**2.2 PCR-based markers**

The idea of polymerase chain reaction (PCR) was conceived by Kary Mullis in 1983, and invented the process in 1985 which is based on denaturation, annealing, and extension [30]. The PCR based markers use primer dependent PCR amplification and/ or DNA hybridization followed by electrophoresis. Polymorphism is detected based on the presence or absence of an amplicon or based on the band size and mobility. The most commonly used PCR based markers are Randomly amplified polymorphic DNA (RAPD) [31], Amplified fragment length polymorphism (AFLP) [32], microsatellites or simple sequence repeats (SSRs) [33], sequence-related amplified polymorphism (SRAP) [34], inter simple sequence repeat (ISSR) [35], cleaved amplified polymorphic sequences [36], sequence characterized amplified region (SCAR) [37].

### **2.3 Sequence-based markers**

Sequencing technique is characterized by the identification of nucleotide sequences and their order along with the DNA strand [38]. Sequence-based markers are designed as per a specific sequence of DNA in a pool of unknown DNA. The modern sequencing techniques are genotyping by sequencing (GBS) and nextgeneration sequencing (NGS), which help to develop a large array of polymorphism at the nucleotide level; however, the most commonly used marker are single nucleotide polymorphisms (SNPs) [39] and diversity array technology (DArT Seq), which are known to be more accurate and reliable [22, 40].


#### **Table 1.**

*A chronology of the historical steps in molecular breeding.*

The historical development of molecular markers is also represented in the **Table 1**, which is adapted and modified from: Singh and Singh [41].

We have discussed several molecular marker systems; however, the most commonly used markers in plant breeding are RFLP, SSR, RAPD, AFLP, SCAR, and SNP [42]. The single-locus markers are RFLP, VNTR, SSLP, STMS, SSR, STS, SNP, CAPS, and SCAR whereas; multi-locus markers are RAPD, AP-PCR, ISSR, AFLP, M-AFLP, and S-SAP marker [43]. All these markers are used in plant breeding for germplasm characterization and protection, gene tagging, genome mapping, linkage map construction and analysis, evolution studies, parental selection, F1 hybrid testing, genetic purity test of seeds, genes or QTLs mapping etc. [44, 45].

### **3. Marker assisted selection (MAS)**

The direct phenotypic selection in plant breeding for crop improvement is labor-intensive, costly, and time-taking. This selection is also affected by target gene expression, their specific biological or environmental condition, and heritability of a trait. Phenotypic selection is less efficient for the quantitative traits that are frequently under the selection [46].

In MAS, the phenotypic selection is made with the help of genotypic markers. This technique helps to avoid difficulties and challenges that are occurred during the conventional crop breeding [47]. It is mostly used by plant breeders in their breeding programmes for the identification of desired dominant or recessive alleles throughout generations, also it helps to identify best genotypes from segregating generations [48]. The prerequisite for an efficient MAS program is reliable markers, quality of DNA extraction method, genetic maps, knowledge of marker-trait association, quick and efficient data processing, and availability of high throughput marker detection system [49]. Marker development pipeline adapted from [5] Collard and Mackill, 2008, in **Figure 1** explain that how marker assisted selection imposed from development of population through various steps.

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