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Development of functional markers of rice stripe disease resistance gene STV11 based on HRM technique

WANG Chan1,2,WU Ying-Ying1,2,LI Wen-Qi2,LI Xia2,WANG Fang-Quan2,ZHOU Tong3,YANG Jie1,2,*   

  1. 1 Jiangsu University, Zhenjiang 212013, Jiangsu, China; 2 Institute of Grain Crops, Jiangsu Academy of Agricultural Sciences / Key Laboratory of Germplasm lnnovation in Downstrem of Huaihe River (Nanjing), Nanjing 210014, Jiangsu, China; 3 Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, Jiangsu, China
  • Received:2024-11-27 Revised:2025-06-01 Accepted:2025-06-01 Published:2025-06-13
  • Supported by:
    This study was supported by the Zhongshan Biological Breeding Laboratory Project (BM2022008-03).

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Abstract:

Rice stripe disease, transmitted by the brown planthopper, poses a major threat to rice (Oryza sativa L.) production, particularly affecting japonica rice (Oryza sativa subsp. japonica). The causal agent is the rice stripe virus (RSV), which causes significant yield losses. To accelerate the breeding of rice varieties resistant to rice stripe disease, this study aimed to develop functional markers for the rapid and accurate identification of RSV resistance genes, thereby improving the efficiency of rice germplasm enhancement. STV11, a resistance gene identified in the indica variety Kasalath, was targeted. Based on a six-base deletion polymorphism in the Kasalath-type resistance allele STV11KAS (LOC_Os11g30910), sequence data from NCBI were analyzed. A PCR-based functional molecular marker, stvHRM-3, was designed according to nucleotide differences at positions 773–779 between resistant and susceptible varieties. PCR amplification and sequencing of the target fragments were conducted to validate the marker’s specificity. Through HRM-PCR detection and sequencing analysis, stvHRM-3 was confirmed as a functional marker for the STV11 gene. Using this marker, the STV11 genotypes of 520 japonica rice accessions—including materials from the Jiangsu Provincial Late Japonica Rice Regional Trials, late-maturing medium japonica preliminary tests, breeding intermediates, and selected varieties—were analyzed. Results showed that 217 accessions carried the resistance allele, 294 carried the susceptibility allele, and nine exhibited a heterozygous genotype. Accessions identified as resistant through marker analysis consistently exhibited high or moderate levels of resistance. The stvHRM-3 marker, developed using HRM-PCR technology, enables rapid, high-throughput genotyping of STV11 alleles and provides an effective tool for the early screening of RSV resistance. This marker holds great potential for application in marker-assisted selection and breeding of stripe virus–resistant rice varieties.

Key words: rice, rice stripe disease, STV11, functional marker, HRM-PCR technology

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