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PubMed1986

Urban cats: characteristics and estimation of mortality due to motor vehicles.

The present study was undertaken to characterize and estimate cat mortality caused by motor vehicles in Baltimore, Md. Analysis of Municipal Animal Shelter records revealed that the number of dead cats annually removed from Baltimore streets averaged 2,721 over 3 years. The number of cats removed per year was notably constant (range 2,621 to 2,917), with a consistently greater number of animals being picked up during summer months. A map of the location of 634 dead cats removed from city streets showed that areas of highest cat mortality were associated with areas of highest human population density. This map was used to stratify Baltimore into areas of high, medium, and low cat mortality for subsequent stratified random placement of tagged dead cats for the mark-recapture study. One hundred fifteen tagged dead cats were placed on city streets during the course of 1 year, and 50.5% were retrieved by the Municipal Animal Shelter. We estimate over 5,000 free-ranging cats are killed by automobiles/year in Baltimore. Analysis of 212 dead cats removed from city streets showed that the majority were male (63%) and that most animals were sexually intact (90%). At least 20% of the dead animals was previously owned, and few kittens or juvenile cats were found in the sample.

Accidents, Traffic↗
PubMed2004

[Mapping QTLs of soybean root weight with RIL population NJRIKY].

The recombinant inbred line (RIL) population, NJRIKY with 184 families derived from a cross Kefeng No.1 x Nannong1138-2 was used in mapping QTLs of root weight of soybean. Based on the linkage map constructed by Wang, with the software Cartographer V. 1.21 of the composite interval mapping procedure, three QTLs of root weight were mapped on N3-B1 and N6-C2 linkage group. The left telomere distance of rw1 was 66.31cM on N3-B1 linkage group, and those of rw2 and rw3 were 169.91cM and 179.71 cM, respectively, on N6-C2 linkage group. The former was located in A520T approximately ACCCAGO5 and the latter were overlapped with OPW13 and ACGCATO6, respectively. Their LOD values were 10.34,4.01 and 3.15, respectively. The QTLs of the root weight explained 26.3%,9.2% and 6.8% of the total variation, and their additive effects were -0.514,-0.303 and -0.260, respectively.

Chromosome Mapping↗
PubMed1976

Mapping of mitochondrial genes in Saccharomyces cerevisiae. Populations and pedigree analysis of retention or loss of four genetic markers in Rho-cells.

1. Retention or loss of mitochondrial markers CR321, OR1, PR454, TR (gene loci RIB1, OLI1, PAR1, TSM1 respectively has been analysed in a large number of ethidium bromide induced primary rho-clones. Retention of one or more of the four markers with a single clone was observed frequently, only 20 to 25% of clones were found to be (TOCOOOPO). Primary clones retaining two or more of the four markers were found to be mixed, i.e. the primary rho- cell contained a heterogeneous population of variously deleted mitDNA molecules which segregated into different cell lines in the corresponding primary clone. 2. A representative sample of the population of ethidium bromide induced rho- mutants has been analysed by a first subcloning performed after some 30 cell generations of vegetative multiplication in the abscence of the drug. At this level the heterogeneous population of mitDNA molecules, generated by the mutagenic treatment in the primary cell, has been sorted out. The cells forming secondary clones are thus essentially homoplasmic. In contrast to primary clones, genotypes of secondary clones therefore could be determined unambiguously, and the frequency of cell types can be regarded as a faithful representation of the frequency of mitDNA molecules. Retention of markers was low, in less than 2% of secondary clones one or several markers have been found. This observation has been interpreted as indicating that induction of rho-mutants by ethidium bromide is accompanied by deletion of very large sequences of mitDNA in a very large fraction of mitDNA molecules. 3. Five individual rho-clones retaining the four markers TRCRORPR have been isolated and analysed for spontaneous deletion of one or several of these markers during successive subclonings (pedigree analysis). High genetic stability (98-99.5% per cell generation) has been observed in these clones. 4. A method has been developed allowing an unambiguous determination of the order of the four markers on a circular map. It is based on the concomitant loss of two markers and retention of the other two markers (double loss/double retention analysis). The results of four out of five pedigrees of individual rho-clones analysed (spontaneous deletion) and the results of the analysis of populations of secondary rho-clones (ethidium bromide induced deletion) were in full agreement and the order of genes has been determined as being P-T-C-O-P. In the fifth pedigree results suggest an inversion of the T and C markers. 5. Relative distances between pairs of markers have been derived from the frequencies of separation of markers by deletion and were found to be C-T less than C-O less than T-O less than T-P less than C-P less than O-P. Linkage of the four markers could be established, and distances calculated are additive. 6. The general relevance of this approach of mapping by deletion and the methods used for the determination of order and distances of mitochondrial genes has been discussed. (ABSTRACT TRUNCATED)

DNA, Mitochondrial↗
PubMed2004

Dog star rising: the canine genetic system.

Purebred dogs are providing invaluable information about morphology, behaviour and complex diseases, both of themselves and humans, by supplying tractable populations in which to map genes that control those processes. The diversification of dog breeds has led to the development of breeds enriched for particular genetic disorders, the mapping and cloning of which have been facilitated by the availability of the canine genome map and sequence. These tools have aided our understanding of canine population genetics, linkage disequilibrium and haplotype sharing in the dog, and have informed ongoing efforts of the need to identify quantitative trait loci that are important in complex traits.

Animals↗
PubMed1995

Influence of infectious dose upon productive replication and transynaptic passage of pseudorabies virus in rat central nervous system.

Pseudorabies virus (PRV) is a neurotropic swine alpha herpesvirus that characteristically invades the nervous system and replicates within synaptically-linked populations of neurons. The invasive characteristics and ability of this family of viruses to replicate in neurons of the central nervous system (CNS) have been exploited to map functionally related populations of neurons in a variety of systems. In this report, we examined the effects of strain and concentration on the ability of PRV to infect retinal ganglion cells and pass transneuronally through central visual circuits. We find that the ability of virulent (PRV-Becker) and attenuated (PRV-Bartha) strains of PRV to produce a productive infection of visual circuitry is directly dependent upon the infectious of the injected virus. Injections of at least 10(5) total plaque forming units produce 100% infectivity, whereas lower infectious doses substantially reduce the percentage of animals exhibiting productive infection via this route of inoculation. Furthermore, the virulent strain of PRV consistently infects a higher percentage of animals across a broader range of titers than attenuated virus. These data demonstrate that viral titer and strain are important variables that should be considered in the design of studies and interpretation of data derived from investigations employing this pathogen for circuit analysis.

Animals↗
PubMed2005

QTL analysis of fruit components in the progeny of a Rennell Island Tall coconut (Cocos nucifera L.) individual.

We investigated the genetic factors controlling fruit components in coconut by performing QTL analyses for fruit component weights and ratios in a segregating progeny of a Rennell Island Tall genotype. The underlying linkage map of this population was already established in a previous study, as well as QTL analyses for fruit production, which were used to complement our results. The addition of 53 new markers (mainly SSRs) led to minor amendments in the map. A total of 52 putative QTLs were identified for the 11 traits under study. Thirty-four of them were grouped in six small clusters, which probably correspond to single pleiotropic genes. Some additional QTLs located apart from these clusters also had relatively large effects on the individual traits. The QTLs for fruit component weight, endosperm humidity and fruit production were found at different locations in the genome, suggesting that efficient marker-assisted selection for yield can be achieved by selecting QTLs for the individual components. The detected QTLs descend from a genotype belonging to the "Pacific" coconut group. Based on the known molecular and phenotypic differences between "Pacific" and "Indo-Atlantic" coconuts, we suggest that a large fraction of coconut genetic diversity is still to be investigated by studying populations derived from crosses between these groups.

Chromosome Mapping↗
PubMed2001

Quantitative trait loci mapping associated with plant regeneration ability from seed derived calli in rice (Oryza sativa L.).

Quantitative trait loci (QTLs), which are associated with the ability of plant regeneration from seed derived calli, were detected using a recombinant inbred (RI) population from a cross between 'Milyang 23 (toingil)' and 'Gihobyeo (japonica)' in rice (Oryza sativa L.). A tongil type cultivar, 'Milyang 23', has a lower frequency of callus induction and plant regeneration than those of japonica 'Gihobyeo'. Transgressive segregations were observed for the callus induction rate and plant regeneration ability from seed derived calli of the RI population. An interval mapping analysis was used to identify the QTL controlling the plant regeneration ability. Two QTLs for the callus induction rate were detected on chromosomes 1 and 2, explaining the 10.9% total phenotypic variation. Four QTLs that are associated with the plant regeneration ability were located on chromosomes 2, 3, and 11, accounting for 25.7% of the total phenotypic variation.

Chromosome Mapping↗
PubMed1997

New microsatellite markers in chicken optimized for automated fluorescent genotyping.

We have isolated and developed 180 new polymorphic chicken microsatellite markers. In addition, primers have been developed for 91 microsatellites derived from the GenBank sequence database (isolated by the laboratory of Terry Burke, Leicester University), of which 89 were polymorphic, and six existing polymorphic markers (HUJ) have been modified. The primer sequences were designed to allow optimal performance of the markers, in sets containing multiple microsatellites, on ABI sequencers. The average number of alleles for the 275 polymorphic markers described was 4.0. Of these markers, 93% were polymorphic in the Wageningen resource population whereas 57% of the markers were polymorphic in the East Lansing reference population and only 44% could be mapped in the Compton reference population. The microsatellite markers described in this paper, in combination with the microsatellite markers published previously, are particularly well suited for performing a total genome scan for the detection of quantitative trait loci (QTL).

Animals↗
PubMed2004

Isolation and mapping of resistance gene analogs from the Avena strigosa genome.

Degenerate primers based on conserved regions of the nucleotide binding site (NBS) domain (encoded by the largest group of cloned plant disease resistance genes) were used to isolate a set of 15 resistance gene analogs (RGA) from the diploid species Avena strigosa Schreb. These were grouped into seven classes on the basis of 60% or greater nucleic acid sequence identity. Representative clones were used for genetic mapping in diploid and hexaploid oats. Two RGAs were mapped at two loci of the linkage group AswBF belonging to the A. strigosa x A. wiestii Steud map, and ten RGAs were mapped at 15 loci in eight linkage groups belonging to the A. byzantina C. Koch cv. Kanota x A. sativa L. cv. Ogle map. A similar approach was used for targeting genes encoding receptor-like kinases. Three different sequences were obtained and mapped to two linkage groups of the hexaploid oat map. Associations were explored between already known disease resistance loci mapped in different populations and the RGAs. Molecular markers previously linked to crown rust and barley yellow dwarf resistance genes or quantitative trait loci were found in the Kanota x Ogle map linked to RGAs at a distance ranging from 0 cM to 20 cM. Homoeologous RGAs were found to be linked to loci either conferring resistance to different isolates of the same pathogen or to different pathogens. This suggests that these RGAs identify genome regions containing resistance gene clusters.

Amino Acid Sequence↗
PubMed2006

QTL mapping for plant architecture traits in upland cotton using RILs and SSR markers.

Xiangzamian 2 (XZM2) is the most widely cultivated cotton hybrid in China. By crossing two parents Zhongmiansuo12 and 8891 and upon subsequent selfings, we got F8 and F9 populations having 180 recombinant inbred lines. Ten plant architecture traits were investigated in two years with this population. A genetic map was constructed mainly with SSR markers. Quantitative trait loci (QTL) conditioning plant architecture traits were determined at the single-locus and double-locus levels. The results showed that epistastic effects as well as additive effects of QTL played an important role as the genetic basis of cotton plant architecture. The QTL detected in our research might provide new information on improving plant architecture traits. The polymorphism of molecular markers between ZMS12 and 8891 were quite limited, while significant differences between their phenotypes were found and the hybrid XZM2 expressed high heterosis in yield. All these could be partly explained by the effect of epistatic QTL.

Breeding↗
PubMed2023

The genetic basis of adaptation to copper pollution in Drosophila melanogaster.

Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity to characterize the genetic mechanisms that contribute to metal resistance in natural populations. Methods: We examined variation in resistance to copper, a common heavy metal contaminant, using wild collections of the model organism Drosophila melanogaster. Flies were collected from multiple sites that varied in copper contamination risk. We characterized phenotypic variation in copper resistance within and among populations using bulked segregant analysis to identify regions of the genome that contribute to copper resistance. Results and Discussion: Copper resistance varied among wild populations with a clear correspondence between resistance level and historical exposure to copper. We identified 288 SNPs distributed across the genome associated with copper resistance. Many SNPs had population-specific effects, but some had consistent effects on copper resistance in all populations. Significant SNPs map to several novel candidate genes involved in refolding disrupted proteins, energy production, and mitochondrial function. We also identified one SNP with consistent effects on copper resistance in all populations near CG11825, a gene involved in copper homeostasis and copper resistance. We compared the genetic signatures of copper resistance in the wild-derived populations to genetic control of copper resistance in the Drosophila Synthetic Population Resource (DSPR) and the Drosophila Genetic Reference Panel (DGRP), two copper-naïve laboratory populations. In addition to CG11825, which was identified as a candidate gene in the wild-derived populations and previously in the DSPR, there was modest overlap of copper-associated SNPs between the wild-derived populations and laboratory populations. Thirty-one SNPs associated with copper resistance in wild-derived populations fell within regions of the genome that were associated with copper resistance in the DSPR in a prior study. Collectively, our results demonstrate that the genetic control of copper resistance is highly polygenic, and that several loci can be clearly linked to genes involved in heavy metal toxicity response. The mixture of parallel and population-specific SNPs points to a complex interplay between genetic background and the selection regime that modifies the effects of genetic variation on copper resistance.

Drosophila↗
PubMed2002

Genetic dissection of seed shattering, agronomic, and color traits in American wildrice ( Zizania palustris var. interior L.) with a comparative map.

A comparative map of American wildrice ( Zizania palustris var. interior L.) was used to identify loci controlling seed shattering, plant height, maturity, tiller number, plant habit, panicle length seed length, and color traits. Two to six significant quantitative-trait-loci (QTLs, P < 0.05) were detected for each trait evaluated, representing the first trait-mapping in wildrice. The chosen population was designed to emphasize the mapping of loci controlling the shattering trait, which is the most important trait in the management of this newly domesticated species. Three loci were detected that controlled the discretely categorized variation between shattering and non-shattering plants. Seed-shattering loci were detected and validated among the F(2) and F(3) generations. A multiple regression model with these three loci described 49.6% of the additive genetic variation. A genetic model with the same three loci including dominance and locus interactions predicted the shattering versus non-shattering phenotype at a success rate of 87%. The comparative map was based on mapped RFLP markers used in white rice ( Oryza sativa L.) and other grass species. Anchor loci provided a reference point for the identification of potential orthologous genes on the basis of white rice mutant loci and consensus grass species QTLs. Candidate orthologous loci were identified among all traits evaluated. The study underscores the benefits of extending trait analysis through comparative mapping, as well as challenges of QTL analysis in a newly domesticated species.

Journal Article↗
PubMed2006

Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize.

Quantitative trait loci (QTL) detection experiments have often been restricted to large biallelic populations. Use of connected multiparental crosses has been proposed to increase the genetic variability addressed and to test for epistatic interactions between QTL and the genetic background. We present here the results of a QTL detection performed on six connected F(2) populations of 150 F(2:3) families each, derived from four maize inbreds and evaluated for three traits of agronomic interest. The QTL detection was carried out by composite interval mapping on each population separately, then on the global design either by taking into account the connections between populations or not. Epistatic interactions between loci and with the genetic background were tested. Taking into account the connections between populations increased the number of QTL detected and the accuracy of QTL position estimates. We detected many epistatic interactions, particularly for grain yield QTL (R(2) increase of 9.6%). Use of connections for the QTL detection also allowed a global ranking of alleles at each QTL. Allelic relationships and epistasis both contribute to the lack of consistency for QTL positions observed among populations, in addition to the limited power of the tests. The potential benefit of assembling favorable alleles by marker-assisted selection are discussed.

Epistasis, Genetic↗
PubMed2005

Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels.

The use of inbred strains of mice to dissect the genetic complexity of common diseases offers a viable alternative to human studies, given the control over experimental parameters that can be exercised. Central to efforts to map susceptibility loci for common diseases in mice is a comprehensive map of DNA variation among the common inbred strains of mice. Here we present one of the most comprehensive high-density, single nucleotide polymorphism (SNP) maps of mice constructed to date. This map consists of 10,350 SNPs genotyped in 62 strains of inbred mice. We demonstrate the utility of these data via a novel integrative genomics approach to mapping susceptibility loci for complex traits. By integrating in silico quantitative trait locus (QTL) mapping with progressive QTL mapping strategies in segregating mouse populations that leverage large-scale mapping of the genetic determinants of gene expression traits, we not only facilitate identification of candidate quantitative trait genes, but also protect against spurious associations that can arise in genetic association studies due to allelic association among unlinked markers. Application of this approach to our high-density SNP map and two previously described F2 crosses between strains C57BL/6J (B6) and DBA/2J and between B6 ApoE(-/-) and C3H/HeJ ApoE(-/-) results in the identification of Insig2 as a strong candidate susceptibility gene for total plasma cholesterol levels.

Animals↗
PubMed1996

Echo-planar MR determination of relative cerebral blood volume in human brain tumors: T1 versus T2 weighting.

PURPOSE: Maps related to relative cerebral blood volume (rCBV) were generated with the use of the T1 effects produced by a low-dose bolus passage of gadopentetate dimeglumine. The T1 maps were evaluated in a tumor population and compared with rCBV maps obtained with T2-weighted measurements. METHODS: Imaging was performed in 19 patients with suspected intraaxial brain tumors. For the T1 rCBV maps, a low-dose bolus of contrast material was given during T1-weighted interleaved spin-echo echo-planar MR imaging. This was followed by a second injection during serial T2-weighted imaging for generation of the T2 rCBV maps. RESULTS: Among patients with low-grade lesions (n = 9), T1-based and T2-based rCBV maps showed comparably low rCBV in 7 subjects. In the other 2 patients, with confirmed tumor dedifferentiation, elevation of rCBV values was seen on maps obtained with both techniques. Among patients with high-grade tumors (n = 10), 4 had no evidence of recurrence and 6 did have tumor recurrence (confirmed by follow-up and positron emission tomography). In patients with the high-grade lesions exhibiting conventional contrast enhancement, lesions tended to have higher estimated values on T1 rCBV maps than on the T2 rCBV maps. CONCLUSION: Although the T1 rCBV maps showed less contrast as compared with the T2 rCBV maps, they provided diagnostic information that was comparable to the T2 rCBV maps in our series of 19 patients with primary brain tumors.

Adult↗
PubMed2002

Mapping of genes controlling aluminum tolerance in rice: comparison of different genetic backgrounds.

Aluminum toxicity is the main factor limiting the productivity of crop plants in acid soils, particularly in the tropics and subtropics. In this study, a doubled-haploid population derived from the rice ( Oryza sativa L.) breeding lines CT9993 and IR62266 was used to map genes controlling Al tolerance. A genetic linkage map consisting of 280 DNA markers (RFLP, AFLP and SSR) was constructed to determine the position and nature of quantitative trait loci (QTLs) affecting Al tolerance. Three characters - control root length (CRL), Al-stressed root length (SRL) and root length ratio (RR) - were evaluated for the DH lines and the parents at the seedling stage in nutrient solution. A total of 20 QTLs controlling root growth under Al stress and control conditions were detected and distributed over 10 of the 12 rice chromosomes, reflecting multigenic control of these traits. The two QTLs of largest effect, qALRR-1-1 and qALRR-8 for root length ratio (a measurement of Al tolerance) were localized on chromosomes 1 and 8, respectively. Three other QTLs in addition to qALRR-8 were apparently unique in the CT9993 x IR62266 mapping population, which may explain the high level of Al tolerance in CT9993. Comparative mapping identified a conserved genomic region on chromosome 1 associated with Al tolerance across three rice genetic backgrounds. This region provides an important starting point for isolating genes responsible for different mechanisms of aluminum tolerance and understanding the genetic nature of this trait in rice and other cereals.

Aluminum↗
PubMed2001

Determinants of mean arterial pressure and pulse pressure in chronic haemodialysis patients.

Hypertension is highly prevalent in the dialysis population, and has been implicated in the pathogenesis of the observed excess of cardiovascular morbidity and mortality in these patients. Nevertheless, there are no reports on the clinical and biochemical determinants of both pulse pressure (PP) and mean arterial pressure (MAP) in dialysis populations. A total of 541 haemodialysed patients from 11 dialysis centres were included in the study. The demographic, clinical, and biological characteristics were recorded. Both pre- and post- dialytic blood pressures (systolic and diastolic) were measured. PP and MAP were calculated. Mean predialytic PP was 67 +/- 17 mm Hg and significantly decreased after dialysis (60 +/- 18 mm Hg; P < 0.0001). In multivariate analysis, a 10 mm Hg increase in PP was positively associated with age (RR, 2.01; 95% CI, 1.35-5.01, for a 10-year increase in age), diabetes mellitus (RR, 1.08; 95% CI, 1.04-1.14), interdialytic weight gain (IWG) (RR, 1.84; 95% CI, 1.07-3.18, for 1% increase in IWG), and current smoking (RR, 2.59; 95% CI, 1.13-5.92) and negatively with Hb concentration (RR, 0.92; 95% CI, 0.84-0.99, for a 1 g/100 ml in Hb). Mean predialytic MAP was 98 +/- 15 mm Hg and significantly decreased after dialysis (91 +/- 16 mm Hg; P < 0.0001). In multivariate analysis, a 10 mm Hg increase in MAP was positively associated with parathyroid hormone (PTH) (RR, 1.32; 95% CI, 1.15-1.6, for 50 ng/ml in PTH), erythropoietin (EPO) treatment (RR, 1.09; 95% CI, 1.03-1.16), and current smoking (RR, 1.87; 95% CI, 1.39-2.41). PP and MAP are associated with different clinical parameters. Most of these factors are potentially reversible. Smoking cessation, correction of anaemia and limitation of IWG should be important challenges for physicians in care of dialysis patients.

Age Factors↗
PubMed2004

Mapping genes for common diseases: the case for genetic (LD) maps.

We examine the current effort to develop a haplotype map of the human genome and suggest an alternative approach which represents linkage disequilibrium patterns in the form of a metric LD map. LD maps have some of the useful properties of genetic linkage maps but have a much higher resolution which is optimal for SNP-based association mapping of common diseases. The studies that have been undertaken to date suggest that LD and recombination maps show some close similarities because of abundant, narrow, recombination hot spots. These hot spots are co-localised in all populations but, unlike linkage maps, LD maps differ in scale for different populations because of differences in population history. The prospects for developing optimized panels of SNPs and the use of linkage disequilibrium maps in disease gene localisation are assessed in the light of recent evidence.

Chromosome Mapping↗