Characterization, validation, and cross-species transferability of newly developed EST-SSR markers and their application for genetic evaluation in crape myrtle (Lagerstroemia spp)

Abstract

Crape myrtle is an important ornamental woody plant, due to its long-lasting midsummer bloom and rich color. However, limited molecular markers on this species hinder the breeding and genetic studies. In this work, 8652 EST-SSRs were identified from L. indica transcriptome data. Di-nucleotide repeats (57.1%) were the most abundant type followed by tri-, tetra-, penta-, and hexa-nucleotide repeats, with the AG/CT motif occurring most frequently. Of the 1200 synthesized primer pairs, 761 EST-SSRs (63.4%) were successfully amplified and 245 EST-SSRs (20.4%) showed polymorphic. High cross-species transferabilities of these markers were observed except in L. speciosa (26.7%). The polymorphic information content (PIC) for each locus ranged from 0.210 to 0.813 with a mean of 0.589, suggesting a high level of informativeness. Using 30 polymorphic EST-SSRs, structure and cluster analyses roughly divided the 73 genotypes into three major groups with some admixtures. This work contributes to the better understanding of the genetic diversity and germplasm resources conservation in Lagerstroemia species. Thus, the newly developed EST-SSRs will provide a valuable tool for genetic analysis, linkage map construction, and marker-assisted selection breeding in crape myrtle.