Haodan  Zeng^1,2 , Yanling  Wen^1,2 , Jungui  Xu³ , Jianhong  Xu ^1,2 , Zhen  Liu¹

1 Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572026, China
2 Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
3 Hainan Huitian Agriculture Co., Ltd., Yazhou Bay Science and Technology City, Sanya, 572026, China
Author    Correspondence author
Genomics and Applied Biology, 2026, Vol. 17, No. 1   
Received: 21 Nov., 2025    Accepted: 07 Jan., 2026    Published: 14 Feb., 2026

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Gene chip integrates multiple oligonucleotide sequences (probes) onto a solid-phase carrier or in a solution. Through the hybridization of probes with sample DNA and subsequent signal detection or sequence analysis, gene expression levels or genotypes can be detected. Single nucleotide polymorphisms (SNPs) are widely distributed across the genome and easily detectable, making them commonly used molecular markers for genotype detection and the development of gene chips. The development of SNP-based gene chips has gone through two stages: solid-phase and liquid-phase. Particularly since the application of high-throughput genome sequencing technology, a large number of SNPs have been identified in various crops, leading to the development of different SNP chips. These chips are widely used in variety identification, kinship analysis, genome-wide association analysis, genomic selection analysis, and other areas to assist breeding. This review introduces the detection principles related to gene chips, summarizes the SNP chips developed for different crops, and outlines the current application status of SNP chips, their existing defects and limitations, as well as future development trends. The aim is to provide a solid theoretical foundation for the optimization and innovation of gene chips in the future, promoting the continuous progress and refinement of related technologies.

Crop; Gene chip; Genotyping; Single nucleotide polymorphism