Zufan Chen , Yuandong Hong , Jianquan Li

Hier Rice Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China
Author    Correspondence author
Rice Genomics and Genetics, 2025, Vol. 16, No. 6   
Received: 20 Sep., 2025    Accepted: 30 Oct., 2025    Published: 21 Nov., 2025

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.

Structural Variants (SVs), including insertions, deletions, inversions and translocations, are the key factors shaping the genomic structure and phenotypic diversity of rice (Oryza genus). However, due to the limitations of short-read sequencing technology in terms of read length and alignment accuracy, traditional methods often have insufficient accuracy when identifying complex or large-scale SVS. This study constructed an integrated framework using long-read sequencing technology, mainly including PacBio HiFi and Oxford Nanopore platforms, to achieve high-resolution detection and annotation of SV in multiple rice genomes, and systematically analyzed the biological significance of SV in regulating agronomic traits such as yield, stress resistance and adaptability. In the comparative analysis among japonica rice, indica rice and wild rice varieties, a large number of structural variation differences were found in the study, and insertion and deletion sites related to key phenotypic traits were identified. The expression analysis and PCR verification of the candidate SV loci further revealed their potential role in gene regulation. This study has laid the foundation for integrating SV data into a multi-omics breeding platform, which is expected to accelerate the precise improvement of rice varieties in the context of modern agriculture.

Rice genome; Long-read sequencing; Structural variation; Precise genome assembly; Molecular breeding