*3.2.1.1 SSRs as a sequence based marker*

These markers are group of tedious DNA chain typically two to six base pairs. It is a form of VNTRs (Variable Number Tandem Repeats) [93]. These markers are wellknown as STRs (short tandem repeats). The rate of different STRs length is feature of microsatellite loci in rice [75]. They consist of dinucleotide; trinucleotide as well as tetranucleotide repeats for genetic analysis. Dinucleotides are the key form present in most vertebrates. Trinucleotide repeat are rich in plants [94]. Microsatellite markers are believed to be suitable over different array of markers due to following reasons. These are scattered all over the genome of extremely conserved region. These markers have various qualities of simplicity, high polymorphism, rapidity as well as stability. These markers have been model for examination of germplasm, genetic diversity [95], heterosis, purity test, gene mapping, fingerprints assembly, phylogenetic comparison as well as marker aided selection [75, 95]. A random collection of SSRs assist in estimation of rice genetic diversity and rice cultivar classification without mistakes [96]. Particularly SSRs markers have been extensively employed in rice genetic analysis for high allelic detection [97]. Microsatellite exposed unreliable level of genetic relationship among the domesticated as well as wild collection of rice [98].

## *3.2.1.2 SNPs as genetic markers from high-throughput sequencing*

SNPs (single nucleotide polymorphisms) signify a strong group of genetic markers [99] among different categories of molecular markers due to following reason [100]. These markers detect single-base pair location depend upon sequence variation in genomes [101]. SNPs markers offer a huge marker density in genomes [102]. SNPs markers have achieved significant importance in plant genetic analysis due to their brilliant genetic qualities, genetic diversity, evolutionary interaction [103], high throughput genetic mapping [104], population substructure [105], genomewide linkage disequilibrium [106] as well as association mapping [107]. Availability of high quality reference genome sequence made it easier to scan out mutation by re-sequencing the species genotypes through next generation sequencing (NGS) approaches and to identify the variation in targeted genotype through mapping techniques as genome-wide association mapping [108].

Classically, a quite large sequencing attempt is faithful to recognize polymorphic location in a genome among a set of various breeding lines [109]. A precise

multiplexed SNPs genotyping analysis is necessary to utilize the huge SNPs source for high-throughput genetic test in rice [110]. It will become routine to re-sequence the plants genome with current SNPs platforms as the price of genome sequencing keep on to reduce [111].

SNPs genotyping have been applied in many organism including rice [112–114], *Arabidopsis* [115], maize [116], soybean [117] and wheat [118]. The high class order of the rice genome has offered genome-wide SNPs source [119]. Polymorphic loci (5.41 million) were detected between the two main domesticated rice subspecies (*Indica* and *Japonica*) by SNPs genotyping [120].

A complete map of rice genome builds 6,119,311 SNPs variants for 1529 genome orders. SNPs (213,188) were located in *Indica* and *Japonica* rice. Asian and African rice were established 9595 SNPs [121]. Three thousand rice genomes project [122] submit for rice clustering of aus/boro genotypes. Only 208 accessions are categorized as aus/boro depends upon SNPs markers of 200,000. It is also exposed from further study that aus group was genetically related by 376,000 SNPs markers [123].
