Based on the considerable developments in biotechnology, plant breeders developed more efficient selection systems to replace traditional phenotypic-pedigree-based selection systems. Conventional breeding is time consuming and much dependent on the environmental conditions. Breeding a new variety takes between eight to twelve years and even then the release of an improved variety cannot be guaranteed. Hence, breeders are extremely interested in new technologies that could make this procedure more efficient. Molecular marker technology offers such a possibility by adopting a wide range of novel approaches to improve the selection strategies in breeding. Markers can aid selection for target alleles that are not easily assayed in individual plants, minimize linkage drag around the target gene, and reduce the number of generations required to recover a very high percentage of the recurrent parent genetic background. Marker assisted selection (MAS) is indirect selection process where a trait of interest is selected based on a marker linked to it and not on the trait itself (Rosyara, 2006; Ribaut and Hoisington, 1998). For example if MAS is being used to select a crop  with a disease resistance, the level of disease is not quantified but rather a marker allele which is linked with the disease is used to determine the presence of the disease. The assumption is that linked allele gets associated with the gene and/or quantitative trait locus (QTL) of interest. MAS can be useful for traits that are difficult to measure, exhibit low heritability, and/or are expressed late in development.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" />


Molecular markers

What are they?

A marker is a gene or piece of DNA with easily identified phenotype such that cells or individuals with different alleles are distinguishable. For example a gene with a known function or a single nucleotide change in DNA


A readily detectable sequence of DNA or protein whose inheritance can be monitored


To become a useful molecular marker, it must possess certain characteristics:

  • Polymorphic: A polymorphism is a detectable and heritable variation at a locus.

A marker is polymorphic if the most abundant allele comprises less than X% of all the alleles, usually 95%.

  • Reproducible: Should give similar results in different experiments irrespective of the time and the place.
  • Preferably displays co-dominant inheritance (both forms are detectable in heterozygotes).  
  • The detection of marker must be fast and inexpensive.
  • Demonstrates measurable difference(s) in expression between trait types and/or alleles of interest, early in the development of the organism.
  • Has no effect on the trait of interest that varies depending on the allele at the marker loci.
  • Low or null interaction among the markers allowing the use of many markers at the same time in a segregating population


Types of markers


Morphological markers

o    Seed color, for example  Kernel color in maize, hylum color in soybean seeds

o    Pubescence (small hair like growth on stems, leaves)

o    Function based like Plant height associated with the salt tolerance in rice.


Limitations of the morphological markers

Morphological markers are associated with several general deficits that reduce their usefulness including:

  • The delay in morphological marker expression until late into the development of the organism, for example flower color.
  • Dominance of the markers: homozygotes and heterozygotes are not distinguishable.
  • Deleterious effects
  • Pleiotropy
  • Confounding effect(s) of the genes unrelated to the gene or the trait of interest. However, that also affect the morphological marker (epistasis)
  • Rare polymorphism
  • Frequent confounding effect(s) of the environmental factors which affect the morphological characteristics of the organism.
  • Most phenotypic markers are undesirable in the final product (Yellow color in maize).
  • Sometimes dependent on the environment for expression, for example height of the plants.


Non-DNA or Protein molecular markers such as isozyme markers:

Markert and Moller (1959) were first to describe the differing forms of bands that they were able to visualize with specific enzyme stains. They were the first to introduce the term biochemical polymorphisms often referred  as allozyme or isozyme markers. By the early 1980s, biochemical markers had been employed as a general tool for mapping QTL (Weller et al., 1988). Isozyme markers are still useful as these are simple, inexpensive means for detection of the gene introgression and recombination, for comparative mapping, and for determination of the genetic diversity and phylogenetic relationships among plant species (Hart and Langston, 1977; Hoffman, 1999; Horandl et al., 2000; Yu et al., 2001).


Isozyme markers: Multiple forms of the same enzyme coded by the different genes.

- Isozyme: one enzyme, more than one locus (gene duplication; gene families)

- Allozyme: one enzyme; one locus; two or more alleles in a population

Isozymes are proteins with same enzymatic function but different structural, chemical, or immunological characteristics (coded by the different genes). To be useful as marker, isoforms must be electrophoretically resolvable, and detectable by in-gel assay methods (Fig. 1)

w     Differences: amino acid composition/ sequence

w     Differences visualized: gel electrophoresis, mass spectrometry, etc.

w     Restricted due to limited number of enzyme systems available (about 30)


<?xml:namespace prefix = v ns = "urn:schemas-microsoft-com:vml" />




Dimeric Allozyme







<?xml:namespace prefix = w ns = "urn:schemas-microsoft-com:office:word" />

Fig. 1    Elecrophoretic resolvation of dimeric allozymes


Source for further reading:


Sanjeev Yadav, Neha Garg,  Sarika Garg  and Anil Kumar*

School of Biotechnology, Devi Ahilya University Indore-452001, INDIA
In Plant Genetic Transformation&Molecular Markers 
by Ashwani Kumar (eds)
ISBN13: 978-81-7132-613-6