Genomics and Applied Biology 2026, Vol.17, No.1, 1-15 http://bioscipublisher.com/index.php/gab 2 Recent advances in association analysis enable the integration of genotyping data from gene chip with crop phenotypes. This integration marks a key shift from conventional to molecular assisted breeding, supporting the sustainable genetic improvement of crop varieties. However, current gene chip still face several limitations: (1) Restricted system-they can only detect known variants based on pre-designed probes, making it difficult to capture novel mutations or large-scale structural variants; (2) High customization thresholds and platform dependency-solid-phase gene chip entails high development costs. Liquid-phase gene chip, while offering greater flexibility, requires continuous optimization of probe pools, posing challenges for small and medium-sized breeding institutions; (3) Insufficient data standardization-batch effects (Luo et al., 2010) across different chips often hinder cross-project data integration. These effects can arise from factors such as different chips type/lot/platform or variations in sample preparation protocols. This study systematically reviews the fundamental principles, types, applications, and future prospects of crop gene chip. We aim to provide valuable insights for crop variety improvement and the refinement of gene chip. 2 Classification and Principles of Gene Chip Gene chips are categorized into two types according to their reaction environment: Solid-phase and liquid-phase (Li et al., 2024). Since advent, chips have been developed using SNPs as markers. Hence they are also referred to SNP arrays. The solid-phase gene chip emerged in the late 1980s to early 1990s. A key commercial milestone was the GeneChip® microarrays based on photolithographic synthesis, developed by company Affymetrix in the early 1990s. And in 1994, it produced the first commercial solid-phase gene chip for HIV genotyping (John et al., 2000; Cook et al., 2002). Subsequently, Illumina introduced its GoldenGate and Infinium assays based on its BeadArray/BeadChip technology, thereby becoming a popular provider of cost-effective genomic platforms. Meanwhile, Beckman Coulter focused on developing chips with lower SNP throughput but ultra-high sample capacity, carving out a unique market niche with its SNPstream platform (Gupta et al., 2008). With the maturation of solid-phase gene chip applications in the medical field, Akhunov et al. (2009) employed the Illumina GoldenGate assay to genotype 96 SNP loci across 53 homozygous tetraploid and 38 homozygous hexaploid wheat lines. They obtained high-quality genotyping data and thereby marking the beginning of solid-phase gene chip application in crops. Today, both Affymetrix and Illumina have established mature solid-phase gene chip platforms, offering distinct array fabrication assay and software analysis packages for genotyping. Despite these differences, their hybridization and signal detection principles remain similar: Following nucleic acid extraction, the target is amplified and labeled with biotin. After hybridization, the array undergoes automated washing and staining with a fluorescent streptavidin-phycoerythrin conjugate (SAPE) that binds to the biotin, enabling the detection of hybridized targets by scanning the array for fluorescence intensity (Dalma-Weiszhausz et al., 2006). Crop ploidy significantly influences the effect of solid-phase gene chips application. In diploid crops, each SNP loci typically generates three fluorescence signal types-two homozygous (AA and BB) and one heterozygous (AB)-each clustering distinctly to enable accurate genotyping. However, in auto- or allopolyploid species, each SNP loci may produce more than three signal types, substantially complicating the analysis of genotyping results. You et al. (2018) systematically reviewed the limitations of solid-phase gene chips in polyploid crops by comparing the principles of various platforms and analytical software, offering valuable strategies for genotyping polyploid species. As solid-phase gene chips are custom-designed for specific known SNPs with fixed marker loci, they lack flexibility for study-specific adjustments. Coupled with their high cost, these limitations restrict their widespread adoption in breeding programs (Guo et al., 2019). The liquid-phase gene chip was developed based on high-throughput genome sequencing technology. It is also known as Genotyping-by-Target-Sequence (GBTS). Unlike whole-genome sequencing, this approach first captures targeted genomic regions before sequencing them. Two primary methods are used for targets capture: The first is solution-phase probes hybridization, where custom-designed probes hybridize with target DNA fragments in a liquid environment through base complementarity, thereby enriching the target regions. Subsequent steps include sequencing library construction and sequencing. Representative products employing this method include NimbleGen, SureSelect, and GenoBaits (Guo et al., 2019). The second method relies on multiplex PCR, which
RkJQdWJsaXNoZXIy MjQ4ODYzNA==