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including allele‐specific hybridization, (ii) enzymatic reactions including primer extension, and mini‐sequencing (Ding and Jin 2009). For making SNP arrays, the first step is the identification of genome‐wide SNPs by sequencing (preferably WGR) of a large diverse panel. The SNPs arrays may include SNPs from coding (genic) regions only and/or genome‐wide SNPs from other noncoding regions. SNPs are in silico validated with several custom tools and final filtered SNPs are identified. The oligonucleotide probes containing SNP alleles are designed and bound on a solid glass plate surface. SNP chips can be custom designed commercially from two widely used platforms: Affymetrics (www.affymetrics.com) as Axiom Affymetrics SNP Chips (Affymetrix/Thermo Fisher Axiom®) or Illumina (https://www.illumina.com/science/technology/microarray.html) as Immunia Infinium assay (Illumina Infinium®). Affymetrics SNP array relies on differential hybridization due to different melting temperatures for matched and mismatched SNPs binding to target DNA sequence. On the other hand, Illumina Infinium assay uses Illumina BeadArray technology that relies on primer extension to distinguish two SNP alleles. The Affymetrix SNP array uses 25‐mer for SNP calling while the Illumina BeadArray uses 50‐mer for target capture. In rice, a high‐resolution 44K Affymetrix array, 50K Infinium array, and 700K high‐density rice array are available for rice SNP genotyping (McCouch et al. 2010; Tung et al. 2010; Chen et al. 2013; McCouch et al. 2015). Additionally, high‐density SNP arrays have been developed for other crop plants such as maize (Ganal et al. 2011) and sunflower (Bachlava et al. 2012) as well as domestic animal species, including cattle (Gibbs et al. 2009; Matukumalli et al. 2009) and pig (Ramos et al. 2009). One major advantage of SNP arrays is the reproducibility of data points where GBS does have some shortcomings. However, the disadvantage is the less polymorphism as compared to GBS and WGR and detection of only alleles present in the array (Table 1.2).

SSR GBS WGR SNP array KASP™
DNA quality Moderate High High High High
PCR‐based Yes Yes No No No
Allele detection High High High Low Low
Polymorphism High High High Low Low
Ease to use Easy Not easy Not easy Easy Easy
Reproducibility High Low High High High
Cost Moderate Low to moderate High High moderate
Cost for analysis High High High Low Low
Suitability for different approaches
Genetic diversity analysis High Moderate High (cost concerns) High High
Bi‐parental QTL mapping High High High High High
Genome wide association analysis Moderate High High High Low
Genomic selection Low Moderate High (cost concerns) High Low

      1.5.4 Kompetitive Allele‐Specific PCR (KASP)

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