Evaluation of SNP Loci for Rice Variety Authenticity Verification

doi:10.16819/j.1001-7216.2025.241114

Abstract

Abstract:

【Objective】 A highly discriminative combination of SNP loci is crucial for developing efficient, accurate, and cost-effective rice variety verification technologies, which can be widely applied in seed regulation, variety breeding and other fields.【Method】 This study established fingerprints for 1,383 inbred and 2,702 hybrid rice varieties using the 96 SNP panel from the agricultural industry standard, designated RGIsnp96.【Result】 The results demonstrated that RGIsnp96 exhibited high polymorphism and strong discriminative power for variety identification. For 1,387 inbred varieties, the heterozygous rate, average polymorphic information content (PIC), and average minor allele frequency (MAF) of SNPs in RGIsnp96 were 0.03, 0.30, and 0.27, respectively. For 2702 hybrid varieties, the corresponding values were 0.39, 0.30, and 0.29, respectively. The identification rates, represented by the proportion of distinguishable variety pairs, for inbred and hybrid rice varieties were 99.94% and 99.99%, respectively. A good equivalence between RGIsnp96 and 48 SSRs in agricultural industry standards (designated RGIssr48 in the following) was evaluated by comparing similarities of variety pairs measured by the two marker sets for both inbred and hybrid varieties. Furthermore, combining RGIsnp96 and RGIssr48, representing different types of markers, could generate better results than using a single type of marker for differentiating certain inbred rice varieties, and corresponding strategies were recommended.【Conclusion】 RGIsnp96 demonstrates exceptional capability in rice variety identification, providing robust technical support for improving rice seed quality, regulating the seed market order, and safeguarding farmers' rights and interests.

Key words: rice variety, allthenticity verification, RGIsnp96, single nucleotide polymorphism, variety identification

摘要：

【目的】高鉴别力的SNP位点组合对建立高效、精准、低成本的水稻品种验证技术至关重要，可广泛应用于种子监管和品种创新等领域。【方法】利用农业行业标准推荐的96个SNP标记(RGIsnp96)，构建1383个常规种和2702个杂交种水稻品种的SNP指纹图谱。【结果】发现在常规种中，杂合基因型比率、平均多态性信息成分(PIC)、平均次要等位基因频率(MAF)分别为0.03、0.30和0.27；在杂交种中，相关指标分别为0.39、0.30和0.29。RGIsnp96对常规稻、杂交稻的品种识别率分别为99.94%、99.99%。基于品种间异同基因型位点的比例，对RGIsnp96与农业行业标准推荐的48个SSR标记(RGIssr48)的鉴定结果进行比较，结果显示，不论是对于常规种、还是杂交种，这两套标记均具有良好的等效性。同时，还发现对部分常规品种的鉴别，组合不同类型的标记，比单一类型的标记能取得更好的效果，并推荐了相应的策略。【结论】RGIsnp96展现出卓越的水稻品种鉴别能力，为提升水稻种子质量、规范种子市场秩序以及保障农民权益提供了坚实的技术支持。

关键词: 水稻品种, 真实性鉴定, RGIsnp96, 单核苷酸多态性, 品种鉴定

XU Qun, WANG Shan, YUAN Xiaoping, JIN Shiqiao, JIN Fang, HAO Wanjun, WU Xiaobi, FENG Yue, YU Hanyong, SUN Yanfei, YANG Yaolong, WEI Xinghua. Evaluation of SNP Loci for Rice Variety Authenticity Verification[J]. Chinese Journal OF Rice Science, 2025, 39(5): 635-642.

徐群, 王珊, 袁筱萍, 金石桥, 晋芳, 郝万军, 吴小碧, 冯跃, 余汉勇, 孙燕飞, 杨窑龙, 魏兴华. 用于水稻品种真实性验证的SNP位点评价[J]. 中国水稻科学, 2025, 39(5): 635-642.

Figures/Tables 5

Fig. 1. Distribution of RGIsnp96 on rice reference genome IRGSP-1.0

Fig. 2. Distribution of PIC, MAF, heterozygous genotype rates of RGIsnp96 in 2702 hybrid rice and 1383 inbred rice varieties

Fig. 3. Variety discrimination rate based on optimal loci combination

Fig. 4. Distribution of the number of different SNPs obtained by pairwise analysis of hybrid rice and inbred rice varieties, respectively

Fig. 5. Distribution of pairwise similarity of 1383 inbred rice and 2702 hybrid rice varieties based on RGIsnp96 and RGIssr48

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