不同倍性甘薯及近缘材料的SNP鉴定流程

SNP Identification Process of Sweet Potato Varieties and Related Wild Materials with Varied Ploidy

基因组上的SNP变异具有丰富的数量和多态性的特点,SNP鉴定在作物遗传多样性、群体结构关系、育种等方面有重要作用。然而多倍体作物由于倍性高、杂合性高等问题,使得SNP的开发、验证和检测较为困难。甘薯及不同倍性近缘野生种均属于番薯属,由于甘薯近缘物种倍性变化较大,本研究选取二倍体、四倍体、六倍体的Ipomoea trifida以及五倍体和六倍体的甘薯为材料,采用简化基因组测序技术——RAD-seq进行测序,以栽培甘薯‘泰中6号’基因组序列为参考,通过与参考基因组的比对、排序、PCR标记去重复以及变异检测,建立了一套基于甘薯参考基因组进行不同倍性材料SNP鉴定的分析流程。通过IQ-TREE对SNP标记进行系统发育树构建,结果验证了本流程具有较高的可靠性。本研究开发的数据处理流程,不仅可用于不同倍性野生材料遗传关系的鉴定,还可为甘薯品种的遗传多样性分析和育种的亲本选择以及其他多倍体植物SNP标记开发鉴定提供借鉴和参考。

The SNP variation in the genome is characterized by abundant quantity and polymorphism.SNP identification plays an important role in exploring genetic diversity,population structure relationship and breeding in crops.Due to the high degree of ploidy complexity and high degree of heterozygosity,it is difficult to develop,verify and detect SNP in polyploid crops.Sweet potato(Ipomoea batatas(L.)Lam.)and its related different polyploidy wild species I.trifida are all from the family of Convolvulaceae,in view of the large ploidy changes within sweet potato species,we selected the diploid,tetraploid and hexaploid I.trifida,as well as the pentaploid and hexaploid I.batatas for reduced-representation genome sequencing using RAD-seq technology.Taking the genome of cultivated sweet potato'Taizhong6'as a reference,the process of SNP identification in different ploidy materials was established through mapping,sort,PCR marker duplication and variation detection.The results of IQ-TREE analysis of SNP markers confirmed that this process has high reliability.The study use sweet potato genome as reference to obtain SNP markers from different ploidy materials and identify the genetic relationship of wild and cultivated sweet potato with different ploidy which help to facilitate the parental selection of breeding and the identification for SNP markers of other polyploid crop plants.