Construction of molecular ID for Osmanthus fragrans cultivars based on phenotypic traits and single nucleotide polymorphisms (SNPs)

WANG Yihan, LIU Jiaojiao, JIN Peiquan, LI Shuqing, WEI Jianfen, GUO Peng, SHANG Fude

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (4) : 12-24.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (4) : 12-24. DOI: 10.12302/j.issn.1000-2006.202405026

Construction of molecular ID for Osmanthus fragrans cultivars based on phenotypic traits and single nucleotide polymorphisms (SNPs)

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Abstract

【Objective】This study selected core genomic single-nucleotide polymorphism (SNP) loci to establish a rapid SNP genotyping method on the KASP platform, and to construct molecular IDs for Osmanthus fragrans cultivars. This study provides a theoretical foundation for identifying, tracing and protecting the intellectual property of O. fragrans cultivars.【Method】Field surveys were conducted to investigate key phenotypic characteristics of O. fragrans cultivars. Following two rounds of rigorous screening, we identified a set of core SNP markers capable of completely distinguishing previously sequenced cultivars. Subsequently, we analyzed the polymorphic information content (PIC) and expected heterozygosity (He) of each SNP locus. Using the genome sequences of ‘Rixianggui’ as a reference, species-specific KASP primers were designed for PCR amplification. Based on the genotyping results, we constructed cultivar DNA fingerprints and assessed the efficiency of core SNP markers for cultivar identification. Molecular IDs for O. fragrans cultivars were established by integrating phenotypic information codes with molecular fingerprint codes.【Result】We retained a total of 14 core SNP loci from genomic SNPs that fully discriminated the sequenced cultivars. The PIC values of these loci ranged from 0.246 to 0.375, with an average of 0.335, and the He indices ranged from 0.288 to 0.500, averaging 0.431. The KASP primers designed for these core SNP loci produced accurate genotyping results, enabling us to construct DNA fingerprints capable of distinguishing all 90 tested cultivars, including those not previously sequenced. Each cultivar was assigned a molecular ID composed of 34 digits.【Conclusion】In conclusion, 14 core SNP loci (SNP1 to SNP14) were identified that effectively discriminate among at least 90 O. fragrans cultivars. Unique molecular ID codes were constructed using DNA fingerprint codes along with serial codes derived from cultivar group types and phenotypic characteristics. Finally, barcode and quick response (QR) codes were generated for each cultivar.

Key words

Osmanthus fragrans / cultivar identification / single nucleotide polymorphism (SNP) / phenotype / molecular ID

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WANG Yihan , LIU Jiaojiao , JIN Peiquan , et al . Construction of molecular ID for Osmanthus fragrans cultivars based on phenotypic traits and single nucleotide polymorphisms (SNPs)[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2024, 48(4): 12-24 https://doi.org/10.12302/j.issn.1000-2006.202405026

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