Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2000-10-05
2002-04-09
Whisenant, Ethan C. (Department: 1655)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C536S023100, C536S024300
Reexamination Certificate
active
06368806
ABSTRACT:
TECHNICAL FIELD
The present invention relates generally to the field of plant breeding. More specifically, it relates to gene identification in plants.
BACKGROUND OF THE INVENTION
The ability to predict the inheritance of certain traits is of tremendous value to agricultural, horticultural, and medical endeavors. For traits controlled by single genes, predicting inheritance patterns is often no more difficult than understanding simple Mendelian principles. However, traits controlled by more than one locus offer unique challenges. Statistical methods and experimental designs have been created in an attempt to predict the inheritance of numerous quantitatively inherited phenotypic traits.
However, attempts to compare gene expression between groups of organisms separated on the basis of phenotype of complexly inherited traits have still been frustrating because phenotypes are the result of environmental factors plus the effects of many genes. If a trait is complexly inherited, no individual in a segregating population is expected to carry all favorable or unfavorable alleles. Therefore, each group consists of expression products of both favorable and unfavorable alleles at loci affecting the trait.
What is needed in the art is a method to associate a gene or an expression product with a phenotypic trait of interest for use in such applications as predicting the inheritance of quantitatively inherited phenotypic traits and in separating groups of organisms on the basis of allelic variation rather than solely on phenotypic variation. The present invention provides these and other advantages.
SUMMARY OF THE INVENTION
Generally, it is the object of the present invention to provide methods of selection of a gene associated with a phenotypic trait. It is an object of the present invention to provide a method of associating a gene with a phenotypic trait of interest and methods of associating an expression product with a phenotypic trait of interest.
Therefore, in one aspect, the present invention relates to a method of associating a gene with a phenotypic trait of interest comprising (a) segregating members of a biological population by the presence or absence of one or more genetic markers statistically associated with a quantitatively inherited phenotypic trait; (b) expression profiling segregated members of (a); and, (c) determining from expression profiles of (b) the gene associated with said phenotypic trait.
In another aspect, the present invention relates to a method of associating an expression product with a phenotypic trait of interest comprising (a) segregating members of a population consisting of a biological population by the presence or absence of one or more genetic markers statistically associated with said phenotypic trait, wherein said phenotypic trait has a statistical association with more than one genetic locus; (b) expression profiling at least one segregated member of (a) possessing said genetic marker and at least one segregated member of (a) lacking said genetic marker; and, (c) determining from said expression profiles of (b) an expression product associated with said phenotypic trait.
In yet another aspect, the present invention relates to associating an expression product with a phenotypic trait of interest, comprising: (a) expression profiling a plurality of members of a biological population having one or more genetic markers statistically associated with a phenotypic trait of interest wherein said phenotypic trait exhibits statistical association with more than one genomic locus; (b) expression profiling a plurality of members from said population lacking said genetic marker; and, (c) determining from expression profiles of (a) and (b) an expression product associated with said phenotypic trait.
Definitions
The terms defined below are more fully defined by reference to the specification as a whole. Units, prefixes, and symbols may be denoted in their SI accepted form. Numeric ranges are inclusive of the numbers defining the range and include each integer within the defined range.
The phrase “biological population” includes reference to a group of individuals having the capacity to be genetically crossed, regardless of species. For example, a group of
Glycine soja
and
Glycine max
plants would be considered a “biological population” because they are capable of being crossed. Individuals, as used herein, will refer to whole organisms, organism organs, cells, and progeny of same. For example, a plant biological population would include reference to whole plants, plant organs, plant cells, seeds, suspension cultures, embryos, meristematic regions, callus tissue, leaves, roots, shoots, gametophytes, sporophytes, pollen, and microspores.
The phrase “expression profiling” includes reference to generating an expression profile. By “expression profile” is meant the quantitation of a plurality of DNA, RNA, or protein expression products from a cell, tissue or whole organism. Many RNA expression products of a cell or tissue can simultaneously be detected on a nucleic acid array, or by the technique of differential display or modification thereof, such as those described in WO 97/15690 by Rothberg et al. and U.S. Pat. No. 5,719,060.
By “genetic locus” is meant a location on a chromosome. By “genomic locus” is meant a location within the entire set of chromosomes of an organism.
As used herein, “linkage disequilibrium” refers to a statistical association between two loci or between a trait and a marker.
As used herein, “marker” includes reference to a locus on a chromosome that serves to identify a unique position on the chromosome. A genotype may be defined by use of one or a plurality of markers.
“Phenotypic traits” may be comprised of, but are not limited to, a combination of measurable traits reflected in, but not limited to, the following:
Barren plants: The percent of plants per plot that were barren (lack ears).
Brittle Stalks: This is a measure of the stalk breakage near the time of pollination, and is an indication of whether the stalk of a hybrid or inbred would snap or break near the time of flowering under severe winds.
Yield: Yield of the grain at harvest in bushels per acre adjusted to 15.5% moisture.
Disease resistance: Resistance to any plant pathogen or group of plant pathogens.
Drydown: The relative rate at which a hybrid will reach acceptable harvest moisture compared to other hybrids.
Dropped Ears: A measure of the number of dropped ears per plot and represents the percentage of plants that dropped ears prior to harvest.
Ear height: Ear height is a measure from the ground to the highest placed developed ear node attachment and is measured in inches.
General Ear Mold: This is based on overall rating for ear mold of mature ears without determining the specific mold organism, and may not be predictive for a specific ear mold.
European Corn Borer feeding resistance (Ostrinia nubilalis): Average inches of tunneling per plant in the stalk or post flowering degree of stalk breakage and other evidence of feeding by European Corn Borer.
European Corn Borer Dropped Ears (Ostrinia nubilalis): Dropped ears due to European Corn Borer. Percentage of plants that dropped ears under second generation corn borer infestation.
Early Growth: scored when two leaf collars are visible.
Early Stand Count: This is a measure of the stand establishment in the spring and represents the number of plants that emerge on per plot basis for the inbred or hybrid.
Growing Degree Units: Using the Barger Heat Unit Theory, that assumes that maize growth occurs in the temperature range 50° F.-86° F. and that temperatures outside this range slow down growth; the maximum daily heat unit accumulation is 36 and the minimum daily heat unit accumulation is 0. The seasonal accumulation of GDU is a major factor in determining maturity zones.
GDU to physical maturity: The number of growing degree units required for an inbred or hybrid line to have approximately 50 percent of plants at physiological maturity from time of planting. Growing degree units are calculated by the Barger method (desc
Bruce Wesley B.
Openshaw Steve
Pioneer Hi-Bred International , Inc.
Pioneer Hi-Bred International Inc.
Ran David B.
Whisenant Ethan C.
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