Plant Breeding and Genomics August 22, 2011 Print Friendly and PDF


David Francis, The Ohio State University

Heather L. Merk, The Ohio State University

Deana Namuth Covert, University of Nebraska - Lincoln

Matthew Robbins, The Ohio State University

This page provides glossary definitions and links to further information when appropriate.

Backcross Breeding: A breeding method used to move one or a few desirable genes from an agronomically poor line to an elite line. This is done by crossing the line having a few desirable genes (donor parent line) to an elite line (recurrent parent line), and crossing offspring with the desired gene(s) to the recurrent parent. For more information, see the Backcross Breeding article.

Backcross Population: A population of individuals derived by making crosses between hybrid progeny and one of the parents. Backcross populations are often used in plant breeding to introgress desirable traits from a donor parent, while maintaining most of the genetic background of the recurrent parent. For more information, see the Backcross Breeding article.

Balanced Population: Individuals in a balanced population have equal genetic contributions from each parent. Examples of populations with balanced design include F2 and recombinant inbred line (RIL) populations. See also, unbalanced population.

BLAST: A bioinformatic search tool used to compare biological sequences, including nucleotide and amino acid sequences. BLAST is an acronym for Basic Local Alignment Search Tool and can be found at:

CAP(S): A type of molecular marker that uses restriction enzymes to exploit differences in DNA sequence. CAP(S) is an acronym for Cleaved/Cut Amplified Polymorphism (Sequence). For more information, see the Overview of Traditional Molecular Markers article.

Codominant: A form of inheritance where the heterozygote can be distinguished from homozygotes. For example, most SSR markers are codominant because each homozygote produces a distinct band and the heterozygous progeny of a cross between the homozygotes produces both bands.

Donor parent: The parent from which one or a few genes are transferred to the recurrent parent in backcross breeding. For more information, see the Backcross Breeding article.

Electrophoresis: A laboratory method that uses electric current to separate DNA, RNA, or protein fragments by size. For more information, see the gel electrophoresis article.

FASTA format: A widely accepted format for documenting DNA or protein sequences. The basic format consists of the first line as the definition of the sequence (a comment or name) followed by the sequence starting on the second line. The definition line consists of the > symbol, followed by the definition, followed by a hard return.

Genome: All of the genetic material in the full set of haploid chromosomes in an individual. The full DNA sequence of an organism.

Genotype: The genetic makeup of a cell, organism, or individual, often with regard to a particular gene of interest.

Germplasm: a collection of individual plants that contains a species' genetic variation. It can be represented and propagated by any living propagule such as seeds, cuttings, or even cells. Germplasm is the basis of plant breeding programs. It is usually limited to any sexually compatible species for a given crop.

Heterozygous: Case where an individual has different alleles at a given gene or marker locus, such as Aa instead of AA or aa.

Homozygous: Case where an individual has two copies of the same allele at a given gene or marker locus, such as AA or aa rather than Aa.

Hypersensitive Response: This is one mode of plant resistance or defense against a plant pathogen. It is characterized by a localized region of cell death in the plant. This sacrifices a few cells of the plant, but prevents spread of the pathogen, thereby conferring overall resistance to the disease pathogen.

IBC: Abbreviation for Inbred backcross. A population developed from two parents by backcrossing, then selfing for several generations. For more information, see the Inbred Backcross (IBC) Populations article.

Indel: Abbreviation for Insertion/deletion. A difference in length between DNA sequences based on an insertion of DNA base(s) in the longer sequence or deletion of DNA base(s) in the shorter sequence.

Introgress: Moving a gene (or genes) from one species to another, utilizing backcross breeding techniques.

Marker-Assisted Selection: MAS is a technique used in plant breeding programs to facilitate selection.  The decision of which individuals or lines to move forward (or eliminate) in the improvement program is aided by the use of molecular markers and genetic linkage between markers and traits. MAS is usually applied in combination with phenotypic selection.

Molecular Marker: An identifiable DNA sequence on a chromosome. A marker can be a gene, part of a gene, or a sequence in a non-gene region. SSR and SNP are acronyms for commonly used types of markers. A molecular marker may also be referred to as a DNA marker or genetic marker. For more information, see the Overview of Molecular Markers article.

Molecular weight: The size of a molecule in specific units. Units depend on the molecule. DNA and RNA fragments are often measured in base pairs (bp), proteins are often measured in daltons (Da), and so forth. See description of a molecular weight ladder in the Scoring a Marker by Gel Electrophoresis article.

mRNA: Abbreviation for messenger RNA. mRNA is a single-stranded nucleic acid similar to DNA, but having a ribose sugar rather than deoxyribose sugar and a uracil rather than thymine as one of the bases. mRNA is usually transcribed into protein.

NCBI: National Center for Biotechnology Information, which can be located at A public resource with databases and tools for analysis of molecular data. Training and tutorials can be found at

Nucleus (plural: nuclei): Part of the cell that contains the nuclear DNA, which is packaged in chromosomes. The nucleus is surrounded by the nuclear membrane.

Phenotype: The observable physical or biochemical characteristics of an organism that are determined by a combination of the genetic composition (genotype) and the environment of the individual (P = G x E).

Polymorphism: Polymorphism means having several shapes or forms. Differences that exist between phenotypes, DNA or protein sequence, gene expression levels, molecular marker genotypes, and so forth. For example, the DNA sequence is …ATGGC… in one individual and …ATGTC… in another individual.

Positive Control: A representative sample or treatment for which the outcome is known with certainty. A positive control gives credibility to the experiment and provides an overall reliability measure of the experiment's data. For example, when verifying PCR amplification on an agarose gel, DNA from an individual known to have visible PCR products on a gel is included. If are no visible PCR products from this individual, it suggests that the PCR amplification was not performed correctly.

Qualitative: A trait in which variation is discontinuous, such that phenotypes can be classified into discrete categories. An example would be tomato fruit color, where plant fruit could be categorized as red or yellow. This is in contrast to a quantitative trait, in which phenotypic variation is continuous so that classification into discrete categories is not possible. An example would be tomato fruit yield.

Quantitative: A trait in which variation is continuous, such that phenotypes cannot be classified into discrete categories. Typically, many genes control this type of trait and environmental factors have a large influence on the plant's phenotype. An example of this would be tomato fruit yield. In contrast to a qualitative trait, in which phenotypic variation is discontinuous so that classification into discrete categories is possible. An example would be tomato fruit color, for which fruit can be categorized as red or yellow.

QTL: Abbreviation for Quantitative Trait Locus. This is a location of a chromosome region which contributes significantly to the overall phenotypes of a quantitative trait. It may be (1) a locus that influences the expression of a quantitative trait, or (2) a chromosome region detected by statistical analysis that is significantly associated with variation for a quantitative trait.

Race Specific Resistance: Resistance to one, or a few, races of a disease. This type of resistance is often conferred by a single gene and is typically ineffective when new races of a disease-causing pathogen emerge. It is also known as qualitative resistance, single gene resistance, or vertical resistance.

Race Non-Specific Resistance: Resistance to multiple races of a pathogen. This type of resistance is often conferred by multiple genes and typically slows, but does not stop, disease progress. Race Non-Specific Resistance is also known as quantitative resistance, polygenic resistance, field resistance, or horizontal resistance.

Recombinant Inbred Line (RIL): A recombinant inbred line (RIL) population is developed through single seed descent from the F2 generation. The result is a set of homogeneous, homozygous lines for which large amounts of seed can be produced for replicated trials. This type of population is often useful for mapping QTLs.

Recurrent parent: The parent to which successive backcrosses are made in backcross breeding. For more information, see the Backcross Breeding article.

Restriction Endonuclease (or Restriction Enzyme): An enzyme that cuts single- or double-stranded DNA at a specific base sequence called a recognition site, with each restriction enzyme detecting a different sequence. Restriction endonucleases are used for CAP(S) markers.

Segregation: This term has two meanings in genetics and plant breeding. Segregation can refer to the separation of genes and their respective alleles during meiosis into new daughter cells. This is also referred to as Mendel's first law or the Principle of Segregation.
Segregation—or a segregating population—can also refer to a population in which there is phenotypic variation. For example, a population may have both resistant and susceptible individuals with respect to bacterial spot.

Single-seed descent (SSD): Deriving a population of inbred plants by self-pollinating individuals for several generations. Each individual from a segregating population, such as an F2, is self-pollinated and seed are collected separately for each individual. A single seed from each individual is sown, self-pollinated, and seed are collected separately in each generation. After 5–6 generations each line is considered inbred.

SNP: Abbreviation for Single Nucleotide Polymorphism. A single position in a given DNA sequence that contains allelic variations within a population at relatively high frequencies. The replacement of a guanine (G) with a thymine (T) nucleotide is an example of a SNP. The high frequency of SNPs in the genome facilitates the development of high-density marker maps.

SSR: An abbreviation for Simple Sequence Repeat and sometimes referred to as microsatellites. The "repeat" in Simple Sequence Repeat refers to a short nucleotide repeat, typically two to three nucleotides (e.g., …ACGCGCGT…). Variations in the number of repeats forms the basis for SSR markers. For information about how SSRs are used as molecular markers, see the Overview of Molecular Markers article.

Unbalanced Population: Individuals in an unbalanced population do not have equal genetic contributions from each parent. Advanced backcross and inbred backcross (IBC) populations are examples of structured populations that are unbalanced. See also, balanced population.

Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

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This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.