National Plant Genome Initiative (October 1999 Report): Glossary

Glossary

Base Pair (bp): Nucleotide bases (adenine, thymine, guanine and cytosine) are the building blocks of DNA. Two molecules of nucleotide bases held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs. The number of base pairs is used to describe the size of a DNA molecule.

Chromosome: The self-replicating genetic structure of cells containing the cellular DNA that bears in its nucleotide sequences the linear array of genes. In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome. Plant genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins.

Clone: An exact copy made of biological material such as a DNA segment (a gene or other region), a whole cell, or a complete organism.

Cloning Vector: A piece of DNA, such as a plasmid, into which a DNA segment can be inserted, transferred into an organism, and replicated or reproduced.

DNA (deoxyribonucleic acid): The molecule that encodes genetic information. DNA is a double stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases: adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner.

EST: Expressed Sequence Tag: A unique, short DNA sequence derived from a cDNA library. ESTs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as identifying landmarks on the developing physical map of a plant genome.

Expression Pattern: Gene expression is the process by which a gene's coded information is converted into the structures or molecules present and operating in the cell. Expression pattern refers to a set of genes expressed under a set conditions (e.g. genes expressed in plants grown under drought condition).

Functional Genomics: Studies of the relationship between the structure and organization of the genome and the function of the genome as it directs growth, development, physiological activities, and other life processes of the organism.

GenBank: A public database where DNA sequences are deposited and made public. It is operated and supported by the National Library of Medicine, part of the National Institutes of Health, and is part of an international consortium of a gene sequence database.

Gene: The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule).

Genetic Map: A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together.

Genetics: The study of the patterns of inheritance of specific traits.

Genome: All the genetic material in the chromosomes of a particular organism; its size is generally given as its total number of base pairs.

Genome Project: Research and technology development effort aimed at mapping and sequencing some or all of the genome of human beings and other organisms.

High Throughput Biology: An experimental approach that generates massive amounts of raw data at the production scale using highly automated technologies such as genome sequencing technology or microarray technology, and processes the data by a batch method using computational and other information management tools.

Human Genome Project: The national effort, led by DOE and NIH, was started in the late 1980's. It includes several projects to (1) create an ordered set of DNA segments from known chromosomal locations, (2) develop new computational methods for analyzing genetic map and DNA sequence data, and (3) develop new techniques and instruments for detecting and analyzing DNA. While the ultimate objective is to understand the structure, organization and function of the human genome, the Human Genome Project supports studies on several model microbial and animal genomes. No plant genomes are targeted by the Human Genome Project.

Informatics: The study of the application of computer and statistical techniques to the management of information. In genome projects, informatics includes the development of methods to search databases quickly, to analyze DNA sequence information, and to predict protein sequence and structure from DNA sequence data.

Library: An unordered collection of clones (i.e., cloned DNA from a particular organism), whose relationship to each other can be established by physical mapping.

Microarray Technology: New approach to the study of how large numbers of genes interact with each other. This technology provides a quantitative assessment of how a cell's regulatory networks control extensive gene sets simultaneously. The method uses a robot to precisely apply tiny droplets containing functional DNA to glass slides. Researchers then attach fluorescent labels to DNA from the cell they are studying. The slides are put into a scanning microscope that can measure the brightness of each fluorescent dot; brightness reveals how much of a specific DNA fragment is present, an indicator of how active it is.

Physical Map: A map of the physical locations of identifiable landmarks on DNA (e.g., restriction enzyme cutting sites, genes); distance is measured in base pairs. The highest resolution map would be the complete nucleotide sequence of the chromosomes.

Reverse Genetics: An experimental approach that begins with information about the primary DNA or protein sequence and uses this knowledge to generate targeted mutations (heritable changes) or altered expression levels. Observation of the resulting effects on the organism (a physical attribute such as the color of the flower or the shape of the leaf) yields information about the physiological function of the gene or protein. This is the reverse strategy to a classical genetics approach that proceeds from observing a defined genetic trait towards obtaining sequence information for a specific gene.

Sequencing: Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein.

Structural Genomics: Studies of the structure and organization of the genome including DNA sequencing and physical and genetic mapping.

Syntenic Map: Chromosomal maps showing the collinear relationships between the genomes of different organisms. Often these chromosomal regions from related organisms (such as various grass species) contain corresponding genetic information and similar gene order.

Technology Transfer: The process of converting scientific findings from research laboratories into useful products by the commercial sector.