Background: Analysis of genetic diversity is important for the authentication of a species. Litchi (
Litchi chinensis
Sonn.) is a subtropical evergreen tree. Recently,
L. chinensis has been characterized by an improved random
amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) analysis. The goal of this study
was to develop sequence-characterized amplified region (SCAR) markers from the improved RAPD fragments
for the genetic analysis of
L. chinensis.
Results: The improved RAPD fragments from
L. chinensis were cloned, sequenced and converted into stable SCAR
markers. Sequencing of three cloned RAPD fragments revealed that the clone L7-16 consisted of 222 nucleotides
(GenBank accession number KM235222), clone L9-6 consisted of 648 nucleotides (GenBank accession number
KM235223), and clone L11-26 consisted of 369 nucleotides (GenBank accession number KM235224). Then,
specific primers for SCAR markers L7-16, L9-6, and L11-26 were designed and synthesized. PCR amplification
was performed using DNA templates from 24 different samples, including 6 samples of
L. chinensis and other
plants. The SCAR marker L9-6 was specific for all of the
L. chinensis samples, the SCAR marker L11-26 specific
for five
L. chinensis samples, and the SCAR marker L7-16 only specific for the samples from Luzhou.
Conclusions: This study developed stable SCAR markers for the identification of
L. chinensis by the cloning of the
improved RAPD fragments. Combining RAPD and SCAR markers provides a simple and reliable tool for the
genetic characterization of plant species.
