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2020), and maize (Zhang et al. 2017; Su et al. 2016).

Schematic illustration of the steps in KASP reaction: (a) annealing: allele-specific primer binds to target SNP, (b) extension: anti tail sequence generation leading to disassembly of allele-specific FRET cassette, and (c) fluorescent emission: sample emitting fluorescence on exposing to a specific wavelength.

      Source: The figure is reproduced from Rosas et al. (2014) available with CC‐BY‐4.0.

SNP database Organism URL
dbSNP Human http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp
Ensembl Human http://www.ensembl.org/Homo_sapiens/index.html
1001 Genomes Arabidopsis https://1001genomes.org/
CropSNPdb Brassica crops, wheat http://snpdb.appliedbioinformatics.com.au
SNP‐Seek Database Rice 3K panel https://snp‐seek.irri.org/
MaizeSNPDB 1210 Maize inbred lines http://150.109.59.144:3838/MaizeSNPDB/
CerealDB Wheat http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php

      1.7.1 Application of Molecular Markers in Crop Improvement

      Molecular markers have several applications in genetic studies and crop improvement programs. These have been used in the development of saturated linkage maps, gene/QTL mapping, map‐based cloning of genes, orthologous gene mapping, and marker‐assisted transfer of targeted genes/QTLs in the background of different cultivars/lines. Saturation of linkage maps refers to increased marker density to cover the entire chromosomal region. In general, when molecular markers are arranged on a linkage map with less than 1 cM distance apart, is considered as saturated linkage map. The development of saturated linkage maps could only be possible with the availability of molecular markers. These maps are prerequisite for gene/QTL mapping, map‐based cloning of genes, and MAS. Several molecular markers‐based saturated linkage maps have been developed in crop plants including rice (Harushima et al. 1998; McCouch et al. 2002; IRGSP 2005; Zhu et al. 2017; Kumar et al. 2018), wheat (Somers et al. 2004; Song et al. 2005; Poland et al. 2012; Li et al. 2015; Hussain et al. 2017), maize (Sharopova et al. 2002; Zhou et al. 2016; Su et al. 2017), and tomato (Tanksley et al. 1992; Haanstra et al. 1999; Sim et al. 2012). In one of the studies, a rice genetic map helped to enrich the genetic region of Ph1 locus of wheat and facilitated the identification of candidate genes governing the locus (Sidhu et al. 2008).

      1.7.2 Role of Molecular Markers in Germplasm Characterization

      Molecular markers are also used in DNA fingerprinting for varietal identification, germplasm evaluation, phylogenetic and evolutionary studies, etc. The molecular marker‐based DNA fingerprinting data are useful for the characterization of plant germplasm accessions, quantification of genetic diversity, and protection of proprietary germplasm (Smith and Smith 1992). Molecular markers have been utilized to distinguish closely related crop cultivars (Melchinger et al. 1991; Paull et al. 1998), in sex identification of dioecious plants (Parasnis et al. 1999). They are also used to understand evolutionary relationships within and between species, genera, or higher taxonomic groups. Such studies involve large number of markers to study similarities and differences among taxa (Paterson et al. 1991). Although phylogeny has been established for many plant species based on morphological markers, biochemical markers, and chromosome homology,

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