Christopher J. Basten

Estimating the genetic architecture of quantitative traits.

Understanding and estimating the structure and parameters associated with the genetic architecture of quantitative traits is a major research focus in quantitative genetics. With the availability of a well-saturated genetic map of molecular markers, it is possible to identify a major part of the structure of the genetic architecture of quantitative traits and to estimate the associated parameters. Multiple interval mapping, which was recently proposed for simultaneously mapping multiple quantitative trait loci (QTL), is well suited to the identification and estimation of the genetic architecture parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance. With multiple traits and multiple environments involved in a QTL mapping experiment, pleiotropic effects and QTL by environment interactions can also be estimated. We review the method and discuss issues associated with multiple interval mapping, such as likelihood analysis, model selection, stopping rules and parameter estimation. The potential power and advantages of the method for mapping multiple QTL and estimating the genetic architecture are discussed. We also point out potential problems and difficulties in resolving the details of the genetic architecture as well as other areas that require further investigation. One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.

Correlation of mitochondrial haplotypes with cuticular hydrocarbon phenotypes of sympatric Reticulitermes species from the southeastern United States.

Three sympatric Reticulitermes species have been identified in Georgia, USA, based on morphological characters from alates and soldiers: R. flavipes, R. virginicus, and R. hageni, but species identification at individual collection sites is often difficult because alate production is seasonal and soldiers comprise 1–3% of the colony. We therefore set up an experiment to determine if chemical phenotypes and mtDNA haplotypes can be used together to separate species of subterranean termites. Subterranean termites of the order Reticulitermes (Isoptera: Rhinotermitidae) were collected from 20 inspection ports across four soil provinces in Georgia. Each collection was identified to species using dichotomous keys. Two collections, HH11 and BH25, however, could not be unequivocally keyed to species and were classified as unknown. The mitochondrial cytochrome oxidase II (COII) gene was sequenced from individual members of each collection and the variation in cuticular hydrocarbon phenotypes from these same collections was characterized. The cuticular hydrocarbon and mtDNA phylogenetic analyses show agreement with both unknown collections falling out in a separate clade. Specimens from HH11 nad BH25 are different morphologically, chemically, and genetically from the three known sympatric species in Georgia. Our results suggest that these two collections may represent at least one new taxon in Reticulitermes. Furthermore, the association of cuticular hydrocarbon phenotypes and mtDNA haplotypes demonstrates that, when combined with morphological characters, they are useful in separating known species, determining new species, and understanding termite evolution.

A PCR Multiplex and Database for Forensic DNA Identification of Dogs

Animal-derived trace evidence is a common finding at crime scenes and may provide an important link between victim(s) and suspect(s). A database of 558 dogs of pure and mixed breeds is described and analyzed with two PCR multiplexes of 17 microsatellites. Summary statistics (number of alleles, expected and observed heterozygosity and power of exclusion) are compared between breeds. Marked population substructure in dog breeds indicates significant inbreeding, and the use of a conservative theta value is recommended in likelihood calculations for determining the significance of a DNA match. Evidence is presented that the informativeness of the canine microsatellites, despite inbreeding, is comparable to the human CODIS loci. Two cases utilizing canine DNA typing, State of Washington v. Kenneth Leuluaialii and George Tuilefano and Crown v. Daniel McGowan, illustrate the potential of canine microsatellite markers for forensic investigations.

Constraints and normalized measures for cytonuclear disequilibria

The full bounds are derived for cytonuclear disequilibria in two-locus systems with an arbitrary number of alleles at the cytoplasmic and nuclear markers. The associated marginal frequencies constrain the nonrandom associations between cytoplasmic alleles and nuclear genotypes in the same way that the allele frequencies constrain the linkage disequilibrium between two nuclear loci. Additional constraints are imposed on the nonrandom associations between cytoplasmic and nuclear alleles, however, by the marginal frequencies of nuclear genotypes carrying either two or no copies of the associated nuclear allele. These bounds are analysed and used to define normalized measures of cytonuclear disequilibria, whose practical utility is illustrated through applications to two sets of recent nuclear-mitochondrial data.

Use of Combined Frequencies for RFLP and PCR Based Loci in Determining Match Probability

Statistical analysis was performed on a subset of the Pennsylvania State Police Caucasian, African American and Hispanic database for the purpose of determining Hardy-Weinberg equilibrium and associations across the RFLP loci D1S7, D2S44, D4S139, D5S110, D10S28 and D17S79 and the PCR-based loci HLA-DQA1, LDLR, GYPA, HBGG, D7S8 and Gc. Overall, the statistical results are consistent with a population in equilibrium both within and between loci. The assumption for independence is valid.

Effect of gene conversion on variances of digenic identity measures.

The variances and covariances of digenic descent measures are studied for a two-locus model incorporating mutation, gene conversion, recombination, drift, and finite sampling. Gene conversion can occur between allelic pairs of genes or between non-allelic pairs on the same or different gametes within individuals. Most interest therefore centers on pairs of genes, and five digenic identity measures are required. The behavior over time of these measures is studied, with an emphasis on the effects of gene conversion. Because of the stochastic nature of the forces of drift, recombination, mutation, and conversion, the actual identity status of gene pairs can vary from expectation among replicate populations. To study this variation we compute the expected variances and covariances of the measures, and show that this requires the introduction of trigenic and quadrigenic measures. Allowing for conversion between genes on different gametes requires a large number of these higher-order measures.