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PubMed1986

EXPERFARM: a new package in BASIC for teaching genetics.

We have developed two interactive computer programs (together referred to as EXPERFARM), which enable simulation of a great variety of genetic situations. This package is designed for teaching basic genetics as well as quantitative and population genetics. The main advantages of EXPERFARM are its great versatility, as different situations can be simulated by simply changing the inputs, and the small amount of training necessary for the users.

Computer-Assisted Instruction↗
PubMed2005

Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.

By analyzing 1,780,295 5'-end sequences of human full-length cDNAs derived from 164 kinds of oligo-cap cDNA libraries, we identified 269,774 independent positions of transcriptional start sites (TSSs) for 14,628 human RefSeq genes. These TSSs were clustered into 30,964 clusters that were separated from each other by more than 500 bp and thus are very likely to constitute mutually distinct alternative promoters. To our surprise, at least 7674 (52%) human RefSeq genes were subject to regulation by putative alternative promoters (PAPs). On average, there were 3.1 PAPs per gene, with the composition of one CpG-island-containing promoter per 2.6 CpG-less promoters. In 17% of the PAP-containing loci, tissue-specific use of the PAPs was observed. The richest tissue sources of the tissue-specific PAPs were testis and brain. It was also intriguing that the PAP-containing promoters were enriched in the genes encoding signal transduction-related proteins and were rarer in the genes encoding extracellular proteins, possibly reflecting the varied functional requirement for and the restricted expression of those categories of genes, respectively. The patterns of the first exons were highly diverse as well. On average, there were 7.7 different splicing types of first exons per locus partly produced by the PAPs, suggesting that a wide variety of transcripts can be achieved by this mechanism. Our findings suggest that use of alternate promoters and consequent alternative use of first exons should play a pivotal role in generating the complexity required for the highly elaborated molecular systems in humans.

Base Sequence↗
PubMed1996

Quantitative trait loci contributing to phencyclidine-induced and amphetamine-induced locomotor behavior in inbred mice.

Phencyclidine (PCP) and amphetamine (AMP) can induce psychotic syndromes in humans, whereas administration of these drugs to mice results in behavioral activation that is influenced by genetic factors. Quantitative trait loci (QTL) underlying genetic differences in response to PCP and AMP in mice were provisionally identified by correlating allelic variation at known marker loci in the BXD series of recombinant inbred (RI) mice and its progenitors (C57BL/6J and DBA/2J inbred strains) with the locomotor response of each strain to PCP and AMP. Total distance traveled for individual mice from each of the 26 BXD RI and two progenitor strains was measured after injections of normal saline and 7.5 mg/kg i.p. injection of PCP. This procedure was repeated after 1 week, using 5.0 mg/kg of AMP, instead of PCP. Markers significantly (p < .01) correlated with response to PCP map to murine chromosomes 1, 14, and 15. Response to amphetamine was correlated with markers mapping to chromosomes 4, 5, 6, 8, 14, and 18. Identification of the QTL underlying PCP-induced and AMP-induced behavior in mice may provide clues into the complicated genetics of psychosis in humans.

Amphetamine↗
PubMed2002

Strategies for continual application of marker-assisted selection in an open nucleus population.

The objectives of this study were to develop and simulate the implementation of several strategies for repeated application of quantitative trait loci (QTL) detection and marker-assisted selection (MAS) and to compare the short-term and continual genetic responses. A finite locus model was simulated with 20 QTL randomly distributed across 30 chromosome. Three hundred markers were evenly spaced across the genome. Allelic effects were sampled from a double exponential distribution. A daughter design was used every generation to determine the marker alleles favorably associated to QTL alleles. The MAS was applied within family to young bulls, before progeny testing, as part of an open nucleus. Young bulls were selected using strategies based on 1) the single marker with greatest contrast (BEST1), 2) the sum of n greatest contrasts (BESTn), 3) the best n contrasts, limited to one per chromosome (LIMn), 4) the sum of all contrasts exceeding a given threshold n (THRESn), and 5) the sum of contrasts exceeding a threshold, but limited to one per chromosome (LIMT). The maximum progress was achieved by strategies that selected upon several markers flanking multiple QTL in each generation. When THRES was applied, the mean true breeding value (TBV) of selected bulls was increased by 11.98% (over conventional selection) versus 6.73% for BEST1 in the first generation. Applying a full genome scan in each generation allowed selection for different QTL across time. By selecting for multiple QTL over time, MAS maintained superiority over conventional selection for many generations.

Alleles↗
PubMed2002

Contrasting patterns of divergence in quantitative traits and neutral DNA markers: analysis of clinal variation.

Clinal variation in quantitative traits is often attributed to the effects of spatially varying selection. However, identical patterns can be produced by the interplay between purely stochastic processes (i.e. drift in combination with spatially restricted gene flow). One means of distinguishing between adaptive and nonadaptive causes of geographical variation is to compare relative levels of between-population divergence in quantitative traits and neutral DNA markers. Such comparisons can be used to test whether levels of trait divergence attributable to additive genetic effects (as measured by QST) exceed null expectations based on the level of divergence at neutral marker loci (as measured by FST). The purpose of this study was to use an approach based on 'QST vs. FST' contrasts to test for evidence of diversifying selection on body size of an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae). Specifically, relative levels of between-population divergence in body size and microsatellite DNA markers were compared to assess whether the observed pattern of clinal size variation could be explained by a neutral model of isolation by distance. QST for body size was calculated using unbiased estimators of within- and between-population variance of principal component scores. The association between body size variation and geographical/environmental distance was tested using pairwise and partial matrix correspondence tests (MCTs). Independent variables (representing causal hypotheses) were constructed as between-locality distance matrices. The effects of neutral genetic divergence were assessed by including a matrix of pairwise FST as an independent variable. Partial MCTs revealed highly significant associations between phenotypic divergence (QST) and both geographical and environmental distance, even when the effects of neutral genetic divergence (FST) were partialled out. Results of the tests confirmed that migration-drift equilibrium is not a sufficient explanation for the latitudinal pattern of clinal size variation in C. sphinx. The geographical patterning of pairwise QST is most likely attributable to spatially varying selection and/or the direct influence of latitudinally ordered environmental effects.

Animals↗
PubMed2006

A genetic linkage map of Pacific white shrimp (Litopenaeus vannamei): sex-linked microsatellite markers and high recombination rates.

Pacific white shrimp (Litopenaeus vannamei) is the leading species farmed in the Western Hemisphere and an economically important aquaculture species in China. In this project, a genetic linkage map was constructed using amplified fragment length polymorphism (AFLP) and microsatellite markers. One hundred and eight select AFLP primer combinations and 30 polymorphic microsatellite markers produced 2071 markers that were polymorphic in either of the parents and segregated in the progeny. Of these segregating markers, 319 were mapped to 45 linkage groups of the female framework map, covering a total of 4134.4 cM; and 267 markers were assigned to 45 linkage groups of the male map, covering a total of 3220.9 cM. High recombination rates were found in both parental maps. A sex-linked microsatellite marker was mapped on the female map with 6.6 cM to sex and a LOD of 17.8, two other microsatellite markers were also linked with both 8.6 cM to sex and LOD score of 14.3 and 16.4. The genetic maps presented here will serve as a basis for the construction of a high-resolution genetic map, quantitative trait loci (QTLs) detection, marker-assisted selection (MAS) and comparative genome mapping.

Animals↗
PubMed2001

Detection and characterization of quantitative trait loci for meat quality traits in pigs.

In an experimental cross between Meishan and Dutch Large White and Landrace lines, 785 F2 animals with carcass information and their parents were typed for molecular markers covering the entire porcine genome. Linkage was studied between these markers and eight meat quality traits. Quantitative trait locus analyses were performed using interval mapping by regression under two genetic models: 1) the line-cross approach, where the founder lines were assumed to be fixed for different QTL alleles and 2) a half-sib model where a unique allele substitution effect was fitted within each of the 38 half-sib families. The line-cross approach included tests for genomic imprinting and sex-specific QTL effects. In total, three genome-wide significant and 26 suggestive QTL were detected. The significant QTL on chromosomes 3, 4, and 13, affecting meat color, were only detected under the half-sib model. Failure of the line-cross approach to detect the meat color QTL suggests that the founder lines have similar allele frequencies for these QTL. This study provides information on new QTL affecting meat quality traits. It also shows the benefit of analyzing experimental data under different genetic and statistical models.

Alleles↗
PubMed1986

Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers.

A method is presented to estimate the biometric parameters of a quantitative trait locus linked to a genetic marker when both loci are segregating in the F-2 generation of a cross between two inbred lines. The method, which assumes underlying normal distributions, is a combination of maximum likelihood and moments methods and uses the statistics of the genetic marker genotype samples for the quantitative trait to estimate the recombination frequency between the two loci and the means and variances of the genotypes of the quantitative trait locus. With this method, the genetic parameters of a locus affecting plant height linked to an electrophoretic marker for esterase were accurately estimated from a sample of 1596 F-2 progeny of a cross between two species of Lycopersicon (tomato). Linkage distance between the two loci was 38 map units and the effect of the quantitative trait locus was 1.6 phenotypic standard deviation units. Accurate estimates of the genetic parameters and linkage distance for populations of 2000 individuals simulated with a segregating codominant locus with an effect of 1.63 standard deviations linked to a genetic marker with .2 recombination were also derived by this method. The method is not effective in distinguishing between complete and partial linkage in samples of only 500 individuals or for quantitative loci with effects less than a phenotypic standard deviation. The method is more effective for codominant than for dominant loci.

Algorithms↗
PubMed1997

Quantitative trait loci affecting methamphetamine responses in BXD recombinant inbred mouse strains.

Individual differences in most behavioral and pharmacological responses to abused drugs are dependent on both genetic and environmental factors. The genetic influences on the complex phenotypes related to drug abuse have been difficult to study using classical genetic analyses. Quantitative trait locus (QTL) mapping is a method that has been used successfully to examine genetic contributions to some of these traits by correlating allelic variation in polymorphic genetic markers of known chromosomal location with variation in drug-response phenotypes. We evaluated several behavioral responses to multiple doses of methamphetamine (METH) in C57BL/6J (B6), DBA/2J (D2), and 25 of their recombinant inbred (BXD RI) strains. Stereotyped chewing, horizontal home cage activity, and changes in body temperature after 0, 4, 8, or 16 mg/kg METH, as well as stereotyped climbing behavior after 16 mg/kg METH, were examined. Associations (p < 0.01) between METH sensitivity and allelic status at multiple microsatellite genetic markers were subsequently determined for each response. QTLs were provisionally identified for each phenotype, some unique to a particular behavior and others that appeared to influence multiple phenotypes. Candidate genes suggested by these analyses included several that mapped near genes relevant for the neurotransmitters acetylcholine and glutamate. The locations of QTLs provisionally identified by this analysis were compared with QTLs hypothesized in other studies to influence methamphetamine- and cocaine-related phenotypes. In several instances, QTLs appeared to overlap, which is consistent with idea that common neural substrates underlie some responses to psychostimulants.

Alleles↗
PubMed2005

Two quantitative trait loci for prepulse inhibition of startle identified on mouse chromosome 16 using chromosome substitution strains.

Prepulse inhibition (PPI) of acoustic startle is a genetically complex quantitative phenotype of considerable medical interest due to its impairment in psychiatric disorders such as schizophrenia. To identify quantitative trait loci (QTL) involved in mouse PPI, we studied mouse chromosome substitution strains (CSS) that each carry a homologous chromosome pair from the A/J inbred strain on a host C57BL/6J inbred strain background. We determined that the chromosome 16 substitution strain has elevated PPI compared to C57BL/6J (P = 1.6 x 10(-11)), indicating that chromosome 16 carries one or more PPI genes. QTL mapping using 87 F(2) intercross progeny identified two significant chromosome 16 loci with LODs of 3.9 and 4.7 (significance threshold LOD is 2.3). The QTL were each highly significant independently and do not appear to interact. Sequence variation between B6 and A/J was used to identify strong candidate genes in the QTL regions, some of which have known neuronal functions. In conclusion, we used mouse CSS to rapidly and efficiently identify two significant QTL for PPI on mouse chromosome 16. The regions contain a limited number of strong biological candidate genes that are potential risk genes for psychiatric disorders in which patients have PPI impairments.

Animals↗
PubMed2006

On the evolution of epistasis II: a generalized Wright-Kimura framework.

The evolution of fitness interactions between genes at two major loci is studied where the alleles at a third locus modify the epistatic interaction between the two major loci. The epistasis is defined by a parameter epsilon and a matrix structure that specifies the nature of the interactions. When epsilon=0 the two major loci have additive fitnesses, and when these are symmetric the interaction matrices studied here produce symmetric viabilities of the Wright [1952. The genetics of quantitative variability. In: Reeve, E.C.R., Waddington, C.H. (Eds.), Quantitative Inheritance. Her Majesty's Stationary Office, London]-Kimura [1956. A model of a genetic system which leads to closer linkage by natural selection. Evolution 10, 278-281] form. Two such interaction matrices are studied, for one of which epistasis as measured by |epsilon| always increases, and for the other it increases when the linkage between the major loci is tight enough and there is initial linkage disequilibrium. Increase of epistasis does not necessarily coincide with increase in equilibrium mean fitness.

Alleles↗
PubMed2006

Flanking HS-62.5 and 3' HS1, and regions upstream of the LCR, are not required for beta-globin transcription.

The locus control region (LCR) was thought to be necessary and sufficient for establishing and maintaining an open beta-globin locus chromatin domain in the repressive environment of the developing erythrocyte. However, deletion of the LCR from the endogenous locus had no significant effect on chromatin structure and did not silence transcription. Thus, the cis-regulatory elements that confer the open domain remain unidentified. The conserved DNaseI hypersensitivity sites (HSs) HS-62.5 and 3'HS1 that flank the locus, and the region upstream of the LCR have been implicated in globin gene regulation. The flanking HSs bind CCCTC binding factor (CTCF) and are thought to interact with the LCR to form a "chromatin hub" involved in beta-globin gene activation. Hispanic thalassemia, a deletion of the LCR and 27 kb upstream, leads to heterochromatinization and silencing of the locus. Thus, the region upstream of the LCR deleted in Hispanic thalassemia (upstream Hispanic region [UHR]) may be required for expression. To determine the importance of the UHR and flanking HSs for beta-globin expression, we generated and analyzed mice with targeted deletions of these elements. We demonstrate deletion of these regions alone, and in combination, do not affect transcription, bringing into question current models for the regulation of the beta-globin locus.

5' Flanking Region↗
PubMedDate not supplied

Assessing the contribution of breeds to genetic diversity in conservation schemes.

The quantitative assessment of genetic diversity within and between populations is important for decision making in genetic conservation plans. In this paper we define the genetic diversity of a set of populations, S, as the maximum genetic variance that can be obtained in a random mating population that is bred from the set of populations S. First we calculated the relative contribution of populations to a core set of populations in which the overlap of genetic diversity was minimised. This implies that the mean kinship in the core set should be minimal. The above definition of diversity differs from Weitzman diversity in that it attempts to conserve the founder population (and thus minimises the loss of alleles), whereas Weitzman diversity favours the conservation of many inbred lines. The former is preferred in species where inbred lines suffer from inbreeding depression. The application of the method is illustrated by an example involving 45 Dutch poultry breeds. The calculations used were easy to implement and not computer intensive. The method gave a ranking of breeds according to their contributions to genetic diversity. Losses in genetic diversity ranged from 2.1% to 4.5% for different subsets relative to the entire set of breeds, while the loss of founder genome equivalents ranged from 22.9% to 39.3%.

Animals↗
PubMed2004

Genetic parameters for six measures of length of productive life and three measures of lifetime production by 6 yr after first calving for Hereford cows.

Genetic parameters for length of productive life given the opportunity (LPL/O), measured as days between first calving and disposal conditioned on one of six opportunity groups, L1 through L6 (e.g., L2 is length of productive life in days given the opportunity to live 2 yr after first calving), and lifetime production (LP), measured as the number of calves born (NB), number of calves weaned (NW), and cumulative weaning weight (CW) by 6 yr after first calving, were estimated using records of 1,886 Hereford cows from a selection experiment with three selected lines and a control line. Weaning weights were adjusted to 200 d of age and for sex and age of dam. Estimates of heritability and genetic and environmental correlations were obtained by restricted maximum likelihood with bivariate animal models, with year of birth of cow as a fixed effect and direct genetic and residual as random effects. Genetic trends were estimated by regressing means of estimated breeding values by year of birth and line on birth year. Estimates of heritability (SE) for LPL/O ranged from 0.05 (0.01) to 0.15 (0.03). Estimates of genetic correlations (SE) among LPL/O ranged from 0.74 (0.14) to 1.00 (0.00), and estimates of environmental correlations ranged from 0.67 (0.05) to 0.98 (0.01). Estimates of heritability (SE) for NB, NW, and CW were 0.17 (0.05), 0.21 (0.06), and 0.18 (0.01). Estimates of genetic correlations (SE) among NB, NW, and CW ranged from 0.96 (0.02) to 0.99 (0.01). Estimates of environmental correlations (SE) ranged from 0.93 (0.01) to 0.99 (0.01). Estimates of genetic correlations for L6 with NB, NW, and CW were near 1.00 (0.09). Estimates of environmental correlations (SE) ranged from 0.57 (0.03) to 0.60 (0.03). Estimates of genetic change per year (SE) for L6 were low for all lines and ranged from -3.53 (2.09) to 4.63 (2.11) d/yr. Genetic trends for NB and NW were negligible for all lines. Genetic trends for CW were low and ranged from -2.81 (1.67) to 3.29 (1.76) kg/yr. Differences in genetic trends between selected lines and control were not significant (P > 0.05). Estimates of environmental trends (SE) over all lines were -104.00 (25.48) d/yr, -0.26 (0.02) calves/yr, -0.25 (0.02) calves/yr, and -55.10 (15.63) kg/yr, for L6, NB, NW, and CW, respectively. Selection for LPLIO or LP could be successful in a breeding program, but may be relatively slow due to the low magnitude of heritability and extended generation interval.

Animals↗
PubMed2003

Primary factors affecting the evaluation accuracy of animal model MBLUP.

Marker-assisted best linear unbiased prediction (MBLUP) is one important method of implementing marker-assisted selection (MAS). The computer stochastic simulation method was used to study the effects of heritability of trait, QTL variance and map distance between two adjacent markers on the evaluation accuracy of animal model MBLUP. With the higher heritability, the smaller QTL variance and the shorter map distance between two adjacent markers, the evaluation accuracy of animal model MBLUP would be increased. On the contrary, the evaluation accuracy of animal model MBLUP would be decreased when the heritability was lower, QTL variance was larger and map distance between two adjacent markers was longer.

Animals↗
PubMed2004

Quantitative trait locus dissection in congenic strains of the Goto-Kakizaki rat identifies a region conserved with diabetes loci in human chromosome 1q.

Genetic studies in human populations and rodent models have identified regions of human chromosome 1q21-25 and rat chromosome 2 showing evidence of significant and replicated linkage to diabetes-related phenotypes. To investigate the relationship between the human and rat diabetes loci, we fine mapped the rat locus Nidd/gk2 linked to hyperinsulinemia in an F2 cross derived from the diabetic (type 2) Goto-Kakizaki (GK) rat and the Brown Norway (BN) control rat, and carried out its genetic and pathophysiological characterization in BN.GK congenic strains. Evidence of glucose intolerance and enhanced insulin secretion in a congenic strain allowed us to localize the underlying diabetes gene(s) in a rat chromosomal interval of approximately 3-6 cM conserved with an 11-Mb region of human 1q21-23. Positional diabetes candidate genes were tested for transcriptional changes between congenics and controls and sequence variations in a panel of inbred rat strains. Congenic strains of the GK rats represent powerful novel models for accurately defining the pathophysiological impact of diabetes gene(s) at the locus Nidd/gk2 and improving functional annotations of diabetes candidates in human 1q21-23.

Animals↗
PubMed2000

Genomic instability induced by high and low LET ionizing radiation.

Genomic instability is the increased rate of acquisition of alterations in the mammalian genome, and includes such diverse biological endpoints as chromosomal destabilization, aneuploidy, micronucleus formation, sister chromatid exchange, gene mutation and amplification, variations in colony size, reduced plating efficiency, and cellular transformation. Because these multiple endpoints persist long after initial radiation exposure, genomic instability has been proposed to operate as a driving force contributing to genetic plasticity and carcinogenic potential. Many of these radiation-induced endpoints depend qualitatively and quantitatively on genetic background, dose and LET. Differences in the frequency and temporal expression of chromosomal instability depend on all three of the foregoing factors. On the other hand, many of these endpoints appear independent of dose and show bystander effects, implicating non-nuclear targets and epigenetic regulatory mechanisms. The present work will survey results concerning the LET dependence of genomic instability and the role of epigenetic mechanisms, with a particular emphasis on the endpoint of chromosomal instability.

Animals↗
PubMed2005

The self-incompatibility locus (S) and quantitative trait loci for self-pollination and seed dormancy in sunflower.

Wild populations of common sunflower (Helianthus annuus L.) are self-incompatible and have deep seed dormancy, whereas modern cultivars, inbreds, and hybrids are self-compatible and partially-to-strongly self-pollinated, and have shallow seed dormancy. Self-pollination (SP) and seed dormancy are genetically complex traits, the number of self-compatibility (S) loci has been disputed, and none of the putative S loci have been genetically mapped in sunflower. We genetically mapped quantitative trait loci (QTL) for self-incompatibility (SI), SP, and seed dormancy in a backcross population produced from a cross between an elite, self-pollinated, nondormant inbred line (NMS373) and a wild, self-incompatible, dormant population (ANN1811). A population consisting of 212 BC(1) progeny was subsequently produced by backcrossing a single hybrid individual to NMS373. BC(1) progeny produced 0-838 seeds per primary capitula when naturally selfed and 0-518 seeds per secondary capitula when manually selfed and segregated for a single S locus. The S locus mapped to linkage group 17 and was tightly linked to a cluster of previously identified QTL for several domestication and postdomestication traits. Two synergistically interacting QTL were identified for SP among self-compatible (ss) BC(1) progeny (R(2)=34.6%). NMS373 homozygotes produced 271.5 more seeds per secondary capitulum than heterozygotes. Germination percentages of seeds after-ripened for 4 weeks ranged from 0% to 100% among self-compatible BC(1)S(1) families. Three QTL for seed dormancy were identified (R(2)=38.3%). QTL effects were in the predicted direction (wild alleles decreased self-pollination and seed germination). The present analysis differentiated between loci governing SI and SP and identified DNA markers for bypassing SI and seed dormancy in elite x wild crosses through marker-assisted selection.

Chromosome Mapping↗