多倍体植物中单核苷酸多态性(SNPs)的开发

Single nucleotide polymorphism(SNP) discovery in polyploid plants

单核苷酸多态性(SNP)是指在基因组水平上由单核苷酸的变异所引起的一种DNA序列多态性.在人、拟南芥、水稻等二倍体生物中,已经开发出大量的SNP标记并被用于群体结构分析、关联作图等研究,而在棉花、油菜、小麦等多倍体植物中,SNP的开发与应用却进展迟缓.为促进多倍体植物中SNP的开发,本文对多倍体植物中SNP标记开发所遇到的难题进行了阐述,并对多倍体中SNP标记开发方法进行了梳理,包括位点特异性引物的PCR片段直接测序,利用多倍体的近缘二倍体区分SNPs和部分同源序列间的差异(homoeologous sequence variants,HSVs),利用2代测序技术大规模发掘SNPs,基于公共数据库的序列通过生物信息学分析获取候选SNPs,通过遗传(分离)模式的研究验证SNPs等.利用上述方法可实现多倍体植物中SNP标记的大规模开发.

Single nucleotide polymorphism（SNP） is a kind of DNA polymorphism in genome which results from the variance of single nucleotide.In diploid organisms（such as human,Arabidopsis thaliana,Oryza sativa,etc.）,many SNP markers were discovered as genetic markers,and had been widely used for population parameter estimation and association mapping.However, SNP discovery and application in the polyploid organisms（such as Gossypium hirsutum,Brassica napus,Triticum aestivum,etc.） were limited and lagged.In order to facilitate SNP discovery in polyploid plants,this paper reviewed the genomic complexity of polyploidy,the obstacle and the solutions of SNPs discovery in polyploid plants,including these methods of sequencing of polymerase chain reaction（PCR） amplicons from locus-specific primer,distinguishing SNPs from homoeologous sequence variants（HSVs） through living models of allopolyploid ancestral genomes,use of next-generation sequencing for SNP discovery,scanning along seeking potential SNPs by bioinformatics tool,Mendelian transmission test of candidate SNPs.In conclusion,the applications of solutions mentioned above are feasible and reliable for the high-throughput SNP discovery in polyploid plants.