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At least 1,117 records · Page 62Linked to original sources
PubMed2005

QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments.

To genetically dissect drought resistance associated with japonica upland rice, we evaluated a doubled haploid (DH) population from a cross between two japonica cultivars for seven root traits under three different growing conditions (upland, lowland and upland in PVC pipe). The traits included basal root thickness (BRT), total root number (RN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), ratio of root fresh weight to shoot fresh weight (RFW/SFW) and ratio of root dry weight to shoot dry weight (RDW/SDW). The BRT was significantly correlated with the index of drought resistance, which was defined as the ratio of yield under the stress of the upland condition to that under the normal lowland condition. A complete genetic linkage map with 165 molecular markers covering 1,535 cM was constructed. Seven additive quantitative trait loci (QTLs) and 15 pairs of epistatic loci for BRT and RN were identified under upland and lowland conditions, and 12 additive QTLs and 17 pairs of epistatic QTLs for BRT, RN, MRL, RFW, RFW/SFW and RDW/SDW were identified under the PVC pipe condition. Four additive QTLs and one pair of epistatic QTLs controlling IDR were also found. These QTLs individually explained up to 25.6% of the phenotypic variance. QTL x environment (Q x E) interactions were detected for all root traits, and the contributions of these interactions ranged from 1.1% to 19.9%. Five co-localized QTLs controlling RFW and RDW, RFW/SFW, RDW/SDW and IDR, BRT and RN, RN, MRL and IDR were found. Four types of QTLs governing BRT and RN were classified by their detection in the upland and lowland conditions. Some common QTLs for root traits across different backgrounds were also revealed. These co-localized QTLs and common QTLs will facilitate marker-assisted selection for root traits in rice breeding programs.

Adaptation, Physiological↗
PubMed2001

Markers for mapping by admixture linkage disequilibrium in African American and Hispanic populations.

Population linkage disequilibrium occurs as a consequence of mutation, selection, genetic drift, and population substructure produced by admixture of genetically distinct ethnic populations. African American and Hispanic ethnic groups have a history of significant gene flow among parent groups, which can be of value in affecting genome scans for disease-gene discovery in the case-control and transmission/disequilibrium test designs. Disease-gene discovery using mapping by admixture linkage disequilibrium (MALD) requires a map of polymorphic markers that differentiate between the founding populations, along with differences in disease-gene allele frequencies. We describe markers appropriate for MALD mapping by assessing allele frequencies of 744 short tandem repeats (STRs) in African Americans, Hispanics, European Americans, and Asians, by choosing STR markers that have large differences in composite delta, log-likelihood ratios, and/or I*(2) for MALD. Additional markers can be added to this MALD map by utilization of the rapidly growing single-nucleotide-polymorphism databases and the literature, to achieve a 3-10-cM scanning scale. The map will be useful for studies of diseases, including prostate and breast cancer, diabetes, hypertension, and end-stage renal disease, that have large differences in incidence between the founding populations of either Hispanics or African Americans.

Black or African American↗
PubMed2006

Developmental expression of Bis protein in the cerebral cortex and hippocampus of rats.

Bis (Bcl-2 interacting death suppressor), identified as a Bcl-2-binding protein, has been suggested to have diverse functions in addition to binding to Bcl-2, thereby regulating cell death. To investigate the potential role of Bis in the developing brain, the spatiotemporal expression of Bis protein was studied in the rat forebrain during prenatal and early postnatal development using immunohistochemistry. Initial expression of Bis was detected in the medial telencephalic wall of the lateral ventricle, the area most likely corresponded to the cortical hem from the earliest age examined (E13). There was an abrupt increase of immunoreactive neurons in the cortex and hippocampus during the first postnatal week, which declined thereafter. Two populations of Bis-immunoreactive neurons can be clearly distinguished in the developing forebrain: a population of differentiating and postmitotic neurons coexpressing Bis and microtubule-associated protein-2 (MAP-2), and a population of neurons with the characteristic morphology of Cajal-Retzius cells located exclusively in the marginal zone/layer I of the cortex and in the hippocampal equivalents of the marginal zone. The latter neurons were colabeled with reelin, a marker for Cajal-Retzius cells. While Bis expression in the cerebral cortex and hippocampus exists only transiently by P14, considerable expression was found to be maintained in the rostral migratory stream and the subventricular zone of the lateral ventricle, where Bis-immunoreactive cells were glutamine synthetase-positive glial cells. Our results suggest that Bis may contribute to the developmental processes, including the differentiation and maturation of specific neuronal populations in relation to Bcl-2 in the developing rat forebrain.

Adaptor Proteins, Signal Transducing↗
PubMed1988

Microcomputer mapping helps healthcare planners target market.

In the highly competitive healthcare arena, microcomputer maps illustrating everything from population shifts to sources of patient referrals are becoming important planning and marketing tools. Mapping can help facilities focus their marketing on the physician community in general or on particular physicians who may refer patients for specialized care. It can locate patients by type, physician, and other data; it can be used to illustrate requests for state approval of expansions and acquisitions; and it can help organizations target certain areas for changes in service delivery, marketing, or physician placement. Five basic components are needed to create microcomputer maps: a computer with graphics capabilities; an output device such as a printer or plotter; a data file; a boundary file; and mapping software.

Catchment Area, Health↗
PubMed2002

Detection of quantitative trait loci for protein percentage in muscle in resource pig population.

An intercross between Meishan and Large White pig population was used to map quantitative trait loci(QTL) for protein percentage in muscle. In the present study, all 135 F2 animals, their parents and their grandparents were genotyped for 24 microsatellites, which were in 1, 2 and 6 chromosome. The marker genotypes were used to calculate the additive and dominant coefficients at fixed position in the genome of each F2 animal, and the protein percentage were regressed on to the coefficients in intervals of 1 cM. Three significant QTLs effects were found for protein percentage in muscle. They were located between markers Sw1332 and Sw2130 at chromosome 1, between Sw2516 and Sw1201 at chromosome 2 and between Sw322 and Sw607 at chromosome 6(P < 0.05), and the explained residual variance were 0.91%, 12.76% and 4.60%, respectively. The results show that QTLs, which affect protein percentage, may be located in different chromosomes.

Animals↗
PubMed1996

[Use of body surface heart potential mapping for registration of electrical phenomenal in the atrium].

Research on body surface potential mapping concerned predominantly the ventricular excitation process. There is only very limited data available documenting surface potential distribution during atrial electric events. The goal of this study was to establish the pattern and criteria of the atrial potential maps in the healthy population, which is substantial for a prospective usefulness of the noninvasive registrations of surface maps in atrial arrhythmias. A group of 54 subjects in whom there was no clinical evidence of cardiac dysfunction underwent a procedure of body surface potential mapping. The recordings were performed using the HPM-7100 system simultaneously from 87 leads covering the entire thorax. Isopotential maps registered during the P wave were subjected to the statistical analysis by means of the own system "Heart Map" enabling the qualitative and quantitative estimation of the atrial maps. To avoid a problem of variable heart rate, a time standardization, by the division of the P wave into 10 time intervals, was applied. In order to eliminate an interindividual variability of heart location in the thorax, a distribution of the constituent values without subordinating them to the individual electrodes was proposed. In consequence, the group-mean isopotential maps of the wave P for the normal subjects were created. According to the migration of the maximum throughout the thoracic surface during the P wave, three phases of the isopotential atrial maps were determined: phase 1 (P1-P4) comprising initial 40% of the P wave, phase 2 (P5,P6)-next 20% of the P wave and phase 3 (P7-P10)-the terminal 40% of the P wave duration. These phases reflect the successive sequences of atrial excitation. During the whole atrial depolarization the minimum of potential, changing its value, was located around lead D7. Furthermore, in the results of the analysis of the constituent values sequences, for the P wave time intervals the additional quantitive parameters were calculated, i.e. areas designated by positive and negative potential and the ratio of these areas. The presented findings revealed that surface maps give the precious insight into spread of atrial excitation. Establishing of the distribution pattern and the criteria of the atrial potential maps for normals enables to undertake the further research on the use of this technique in a various atrial pathology.

Adult↗
PubMed2001

Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses.

Two complementary segregating plant populations of Coffea canephora were produced from the same clone. One population (DH) comprised 92 doubled haploids derived from female gametes, while the other population (TC) was a test cross consisting of 44 individuals derived from male gametes. Based on the DH population, a genetic linkage map comprising 160 loci was constructed. Eleven linkage groups that putatively correspond to the 11 gametic chromosomes of C. canephora were identified. The mapped loci included more than 40 specific sequence-tagged site markers, either single-copy RFLP probes or microsatellites, that could serve as standard landmarks in coffee-genome analyses. Furthermore, comparisons for segregation distortion and recombination frequency between the two populations were performed. Although segregation distortions were observed in both populations, the frequency of loci exhibiting a very pronounced degree of distortion was especially high in the DH population. This observation is consistent with the hypothesis of strong zygotic selection among the DH population. The recombination frequencies in both populations were found to be almost indistinguishable. These results offer evidence in favour of the lack of significant sex differences in recombination in C. canephora.

Cloning, Molecular↗
PubMed2003

Genetic analysis and molecular mapping of maize (Zea mays L.) stalk rot resistant gene Rfg1.

One single pathogen Fusarium graminearum Schw. was inoculated to maize inbred lines 1,145 (Resistant) and Y331 (Susceptive), and their progenies of F(1), F(2) and BC(1)F(1) populations. Field statistical data revealed that all of the F(1) individuals were resistant to the disease and that the ratio of resistant plants to susceptive plants was 3:1 in the F(2) population, and 1:1 in the BC(1)F(1 )population. The results revealed that a single dominant gene controls the resistance to F. graminearum Schw. The resistant gene to F. graminearum Schw. was denominated as Rfg1 according to the standard principle of the nomenclature of the plant disease resistant genes. RAPD (randomly amplified polymorphic DNA) combined with BSA (bulked segregant analysis) analysis was carried out in the developed F(2) and BC(1)F(1 )populations, respectively. Three RAPD products screened from the RAPD analysis with 820 Operon 10-mer primers showed the linkage relation with the resistant gene Rfg1. The three RAPD amplification products (OPD-20(1000), OPA-04(1100) and OPY-04(900)) were cloned and their copy numbers were determined. The results indicated that only OPY-04(900) was a single-copy sequence. Then, OPY-04(900) was used as a probe to map the Rfg1 gene with a RIL F(7) mapping population provided by Henry Nguyen, which was developed from the cross "S3xMo17". Rfg1 was primarily mapped on chromosome 6 between the two linked markers OPY-04(900) and umc21 (Bin 6.04-6.05). In order to confirm the primary mapping result, 25 SSR (simple sequence repeat) markers and six RFLP (restriction fragment length polymorphism) markers in the Rfg1 gene-encompassing region were selected, and their linkage relation with Rfg1 was analyzed in our F(2) population. Results indicated that SSR marker mmc0241 and RFLP marker bnl3.03 are flanking the Rfg1 gene with a genetic distance of 3.0 cM and 2.0 cM, respectively. This is the first time to name and to map a single resistant gene of maize stalk rot through a single pathogen inoculation and molecular marker analysis.

Chromosome Mapping↗
PubMed2003

Homoeologous loci control the accumulation of seed glucosinolates in oilseed rape (Brassica napus).

The genetic control of seed glucosinolate content in oilseed rape was investigated using two intervarietal backcross populations. Four QTLs segregating in the population derived from a Brassica napus L. 'Victor' x Brassica napus L. 'Tapidor' cross, together accounting for 76% of the phenotypic variation, were mapped. Three of these loci also appeared to control the accumulation of seed glucosinolates in a Brassica napus L. 'Bienvenu' x 'Tapidor' cross, and accounted for 86% of the phenotypic variation. The three QTLs common to both populations mapped to homoeologous regions of the B. napus genome, suggesting that seed glucosinolate accumulation is controlled by duplicate genes. It was possible to extend the comparative analysis of QTLs controlling seed glucosinolate accumulation by aligning the published genetic maps generated by several research groups. This comparative mapping demonstrated that high-glucosinolate varieties often carry low-glucosinolate alleles at one or more of the loci controlling seed glucosinolate accumulation.

Brassica napus↗
PubMed1999

Use of unlinked genetic markers to detect population stratification in association studies.

We examine the issue of population stratification in association-mapping studies. In case-control studies of association, population subdivision or recent admixture of populations can lead to spurious associations between a phenotype and unlinked candidate loci. Using a model of sampling from a structured population, we show that if population stratification exists, it can be detected by use of unlinked marker loci. We show that the case-control-study design, using unrelated control individuals, is a valid approach for association mapping, provided that marker loci unlinked to the candidate locus are included in the study, to test for stratification. We suggest guidelines as to the number of unlinked marker loci to use.

Alleles↗
PubMed1991

Restriction fragment length polymorphism-mediated targeting of the ml-o resistance locus in barley (Hordeum vulgare).

The ml-o locus in barley confers resistance to all known races of the fungus Erysiphe graminis f.sp. hordei. Since the molecular mechanisms underlying ml-o-mediated resistance are currently undefined, experiments have been initiated to isolate the gene by means of its map position. A collection of backcross lines containing ml-o alleles derived from six barley genotypes allowed us to identify a set of DNA markers very tightly linked to the resistance locus. These markers span an unexpectedly small segment of 8.6 centimorgans on chromosome 4 that includes the Ml-o locus. Two of the markers cosegregate with the resistance locus on the basis of 44 homozygous resistant plants identified within a segregating F2 population derived from an intravarietal cross. Colinearity of the resistance-linked markers was confirmed in an F2 mapping population derived from a wide cross between Hordeum vulgare subsp. vulgare and Hordeum vulgare subsp. spontaneum. The two markers cosegregating with the resistance locus in the former cross define in the latter cross an interval of 2.4 centimorgans within which Ml-o is most probably situated. The set of linked markers opens up the possibility of carrying out a bidirectional chromosomal walk or jump to the gene.

Journal Article↗
PubMed2004

Optimal designs for linkage disequilibrium mapping and candidate gene association tests in livestock populations.

Simulation was used to evaluate the performance of different selective genotyping strategies when using linkage disequilibrium across large half-sib families to position a QTL within a previously defined genomic region. Strategies examined included standard selective genotyping and different approaches of discordant and concordant sib selection applied to arbitrary or selected families. Strategies were compared as a function of effect and frequency of QTL alleles, heritability, and phenotypic expression of the trait. Large half-sib families were simulated for 100 generations and 2% of the population was genotyped in the final generation. Simple ANOVA was applied and the marker with the greatest F-value was considered the most likely QTL position. For traits with continuous phenotypes, genotyping the most divergent pairs of half-sibs from all families was the best strategy in general, but standard selective genotyping was somewhat more precise when heritability was low. When the phenotype was distributed in ordered categories, discordant sib selection was the optimal approach for positioning QTL for traits with high heritability and concordant sib selection was the best approach when genetic effects were small. Genotyping of a few selected sibs from many families was generally more efficient than genotyping many individuals from a few highly selected sires.

Alleles↗
PubMed1997

World population in a grid of spherical quadrilaterals.

"We report on a project that converted subnational population data to a raster of cells on the earth. We note that studies using satellites as collection devices yield results indexed by latitude and longitude. Thus it makes sense to assemble the terrestrial arrangement of people in a compatible manner. This alternative is explored here, using latitude/longitude quadrilaterals as bins for population information.... The results to date of putting world boundary coordinates together with estimates of the number of people are described. The estimated 1994 population of 219 countries, subdivided into 19,032 polygons, has been assigned to over six million five minute by five minute quadrilaterals covering the world."

Data Collection↗
PubMed2007

Short communication: detection of quantitative trait loci influencing somatic cell score in Spanish Churra sheep.

Eleven half-sib ovine families, including 1,421 Spanish Churra ewes, were analyzed for 181 microsatellite markers spanning the entire autosomic ovine genome. Using a multimarker regression method, a daughter experimental design was used to identify putative quantitative trait loci (QTL) affecting the somatic cell score (SCS). Chromosome-wise significance thresholds were set empirically by permuting the phenotypic data. Marker order and genetic distances of the autosomic linkage map built for this commercial population were in accordance with the published ovine linkage map. An across-family association analysis revealed a region on chromosome 20 suggestive of evidence for a QTL. Segregation of the QTL into 2 families was inferred from the within-family analysis, and differences in the position of the suggested QTL were found between the 2 half-sib groups. This could be the result of incomplete information associated with the markers for the significant families. The location of the major histocompatibility complex in proximity to the across-family effect suggests this region may harbor a segregating QTL for the SCS in the Churra population. Studies in dairy cattle examining the SCS have reported linkage associations on corresponding bovine orthologous regions, supporting the validity of our findings.

Animals↗
PubMed2006

Development of a linkage map and mapping of phenotypic polymorphisms in a free-living population of Soay sheep (Ovis aries).

An understanding of the determinants of trait variation and the selective forces acting on it in natural populations would give insights into the process of evolution. The combination of long-term studies of individuals living in the wild and better genomic resources for nonmodel organisms makes achieving this goal feasible. This article reports the development of a complete linkage map in a pedigree of free-living Soay sheep on St. Kilda and its application to mapping the loci responsible for three morphological polymorphisms for which the maintenance of variation demands explanation. The map was derived from 251 microsatellite and four allozyme markers and covers 3350 cM (approximately 90% of the sheep genome) at approximately 15-cM intervals. Marker order was consistent with the published sheep map with the exception of one region on chromosome 1 and one on chromosome 12. Coat color maps to chromosome 2 where a strong candidate gene, tyrosinase-related protein 1 (TYRP1), has also been mapped. Coat pattern maps to chromosome 13, close to the candidate locus Agouti. Horn type maps to chromosome 10, a location similar to that previously identified in domestic sheep. These findings represent an advance in the dissection of the genetic diversity in the wild and provide the foundation for QTL analyses in the study population.

Animals↗
PubMed1997

Statistical methods in computational anatomy.

This paper reviews recent developments by the Washington/Brown groups for the study of anatomical shape in the emerging new discipline of computational anatomy. Parametric representations of anatomical variation for computational anatomy are reviewed, restricted to the assumption of small deformations. The generation of covariance operators for probabilistic measures of anatomical variation on coordinatized submanifolds is formulated as an empirical procedure. Populations of brains are mapped to common coordinate systems, from which template coordinate systems are constructed which are closest to the population of anatomies in a minimum distance sense. Variation of several one-, two- and three-dimensional manifolds, i.e. sulci, surfaces and brain volumes are examined via Gaussian measures with mean and covariances estimated directly from maps of templates to targets. Methods are presented for estimating the covariances of vector fields from a family of empirically generated maps, posed as generalized spectrum estimation indexed over the submanifolds. Covariance estimation is made parametric, analogous to autoregressive modelling, by introducing small deformation linear operators for constraining the spectrum of the fields.

Algorithms↗
PubMed2002

Genetic analysis and QTL mapping of early root bulking in an F1 population of non-inbred parents in cassava ( Manihot esculenta Crantz).

The genetic basis of early bulking in cassava was studied in a replicated, multi-locational trial using 144 F1 progeny derived from an intra-specific cross between two non-inbred parents. A second, sequential harvest experiment examined the relative importance of eight yield-related traits on early bulking and their QTLs during the crop growth cycle. Our objectives were to identify traits, and genes controlling them, strongly associated with early yield as a first step to marker-assisted improvement of the trait. Multiple linear regression analysis and stepwise regression of early yield on eight yield-related traits revealed harvest index, dry foliage weight and root diameter as the most important factors associated with early yield. A total of 18 QTLs controlling early yield were identified in the first and second experiments and 27 QTLs, 2 for dry foliage weight, 8 for harvest index and 17 for root diameter, in the second experiment. The individual effects of alleles at these QTLs identified ranged from 7% to 33% of the phenotypic variance explained. Seven of 18 QTLs found for early yield (39%) coincided with QTLs associated with one or more traits with significant influence on early yield. The results show that sink and source capacities are very important in determining early yield. The identification of a number of QTLs with positive effect for increased early yield provides an opportunity for marker-assisted selection and improvement of early bulking potential in cassava.

Chromosome Mapping↗
PubMed1994

Approximate thresholds of interval mapping tests for QTL detection.

A general method is proposed for calculating approximate thresholds of interval mapping tests for quantitative trait loci (QTL) detection. Simulation results show that this method, when applied to backcross and F2 populations, gives good approximations and is useful for any situation. Programs which calculate these thresholds for backcross, recombinant inbreds and F2 for any given level and any chromosome with any given distribution of codominant markers were written in Fortran 77 and are available under request. The approach presented here could be used to obtain, after suitable calculations, thresholds for most segregating populations used in QTL mapping experiments.

Biometry↗