基于表型性状和SNP标记构建桂花主要品种资源的分子身份证OA北大核心CSTPCD
Construction of molecular ID for Osmanthus fragrans cultivars based on phenotypic traits and single nucleotide polymorphisms(SNPs)
[目的]筛选核心单核苷酸多态性(single nucleotide polymorphism,SNP)位点,建立基于KASP 平台的桂花(Osmanthus fragrans)品种基因型快速检测方法,构建品种特异性分子身份证,为桂花品种鉴定、溯源、知识产权保护等提供理论基础.[方法]实地调查主流桂花栽培品种的重要表型特征.通过两轮严格筛选,从基因组SNP中保留一组能够完全鉴别测序品种的最优SNP标记,计算SNP 位点的多态信息含量(PIC)、期望杂合度(He)等信息.以'日香桂'('Rixianggui')基因组为参考,设计桂花特异性KASP引物并进行批量扩增,根据基因分型结果建立品种指纹图谱,评估核心SNP标记的品种鉴别力.结合品种表型信息码和品种分子指纹码构建桂花品种资源的分子身份证.[结果]筛选出 14 个能够完全鉴别测序品种的核心SNP 位点.各位点PIC值的变化范围为 0.246～0.375,平均值为 0.335;He的变化范围为 0.288～0.500,平均值为 0.431.针对核心位点设计的KASP引物基因分型准确.根据扩增结果构建DNA指纹图谱,可区分全部包括未测序品种在内的 90 个参试品种.对品种表型特征赋值,结合指纹码构建由 34 位数字组成的桂花品种资源分子身份证.[结论]确定了 SNP1—SNP14 共 14 个核心SNP位点,能够实现至少 90 个桂花品种的有效鉴别.结合品种群类型、表型特征和分子指纹码构建了 90 个桂花品种的唯一分子身份证,并生成对应的条形码和二维码.
[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.
王一涵;刘姣姣;金沛权;李书情;魏建芬;郭朋;尚富德
河南农业大学生命科学学院,河南省桂花种质创新与资源利用工程研究中心,河南 郑州 450046杭州桂花国家种质资源库,浙江 杭州 310020
园艺学与植物营养学
桂花品种鉴别单核苷酸多态性表型性状分子身份证
Osmanthus fragranscultivar identificationsingle nucleotide polymorphism(SNP)phenotypemolecular ID
《南京林业大学学报（自然科学版）》 2024 (004)
12-24 / 13
国家自然科学基金项目(32371911);河南省重大公益专项(201300110900).
评论