Published in Probe Volume 1(3-4): Fall-Winter 1991
Nevin Dale Young, Assistant Professor
Department of Plant Pathology
University of Minnesota, St. Paul
As scientists develop new techniques to examine the genetic constitution of individual plants, there is a growing need for simple methods to display the information. For example, detailed genetic maps based on deoxyribonucleic acid (DNA) markers (such as RFLP's) make it possible to describe the ancestry of an individual throughout its entire genome. While it is widely agreed that this kind of information will make it possible to develop better plants faster, scientists face a serious problem of effectively making sense of so much information. One computer program that addresses this problem is "HyperGene."
Graphical Genotype Display
HyperGene a MacIntosh program, uses DNA marker data to create a graphical image for the genomic constitution of an individual. The program actually draws a genetic map showing segments of DNA from different ancestors in different shades or colors. This way of looking at a mosaic of inherited chromosomal regions is called a "graphical genotype."
HyperGene was originally developed by Dr. Nevin Young working with Steve Tanksley at Cornell University. Dr. Young, who has since moved to the University of Minnesota, is now expanding the program to have more powerful display routines and improved decision-making capacities. The program is also being adapted so that is will work in conjunction with USDA's Plant Genome Database Project. As a model system for developing these new features, Dr. Young and his associates are focusing on soybean and the soybean genome mapping database.
Selecting Target Individuals
In addition to displaying graphical genotypes, HyperGene also makes it possible to select target individuals out of a population by simply "painting" the desired genome using a computer mouse. If more than one individual in the population has the desired configuration, HyperGene can compare the selected individuals and pinpoint the best for future breeding.
HyperGene, and programs like it, provide a powerful tool for applying genetic data to crop improvement. The program considers the genome as a whole by integrating the results from many discrete DNA markers. In this way, scientists can get the "big picture" instead of being burdened by an overload of detail. And since users can precisely describe a target genome in terms of DNA genotype, HyperGene should also make plant breeding a more deterministic process. See below for disk information.
A Graphical Genotype for an F2 individual. Dark regions indicate DNA segments derived from one parent; light regions DNA regions from the other parent.
Hypergene is written for the Macintosh computer. The program requires at least 2 megabytes of RAM and a math coprocessor. All non-profit scientists may receive a copy at no cost by sending a formatted Macintosh diskette and a stamped, self-addressed diskette mailer to:
Nevin Dale Young
Department of Plant Pathology
495 Borlaug Hall
University of Minnesota
St. Paul, MN 55108