RT Journal Article
SR Electronic
T1 A novel method for large-scale identification of polymorphic microsatellites through comparative transcriptome analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 114645
DO 10.1101/114645
A1 Wei Luo
A1 Hongyue Qu
A1 Xin Wang
A1 Qin Zhan
A1 Qiang Lin
YR 2017
UL http://biorxiv.org/content/early/2017/03/07/114645.abstract
AB Microsatellite (SSR) is one of the most popular markers for applied genetic research, but generally the current methods to develop SSRs are relatively time-consuming and expensive. Although high-throughput sequencing (HTS) approach has become a practical and relatively inexpensive option so far, only a small percentage of SSR markers turn out to be polymorphic. Here, we designed a new method to enrich polymorphic SSRs through the comparative transcriptome analysis. This program contains five main steps: 1) transcriptome data downloading or RNA-seq; 2) sequence assembly; 3) SSR mining and enrichment of sequences containing SSRs; 4) sequence alignment; 5) enrichment of sequences containing polymorphic SSRs. A validation experiment was performed and the results showed almost all markers (> 90%) that were indicated as putatively polymorphic by this method were indeed polymorphic. The frequency of polymorphic SSRs was significantly higher (P < 0.05) but the cost and running time were much lower than those of traditional and HTS approaches. The method has a practical value for polymorphic SSRs development and might be widely used for genetic analyses in any species.