Pioneer Hi-Bred International, Inc.
Computerized two-dimensional electrophoretic protein profiles of 37 inbred lines and one hybrid line
--J. W. Higginbotham, J. S. C. Smith, and O. S. Smith
A dataset of protein spot densities obtained from 69 computerized two-dimensional (2-D) electrophoretic protein profiles of 37 inbred lines and one hybrid line has been constructed. Fluorographs showing the separation of 35-S methionine labeled seedling proteins were generated at Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. They were, subsequently, scanned, spot detected, and spot quantified at Protein Databases, Inc., Huntington Station, NY. The fluorographic images were matched with the aid of PDQUESTtm software. Densities for over 1500 protein spots are included in the resulting dataset. Eleven inbred lines are represented by one protein profile image. Twenty-three inbred lines and the hybrid line are represented by two protein profile images each. For the 23 inbred lines, each fluorographic image was obtained from a different gel. For the hybrid line, two fluorographs of differing exposures from the same gel are included. Three images each are included for two inbred lines. The three images were obtained from two different gels with two exposures of one of the gels being included. Four images are included for one inbred line and represent two exposures each of two different gels. To summarize, the 69 protein profile images represent 64 different gels. Two exposures per gel were included only when the appropriate exposure could not be determined a priori. The methodology used in constructing this dataset is given in Higginbotham, Smith, and Smith (Electrophoresis, in press).
Because many inbred lines are represented by more than one gel, it is possible to select by analysis of variance only those protein spots which vary significantly among the inbred lines. Details of this method of spot selection are given in Higginbotham et al. (in press). This is not the only method by which subsets of spots have been selected. Another subset consists solely of spots varying in their presence or absence among the inbred lines.
Information from this 2-D dataset is being used to determine genetic relationships among inbred lines, to resolve heterotic groups of lines, and to identify spots or spot clusters which diagnose lines.
The 2-D data are being used in comparisons with field derived, other
lab derived, and pedigree data, as well. The 2-D data and RFLP data (for
35 of the 37 inbred lines in the 2-D dataset) are being modeled, separately
and in combination, against heterosis yield and F1 yield. Correlations
between 2-D data and morphological traits are being generated as well.
For these correlations, the 2-D data are being divided into a subset of
spots which varies among the lines qualitatively and another subset which
varies among the lines quantitatively. The objective is to determine if
the two kinds of spot variability yield different information and, if so,
which is more informative (Damerval, Hebert, and deVienne, Theor. Appl.
Genet. 74:194, 1987).
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