Genomics and Applied Biology 2026, Vol.17, No.1, 1-15 http://bioscipublisher.com/index.php/gab 4 Figure 2 Flowchart for genotyping by target sequencing with GenoPlexs (Adopted from Xu et al., 2020) 3 Applications of Gene Chips 3.1 Genetic research Cultivar identification is the process of analyzing the genotypic or phenotypic characteristics of plant varieties to confirm their genetic background, and varietal purity. It is also an important aspect of crop breeding, germplasm management, and intellectual property protection (Korir et al., 2012; Samarina et al., 2025). Misidentification of crop varieties is relatively common: crops with the same genotype may be assigned different names, while those with different genotypes may be incorrectly classified as the same variety. This situation seriously infringes upon the rights of breeders. To avoid this problem, scientific identification of crop varieties is particularly important. Gene chips have thus become a key tool in addressing this issue. Liu et al. (2025a) developed the TEA5K mSNP array based on GBTS, stably identifying 5 781 (5K) mSNP markers and 36 357 (36 K) SNP markers in a diverse set of tea germplasm. Among the 36K markers, 5K markers (core SNP) exhibited higher polymorphism, with high PIC and GD values. The study calculated genetic similarity for all possible variety combinations (different individuals of the same variety, homologous but artificially mutagenized varieties, and bud mutant varieties) using three marker sets (5K core SNP, 36K SNP, and 5K mSNP). Theoretically, the genetic similarity between different individuals of the same variety should be 100%. Through comparison, it was found that the 5K core SNP panel
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