基于松树EST序列的马尾松SSR引物开发

Designing Pinus massoniana SSR Primers from Pinus EST Sequences

本文用生物信息学方法对松树359521条EST进行处理,得到无冗余EST序列56776条,其中有2315个SSR分布于2057条EST中,出现频率是4.08%,平均距离是22.06kb。检测到二、三碱基重复SSR总数为1631个,四碱基至六碱基重复SSR共117个。在所得二碱基以上重复SSR中,多态潜能高的有488个,占27.92%;多态潜能次高的有1260个,占72.08%。选择整体长度不小于24个碱基的SSR位点用于开发马尾松SSR引物,设计出135对备选引物,最终有51对引物在马尾松中得到扩增,有效扩增率为37.78%;其中39对有多态性,多态率为28.89%。在51对可扩增引物所对应的SSR类型中,P型占74.51%,I型占3.92%,C型占21.57%。

In this study, bioinformatics method was used to deal with 359 521 P/nus EST sequences to get 56 776 non-redundant EST sequences. There were 2 315 SSRs distributed in 2 057 ESTs, the frequency of occurrence is 4.08%, and the average distance is 22.06 kb. 1 631 SSRs of dinucleotide and trinucleotide repeats, 117 SSRs of tetranucelotide, pentanucleotide and hexanucleotide were detected. Among all the SSRs except mononucleotide repeats, 488 had the highest potential of polymorphism, accounting for 27.92%; 1 260 SSRs had the second high potential of polymorphism, accounting for 72.08%. We chose SSR loci with the overall length of no less than 24 base pairs for the designing of Pinus massoniona SSR primers, designed 135 pairs of primers options, and ultimately amplified 51 pairs of primers in Pinus massoniana with the effective amplification rate of 37.78%, 39 pairs of which had polymorphism and the rate was 28.89%. Analyzing the 51 primer pairs of SSRs, P-type accounted for 74.51%, I-type accounted for 3.92%, and C-type accounted for 21.57%.