用于玉米品种真实性鉴定的最优核心SNP位点集的研发  

Development of an optimal core SNP loci set for maize variety genuineness identification

作　　者：田红丽[1] 杨扬[1] 范亚明 易红梅[1] 王蕊[1] 金石桥[2] 晋芳[2] 张云龙 刘亚维 王凤格[1] 赵久然[1] TIAN Hong-Li;YANG Yang;FAN Ya-Ming;YI Hong-Mei;WANG Rui;JIN Shi-Qiao;JIN Fang;ZHANG Yun-Long;LIU Ya-Wei;WANG Feng-Ge;ZHAO Jiu-Ran(Maize Research Institute,Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization of the Ministry of Agriculture and Rural Affairs(Co-construction by Ministry and Province)/Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding,Beijing 100097,China;National Agricultural Technology Extension and Service Center,Beijing 100026,China)

机构地区：[1]北京市农林科学院玉米研究所/农业农村部农作物DNA指纹创新利用重点实验室(部省共建)/玉米DNA指纹及分子育种北京市重点实验室,北京100097 [2]全国农业技术推广服务中心,北京100125

出　　处：《作物学报》2024年第5期1115-1123,共9页Acta Agronomica Sinica

基　　金：国家科技创新重大项目(2022ZD04019);北京市农林科学院财政项目(KJCX20230301,CZZJ202206)资助。

摘　　要：品种真实性是种子质量监测的一个重要指标。为建立准确可靠、快速简便、高通量、低成本的玉米品种真实性鉴定技术,本文利用200个核心SNP位点构建的5816个玉米杂交品种,3274个自交系的指纹数据,基于遗传算法、品种识别率评估确定了一套高鉴别力的核心SNP位点集,包含96个SNP位点。这96个SNPs全部位于基因内区域,相对均匀分布在10对染色体上。采用上述杂交品种和自交系的指纹数据评估显示这96个位点具有较高多态性和品种区分能力,PIC、MAF、DP平均值分别为0.36、0.40、0.60和0.36、0.39、0.48,对杂交品种、自交系的品种识别率达到99.14%和99.24%。两两样品成对比较结果显示,99.99%的品种间差异位点数目≥3个,杂交品种和自交系中96.74%和95.67%的成对比较差异位点数目集中在30~65个和30~60个。基于221个主推杂交品种的40个SSR位点、96个SNP位点的基因型数据分析结果显示,这2组标记集的鉴定结果具有较高的一致性。综上所述,本研究报道了一套具有位点数量最少、区分能力最强,兼容多平台、适于自动化分型等优点的最优核心SNP集。期望位点集将在玉米品种真实性监测、种子质量控制中得到广泛应用,进而维护玉米种子市场秩序、保障育种者权利以及保护农民利益。Variety genuineness is an important indicator for seed quality monitoring.In order to establish accurate,reliable,fast,simple,high-throughput,and low-cost maize variety genuineness identification technology,we evaluated and determined a set of high discriminative power core SNP loci set including 96 SNPs based on SNP fingerprint data of 5816 maize hybrids and 3274 inbred lines using the genetic algorithm and variety recognition rate.All 96 SNPs were located in the intra-gene region,generally distributed evenly on 10 pairs of chromosomes.The evaluation results using the above hybrid and inbred line data showed that 96 SNPs set had high polymorphism and variety discrimination power.The average values of PIC,MAF,and DP were 0.36,0.40,0.60,and 0.36,0.39,0.48 for hybrids and inbred lines,respectively.The variety discrimination power for hybrids and inbred lines reached 99.14%and 99.24%,respectively.Pairwise comparison between varieties showed that 99.99%of the comparisons had at least three differential loci.About 96.74%of hybrids and 95.67%of inbred lines mostly had the 30−65 and 30−60 differential loci between varieties,respectively.Compared with the 40 SSRs genotype dataset using 221 hybrids,the 96-SNPs set had high consistency in the identification results of the two marker sets.In summary,the optimal core SNPs set reported in this study had the advantage of the minimum number of loci,the highest discrimination power,the strongest differentiation platforms,and the automatic genotyping.It is expected that the extensive application of this core SNP loci set will be widely used in maize variety genuineness monitor and seed quality control for maintaining seed market order,so as to defend the breeders’rights and protecting interests of farmers.

关 键 词：玉米品种 真实性鉴定 SNP位点集 高鉴别力 

分 类 号：S513[农业科学—作物学]