基于RAD测序技术的瓦氏黄颡鱼(Pelteobagrus vachellii)微卫星标记的开发

Isolation of microsatellite markers for Pelteobagrus vachellii based on RAD sequencing

采用RAD测序技术对瓦氏黄颡鱼进行简化基因组测序,利用MISA软件对拼接的数据进行SSR搜索。结果共获得2275778条contig序列,共检测到466983个SSR位点,其中二碱基重复位点最多,有335095个,占总数的71.8%。随机挑选碱基重复次数较多的微卫星引物25对进行合成,有19对引物通过PCR扩增可以获得目的片段。用长江武汉段30个瓦氏黄颡鱼样本进行多态性验证,其中13个SSR验证为高多态性标记。这些高多态性瓦氏黄颡鱼标记可应用于其群体遗传学、亲子鉴定、分子标记辅助育种等方面的研究。

In this study,we used RAD-seq technology to obtain the reduced-representation genome data of the Pelteobagrus vachellii,and from which,SSR markers were detected by the MISA program.Totally,2275778 contig were obtained,including 466983 SSRs.Of 466983 SSRs,most of them were di-nucleotide repeats(3335095),with the percentage of 71.8%.The set of 25 primer pairs with high number of base repeats were randomly selected to synthesize,and 19 primer pairs produced clear bands with their expected sizes.Polymorphisms were assessed using 30 individuals from the Wuhan section of the Yangtze river,all of 13 SSRs showed high polymorphism.These polymorphic SSRs could be used in population genetics,parentage analysis,and molecular marker assisted breeding of P.vachellii.