An improved technique for isolating codominant compound microsatellite markers

Abstract

An approach for developing codominant polymorphic markers (compound microsatellite (SSR) markers), with substantial time and cost savings, is introduced in this paper. In this technique, fragments flanked by a compound SSR sequence at one end were amplified from the constructed DNA library using compound SSR primer (AC)6(AG)5 or (TC)6(AC)5 and an adaptor primer for the suppression-PCR. A locus-specific primer was designed from the sequence flanking the compound SSR. The primer pairs of the locus-specific and compound SSR primers were used as a compound SSR marker. Because only one locus-specific primer was needed for design of each marker and only a common compound SSR primer was needed as the fluorescence-labeled primer for analyzing all the compound SSR markers, this approach substantially reduced the cost of developing codominant markers and analyzing their polymorphism. We have demonstrated this technique for Dendropanax trifidus and easily developed 11 codominant markers with high polymorphism for D. trifidus. Use of the technique for successful isolation of codominant compound SSR markers for several other plant species is currently in progress.

Development and characterization of polymorphic microsatellite markers for Castanopsis hystrix (Fagaceae)

“…An improved technique for isolating codominant compound microsatellite markers (Lian et al, 2006) was used to develop simple sequence repeat (SSR) markers for C. hystrix. First, an adaptor-ligated DNA library was constructed according to the protocol of Lian et al (2001).…”

Methods for Development of Microsatellite Markers: An Overview

“…Another improved protocol described by Lian et al (2006) differed from the earlier protocol in that a compound SSR primer and adapter primers were used for constructing genomic library. A specific primer (IP1) designed from the nucleotide sequence flanking the SSR and the initial compound SSR primer were used as a compound SSR marker.…”

Short Communication Development and characterization of nine polymorphic microsatellites for the small brown planthopper Laodelphax striatellus (Hemiptera: Delphacidae)

“…Microsatellites were isolated from a genomic DNA library using the suppression-PCR procedure described by Lian et al (2006). Briefly, genomic DNA was extracted from a pool of L. striatellus using a CTAB method (Zhou et al, 1999).…”

“…It is important to understand the genetic structure and the ecological features of local populations for effective pest management of insect populations (Hoshizaki, 1997). In this study, nine polymorphic microsatellites were first isolated from the SBPH genome using the suppression-PCR method (Lian et al, 2006). These microsatellites were tested in 141 individuals of three populations sampled from three provinces of China.…”