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At least 73 records · Page 4Linked to original sources
PubMed2003

Genetic analysis of Agrobacterium tumefaciens susceptibility in Brassica oleracea.

The genetic control and heritability of Agrobacterium tumefaciens susceptibility was investigated using a doubled haploid (DH) mapping population of Brassica oleracea and the associated RFLP map. Preliminary studies were carried out by analysis of an 8 x 8 diallel, for which the parental lines were selected to include a range of susceptibilities to A. tumefaciens. The variation observed within the diallel was attributed to both additive and dominant gene effects, with additive gene effects being more important. A broad sense heritability value of 0.95 suggested that 95% of the observed variation was due to genetic effects, with just 5% attributed to non-genetic or environmental effects. A high narrow-sense heritability value of 0.79 suggested that 79% of this trait was controlled by additive gene effects and, therefore, the potential to introduce this trait into breeding material is high. Fifty-nine DH lines from the mapping population were screened for susceptibility towards A. tumefaciens. Variation in susceptibility was observed across the population. The results of the DH screen were entered into the mapping programme MAPQTL and a highly significant quantitative trait loci (QTL) associated with susceptibility to A. tumefaciens was identified on linkage group 09. The use of substitution lines covering this region confirmed the location of this QTL. This work shows that susceptibility to A. tumefaciens is a heritable trait, and the transfer of susceptibility into resistant lines is demonstrated. These findings may help to overcome genotype restrictions to genetic transformation.

Agrobacterium tumefaciens↗
PubMed2001

The replicability of QTLs for murine alcohol preference drinking behavior across eight independent studies.

On the basis of eight independent quantitative trait loci (QTL) studies of ethanol (alcohol) preference drinking in mice, a meta-analysis was carried out to examine the replicability of QTLs across studies and to enhance the power of QTL detection and parameter estimation. To avoid genetic heterogeneity, we analyzed only studies of mapping populations derived from the C57BL/6 (B6) and DBA/2 (D2) inbred progenitor strains. Because these studies were carried out in five different laboratories, there were substantial differences in testing procedure, data analysis, and especially in the choice of mapping population (BXD recombinant inbred strains, F2, backcross, selected lines, or congenic strains). Despite this, we found several QTLs that were sufficiently robust as to appear consistently across studies given the strengths and weaknesses of the mapping populations employed. These were on Chromosomes (Chrs) 2 (proximal to mid), 3 (mid to distal), 4 (distal), and 9 (proximal to mid). The P value for each of these QTLs, combined across all applicable studies, ranged from 10(-7) to 10(-15), with the additive effect of each QTL accounting for 3-5% of the trait variance extrapolated to an F2 population. Two other QTLs on Chrs 1 (distal) and 11 (mid) were less consistent, but still reached overall significance (P <.0001).

Alcohol Drinking↗
PubMed1985

Mapping practice population and morbidity with a computer.

A method of dividing a map of the practice area into a grid based on postcode locations is described. The distribution of the practice population may thus be shown graphically and trends observed. The geographical incidence and prevalence of morbidity may also be charted and variations of statistical significance determined. This is a practical tool that will have greater potential as information technology in general practice develops.

Aged↗
PubMed2002

An AFLP marker tightly linked to apomixis reveals hemizygosity in a portion of the apomixis-controlling locus in Paspalum simplex.

A mapping population of Paspalum simplex segregating for apomixis (asexual reproduction through seeds) was screened with AFLPs to find apomixis-linked markers. Four AFLPs linked to apomixis in coupling phase were found. Three of them did not show recombinants among the 87 individuals of the mapping population, whereas the other was more loosely linked. Integrating the AFLP data with those obtained previously with rice RFLP anchor markers, a map was drawn for the chromosome region of P. simplex encompassing apomixis. We cloned the three AFLPs tightly linked with apomixis into plasmid vectors and used them as probes to hybridize the restriction digested DNA of the mapping population. Two of them revealed RFLP bands linked to apomixis together with other alleles, whereas one was proven to belong to a hemizygous portion of the apomixis locus. The total picture resulting from AFLP and RFLP analyses was that a cluster of markers tightly linked with apomixis was detected in P simplex together with two other markers that were more loosely linked. These two markers enclosed a relatively large chromosome segment characterized by strong repression of recombination. The block of recombination may have caused sequence divergence and, therefore, hemizygosity of some regions belonging to the apomixis-controlling chromosome segment of P. simplex. The potential of developing an apomixis-specific sequence for screening large-fragment libraries for the physical isolation of the locus encompassing apomixis is discussed.

Blotting, Southern↗
PubMed2004

A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers.

A linkage map of cacao based on codominant markers has been constructed by integrating 201 new simple sequence repeats (SSR) developed in this study with a number of isoenzymes, restriction fragment length polymorphisms (RFLP), microsatellite markers and resistance and defence gene analogs (Rgenes-RFLP) previously mapped in cacao. A genomic library enriched for (GA)(n) and (CA)(n) was constructed, and 201 new microsatellite loci were mapped on 135 individuals from the same mapping population used to establish the first reference maps. This progeny resulted from a cross between two heterozygous cacao clones: an Upper-Amazon Forastero (UPA 402) and a Trinitario (UF 676). The new map contains 465 markers (268 SSRs, 176 RFLPs, five isoenzymes and 16 Rgenes-RFLP) arranged in ten linkage groups corresponding to the haploid chromosome number of cacao. Its length is 782.8 cM, with an average interval distance between markers of 1.7 cM. The new microsatellite markers were distributed throughout all linkage groups of the map, but their distribution was not random. The length of the map established with only SSRs was 769.6 cM, representing 94.8% of the total map. The current level of genome coverage is approximately one microsatellite every 3 cM. This new reference map provides a set of useful markers that is transferable across different mapping populations and will allow the identification and comparison of the most important regions involved in the variation of the traits of interest and the development of marker-assisted selection strategies.

Cacao↗
PubMed1994

Dietary obesity linked to genetic loci on chromosomes 9 and 15 in a polygenic mouse model.

Loci linked to sensitivity to dietary obesity were identified by Quantitative Trait Locus (QTL) analysis of two mapping populations derived from a cross between AKR/J and SWR/J mice. AKR/J mice are sensitive to dietary obesity when fed a high fat diet while SWR/J mice are resistant. Intercrosses between these strains segregate the phenotype of sensitivity to dietary obesity. Using an F2 mapping population of 931 male mice we found significant linkage with a QTL on chromosome 9 (Likelihood of the Odds [LOD] ratio of 4.85) and another QTL on chromosome 15 (LOD = 3.93). The presence of a QTL on chromosome 15 was confirmed in a separate mapping population of 375 male F1 x SWR/J mice (LOD = 3.82). These two loci are designated dietary obese 2 (Do2) and dietary obese 3 (Do3) for the chromosome 9 and 15 loci, respectively. Both of these chromosomal regions contain candidate genes which may contribute to variation in the phenotype. These loci also exert a significant control over individual adipose depot weights.

Adipose Tissue↗
PubMed1999

Mapping of histologically identified long fiber tracts in human cerebral hemispheres to the MRI volume of a reference brain: position and spatial variability of the optic radiation.

The interpretation of the anatomical basis of functional deficits after subcortical infarcts could be considerably improved, if the precise topography and interindividual variability in size and course of long fiber tracts in adult human cerebral hemispheres were available in a spatial reference system. We therefore developed a method enabling the mapping of long fiber tracts to the volume of a standard reference brain. The examined fiber tracts were identified in myelin-stained histological serial sections of 10 human brains. The reference brain is a 3-D reconstruction of in vivo obtained magnetic resonance images (MRIs). The warping of histological volumes with the labeled fiber tracts to the reference brain by means of linear and nonlinear transformation procedures results in population maps that demonstrate the interindividual variability in position, size, and course of fiber tracts. In this paper, we present population maps of the optic radiation and the lateral geniculate body as a first example of this mapping strategy. Both structures present a considerable interindividual variability. Furthermore, voxel-based morphometry shows significant side differences with larger volumes of both structures in the left hemisphere than in the right hemisphere. A more than twofold variability of size in the interhemispheric extension of the optic radiation and the lateral geniculate body is found even after normalization of absolute brain size. Our observations demonstrate that the present approach based on population maps of fiber tracts and nuclei can improve the anatomical localization and interpretation of brain lesions visible in MRIs at the level of microstructurally identified architectonical units.

Adult↗
PubMed2005

The late blight resistance locus Rpi-bib3 from Solanum bulbocastanum belongs to a major late blight R gene cluster on chromosome 4 of potato.

Late blight, caused by Phytophthora infestans, is one of the most devastating diseases in cultivated potato. Breeding of new potato cultivars with high levels of resistance to P. infestans is considered the most durable strategy for future potato cultivation. In this study, we report the identification of a new late-blight resistance (R) locus from the wild potato species Solanum bulbocastanum. Using several different approaches, a high-resolution genetic map of the new locus was generated, delimiting Rpi-blb3 to a 0.93 cM interval on chromosome 4. One amplification fragment length polymorphism marker was identified that cosegregated in 1,396 progeny plants of an intraspecific mapping population with Rpi-blb3. For comparative genomics purposes, markers linked to Rpi-blb3 were tested in mapping populations used to map the three other late-blight R loci Rpi-abpt, R2, and R2-like also to chromosome 4. Marker order and allelic conservation suggest that Rpi-blb3, Rpi-abpt, R2, and R2-like reside in the same R gene cluster on chromosome 4 and likely belong to the same gene family. Our findings provide novel insights in the evolution of R gene clusters conferring late-blight resistance in Solanum spp.

Base Sequence↗
PubMed2002

[Comparison between two methods of establishing DH population for mapping lox-3 gene in rice (Oryza sativa L.)].

Crosses were produced by using a storable rice variety (Daw Dam) and 2070, Ming Hui 63, as well as Dulur/Xie Qing Zao B as parents, among these materials there are abundant polymorphisms of DNA molecular markers. Their F1's were applied to generate DH lines by an improved method of direct induction of pollen plant. The method of the direct induction of pollen plant was used as check treatment to evaluate the improved method. The results showed that the improved method increased the re-differentiation percentage of pollen callus, the percentage of regeneration plantlets, and the percentage of green regeneration plantlets and produced more vigorous seedlings. The improved method was a competent method of establishing DH population for mapping lox-3 gene. It was also showed that the efficiency of the new method was different among genotypes and out of three experimental crosses Daw Dam/2070 and Daw Dam/Minghui 63 showed more efficient. More than 60 DH lines have been obtained in this experiment.

English Abstract↗
PubMed1997

Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.).

Chromosomal regions associated with marker segregation distortion in rice were compared based on six molecular linkage maps. Mapping populations were derived from one interspecific backcross and five inter-subspecific (indica/japonica) crosses, including two F2 populations, two doubled haploid (DH) populations, and one recombinant inbred (RI) population. Mapping data for each population consisted of 129-629 markers. Segregation distortion was determined based on chi-square analysis (P < 0.01) and was observed at 6.8-31.8%, of the mapped marker loci. Marker loci associated with skewed allele frequencies were distributed on all 12 chromosomes. Distortion in eight chromosomal regions bracketed previously identified gametophyte (ga) or sterility genes (S). Distortion in three other chromosomal regions was found only in DH populations, where japonica alleles were over-represented, suggesting that loci in these regions may be associated with preferential regeneration of japonica genotypes during anther culture. Three additional clusters of skewed markers were observed in more than one population in regions where no gametophytic or sterility loci have previously been reported. A total of 17 segregation distortion loci may be postulated based on this study and their locations in the rice genome were estimated.

Alleles↗
PubMed2005

An entropy-based measure of founder informativeness.

Optimizing quantitative trait locus (QTL) mapping experiments requires a generalized measure of marker informativeness because variable information is obtained from different marker systems, marker distribution and pedigree types. Such a measure can be derived from the concept of Shannon entropy, a central concept in information theory. Here we introduce entropy-based founder informativeness (EFI), a new measure of information content generalized across pedigrees, maps, marker systems and mating configurations. We derived equations for inbred- and outbred-derived mapping populations. Mathematical properties of EFI include enhanced sensitivity to mapping population type and extension to any number of founders. To illustrate the use of EFI, we compared experimental designs for QTL mapping for three examples: (i) different marker systems for an F2 pedigree, (ii) different marker densities and sampling sizes for a BC1 pedigree and (iii) a comparison of haplotypic versus zygotic analyses of an outbred pedigree. As an a priori generalized measure of information content, EFI does not require phenotypic data for optimizing experimental designs for QTL mapping.

Alleles↗
PubMed2002

Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats.

Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.

Alleles↗
PubMed2001

Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield.

To understand the genetic basis of inbreeding depression and heterosis in rice, main-effect and epistatic QTL associated with inbreeding depression and heterosis for grain yield and biomass in five related rice mapping populations were investigated using a complete RFLP linkage map of 182 markers, replicated phenotyping experiments, and the mixed model approach. The mapping populations included 254 F(10) recombinant inbred lines derived from a cross between Lemont (japonica) and Teqing (indica) and two BC and two testcross hybrid populations derived from crosses between the RILs and their parents plus two testers (Zhong 413 and IR64). For both BY and GY, there was significant inbreeding depression detected in the RI population and a high level of heterosis in each of the BC and testcross hybrid populations. The mean performance of the BC or testcross hybrids was largely determined by their heterosis measurements. The hybrid breakdown (part of inbreeding depression) values of individual RILs were negatively associated with the heterosis measurements of their BC or testcross hybrids, indicating the partial genetic overlap of genes causing hybrid breakdown and heterosis in rice. A large number of epistatic QTL pairs and a few main-effect QTL were identified, which were responsible for >65% of the phenotypic variation of BY and GY in each of the populations with the former explaining a much greater portion of the variation. Two conclusions concerning the loci associated with inbreeding depression and heterosis in rice were reached from our results. First, most QTL associated with inbreeding depression and heterosis in rice appeared to be involved in epistasis. Second, most ( approximately 90%) QTL contributing to heterosis appeared to be overdominant. These observations tend to implicate epistasis and overdominance, rather than dominance, as the major genetic basis of heterosis in rice. The implications of our results in rice evolution and improvement are discussed.

Breeding↗
PubMed2005

Complex trait mapping in isolated populations: Are specific statistical methods required?

In this paper, we review the statistical methods that can be used in isolated populations to map genes involved in complex diseases. Our intention is to highlight the fact that if the features of population isolates may help in the identification of susceptibility factors for complex traits, the choice and design of methods for statistical analysis in these populations deserve particular care. We show that methods designed for outbred samples are generally not appropriate for isolated populations and could lead to false conclusions.

Chromosome Mapping↗
PubMed2005

Mapping of genes expressed in Fusarium graminearum-infected heads of wheat cultivar 'Frontana'.

The isolation, physical, and genetic mapping of a group of wheat genes expressed in infected heads of Triticum aestivum 'Frontana' resistant to Fusarium head blight is reported. A cDNA library was built from heads of 'Frontana' through suppressive subtractive hybridization, to enrich for sequences induced by the pathogen Fusarium graminearum during infection. A group of 1794 clones was screened by dot blot hybridization for differential gene expression following infection. Twenty of these clones showed a strong difference in intensity of hybridization between infected and mock-inoculated wheat head samples, suggesting that they corresponded to genes induced during infection. The 20 clones were sequenced and used for mapping analysis. We determined a precise chromosomal location for 14 selected clones by using series of chromosome deletion stocks. It was shown that the 14 clones detected 90 fragments with the use of the restriction enzyme EcoRI; 52 bands were assigned to chromosome bins, whereas 38 fragments could not be assigned. The selected clones were also screened for polymorphisms on a 'Wuhan' x 'Maringa' wheat doubled haploid mapping population. One clone, Ta01_02b03, was related to a quantitative trait locus for type II resistance located on chromosome 2AL, as determined with simple sequence repeat markers on another mapping population, but did not map in the same location on our population. Another clone, Ta01_06f04, was identified by BLAST (basic local alignment search tool) search in public databases to code for a novel beta-1,3-glucanase, homologous to a major pathogenesis-related protein. This clone mapped to chromosomal regions on chromosome 3, including 3BL and 3DL, where B glucanase gene clusters are known to exist. Seven other clones, including 1 coding for an ethylene-response element binding protein and 3 for ribosomal proteins, and 4 clones corresponding to proteins with unknown function, were also mapped.

Chromosome Mapping↗
PubMedDate not supplied

Linkage mapping in populations with karyotypic rearrangements.

A simulation study was used to examine the consequences of karyotypic rearrangements on molecular genetic map construction. Two groups of 50 datasets were created for F2 populations segregating for a reciprocal translocation of chromosomal segments or a reciprocal translocation and inversion. Multiple attempts were made to construct maps for each dataset using MapMaker/EXP. As expected, the markers from segments involved in the translocation formed one linkage group. Maps that corresponded to the known marker order within a segment could be constructed by the following method. The separation of markers distal to the translocation breakpoints into their respective segments could be made by constructing multiple maps, using distinct orders of marker entry, and observing the variances in intermarker distances: variances between pairs of markers from the same segment were an order of magnitude less compared to pairs where markers were from different segments. The order of markers within a segment could be determined from combining the pairwise linkage results from multiple maps, or from maps including all markers from a segment. No bias in map distances was observed. These results indicate that, under conditions similar to those tested, genetic maps corresponding to the segments conserved in translocations can be constructed.

Chromosome Inversion↗
PubMed2000

QTL: their place in engineering tolerance of rice to salinity.

Secondary salinization and its relationship to irrigation are strong incentives to improve the tolerance of crops to salinity and to drought. Achieving this through the pyramiding of physiological traits (phenotypic selection without knowledge of genotype) is feasible. However, wide application of this approach is limited by the practicalities of assessing not only the parents, but also large numbers of individuals and families in segregating generations. Genotypic information is required in the form of markers for any quantitative trait loci involved (marker-assisted selection) or of direct knowledge of the genes. In the absence of adequate candidate genes for salt tolerance, a quantitative trait locus/marker-assisted selection approach has been used here. Putative markers for ion transport and selectivity, identified from analysis of amplified fragment length polymorphism, had been discovered within a custom-made mapping population of rice. Here it is reported that none of these markers showed any association with similar traits in a closely related population of recombinant inbred lines or in selections of a cultivar. Whilst markers will be of value in using élite lines from the mapping population in backcrossing, this has to be considered alongside the effort required to develop and map any given population. This result cautions against any expectation of a general applicability of markers for physiological traits. It is concluded that direct knowledge of the genes involved is needed. This cannot be achieved at present by positional cloning. The elucidation of candidate genes is required. Here the problem lies not in the analysis of gene expression but in devising protocols in which only those genes of interest are differentially affected by the experimental treatments.

Adaptation, Physiological↗
PubMed1993

Development of a core RFLP map in maize using an immortalized F2 population.

A map derived from restriction fragment length polymorphisms (RFLPs) in maize (Zea mays L.) is presented. The map was constructed in an immortalized Tx303 x CO159 F2 mapping population that allowed for an unlimited number of markers to be mapped and pooled F3 seed to be distributed to other laboratories. A total of 215 markers consisting of 159 genomic clones, 16 isozymes and 35 cloned genes of defined function have been placed on 10 chromosomes. An examination of segregation data has revealed several genomic regions with aberrant segregation ratios favoring either parent or the heterozygote. Mapping of cloned genes and isozymes that have been previously mapped by functional criteria has provided 29 points of alignment with the classical maize genetic map. Screening of all mapped RFLP probes against a collection of U.S. Corn Belt germplasm using EcoRI, HindIII and EcoRV has resulted in a set of 97 core markers being defined. The designation of a set of core markers allows the maize genome to be subdivided into a series of bins which serve as the backbone for maize genetic information and database boundaries. The merits and applications of core markers and bins are discussed.

Crosses, Genetic↗