Published in Probe Volume 3(1-2): January-June 1993
Drs. Sam Boutin and Nevin Young
Department of Plant Pathology,
University of Minnesota, Minneapolis; and
Dr. Randy Shoemaker, USDA, Agricultural Research Service,
Department of Agronomy
and
Dr. Lisa Lorenzen,
Department of Zoology and Genetics; Iowa State University, Ames
Genomic analysis based on DNA genetic markers leads to vast amounts of information. This information can be stored in various ways, including spreadsheets and databases, and presented in a multitude of different text or graphical displays.
Graphical display allows for rapid visualization of data and can potentially simplify interpretation. One example is the display of linkage maps and pedigrees derived from DNA marker studies in a color graphic format. Such graphical images give a powerful visual overview of the genetic relationships between individuals in a single population or between varieties in a species.
Supergene™
A recently developed computer software package, Supergene™ was developed to assist in DNA marker analysis using graphical display. Supergene™ converts DNA marker data into a color graphic format and gives the user the ability to (1) draw a graphical genotype for a selected individual, (2) draw a single linkage group for many selected individuals, and (3) draw a DNA-based pedigree to or from a genotype.
Supergene™ enables genetic comparisons on a macro level by comparing whole genomes, as well as more focused comparisons, such as linkage groups. In a graphical genotype, each portion of the genome is drawn to scale based on genetic distance between markers. The region around each marker is colorized according to the DNA genotype. Finally, for DNA marker-based pedigrees, a graphical image for each linkage group (or genome) is simultaneously displayed for a selected individual, its parents, and grandparents.
Interesting genomic regions, such as those that may carry desirable genes, can be highlighted in the graphical genome representations. This should be helpful in breeding programs for selecting individuals based on genotype and in monitoring the DNA genotypes of progeny individuals.
Using Supergene™
Supergene™ can be used in the analysis and comparison of any type of genome. For studies in plants, it has been used to detect differences and similarities in the genomes of various cultivars, plant introductions, and their progeny. Supergene™ allows the user to list various genotypes, their parents, their loci, map location, and their DNA marker scores in a table. The user can then view a graphical representation of an individual's genome, a side-by-side linkage group comparison between individuals or varieties, and graphical displays of the pedigree for a single linkage group or entire genome.
What You See
Data Table
When Supergene™ is first started, a data table containing individual names, DNA marker names, DNA marker loci, parent names, and numerical genotype scores is displayed on the screen. This information can be entered manually, but would be imported from a spreadsheet program. Figure 1 illustrates a typical data table.
The first column of the table contains the genotypes, the second and third columns contain the names of parent lines, and the remaining columns contain the scores for the genetic markers. The name for each marker and its map location are located at the top of these columns. Presently, the table handles up to 200 markers and 335 individuals.
Genetic marker data identifies the genetic constitution of the genomes at a particular locus. If the genomes of the two different individuals are the same at a locus, the score is the same. When the genomes differ at the same locus, the scores differ. With the types of DNA markers currently in use (RFLP and RAPD's), only two alternate alleles are often observed at each locus for inbred crop species. Improved and more polymorphic DNA markers are likely to show several alleles available at a single locus. Supergene™ can handle several alleles at the same locus through the use of different colors.
The user can then display the desired graphic via the Graphics menu. These displays include the entire genome, single linkage group comparison (Fig. 2), linkage group pedigree (Fig. 3), and genome pedigree.
Genome Display
The Create Map command illustrates all the linkage groups of an individual genome with their loci colorized according to their numerical genotype score. After the individual's name is entered, the software draws each linkage group, labels the loci, and colorizes the loci according to the score.
Single Linkage Group Display
Often a side-by-side comparison of the same linkage group from different individuals is desired (Fig. 2). When the Single Linkage Group command in the Graphics menu is selected, the user is prompted for the linkage group number to be drawn. The software draws the same linkage group for all individuals listed in the table. The same locus on the same linkage group among different individuals can be compared by color.
Linkage Pedigree Display
A comparison of the same linkage group among ancestors of a particular individual is often desired (Fig. 3). The Linkage Pedigree command under the Graphics menu prompts the user for an individual name. The software draws the pedigree for the individual, the parents, and grandparents that reside in the table. The same locus on the same linkage group from different ancestors can be compared, since each allele is a different color. The inheritance of that locus through the pedigree can be followed.
Genome Pedigree Display
If a macroscopic comparison of all the genomes in a pedigree is desired, the Genome Pedigree command can be used. The user is again prompted for the individual; the software then draws out the genome for that desired individual, its parents, and grandparents in a pedigree format. All the linkage groups for each individual in the pedigree can then be compared.
Macro and Micro Views
Since both macro and micro views of the genome and linkage groups are of interest, Supergene™ allows for scaling the various graphics. The user has the option of selecting a scaling factor. This allows for squeezing as much into the display as possible or expanding the view so that markers only a few centimorgans apart can be resolved.
What Supergene™ Isn't
The purpose of Supergene™ is to transform data into useful graphical images rendering genetic information. The software does not have sophisticated graphics or spreadsheet capability. However, many packages are available on the market for users who desire additional manipulation of the graphics or data.
The data should be manipulated in a spreadsheet prior to importing it into Supergene™; additional detail should be added to the graphics by copying the drawings and pasting them into a graphics application. Significantly, the graphics output are "draw" objects (as opposed to "paint" or bit-mapped graphic), so each component of a graphical image can be manipulated individually by a suitable computer software application.
Computer Environment
Supergene™ is a stand-alone application written in Supertalk™, a scripting language of Aldus Supercard. Supergene™ runs on all Macintosh II family computers. However, converting numerical data into graphical images requires considerable processing, so the higher end of the line is strongly recommended. A color display is obviously preferred, but the software draws different patterns for black and white models.
Support
Supergene™ was supported by a specific cooperative agreement for the USDA, Agricultural Research Service Plant Genome Database Program. This paper is a contribution of the Minnesota Agricultural Experiment Station series on research conducted under Project 015, supported by GAR funds.
Contact
Readers who desire additional information should contact Sam Boutin via Internet at boutin@molbio.cbs.umn.edu or via FAX (612) 625-9728.
