ mice prevented these performance deficits and attenuated the hypersecretion of ACTH and corticosterone elicited by stressors. The stressor reactivity may have been related to maternal and genetic factors. When BALB/cByJ mice were raised by a C57BL/6ByJ dam, the excessive stress-elicited HPA activity was reduced, as were the behavioral impairments. However, cross-fostering the more resilient C57BL/6ByJ mice to a BALB/cByJ dam failed to elicit the behavioral disturbances. It is suggested that genetic factors may influence dam-pup interactive styles and may thus proactively influence the response to subsequent stressors among vulnerable animals. In contrast, in relatively hardy animals the early-life manipulations may have less obvious effects.

Aging↗
PubMed1998

Genetic variability and diversity for protein and calcium contents in finger millet (Eleusine coracana (L.) Gaertn) in relation to grain color.

Analysis of 36 genotypes of finger millet (Eleusine coracana (L.) Gaertn) with varying seed colors revealed a wide range of protein and calcium contents. White seeded genotypes had higher protein contents, while brown seeded types had a wide range of values. The brown seeded genotype GE 2500 had the highest protein content. Although protein content had significant negative association with calcium content, white seeded types had moderate levels of calcium. The genotypic coefficients of variability were moderate and high for protein and calcium, respectively. High heritability coupled with high genetic advance indicated their governance by additive gene action. A negative significant correlation was observed between protein content and grain yield. Mahalanobis D2 analysis grouped the 36 genotypes into eight clusters. Clustering pattern failed to indicate any relationship between genetic diversity and geographic diversity. Based on genetic diversity and performance, the genotypes MS 1168, MS 174 and CO 13 were found to be suitable for use as parents in a hybridization program for improving yield; the genotypes MS 1168, MS 174 and MS 2869 for protein and Malawi 1915 and CO 11 for calcium. Protein and calcium contents contributed less to genetic divergence.

Calcium↗
PubMed2003

The intra-individual diversity in senescence.

One of the most characteristic and widely observable features of senescence, usually ignored by scientific investigation, is a very variable, dapple distribution of its manifestations, seen within systems, organs, and tissues of the same individual. Different parts of an organ or tissue undergo senescence at different ages. The early aged foci may form only small solitary places in a tissue, an organ, a region, or an organism or in large parts of it. The proportion of early aged parts to later aged ones, as well as their localization, is predestined by individual genetic makeup, thus determining diversity in the course and forms of senile regression and the lifespan of organisms under consideration. It is a kind of biodiversity that is least known. To clear up what we can say about the nature of the phenomenon today, the features of this kind of human body diversity were interpreted using the data and conceptions of immunology, molecular biology and genetics. The results of the interpretation allow us to suppose that different parts of a human body usually have unequal genetic limits of life duration and their own programs of ageing; each of them has its own 'biological watch' which tells a different time. The genesis of this diversity can be explained by hybridization of persons with different genetic susceptibility to internal and/or environmental factors inducing senescence.

Aging↗
PubMed1992

Stochastic developmental variation in the ratio of allelic rDNAs among newly differentiated, heterozygous macronuclei of Tetrahymena thermophila.

Ciliates possess nuclear dimorphism, i.e., they carry two structurally and functionally differentiated types of nuclei. The micronucleus and macronucleus serve as the germline and somatic nuclei, respectively, of the cell. The macronucleus differentiates from a mitotic sister of the micronucleus once per life cycle. Macronuclear differentiation is accompanied by a developmentally programmed set of DNA rearrangements, including chromosome fragmentation, telomere addition, and amplification. Given the diploidy of the MAC anlage, are both homologous copies of a chromosome processed and amplified equally and simultaneously in an individual differentiating MAC? We have approached this question for the case of the rDNA, exploiting previously identified DNA polymorphisms and the sensitivity of PCR. We determined allelic ratios in individual caryonide cells, i.e., the cells carrying the primary products of MAC differentiation, prior to the first division of the newly differentiated MAC. We observed stochastic variability in allelic ratios among caryonides that start with genetically identical heterozygous MACs. Either rDNA type can be in the majority. Appropriate controls make it unlikely that the ratios observed were significantly affected by variation in the assay itself. The variability may well result from the statistical variation associated with the relative timing of individual biochemical events initiating the processing and/or amplification of a few rDNA precursor molecules, presumably 4-8 at the most, in a MAC anlage. In addition to this stochastic variability, we observed a small but distinct bias in favor of the C3 rDNA. Thus the replication advantage of C3 relative to B rDNA in heterozygous MACs, previously detected during vegetative multiplication, may begin to be expressed during developmental amplification.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗
PubMed1991

The potential for genetic change in milk fat composition.

Effecting genetic improvement requires genetic variation, a mechanism of selection, and an economic incentive for the improvement. Limited data suggest that there is within-breed genetic variation in milk fat composition, but accurate estimates are lacking. There is some evidence for modest differences among breeds. Substantial differences exist among species, indicating that substantial genetic change in fat composition is biologically possible. The economic incentives for genetic change are not clear. Changes in fat composition that would improve the quality of one milk product would often be detrimental to other products. Such changes would best work where subpopulations produced milk for specific end products. Such division of the industry would be difficult to organize and might impede existing improvement programs. Changes in fat composition that increased consumer acceptance of milk products, such as reduced saturated fat concentration, might increase the market for milk products. However, only large changes in composition are likely to affect consumer acceptance; thus, the gradual changes of conventional genetic improvement would produce little or no return to the breeder. Genetic changes that reduced processing costs or increased product value might have low to moderate economic value, inducing slow rates of change. Production of transgenic animals might provide a route for genetic alteration of fat composition in the future. Such improvement would most likely be cost effective in a subdivided production industry in which milk from cows of a particular genotype can be directed to a particular milk product. It is concluded that although alteration of fat composition could be achieved, it is unlikely to be an important component of genetic improvement of dairy cattle.

Animals↗