**2. Molecular markers: road for easy and reliable selection**

Any fixed property of an individual showing the heritable variations is termed as a character or trait, whereas marker can be defined as any mark which inherits together with the trait of interest throughout generation [20, 21]. Markers are categorized into four main groups- morphological, biochemical, cytological and molecular (DNA based) markers [22].

Morphological markers are also known as naked eye marker or phenotypic marker, used for quality traits such as flower shape, size, color, seed structure, growth habit, and other agronomic traits in plants. These markers are eco-friendly; easy to use, and need not require any specific instrument; however, their number is limited in crop species and highly influenced by prevailing environmental conditions [22–24].

Biochemical markers, mostly isozymes, are the results of variation in enzymes (protein and amino acid sequences) encoded by various genes, but functionally they are the same [25]. They are the result end product of allelic variation of enzymes. They are co-dominance in inheritance, cost-effective, and easy to use. They have been widely used in plant breeding for the study of gene flow, population structure, and genetic diversity [26]. However, they are limited in number, show

#### *Insights into Marker Assisted Selection and Its Applications in Plant Breeding DOI: http://dx.doi.org/10.5772/intechopen.95004*

less polymorphism, and predominantly affected by plant tissue being used, growth stage, and method of their extraction [27].

Cytological markers are based on prevailing variation in number, shape, size, the position of chromosomes, and their banding pattern. Cytological analysis reveals the unique characteristics of chromosomes such as knob and satellite, and the number of nucleoli in the nucleus, etc. This variation shows a different pattern of euchromatin and heterochromatin in the chromosome [22], such as Giemsa stain recognizes G bands. They have been extensively utilized in plant breeding for the identification of linkage groups and physical mapping [9]. In contrast, molecular markers are defined as nucleotides polymorphism present between individuals as a result of deletion, duplication, insertion, substitution, point mutation and translocation, etc. [27] but do not affect the function of the gene.

Molecular markers do not inevitably target genes, instead, inherit as a 'flag' with the gene of interest during transmission of a trait from one generation to the next generation [28]. Molecular markers associated with the close proximity of genes of interest are known as gene tags *i.e.* linked with target gene [9]. The essential characteristic features of an ideal marker are co-dominance inheritance, high level of polymorphism, high reproducibility, whole-genome coverage, easy and fast to detect, neutral to environmental conditions, high resolution, low cost, and whole-genome coverage [22, 27, 29]. Different types of molecular markers have been developed, and are used in various crops. These molecular markers are mainly categorized into the following classes based on their method of detection.
