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Glossary of Terms

Sources of more information:

Wikipedia, the free encyclopedia http://en.wikipedia.org
Glossary of the Human Genome Project http://www.ornl.gov/sci/techresources/Human_Genome/glossary/
Glossary of Biotechnology terms: http://biotechterms.org

Allele: alternate forms of a genetic locus. For example, at a locus determining eye colour, an individual might have the allele for blue eyes, brown, etc.

Amplicon: the product of a PCR (polymerase chain reaction); the segment of DNA that has been amplified in a PCR reaction

Base/base pair: the four nitrogenous subunits (nucleotides) of DNA: adenine (abbreviated as A), guanine (G), cytosine (C), and thymine (T). In the DNA molecule, they are linked to one another in pairs of long chains, where each member of the pair is complementary to the other. This double-stranded chain is itself twisted into a double helix. The complementarity between the strands is brought about by the interaction between A and T, and between G and C. Since the identity of a base on one strand can be used to infer the identity of the corresponding base on the other strand, the terms “base” and “base pair” are often used interchangeably. The number of bases (or base pairs) is used as a measurement of the size of a genome. For example, the length of the human genome is approximately 3 billion base pairs (abbreviated bp)

Breeding: the intentional development of new forms or varieties of plants or animals by crossing, hybridization, and selection of offspring for desirable characteristics

Candidate gene: a gene located in a chromosomal region thought to be associated with a particular function

Categorical data: data that falls into natural categories, and is not continuous. See also nominal and ordinal

Centimorgan (cM, map unit): the unit of measure of recombination frequency, named after the geneticist Thomas Hunt Morgan. One cM is equal to a 1% chance that a marker at one genetic locus on a chromosome will be separated from a marker (and thus inherited separately) at a second locus due to crossing over in a single generation.

Cloning: to produce copies of a single gene or other segment of DNA to obtain enough material for further study

cDNA: an abbreviation for “complementary DNA”. This is the in vitro transcription product from mRNA. cDNA molecules usually lack intron sequences

Chromosome: the structure in the eukaryotic nucleus and in the prokaryotic cell that carries most of the DNA

Co-dominant: when different alleles for a gene are simultaneously expressed; or, in describing a molecular marker, when the different alleles can be simultaneously identified

Complement, complementarity: refers to the way that the bases that make up the 2 strands of DNA bind preferentially with each other (adenine with thymine, cytosine with guanine), allowing DNA synthesis to take place

Continuous data: data, such as trait scores, that do not fall into discrete categories but rather a Poisson or other continual distribution (as opposed to categorical data types)

Crossing-over: The reciprocal exchange of material between homologous chromosomes during meiosis, which is responsible for genetic recombination. The process involves the natural breaking of chromosomes, the exchange of chromosome pieces, and the reuniting of DNA molecules

DNA: an abbreviation for “deoxyribose nucleic acid”, the carrier molecule of genetic information. The chain of nucleotides is held together on a polymer backbone formed by a sugar (deoxyribose) and a phosphate group (see also base).

EST: an abbreviation for “ expressed sequence tag”. These represent fragments of gene sequences, and are obtained by single-pass sequencing of cDNA. They have been heavily used for gene discovery, particularly in organisms that have not yet been sequenced, and also as a source of sequence for designing genic molecular markers

Exon: the part of a DNA sequence which encodes a protein (usually in conjunction with other exons).

Fine-mapping: genetic mapping at a higher resolution, to a more precise location on a chromosome

Gene: the unit of heredity, transmitted from generation to generation during reproduction. Each gene consists of a sequence of nucleotides, occupying a specific position along a chromosome. Most genes encodes a specific functional product

Genome: all the genetic material of an organism

Genotype: the inherited genetic constitution of an organism, see also phenotype

Genotyping: the process of identifying the genetic make-up of an organism, by using molecular markers, DNA sequencing, etc.

Germplasm: the collection of a set of genetic resources for an organism, which can consist of a seed collection, nursery, or other types

Homozygous: contains identical alleles at a particular locus

Heterozygous: contains different alleles at a particular locus

Introgression: movement of a gene or locus from one species into another by hybridization

Intron: a DNA sequence within a gene which interrupts the exons, and is not usually transcribed

Linkage, genetic linkage: when two chromosomal regions are located physically near each other such that there is a high likelihood they will be inherited together

Linkage drag: the negative association of non-targeted genes that are inherited with a gene of interest due to linkage

Linkage disequilibrium: the non-random association of alleles at two or more loci, i.e. they occur together more often than would be expected by chance

Mapping: the process of identifying the location of a gene or DNA segment along a chromosome. In genetic mapping, this is done by analyzing patterns of inheritance in segregating populations (measured in recombinational units, commonly centimorgans). In physical mapping, this describes the actual location of a sequence in a particular genomic region (measured in bp).

Molecular marker: a gene or DNA sequence that identifies a particular locus on the chromosome (whether the actual location is known or not) and whose inheritance can be followed

Mutation: an abrupt change in the genotype of an organism that is not the result of recombination

NCBI: abbreviation for “National Center for Biotechnology Information”, the organization which manages genbank, pubmed (a database of publications), and other databases (available at http://www.ncbi.nlm.nih.gov).

Nominal data: a type of categorical data where the classes are unrelated, not ordered. For example, scoring fruit shape as round, blocky or long.

Nucleic acid: see base/base pair and DNA.

Nucleotide: the unit of DNA, consisting of one base, one phosphate molecule, and the sugar  deoxyribose. See also base/base pair

Ontology: a structured, controlled vocabulary, agreed upon by members of a particular community (for example: the plant ontology, at Gramene: http://www.gramene.org)

Ordinal data: a type of categorical data where the classes have some relationship to each other, a natural order. For example, scoring red color on a scale of 1 to 5

PCR: abbreviation for “polymerase chain reaction”, the process by which a defined fragment of DNA is replicated in vitro in a so-called thermocycler or PCR machine. It provides a quick, inexpensive way of making a large number (millions) of copies of a specific DNA segment

Phenotype: the visible appearance of an organism. The phenotype reflects the combined action of the genotype and the environment where the individual exists

Polymerase chain reaction: see PCR

Polyploidy: a state in which multiple copies of a complete genome are present. Polyploidy is rare in animals, but common in plants. In animals (and also plants) some tissues within a diploid organism can be polyploid. The polyploid series is haploid (1 copy), diploid (2 copies), triploid (3 copies), tetraploid (4 copies), pentaploid (5 copies), hexaploid (6 copies) etc.

Primer: a short DNA sequence that is used in PCR to initiate DNA synthesis

Quantitative trait loci (QTL): regions of the chromosome associated with the inheritance of polygenic traits

Recombination: the formation among the offspring of a mating of genetic combinations not present in either parent, achieved via the physical exchange of genetic material during meiosis

Restriction enzyme, restriction endonuclease: A class of enzymes that cleave (i.e. Cut) DNA at a specific and unique location (recognition site). These enzymes are naturally produced by bacteria that use them as a defense mechanism against viral infection but are useful in molecular biology as a way of cutting DNA in specific places

Sequencing: determining the order (sequence) of bases in DNA, or amino acids in a protein

SNP: an abbreviation for “single nucleotide polymorphism”, pronounced "snip". A SNP which distinguishes two sequences can be used as a genetic marker.

Transgenic: an organism containing genetic material from another organism transferred by genetic engineering