Genetic evaluation and core collection construction of crape myrtle accessions using newly developed EST-SSR markers

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  Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education and College of Landscape Architecture, Beijing Forestry University, Beijing, China
DOI
10.7287/peerj.preprints.3141v1
Published
Accepted
Subject Areas
Genetics, Plant Science
Keywords
Crape myrtle, EST-SSRs, Cross-species transferability, Genetic diversity, Population structure, Core collection
Copyright
© 2017 Ye et al.
Licence
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
Cite this article
Ye Y, Feng L, Ju Y, Cai M, Cheng T, Wang J, Zhang Q, Pan H. 2017. Genetic evaluation and core collection construction of crape myrtle accessions using newly developed EST-SSR markers. PeerJ Preprints 5:e3141v1

Abstract

Crape myrtle is an important ornamental woody plant, due to its long-lasting mid summer bloom and rich color . However, limited molecular markers on this species hinder the breeding and genetic studies. In this work, 8,652 EST-SSRs were identified from crape myrtle transcriptome data. Di-nucleotide repeats (57.1%) were the most abundant type followed by tri-, tetra-, penta-, 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 accessions into three major groups with some admixtures. Based on the SSR data and clustering analysis, a final core collection (20 accessions) was identified, which captured Na, Ne, I, and PIC value with a retention rate of 92.8%, 113.6%, 110.6% and 109.7%, respectively. Thus, this work contributes to the better understanding of the genetic diversity and germplasm resources conservation in Lagerstroemia species.

Author Comment

This is a preprint submission to Peer J Preprints.

Supplemental Information

Supplemental Table S1 The detailed information of Lagerstroemia accessions used in this study

DOI: 10.7287/peerj.preprints.3141v1/supp-1

Supplemental Table S2 Nucleotide sequences of 761 successfully amplified EST-SSRs in this study

DOI: 10.7287/peerj.preprints.3141v1/supp-2