Haodan Zeng^1,2 , Lexin Yang^1,2 , Yanling Wen^1,2 , Jianhong Xu^1,2 , Zhen Liu^1,2

1 Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya, 572025, China
2 Department of Agronomy, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, 310058, China
Author    Correspondence author
Bioscience Methods, 2026, Vol. 17, No. 4   
Received: 15 Jun., 2026    Accepted: 16 Jul., 2026    Published: 28 Jul., 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.

Liquid-phase chip utilizes genomic capture sequencing to genotype target loci, offering advantages such as high throughput, low cost, and high customizability. Rice research and breeding often require large-scale cultivars detection. This study aimed to develop an accurate, efficient, high-throughput, and low-cost liquid-phase detection chip targeting important functional genes reported in rice. Through literature review, we collected 76 previously reported important functional genes in rice and identified 122 functional natural variation sites within them. These genes primarily control agronomic traits of great interest to breeders, including yield, quality, fertility, biotic and abiotic stress resistance, and nutrient use efficiency. Specific hybridization probes were designed targeting these functional variation loci, leading to the development of the 0.1K rice functional gene chip (RFG 0.1K). To evaluate the performance of this chip, we used it to genotype 35 diverse rice accessions (including indica, japonica, and Aus). The results showed that the call rate for each sample exceeded 90%, the Q30 value for all samples was above 80%, the biological replicate consistency reached 97%, and the accuracy verified by Sanger sequencing was 88%, indicating that the genotyping results of this chip are accurate, reliable, and reproducible. Subsequently, based on the high-quality genotyping results, population genetic analyses were further conducted. The results demonstrated that this chip can effectively distinguish the genetic backgrounds of different rice accessions, showing good application value in rice germplasm resource identification and molecular-assisted breeding.

Rice; Functional genes; Liquid-phase chip; Molecular marker; Genotyping