烟草种质基因分型核心SNP标记的开发  

Development Core SNP Markers for Tobacco Germplasm Genotyping

作　　者：余世洲 曹领改 王世泽 刘勇 边文杰[4] 任学良[1] YU Shi-zhou;CAO Ling-gai;WANG Shi-ze;LIU Yong;BIAN Wen-jie;REN Xue-liang(Guizhou Academy of Tobacco Science,Guiyang 550081;Hebei Normal University of Science&Technology,Qinhuangdao 066004;Henan Agricultural University,Zhengzhou 450002;China Tobacco Anhui Industrial Co.,Ltd.,Hefei 230088)

机构地区：[1]贵州省烟草科学研究院,贵阳550081 [2]河北科技师范学院,秦皇岛066004 [3]河南农业大学,郑州450002 [4]安徽中烟工业有限责任公司,合肥230088

出　　处：《生物技术通报》2023年第3期89-100,共12页Biotechnology Bulletin

基　　金：中国烟草总公司烟草基因组计划与生物育种重大科技项目(110202101032),中国烟草总公司贵州省公司重点研发项目(2021XM05)。

摘　　要：基于KASP(kompetitive allele specific PCR)技术平台,开发并验证可用于烟草核心种质基因分型的SNP(single nucleotide polymorphism)标记和对应检测引物,为烟草种质基因型鉴定评价、遗传多样性分析、核心种质筛选等提供技术和数据支持。利用Python和Perl脚本程序对覆盖烟草全基因组的1 179 154个SNP位点进行KASP引物设计和筛选,并通过试验验证其准确度和可用性。结果共有217 621个SNP位点完成了对应KASP引物设计,选择1 378个SNP位点进行试验验证,明确了732个可作为SNP标记,并确定48个SNP标记作为烟草种质资源基因分型的核心标记。这48个核心标记在烟草24条染色体上平均分布,平均PIC为0.36,平均MAF为0.39。利用确定的48个核心SNP标记,可以将各供试种质特别是将当前主栽烟草品种基因型进行区分,且标记具有极高的可靠性。Based on kompetitive allele specific PCR(KASP)technology platform,the tobacco SNP(single nucleotide polymorphism)markers and corresponding primers were developed and validated,which could assist tobacco germplasm evaluation,genetic diversity analysis,and core germplasm screening.Using Python and Perl tools,1 179 154 SNPs covering tobacco genome were designed and screened for KASP primers,and their accuracy and applicability were verified by experiment.As results,217 621 SNPs were enough for designing corresponding KASP primers.Then 1 378 SNPs were selected for experimental validation,and 732 were approved for SNP marker.Further 48 SNP markers,with an average PIC of 0.36 and an average MAF of 0.39,were finally identified as core markers,and they were evenly distributed on 24 chromosomes of the tobacco genome.The various germplasm,especially the genotypes of current major tobacco cultivars could be distinguished by the 48 core SNPs,and the marking is of extremely high reliability.

关 键 词：烟草 种质资源 单核苷酸多态性 竞争性等位基因特异性PCR 

分 类 号：S572[农业科学—烟草工业]