Molecular Markers

Molecular Markers

Pradip Chandra Deka
Copyright: © 2024 |Pages: 28
DOI: 10.4018/979-8-3693-3026-5.ch050
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Abstract

Conventionally, establishment of relationship between the genotype and phenotype through genetic analysis was considered as key to success in plant breeding. The discovery of molecular markers has changed the entire scenario of genome analysis. Coinheritance of a gene of interest and a marker suggests that they are physically close on the chromosome. A marker must be polymorphic in nature for their identification and utilization. Such polymorphism can be detected at three levels: phenotype (morphological), difference in biomolecules (biochemical), or differences in the nucleotide sequence of DNA (molecular). These markers act as a versatile tool and find their importance in taxonomy, plant breeding, gene mapping, cultivar identification, and forensic science. They have several advantages over the conventional methods of plant breeding for developing new varieties with higher rate of success. This chapter covers the basic principles and applications of various types of markers with special emphasis on molecular markers.
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Classical Markers

During early history of plant breeding, only visible markers were used as selectable markers. They may be classified as morphological markers and cytological markers.

Morphological markers

The morphological features or phenotypes which are governed by genes are considered as morphological markers or phenotypic markers. They are generally qualitative traits like color of the flower, albinism, and altered leaf morphology that can be scored visually. Morphological markers are usually dominant or recessive. Most of the identified morphological markers are alleles of the wild type phenotypes which have accumulated in the population through mutations. Since the rate of spontaneous mutation is slow, number of such mutations found in natural population is also low. The problem is more acute in the case of forestry species and animal systems (Avise, 1994, Grover & Sharma, 2016).

Further, most of the quantitative characters are governed by polygenes, each contributing a small portion. Therefore, they are difficult to identify. Therefore, the genes controlling quantitative traits cannot be used as morphological markers. Availability of good number of genetic marker is the key to success for any plant or animal improvement program. Discovery of biochemical and molecular markers have been able to solve this problem to a large extent.

Cytological markers

Karyotypes and banding patterns of the chromosomes can be used as cytological markers. The physical structure of the chromosomes observed at the metaphase stage of mitosis has been used to construct the karyotypes of the organisms. The banding patters of the chromosomes derived through e.g. G-banding, Q-banding, R-banding etc. can also be used as markers. The color, width, order and position of the bands can be considered as important features of the markers. Different landmarks of the chromosomes are used for characterization and detection of chromosome mutation, linkage group identification and physical mapping. The physical maps developed through cytological and morphological markers are used for construction of linkage maps. However, in plant breeding cytological markers have limited use (Avise, 1994, Grover & Sharma, 2016).

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Biochemical Markers

Biochemical markers are biomolecules which are produced by gene expression. Two biomolecules primarily used as genetic markers are, monoterpenes and allozymes.

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