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At least 757 records · Page 42Linked to original sources
PubMed2004

Comparative high resolution map of the six-rowed spike locus 1 (vrs1) in several populations of barley, Hordeum vulgare L.

Multiple alleles at the vrs1 locus control the development and fertility of the lateral spikelets of barley (Hordeum vulgare L.), which is a key character in the study of yield, utilization and domestication. In this study, six linkage maps of the vrs1 locus were constructed, using different mapping populations developed from nine different barley cultivars (H. vulgare subsp. vulgare) or mutant and wild barley (H. vulgare subsp. spontaneum). A total of 8387 chromosomes (gametes) were sampled for analysis based on a hypothesis that orders of marker loci were the same over the different parental lines. The results showed that four markers and the vrs1 locus in all cases were arranged in the same order, which was in a good agreement with the hypothesis. This makes the linkage maps suitable for the positional cloning of the alleles at the vrs1 locus.

Alleles↗
PubMed2006

The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers.

Characterizing the extent of linkage disequilibrium (LD) in the genome is a pre-requisite for association mapping studies. Patterns of LD also contain information about the past demography of populations. In this study, we focus on the Icelandic population where LD was investigated in 12 regions of approximately 15 cM using regularly spaced microsatellite loci displaying high heterozygosity. A total of 1753 individuals were genotyped for 179 markers. LD was estimated using a composite disequilibrium measure based on unphased data. LD decreases with distance in all 12 regions and more LD than expected by chance can be detected over approximately 4 cM in our sample. Differences in the patterns of decrease of LD with distance among genomic regions were mostly due to two regions exhibiting, respectively, higher and lower proportions of pairs in LD than average within the first 4 cM. We pooled data from all regions, except these two and summarized patterns of LD by computing the proportion of pairs of loci exhibiting significant LD (at the 5% level) as a function of distance. We compared observed patterns of LD with simulated data sets obtained under scenarios with varying demography and intensity of recombination. We show that unphased data allow to make inferences on scaled recombination rates from patterns of LD. Patterns of LD in Iceland suggest a genome-wide scaled recombination rate of rho* = 200 (130-330) per cM (or an effective size of roughly 5000), in the low range of estimates recently reported in three populations from the HapMap project.

Biological Evolution↗
PubMed2004

Mapping disease-susceptibility genes in admixed populations using interval principal component tests.

Family-based association approach for mapping disease-susceptibility genes of complex human diseases is a topical issue in genetic epidemiology. It is well known that admixture between genetically differentiated populations can result in high levels of linkage disequilibrium at loci separated far apart. This property has been capitalized upon to reduce the burden of genotyping in a genomewide association scan. The authors describe a new approach for admixture mapping--the "interval principal component test" (IPCT). The genome is divided into a multitude of non-overlapping "intervals" (with interval length of 10-20 cM) and the information of the markers in the same interval is integrated using the principal component analysis. Monte-Carlo simulation shows that an interval-by-interval scan using IPCT has much better performances than a conventional marker-by-marker scan using the transmission/disequilibrium test (TDT).

Computer Simulation↗
PubMed2001

Bayesian association mapping for quantitative traits in a mixture of two populations.

We introduce a novel Bayesian approach to estimate and account for population structure simultaneously with association mapping of multiple quantitative trait loci. The method is designed for an analysis of unrelated individuals from a mixture of two populations (no admixture), where the individual population memberships are unknown. In our approach, the population structure is estimated and accounted for by using data on additional "grouping" markers which are assumed to be in Hardy-Weinberg equilibrium within the populations but have different allele frequencies between the populations. We use Bayesian hierarchical modeling and Markov chain Monte Carlo estimation, where we allow both population stratification and genetic heterogeneity. In our model the number of quantitative trait loci and their positions are treated as random variables, and we obtain their posterior distributions. Here we select the candidate and the grouping markers based on results from a preliminary SOLAR analysis.

Bayes Theorem↗
PubMed2005

Highly structured Asian Drosophila melanogaster populations: a new tool for hitchhiking mapping?

Mark-recapture experiments showed that D. melanogaster has high dispersal capabilities. Consistent with a highly migratory species, only very low levels of differentiation were described for D. melanogaster populations from the same continent. We reinvestigated the population structure in D. melanogaster using 49 polymorphic markers in 23 natural populations. While European and American D. melanogaster populations showed very low differentiation, Asian D. melanogaster populations were highly structured. Despite the high differentiation of Asian flies, we confirm that all non-African populations are derived from a single colonization event. We propose that the availability of D. melanogaster populations with high and low population structure provides a novel tool for the identification of ecologically important adaptations by hitchhiking mapping.

Animals↗
PubMed2005

Unbiased atlas formation via large deformations metric mapping.

The construction of population atlases is a key issue in medical image analysis, and particularly in brain mapping. Large sets of images are mapped into a common coordinate system to study intra-population variability and inter-population differences, to provide voxel-wise mapping of functional sites, and to facilitate tissue and object segmentation via registration of anatomical labels. We formulate the unbiased atlas construction problem as a Fréchet mean estimation in the space of diffeomorphisms via large deformations metric mapping. A novel method for computing constant speed velocity fields and an analysis of atlas stability and robustness using entropy are presented. We address the question: how many images are required to build a stable brain atlas?

Algorithms↗
PubMed2002

A genetic linkage map for watermelon derived from a testcross population: ( Citrullus lanatus var. citroides x C. lanatus var. lanatus) x Citrullus colocynthis.

A genetic linkage map was constructed for watermelon using a testcross population [Plant Accession Griffin 14113 ( Citrullus lanatus var. citroides) x New Hampshire Midget (NHM; C. lanatus var. lanatus)] x U.S. Plant Introduction (PI) 386015 ( Citrullus colocynthis). The map contains 141 randomly amplified polymorphic DNA (RAPD) markers produced by 78 primers, 27 inter-simple sequence repeat (ISSR) markers produced by 17 primers, and a sequence-characterized amplified region (SCAR) marker that was previously reported as linked (1.6 cM) to race-1 Fusarium wilt [incited by Fusarium oxysporum Schlechtend.:Fr. f. sp. niveum (E.F.Sm.) W.C. Synder & H.N. Hans] resistance in watermelon. The map consists of 25 linkage groups. Among them are a large linkage group that contains 22 markers covering a mapping distance of 225.6 cM and six large groups each with 10-20 markers covering a mapping distance of 68.8 to 110.8 cM. There are five additional linkage groups consisting of 3-7 markers per group, each covering a mapping distance of 36.5 to 57.2 cM. The 13 remaining linkage groups are small, each consisting of 2-11 markers covering a mapping distance of 3.5-29.9 cM. The entire map covers a total distance of 1,166.2 cM with an average distance of 8.1 cM between two markers. This map is useful for the further development of markers linked to disease resistance and watermelon fruit qualities.

Journal Article↗
PubMed2002

A high-density linkage map in Brassica juncea (Indian mustard) using AFLP and RFLP markers.

A high-density genetic linkage map of Brassica juncea (2n = 36) was constructed with 996 AFLP (amplified fragment length polymorphism) and 33 RFLP (restriction fragment length polymorphism) markers using a F1-derived doubled-haploid (DH) population of 123 individuals. This mapping population was developed by crossing a well-adapted, extensively grown Indian variety Varuna and a canola quality line Heera. The two lines are highly divergent and contain a number of contrasting qualitative and quantitative traits of high agronomic value. AFLPs were generated by the use of restriction enzymes EcoRI or PstI in combination with either MseI or TaqI. Using 91 primer pairs, a total of 1,576 parental polymorphic bands were detected of which 996 were used for mapping. In addition, 33 RFLP markers, developed from genomic clones of B. napus, were added to the map. The segregation of each marker and linkage analysis was performed using the program JoinMap version 2.0. The 1,029 mapped-markers were aligned in 18 linkage groups, which is the haploid chromosome number of the species, at LOD values ranging from 5 to 8. The total map length was 1,629 cM with an average marker interval of 3.5 cM. AFLP markers generated by EcoRI were more clustered, whereas PstI markers showed more extensive distribution. A set of 26 primer pairs (9 EcoRI/ MseI, 6 EcoRI/ TaqI, 6 PstI/ MseI and 5 PstI/ TaqI) generating 385 markers were identified for AFLP-based whole-genome selection as these markers covered 96% of the genome mapped with the 91 primer pairs. The map developed in the present study could be used for dissection and the transfer of agronomically important traits and favourable QTLs from ill-adapted exotic germplasm to cultivated Indian varieties.

Crosses, Genetic↗
PubMed2003

Genetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping.

A BC1 population (N = 1000) of an F1 hybrid between a stress-sensitive Lycopersicon esculentum breeding line (NC84173; maternal and recurrent parent) and a germination stress-tolerant Lycopersicon pimpinellifolium accession (LA722) was evaluated for seed germination rate under drought stress (DS) (14% w/v polyethyleneglycol-8000, water potential approximately -680 kPa), and the most rapidly germinating seeds (first 3% to germinate) were selected. The 30 selected BC1 seedlings were grown to maturity and self pollinated to produce BC1S1 progeny seeds. Twenty of the 30 selected BC1S1 progeny families were evaluated for germination rate under DS and their average performance was compared with that of a "nonselected" BC1S1 population of the same cross. Results indicated that selection for rapid germination under DS significantly improved progeny germination rate under DS (selection gain = 19.6%), suggesting a realized heritability of 0.47 for rate of germination under DS in this population. The 30 selected BC1 plants were subjected to restriction fragment length polymorphism (RFLP) analysis, and marker allele frequencies for 119 RFLP markers which spanned 1153 cM of the 12 tomato chromosomes were determined. A distributional extreme marker analysis, which measures statistical differences in marker allele frequencies between a selected and a nonselected population, detected four quantitative trait loci (QTLs) for rate of germination under DS in this population. Of these, two QTLs, located on chromosomes 1 and 9, were contributed by the L. pimpinellifolium donor parent and had larger effects than the other two QTLs, located on chromosomes 8 and 12, which were contributed by the L. esculentum recurrent parent. A few BC1S1 families were identified with all or most of the identified QTLs and with germination rates comparable with that of LA722. These families should be useful for the development of germination drought-tolerant tomato lines using marker-assisted selection (MAS). The overall results indicate that drought tolerance during seed germination in tomato is genetically controlled and potentially could be improved by directional phenotypic selection or MAS.

Chromosome Mapping↗
PubMed2003

Construction of two genetic linkage maps in cultivated tetraploid alfalfa (Medicago sativa) using microsatellite and AFLP markers.

BACKGROUND: Alfalfa (Medicago sativa) is a major forage crop. The genetic progress is slow in this legume species because of its autotetraploidy and allogamy. The genetic structure of this species makes the construction of genetic maps difficult. To reach this objective, and to be able to detect QTLs in segregating populations, we used the available codominant microsatellite markers (SSRs), most of them identified in the model legume Medicago truncatula from EST database. A genetic map was constructed with AFLP and SSR markers using specific mapping procedures for autotetraploids. The tetrasomic inheritance was analysed in an alfalfa mapping population. RESULTS: We have demonstrated that 80% of primer pairs defined on each side of SSR motifs in M. truncatula EST database amplify with the alfalfa DNA. Using a F1 mapping population of 168 individuals produced from the cross of 2 heterozygous parental plants from Magali and Mercedes cultivars, we obtained 599 AFLP markers and 107 SSR loci. All but 3 SSR loci showed a clear tetrasomic inheritance. For most of the SSR loci, the double-reduction was not significant. For the other loci no specific genotypes were produced, so the significant double-reduction could arise from segregation distortion. For each parent, the genetic map contained 8 groups of four homologous chromosomes. The lengths of the maps were 2649 and 3045 cM, with an average distance of 7.6 and 9.0 cM between markers, for Magali and Mercedes parents, respectively. Using only the SSR markers, we built a composite map covering 709 cM. CONCLUSIONS: Compared to diploid alfalfa genetic maps, our maps cover about 88-100% of the genome and are close to saturation. The inheritance of the codominant markers (SSR) and the pattern of linkage repulsions between markers within each homology group are consistent with the hypothesis of a tetrasomic meiosis in alfalfa. Except for 2 out of 107 SSR markers, we found a similar order of markers on the chromosomes between the tetraploid alfalfa and M. truncatula genomes indicating a high level of colinearity between these two species. These maps will be a valuable tool for alfalfa breeding and are being used to locate QTLs.

Alleles↗
PubMedDate not supplied

Health-related quality of life in multiple musculoskeletal conditions: a cross-sectional population based epidemiological study. II. The MAPPING study.

OBJECTIVE: Musculoskeletal conditions are a major burden on individuals, health systems, and social care systems. The objective of the MAPPING study was to assess the impact of musculoskeletal conditions on health-related quality of life (HRQL) in an Italian population sample. METHODS: Trained rheumatologists carried out structured visits in which subjects were asked about musculoskeletal symptoms and socio-demographic characteristics, completed validated instruments for measuring HRQL, such as the Short Form 36 items status survey questionnaire (SF-36), the EUROQoL five item questionnaire (EQ-5D), and chronic pain severity (Chronic Pain Grade - CPG questionnaire), and underwent a standardized physical examination. We considered a sample size of 576 patients diagnosed as having had musculoskeletal conditions. For the purposes of this study, musculoskeletal diseases were classified into 4 diagnostic groups: inflammatory rheumatic diseases (IRD), symptomatic peripheral osteoarthritis (SPOA), low back pain (LBP), and soft tissue disorders (STD). Cases were defined by previously validated criteria. RESULTS: The 4 major musculoskeletal disease groups, compared to non-sufferers, significantly impaired all eight health concepts of the SF-36 in the following order of magnitude: IRD, SPOA, STD, and LBP. Similar results were found for EQ-5D. The most striking impact was seen for SF-36 physical measures. On multiple regression modelling the physical component (PCS) of the SF-36 was influenced by female sex, age, high BMI, and low educational level (all at a p level < 0.001), and by manual occupation (p = 0.028) and chronic co-morbidity (p = 0.035) in LBP In SPOA, factors influencing physical function were age (p = 0.0001), low educational level (p = 0.006), female sex (p = 0.028), and chronic co-morbidity (p = 0.037). Moreover, an association on chronic co-morbidity and low educational level (both at a p level < 0.001), age (p = 0.004), and manual occupation (p = 0.035) was found with IRD, as well as of chronic co-morbidity and low educational level (both at a p level < 0.001), female sex (p = 0.006) and high BMI (p = 0.036) with STD were also found. Similar results were found for EQ-5D. CONCLUSIONS: The MAPPING study indicates that musculoskeletal conditions have a clearly detrimental effect on the HRQL and one third of the adult population in Italy visited at least one physician for musculoskeletal problem in the past year. These results enable a comparison to be made of the burden of musculoskeletal conditions with that of other common chronic conditions.

Adult↗
PubMed2006

The American Association for Pediatric Ophthalmology and Strabismus workforce distribution project.

PURPOSE: To describe data sources and functional utility of the American Association for Pediatric Ophthalmology and Strabismus (AAPOS) workforce database and associated map files. METHODS: Population data from the 2000 U.S. Census and current listings from the AAPOS and American Academy of Ophthalmology (AAO) databases were organized to demonstrate and analyze practitioner-to-population relationships for metropolitan statistical areas nationwide. An interactive map was developed to provide an intuitive graphical display of the data. RESULTS: A total of 749 active AAPOS members were distributed in 154 of 280 defined metropolitan statistical areas. Within these areas, a 0- to 20-year age subgroup varied from 17.8% to 42.6%, with an average of 30.4%. The AAPOS member-to-million-person ratio varied from 1.3 to 27, with higher numbers generally representing regions with population bases inadequately defined by Census Bureau statistical area definitions. Ratios for a majority of larger, better-defined areas ranged from 3 to 4 AAPOS members per million persons. Sizable areas with no AAPOS member presence were identified and tabulated. AAO members with a specified pediatric practice focus who were not AAPOS members were identified in 103 areas, possibly influencing patient choices and practitioner referrals for these regions. CONCLUSIONS: The AAPOS workforce database and related interactive map display practitioner and population data that may assist physicians and planners in targeting practice development and identifying potentially underserved areas.

Databases, Factual↗
PubMed1999

Multipoint linkage disequilibrium mapping with particular reference to the African-American population.

A new approach to scanning the genome is presented to detect linkage disequilibrium caused specifically by population admixture. In contrast to current linkage genome scanning methods to find causal genes for complex diseases, this new method should be powerful to find genes for multilocus traits, particularly those genes that lead to the highest population attributable risk. Such a scan using the African-American population is generally feasible for mapping common diseases. A conservative threshold is also provided for such association mapping.

Alleles↗
PubMed1998

Identification of genetic markers associated with Gilles de la Tourette syndrome in an Afrikaner population.

Because gene-mapping efforts, using large kindreds and parametric methods of analysis, for the neurologic disorder Tourette syndrome have failed, efforts are being redirected toward association studies in young, genetically isolated populations. The availability of dense marker maps makes it feasible to search for association throughout the entire genome. We report the results of such a genome scan using DNA samples from Tourette patients and unaffected control subjects from the South African Afrikaner population. To optimize mapping efficiency, we chose a two-step strategy. First, we screened pools of DNA samples from both affected and control individuals, using a dense collection of 1,167 short tandem-repeat polymorphisms distributed throughout the genome. Second, we typed those markers displaying evidence of allele frequency-distribution shifts, along with additional tightly linked markers, using DNA from each affected and unaffected individual. To reduce false positives, we tested two independent groups of case and control subjects. Strongest evidence for association (P values 10-2 to 10-5) were obtained for markers within chromosomal regions encompassing D2S1790 near the chromosome 2 centromere, D6S477 on distal 6p, D8S257 on 8q, D11S933 on 11q, D14S1003 on proximal 14q, D20S1085 on distal 20q, and D21S1252 on 21q.

Alleles↗
PubMed2002

Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589).

Although tomato has been the subject of extensive quantitative trait loci (QTLs) mapping experiments, most of this work has been conducted on transient populations (e.g., F2 or backcross) and few homozygous, permanent mapping populations are available. To help remedy this situation, we have developed a set of inbred backcross lines (IBLs) from the interspecific cross between Lycopersicon esculentum cv. E6203 and L. pimpinellifolium (LA1589). A total of 170 BC2F1 plants were selfed for five generations to create a set of homozygous BC2F6 lines by single-seed descent. These lines were then genotyped for 127 marker loci covering the entire tomato genome. These IBLs were evaluated for 22 quantitative traits. In all, 71 significant QTLs were identified, 15% (11/71) of which mapped to the same chromosomal positions as QTLs identified in earlier studies using the same cross. For 48% (34/71) of the detected QTLs, the wild allele was associated with improved agronomic performance. A number of new QTLs were identified including several of significant agronomic importance for tomato production: fruit shape, firmness, fruit color, scar size, seed and flower number, leaf curliness, plant growth, fertility, and flowering time. To improve the utility of the IBL population, a subset of 100 lines giving the most uniform genome coverage and map resolution was selected using a randomized greedy algorithm as implemented in the software package MapPop (http://www.bio.unc.edu/faculty/vision/lab/ mappop/). The map, phenotypic data, and seeds for the IBL population are publicly available (http://soldb.cit.cornell.edu) and will provide tomato geneticists and breeders with a genetic resource for mapping, gene discovery, and breeding.

Genome, Plant↗
PubMed2005

QTL analysis of late blight resistance in a diploid potato family of Solanum phureja x S. stenotomum.

Field resistance to Phytophthora infestans (Mont.) de Bary, the causal agent of late blight in potatoes, has been characterized in a potato segregating family of 230 full-sib progenies derived from a cross between two hybrid Solanum phureja x S. stenotomum clones. The distribution of area under the disease progress curve values, measured in different years and locations, was consistent with the inheritance of multigenic resistance. Relatively high levels of resistance and transgressive segregations were also observed within this family. A genetic linkage map of this population was constructed with the intent of mapping quantitative trait loci (QTLs) associated with this late blight field resistance. A total of 132 clones from this family were genotyped based on 162 restriction fragment length polymorphism (RFLP) markers. The genome coverage by the map (855.2 cM) is estimated to be at least 70% and includes 112 segregating RFLP markers and two phenotypic markers, with an average distance of 7.7 cM between two markers. Two methods were employed to determine trait-marker association, the non-parametric Kruskal-Wallis test and interval mapping analysis. Three major QTLs were detected on linkage group III, V, and XI, explaining 23, 17, and 10%, respectively, of the total phenotypic variation. The present study revealed the presence of potentially new genetic loci in this diploid potato family contributing to general resistance against late blight. The identification of these QTLs represents the first step toward their introgression into cultivated tetraploid potato cultivars through marker-assisted selection.

Chromosome Mapping↗
PubMed2007

Chromosome 7p linkage and GPR154 gene association in Italian families with allergic asthma.

BACKGROUND: Several genome scans have reported linkage of markers on chromosome 7p with asthma and related phenotypes in different populations. A fine mapping in Finnish and French-Canadian populations has associated the GPR154 gene (also known as G-protein-coupled receptor for asthma susceptibility, GPRA) with elevated IgE or asthma. OBJECTIVE: To confirm chromosome 7p linkage and candidate gene association in Italian families with atopic asthma. METHODS: In a two-phase approach, we first performed a linkage analysis of chromosome 7, and then a family-based association study on the GPR154 gene for allergic asthma phenotypes in the Italian population. RESULTS: The screening of 117 families with 19 microsatellite markers showed potential linkage for elevated IgE (P<0.002 at 22 cM from p-ter), asthma (P<0.005 at 44 cM), or atopy (P<0.005 at 54 cM). In the second phase of the present study, candidate gene GPR154, which is located in the phase one-linked region, was investigated in 211 families with seven single nucleotide polymorphisms (SNPs) that tag most haplotype variability, by the pedigree disequilibrium test. Elevated IgE levels were associated with two GPR154 gene SNPs (SNP 546333, P=0.0046; rs740 347, P=0.006), and with haplotypes in the global test (P=0.013). Haplotype analysis performed in nuclear families having at least 1 asthmatic parent showed a significant association with asthma (P=0.0173), atopy (P=0.0058), SPT (P=0.0025), and bronchial hyper reactivity (P=0.0163). CONCLUSION: These results support a susceptibility locus for asthma and related phenotypes on chromosome 7, and are in agreement with recent reports suggesting that a common susceptibility factor for atopic manifestations in asthma is likely conferred by the locus containing the GPR154 gene.

Asthma↗
PubMed2005

Cortical maps of separable tuning properties predict population responses to complex visual stimuli.

In the earliest cortical stages of visual processing, a scene is represented in different functional domains selective for specific features. Maps of orientation and spatial frequency preference have been described in the primary visual cortex using simple sinusoidal grating stimuli. However, recent imaging experiments suggest that the maps of these two spatial parameters are not sufficient to describe patterns of activity in different orientation domains generated in response to complex, moving stimuli. A model of cortical organization is presented in which cortical temporal frequency tuning is superimposed on the maps of orientation and spatial frequency tuning. The maps of these three tuning properties are sufficient to describe the activity in orientation domains that have been measured in response to drifting complex images. The model also makes specific predictions about how moving images are represented in different spatial frequency domains. These results suggest that the tangential organization of primary visual cortex can be described by a set of maps of separable neuronal receptive field features including maps of orientation, spatial frequency, and temporal frequency tuning properties.

Animals↗