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Biomedical subjects

Claire G Williams

Publications and source records attributed to Claire G Williams.

10 recordsLinked to original sources
PubMed2006

Modeling seed dispersal distances: implications for transgenic Pinus taeda.

Predicting forest-tree seed dispersal across a landscape is useful for estimating gene flow from genetically engineered (GE) or transgenic trees. The question of biocontainment has yet to be resolved, although field-trial permits for transgenic forest trees are on the rise. Most current field trials in the United States occur in the Southeast where Pinus taeda L., an indigenous species, is the major timber commodity. Seed dispersal distances were simulated using a model where the major determinants were: (1) forest canopy height at seed release, (2) terminal velocity of the seeds, (3) absolute seed release, and (4) turbulent-flow statistics, all of which were measured or determined within a P. taeda plantation established from seeds collected from wild forest-tree stands at the Duke Forest near Durham, North Carolina, USA. In plantations aged 16 and 25 years our model results showed that most of the seeds fell within local-neighborhood dispersal distances, with estimates ranging from 0.05 to 0.14 km from the source. A fraction of seeds was uplifted above the forest canopy and moved via the long-distance dispersal (LDD) process as far as 11.9-33.7 km. Out of 10(5) seeds produced per hectare per year, roughly 440 seeds were predicted to be uplifted by vertical eddies above the forest canopy and transported via LDD. Of these, 70 seeds/ha traveled distances in excess of 1 km from the source, a distance too great to serve as a biocontainment zone. The probability of LDD occurrence of transgenic conifer seeds at distances exceeding 1 km approached 100%.

Ecology↗
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↗
PubMed2005

Evolution of a triplet repeat in a conifer.

The opportunity to trace the evolution of a triplet repeat is rare, especially for seed-plant lineages with a well-defined fossil record. Microsatellite PtTX2133 sequences from 18 species in 2 conifer genera were used to calibrate the birth of a CAGn repeat, from its protomicrosatellite origins to its repeat expansion. Birth occurred in the hard-pine genome ~ 136 million years ago, or 14 million generations ago, then expanded as a polymorphic triplet repeat 136-100 million years before a major North American vicariance event. Calibration of the triplet-repeat birth and expansion is supported by the shared allelic lineages among Old and New World hard pines and the shared alleles solely among North American diploxylon or hard pines. Five CAGn repeat units appeared to be the expansion threshold for Old and New World diploxylon pines. Haploxylon pine species worldwide did not undergo birth and repeat expansion, remaining monomorphic, with a single imperfect 198-bp allele. A sister genus, Picea, had only a region of cryptic simplicity, preceding a proto-microsatellite region. The polymorphic triplet repeat in hard pines is older than some long-lived microsatellites reported for reptiles, yet younger than those reported for insects. Some cautionary points are raised about phylogenetic applications for this long-lived microsatellite.

Alleles↗
PubMed2004

An ancient bottleneck in the Lost Pines of central Texas.

The retreating edge hypothesis for species responding to climate change predicts severe bottlenecks and eventual extinction. The disjunct Lost Pines population at the westernmost edge of the widespread Pinus taeda range is well suited for testing this prediction. The occurrence of one or more genetic bottlenecks in the Lost Pines population was tested using 34 nuclear microsatellite markers and a control sample from the larger, more continuous east Texas P. taeda forests. The Lost Pines population has undergone drastic contractions in effective population size between 3000 and 30 000 years bp. These results were supported by: (i) detection of transient heterozygosity excess, (ii) a mode-shift indicator of allele frequencies, and (iii) a ratio of allele number to allele size range. No bottleneck was detected for the east Texas control using any of the three methods. The distribution of allele frequencies was skewed for the Lost Pines population compared to the control, indicating a loss of rare alleles. However, allelic diversity was similar between the Lost Pines population and its east Texas control; the mean allele number per locus was 5.29 and 5.38, respectively. It is proposed that the Lost Pines population was the western refugium for P. taeda during Pleistocene glaciation and that East Texas P. taeda forests descended from the bottlenecked Lost Pines population.

Climate↗
PubMed2004

Extracting DNA from submerged pine wood.

A DNA extraction protocol for submerged pine logs was developed with the following properties: (i) high molecular weight DNA, (ii) PCR amplification of chloroplast and nuclear sequences, and (iii) high sequence homology to voucher pine specimens. The DNA extraction protocol was modified from a cetyltrimehtylammonium bromide (CTAB) protocol by adding stringent electrophoretic purification, proteinase K, RNAse, polyvinyl pyrrolidone (PVP), and Gene Releaser. Chloroplast rbcL (ribulose-1,5-bisphosphate carboxylase) could be amplified. Nuclear ribosomal sequences had >95% homology to Pinus taeda and Pinus palustris. Microsatellite polymorphism for PtTX2082 matched 2 of 14 known P. taeda alleles. Our results show DNA analysis for submerged conifer wood is feasible.

Cell Nucleus↗
PubMed2003

Haplotypic QTL mapping in an outbred pedigree.

An offspring genome can be viewed as a mosaic of chromosomal segments or haplotypes contributed by multiple founders in any quantitative trait locus (QTL) detection study but tracing these is especially complex to achieve for outbred pedigrees. QTL haplotypes can be traced from offspring back to individual founders in outbred pedigrees by combining founder-origin probabilities with fully informative flanking markers. This haplotypic method was illustrated for QTL detection using a three-generation pedigree for a woody perennial plant, Pinus taeda L. Growth rate was estimated using height measurements from ages 2 to 10 years. Using simulated and actual datasets, power of the experimental design was shown to be efficient for detecting QTLs of large effect. Using interval mapping and fully informative markers, a large QTL accounting for 11.3% of the phenotypic variance in the growth rate was detected. This same QTL was expressed at all ages for height, accounting for 7.9-12.2% of the phenotypic variance. A mixed-model inheritance was more appropriate for describing genetic architecture of growth curves in P. taeda than a strictly polygenic model. The positive QTL haplotype was traced from the offspring to its contributing founder, GP3, then the haplotypic phase for GP3 was determined by assaying haploid megagametophytes. The positive QTL haplotype was a recombinant haplotype contributed by GP3. This study illustrates the combined power of fully informative flanking markers and founder origin probabilities for (1) estimating QTL haplotype magnitude, (2) tracing founder origin and (3) determining haplotypic transmission frequency.

Haplotypes↗
PubMed2003

No clustering for linkage map based on low-copy and undermethylated microsatellites.

Clustering has been reported for conifer genetic maps based on hypomethylated or low-copy molecular markers, resulting in uneven marker distribution. To test this, a framework genetic map was constructed from three types of microsatellites: low-copy, undermethylated, and genomic. These Pinus taeda L. microsatellites were mapped using a three-generation pedigree with 118 progeny. The microsatellites were highly informative; of the 32 markers in intercross configuration, 29 were segregating for three or four alleles in the progeny. The sex-averaged map placed 51 of the 95 markers in 15 linkage groups at LOD > 4.0. No clustering or uneven distribution across the genome was observed. The three types of P. taeda microsatellites were randomly dispersed within each linkage group. The 51 microsatellites covered a map distance of 795 cM, an average distance of 21.8 cM between markers, roughly half of the estimated total map length. The minimum and maximum distances between any two bins was 4.4 and 45.3 cM, respectively. These microsatellites provided anchor points for framework mapping for polymorphism in P. taeda and other closely related hard pines.

Chromosome Mapping↗
PubMed2002

A haplotypic approach to founder-origin probabilities and outbred QTL analysis.

Founder-origin probability methods are used to trace specific chromosomal segments in individual offspring. A haplotypic method was developed for calculating founder-origin probabilities in three-generation outbred pedigrees suited to quantitative trait locus (QTL) analysis. Estimators for expected founder-origin proportions were derived for a linkage group segment, an entire linkage group and a complete haplotype. If the founders are truly outbred, the haplotypic method gives a close approximation when compared with the Haley et al. (1994) method that simultaneously uses all marker information for QTL analysis, and it is less computationally demanding. The chief limitation of the haplotypic method is that some information in two-allele intercross marker-type configurations is ignored. Informativeness of marker arrays is discussed in the framework of founder-origin probabilities and proportions. The haplotypic method can be extended to more complex pedigrees with additional generations.

Founder Effect↗