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Journal of Nucleic Acids
Volume 2017, Article ID 6590902, 9 pages
https://doi.org/10.1155/2017/6590902
Research Article

Systemic Identification of Hevea brasiliensis EST-SSR Markers and Primer Screening

1College of Agriculture, Hainan University, Haikou 570228, China
2Institute of Cereal Research, Hainan Academy of Agricultural Sciences, Haikou 571100, China
3Hainan Tropical Ocean University, Sanya 572202, China
4Key Laboratory of Tropical Crop Molecular Breeding of Sanya, Sanya 572202, China

Correspondence should be addressed to Yaoting Wu; nc.gro.auhgnist@gnitoayuw

Received 4 August 2016; Revised 26 October 2016; Accepted 23 November 2016; Published 23 January 2017

Academic Editor: Yanfeng Zhang

Copyright © 2017 Benjun Hou et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

This research aimed to systematically identify and preliminarily validate the Hevea brasiliensis expressed sequence tag (EST) information using Simple Sequence Repeat (SSR) and provide evidence for further development of SSR molecular marker. The definition of general SSR features of Hevea EST splicing sequences and development of SSR primers founded the basis of diversity analysis and variety identification for Hevea tree resource. 1134 SSR loci were identified in the EST splicing sequence and distributed in 840 Unigene. The occurrence rate of SSR loci was 23.9%, and the average distribution distance of EST-SSR was 2.59 kb. The major repeat type was mononucleotide repeat motif, which accounted for 38.89%, while the corresponding value was 36.95% for dinucleotide repeat motif and 18.17% for trinucleotide repeat motif; the proportion of other motifs was only 5.99%. The superior repeat motifs for mononucleotide, dinucleotide, and trinucleotide were A/T, AG/CT, and AAG/CTT, respectively. 739 pair of primers were designed for 1134 SSR loci. PCR amplification was performed on Hevea Reyan5-11, Reyan87-6-47, and PR107, and 180 pairs of primers were selected which were able to amplify polymorphism bands.