Marker-Assisted Selection Glossary


Amplified Fragment Length Polymorphism. A molecular marker method consisting of (1) DNA cleavage with two restriction enzymes, (2) ligation to synthetic linkers, and (3) two PCR amplification steps using primers 16 to 17 bases in length. The technique results in a large number of DNA bands per analysis (50 to 100 are commonly observed), and thus it can be an efficient way of detecting polymorphic loci. However, the large number of bands can be difficult to score. AFLPs are usually dominant and require no prior genome information. Because AFLP bands are "anonymous" (i.e., their chromosome positions are not known in advance), RFLP or SSR markers are sometimes evaluated in the same population in order to "anchor" the AFLPs to specific chromosome arms. AFLPs can be detected either with radioactive label or silver staining. The technique is described in more detail in S. Grandillo and T.M. Fulton (2002), Approaches to gene mapping. In P.M. Gilmartin and C. Bowler (ed.) Molecular Plant Biology Vol. 1. Oxford Univ. Press, Oxford and New York.


One of the different forms of a gene (or marker) that can exist at a single locus. A single allele for each locus is inherited separately from each parent.


The deliberate mating of two parental types of organisms in a breeding scheme or genetic analysis.


Used to describe a highly improved, well adapted breeding line, variety, or hybrid with superior performance.


The proportion of phenotypic variation that is due to genetics, as opposed to environment or genotype x environment interaction.


A group of plants within a species that are derived from a single plant.


The inherited association of alleles at loci due to their proximity on a chromosome. The degree of linkage is estimated as the percentage of recombination between loci. Linkage maps are thus based on mathematical distances among loci rather than actual physical distances. However, the order of loci along a chromosome in a linkage map should represent the actual order.

linkage drag

The inheritance of undesirable genes along with a beneficial gene due to their close linkage.


The site on a chromosome where a particular gene (or other sequence) is located (plural=loci).

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, RFLP, RAPD, and AFLP are acronyms for commonly used marker techniques.


Quantitative trait locus. (1) a locus that influences the expression of a quantitative trait. (2) a chromosome region detected by statistical analysis that is significantly associated with variation for a quantitative trait.


Random Amplified Polymorphic DNA. These markers involve PCR amplification of DNA fragments using primers that are random 10-base oligonucleotides. A single RAPD reaction may amplify several to many DNA fragments. RAPDs are dominant markers and, therefore, less informative than codominant markers because heterozygous individuals cannot be identified. A major advantage is that no prior knowledge of an organism's genome is necessary for their use. A common problem with RAPDs has been lack of reproducibility among labs. The technique is described in more detail in S. Grandillo and T.M. Fulton (2002), Approaches to gene mapping. pp. 101-136. In P.M. Gilmartin and C. Bowler (ed.) Molecular Plant Biology Vol. 1. Oxford Univ. Press, Oxford and New York.


Restriction Fragment Length Polymorphism. DNA is digested with a restriction enzyme and the fragments are separated by electrophoresis. The DNA fragments are then transferred to a membrane and hybridized with a labeled DNA probe. Polymorphisms are detected as labeled DNA fragments of different sizes. RFLPs are very informative due to their codominant nature (they distinguish between homozygotes and heterozygotes). Large numbers of RFLP markers are available for many species. Disadvantages are that they are relatively expensive and time consuming, and they require a large quantity of DNA. Most commonly, radioactive labeled probes are used, but non-radioactive methods are also available. The technique is described in detail in S. Grandillo and T.M. Fulton (2002), Approaches to gene mapping. pp. 101-136. In P.M. Gilmartin and C. Bowler (ed.) Molecular Plant Biology Vol. 1. Oxford Univ. Press, Oxford and New York.


Sequence characterized amplified region. To improve their specificity and repeatability, a RAPD or AFLP marker can be converted into a SCAR marker. SCARs are developed by obtaining the DNA sequence of a RAPD or AFLP band and designing 18-25 base PCR primers to amplify the same DNA segment. SCARs are easier to employ in marker-assisted selection than RAPDs or AFLPs.


Single Nucleotide Polymorphism. A single position in a given DNA sequence that contains allelic variations within a population at relatively high frequencies. For example, replacement of a guanine (G) with a thymine (T) nucleotide is an example of a SNP. SNPs occur often in many genomes, thus facilitating the development of high-density marker maps. For further discussion of SNP applications in plants see J.A. Rafalski, 2002, Plant Science 162:329-333.


Simple Sequence Repeat, also known as a microsatellite. These DNA markers are based on differences in length of repeated di- and tri-nucleotide sequences. By identifying the conserved flanking sequences of these SSRs, primers can be designed to selectively amplify them via PCR. SSRs are usually codominant and a potentially large number can be identified. Only small amounts of DNA are required, and analyses can be run quickly and relatively inexpensively. However, initial identification of SSRs followed by design, synthesis, and evaluation of primers is a large-scale effort. Tautz (1989, Nucleic Acids Research 17:6463-6471) describes the biological basis of SSRs and their utility for genetic analysis. Roder et al. (1998, Genetics 149:2007-2023) reports on the development and mapping of microsatellites in wheat.


Sequence Tagged Site. A DNA sequence of known location that occurs just once in the genome. STS loci are detectable by PCR, making them useful for a variety of molecular marker applications.


A group of similar plants whose appearance and performance allow it to be distinguished from other varieties of the same species. Often used synonymously with cultivar.