Genomics and Applied Biology 2026, Vol.17, No.1, 1-15 http://bioscipublisher.com/index.php/gab 1 Feature Review Open Access Crop Gene Chip and Its Applications Haodan Zeng1,2, Yanling Wen 1,2, JunguiXu3, Jianhong Xu1,2 , ZhenLiu 1 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 Corresponding authors: zhen2012@zju.edu.cn; jhxu@zju.edu.cn Genomics and Applied Biology, 2026, Vol.17, No.1 doi: 10.5376/gab.2026.17.0001 Received: 21 Nov., 2025 Accepted: 07 Jan., 2026 Published: 14 Feb., 2026 Copyright © 2026 Zeng et al., 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. Preferred citation for this article: Zeng H.D., Wen Y.L., Xu J.G., Xu J.H., and Liu Z., 2026, Crop gene chip and its applications, Genomics and Applied Biology, 17(1): 1-15 (doi: 10.5376/gab.2026.17.0001) Abstract 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. Keywords Crop; Gene chip; Genotyping; Single nucleotide polymorphism 1 Introduction Crop improvement is increasingly relying on the molecular biology analysis. Over the past two to three decades, reference genomes of various crops have been successively sequenced (Kawahara et al., 2013; IWGSC et al., 2018). Notably, the cost of high-throughput sequencing has exhibited an exponential decrease (Xu et al., 2020). Gene editing systems continue to improve (Pacesa et al., 2024), alongside the growing integration of artificial intelligence and multi-omics (Li et al., 2025b). In this context, crop improvement strategies have progressed to the precise manipulation of single genes, single regulatory elements, and even individual nucleotides. With the evolving needs in breeding, numerous deep-seated challenges remain to be overcome. These include the underutilization of existing genetic resources (Wang et al., 2020; Mark et al., 2022), the ineffective mining and utilization of functional genes (Jia et al., 2023). Moreover, the complex correspondence between genotype and phenotype prevents effective improvement of traits controlled by multiple functional genes (Wang et al., 2025). After Sanger sequencing, gene chip emerged as a revolutionary tool in bioscience. It enables efficient genotyping and presents a solution to the aforementioned challenges. Gene chip has two developmental stages: solid-phase and liquid-phase. Solid-phase gene chip consist of thousands of individual DNA sequences arrayed at a high density on a single matrix, usually glass slides or quartz wafers, but sometimes on nylon substrates. Probes with known identity are used to determine complementary binding, thus allowing the analysis of gene expression, DNA sequence variation or protein levels in a parallel format (Zimdahl et al., 2005). With technological advances, the liquid-phase gene chip, also known as “Genotyping by Target Sequencing” (GBTS), has been successfully developed. This innovation overcomes limitations of traditional solid-phase gene chip, such as low flexibility, difficulty of updating. The liquid-phase gene chip not only efficiently captures target genomic regions by specific probes in solution environment, but also utilizes high-throughput sequencing to obtain genotype. As a result, this technology integrates the targeting ability and cost-effectiveness of chip-based methods with the high accuracy and rich information output of sequencing technologies.
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