Jeffrey J. Doyle - US grants

Dr. Jeffrey Doyle of Cornell University will supervise a graduate student, John Freudenstein, in a morphological and biochemical study of the orchid genus Corallorhiza. About 12 species have been recognized in the genus, but because the plants are small, leafless herbs which are superficially similar, their taxonomy is problematic. One primary objective of the study is to re-evaluate the species of Corallorhiza using new multivariate statistical techniques applied to old as well as new characters. These characters will come from a thorough study of the genus with regard to shape and form of their flowers and stems, their internal construction (anatomy), and the mutational changes which can be measured by comparing their DNA (especially chloroplast DNA). In addition to indicating the species boundaries within the genus, this information will be used to address other questions, such as the evolutionary relationships of Corallorhiza species. DNA information, analyzed by computer-aided cladistic methods, will be especially important here. Additional questions in the group include the evolution of self-pollination, possible parallel trends among species in mycotrophy, and evolution of the chloroplast DNA in a leafless group of plants relative to that in leafy plants. Such information will be of general use in further orchid research.

This award provides partial support for purchase of a modern capillary DNA sequencer and supporting computer equipment for the Cornell Evolutionary Genetics Core Facility (EGCF). The instrument will be equipped for both sequence determination and fragment analysis. The facility supports research by evolutionary biologists, population biologists, behavioral ecologists, and systematists. Research in these areas increasingly depends on variation in the DNA sequences of individual organisms to provide information on mating systems, population structure, genealogy, and phylogeny. Automated DNA sequencing and genotyping are critical to studies employing such variation. The facility is used by 19 faculty in seven departments across the Cornell campus, and contributes significantly to their research programs and the educational experience of their graduate and undergraduate students. Their research programs address various aspects of biodiversity, including the origins and maintenance of plant and animal diversity, and the management of taxa of conservation concern or of economic importance. Aside from the impact of each individual user, the facility plays an important role in teaching and training on the Cornell campus. The new equipment will increase throughput and data quality for all users, improve the training of students, and catalyze interactions among evolutionary biologists and ecologists with diverse taxonomic and disciplinary interests.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Polyploidy (whole genome duplication) is one of the most important genetic phenomena in plants. Immediately after its formation, a polyploid plant can be identified simply by counting its chromosomes, because it has twice as many as a diploid. However, after millions of years a polyploid may have as low a chromosome number as a diploid through a process called "diploidization." Genomic studies can detect such cryptic polyploids, and the advent of high-throughput sequencing has made this approach increasingly feasible. Using this new technology, this project will estimate the frequency of polyploidy in the phaseoloid legumes, a group that includes soybean, common bean, cowpea, pigeonpea, and other less familiar crops, by sequencing thousands of transcribed genes from approximately 25 phylogenetically diverse species. Polyploid events will be identified by their characteristic signature, an excess of genes with two copies duplicated at the same time.

The project has broad significance for genetics and systematics, given the importance of polyploidy as a genetic phenomenon, and also for agriculture, because polyploidy is so common among crop plants (e.g., soybean, wheat, maize, cotton). The large numbers of genes will be a resource for subsequent studies in this large and important lineage. A talented female postdoctoral associate will receive training in the generation and analysis of next-generation sequencing data.

The genomes (total cellular DNA) of flowering plants, including all crop species, have undergone multiple rounds of whole genome duplication (WGD, polyploidy). The availability of duplicated genes, combined with extensive genome remodeling that follows WGD events, gives rise to a wide range of novel traits. It is clear that gene expression mediates many of these responses, and selection on gene dosage may drive gene family and network evolution. Yet surprisingly little is known about how genome duplication affects individual gene expression or the entire transcriptome (the combined expression of all genes in the genome in a given tissue). This project will use a suite of novel approaches to estimate whole transcriptome size and to assay expression changes of genes across the genome in response to WGD. Several synthetic and recently formed natural polyploids and their diploid progenitors will be studied in order to determine both the immediate and longer-term effects of genome duplication on gene expression.
This project is of broad significance and impact because quantifying dosage responses on a genomic scale will clarify our understanding of how selection on gene dosage has shaped plant evolution, leading to important traits in species of agricultural importance, such as soybean, whose close relatives are the targets of this project. In addition, the project funds opportunities for undergraduates to participate in the research, and facilitates scientific collaboration between a major research university (Cornell) and an undergraduate-only institution (Reed College).